NGI Stockholm (Genomics Applications)

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SciLifeLab Infrastructure Unit 2013–2019.

Primary: Shown in the list of current labels, if end date is not specified.

Started: 2013

Ended: 2019

Year 2024

PubMed DOI Crossref
Orthopteran Neo-Sex Chromosomes Reveal Dynamics of Recombination Suppression and Evolution of Supergenes.
Jayaprasad S, Peona V, Ellerstrand SJ, ..., Schielzeth H, Palacios-Gimenez OM
Mol. Ecol. - (-) e17567 [2024-10-30; online 2024-10-30]
NGI Long read [Collaborative] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
The lncRNA SNHG26 drives the inflammatory-to-proliferative state transition of keratinocyte progenitor cells during wound healing.
Li D, Liu Z, Zhang L, ..., Sommar P, Xu Landén N
Nat Commun 15 (1) 8637 [2024-10-05; online 2024-10-05]
NGI Short read [Service] NGI Single cell [Service] NGI Spatial omics [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The single-cell transcriptomic atlas iPain identifies senescence of nociceptors as a therapeutical target for chronic pain treatment.
Techameena P, Feng X, Zhang K, Hadjab S
Nat Commun 15 (1) 8585 [2024-10-04; online 2024-10-04]
NGI Single cell [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Rapid and robust isolation of microglia and vascular cells from brain subregions for integrative single-cell analyses.
Preka E, Lastra Romero A, Sun Y, ..., Osman AM, Blomgren K
Heliyon 10 (16) e35838 [2024-08-30; online 2024-08-05]
NGI Single cell [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Origin, structure, and composition of the spider major ampullate silk fiber revealed by genomics, proteomics, and single-cell and spatial transcriptomics.
Sonavane S, Hassan S, Chatterjee U, ..., Reimegård J, Rising A
Sci Adv 10 (33) eadn0597 [2024-08-16; online 2024-08-14]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Spatial omics [Collaborative] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Detection of transcriptome-wide microRNA-target interactions in single cells with agoTRIBE.
Sekar V, Mármol-Sánchez E, Kalogeropoulos P, ..., Biryukova I, Friedländer MR
Nat. Biotechnol. 42 (8) 1296-1302 [2024-08-00; online 2023-09-21]
Bioinformatics Support for Computational Resources [Service] NGI Single cell [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Multi-compartmental diversification of neutralizing antibody lineages dissected in SARS-CoV-2 spike-immunized macaques.
Mandolesi M, Das H, de Vries L, ..., Murrell B, Karlsson Hedestam GB
Nat Commun 15 (1) 6338 [2024-07-27; online 2024-07-27]
NGI Single cell [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Distinct origin and region-dependent contribution of stromal fibroblasts to fibrosis following traumatic injury in mice.
Holl D, Hau WF, Julien A, ..., Dias DO, Göritz C
Nat. Neurosci. 27 (7) 1285-1298 [2024-07-00; online 2024-06-07]
Bioinformatics Long-term Support WABI [Service] Bioinformatics Support, Infrastructure and Training [Service] Integrated Microscopy Technologies Stockholm [Service] NGI Single cell [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Macrophages upregulate mural cell-like markers and support healing of ischemic injury by adopting functions important for vascular support.
Amoedo-Leite C, Parv K, Testini C, ..., Christoffersson G, Phillipson M
Nat Cardiovasc Res 3 (6) 685-700 [2024-06-00; online 2024-06-06]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Single cell [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Maintenance of caecal homeostasis by diverse adaptive immune cells in the rhesus macaque.
Castro Dopico X, Guryleva M, Mandolesi M, ..., Murrell B, Karlsson Hedestam GB
Clin Transl Immunology 13 (5) e1508 [2024-05-02; online 2024-05-02]
NGI Single cell [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Transcriptomic atlas of midbrain dopamine neurons uncovers differential vulnerability in a Parkinsonism lesion model.
Yaghmaeian Salmani B, Lahti L, Gillberg L, ..., Svenningsson P, Perlmann T
Elife 12 (-) - [2024-04-08; online 2024-04-08]
NGI Single cell [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Adaptive introgression reveals the genetic basis of a sexually selected syndrome in wall lizards.
Feiner N, Yang W, Bunikis I, While GM, Uller T
Sci Adv 10 (14) eadk9315 [2024-04-05; online 2024-04-03]
NGI Long read [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
The super-pangenome of Populus unveils genomic facets for its adaptation and diversification in widespread forest trees.
Shi T, Zhang X, Hou Y, ..., Yin T, Wang J
Mol Plant - (-) - [2024-03-13; online 2024-03-13]
NGI Long read [Service] NGI Other [Service] NGI Short read [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Kupffer cells dictate hepatic responses to the atherogenic dyslipidemic insult.
Di Nunzio G, Hellberg S, Zhang Y, ..., Olofsson PS, Malin SG
Nat Cardiovasc Res 3 (3) 356-371 [2024-03-00; online 2024-03-11]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Single cell [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
A Chromosome-Level Genome Assembly and Annotation for the Clouded Apollo Butterfly (Parnassius mnemosyne): A Species of Global Conservation Concern.
Höglund J, Dias G, Olsen RA, ..., Talla V, Backström N
Genome Biol Evol 16 (2) - [2024-02-01; online 2024-02-18]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Long read [Collaborative] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
Spatial Transcriptomics in a Case of Follicular Thyroid Carcinoma Reveals Clone-Specific Dysregulation of Genes Regulating Extracellular Matrix in the Invading Front.
Condello V, Paulsson JO, Zedenius J, Näsman A, Juhlin CC
Endocr. Pathol. - (-) - [2024-01-27; online 2024-01-27]
NGI Short read [Service] NGI Spatial omics [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Molecular blueprints for spinal circuit modules controlling locomotor speed in zebrafish.
Pallucchi I, Bertuzzi M, Madrid D, ..., Higashijima SI, El Manira A
Nat. Neurosci. 27 (1) 78-89 [2024-01-00; online 2023-11-02]
NGI Single cell [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Year 2023

PubMed DOI Crossref
A chromosome-level assembly of the seed beetle Callosobruchus maculatus genome with annotation of its repetitive elements.
Arnqvist G, Westerberg I, Galbraith J, ..., Ewels P, Suh A
G3 (Bethesda) - (-) - [2023-12-13; online 2023-12-13]
Bioinformatics Support for Computational Resources [Service] NGI Other [Service] NGI Short read [Service] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Lokatt: a hybrid DNA nanopore basecaller with an explicit duration hidden Markov model and a residual LSTM network.
Xu X, Bhalla N, Ståhl P, Jaldén J
BMC Bioinformatics 24 (1) 461 [2023-12-07; online 2023-12-07]
NGI Long read NGI Short read [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Range-wide and temporal genomic analyses reveal the consequences of near-extinction in Swedish moose.
Dussex N, Kurland S, Olsen RA, ..., Dalén L, Laikre L
Commun Biol 6 (1) 1035 [2023-10-17; online 2023-10-17]
Bioinformatics Support for Computational Resources [Service] NGI Other [Collaborative] NGI Short read [Service] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Placental growth factor exerts a dual function for cardiomyogenesis and vasculogenesis during heart development.
Witman N, Zhou C, Häneke T, ..., Chien KR, Sahara M
Nat Commun 14 (1) 5435 [2023-09-05; online 2023-09-05]
Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Short read [Service] NGI Single cell [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Long-read whole-genome analysis of human single cells.
Hård J, Mold JE, Eisfeldt J, ..., Michaëlsson J, Ameur A
Nat Commun 14 (1) 5164 [2023-08-24; online 2023-08-24]
Bioinformatics Support for Computational Resources [Service] NGI Long read [Technology development] NGI Single cell [Technology development] NGI Stockholm (Genomics Applications) [Collaborative] NGI Uppsala (Uppsala Genome Center) [Technology development] National Genomics Infrastructure [Technology development]
PubMed DOI Crossref
Decoding pancreatic endocrine cell differentiation and β cell regeneration in zebrafish.
Mi J, Liu KC, Andersson O
Sci Adv 9 (33) eadf5142 [2023-08-18; online 2023-08-18]
NGI Single cell [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Molecular and spatial landmarks of early mouse skin development.
Jacob T, Annusver K, Czarnewski P, ..., Björklund ÅK, Kasper M
Dev. Cell - (-) - [2023-08-13; online 2023-08-13]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Short read [Service] NGI Single cell [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Evaluation of genetic demultiplexing of single-cell sequencing data from model species.
Cardiello JF, Joven Araus A, Giatrellis S, ..., Simon A, Leigh ND
Life Sci. Alliance 6 (8) e202301979 [2023-08-00; online 2023-05-17]
NGI Single cell [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Proteomic and transcriptomic screening demonstrates increased mast cell-derived CCL23 in systemic mastocytosis.
Söderlund S, Boey D, van Midden W, ..., Dahlin JS, Ungerstedt J
J. Allergy Clin. Immunol. 152 (1) 205-213 [2023-07-00; online 2023-02-21]
NGI Single cell [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
An annotated chromosome-scale reference genome for Eastern black-eared wheatear (Oenanthe melanoleuca).
Peona V, Palacios-Gimenez OM, Lutgen D, ..., Suh A, Burri R
G3 (Bethesda) 13 (6) - [2023-06-01; online 2023-04-25]
Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The spatial landscape of gene expression isoforms in tissue sections.
Lebrigand K, Bergenstråhle J, Thrane K, ..., Waldmann R, Lundeberg J
Nucleic Acids Res. 51 (8) e47 [2023-05-08; online 2023-03-18]
NGI Short read [Service] NGI Spatial omics NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The human bone marrow plasma cell compartment in rheumatoid arthritis - Clonal relationships and anti-citrulline autoantibody producing cells.
Hensvold A, Horuluoglu B, Sahlström P, ..., Malmström V, Grönwall C
J. Autoimmun. 136 (-) 103022 [2023-04-00; online 2023-03-29]
NGI Short read [Service] NGI Single cell [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
A small noncoding RNA links ribosome recovery and translation control to dedifferentiation during salamander limb regeneration.
Subramanian E, Elewa A, Brito G, ..., Andersson O, Simon A
Dev. Cell 58 (6) 450-460.e6 [2023-03-27; online 2023-03-08]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Genomic architecture of migration timing in a long-distance migratory songbird.
de Greef E, Suh A, Thorstensen MJ, Delmore KE, Fraser KC
Sci Rep 13 (1) 2437 [2023-02-10; online 2023-02-10]
Bioinformatics Support for Computational Resources [Service] NGI Other [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure
PubMed DOI Crossref
Inversions maintain differences between migratory phenotypes of a songbird.
Lundberg M, Mackintosh A, Petri A, Bensch S
Nat Commun 14 (1) 452 [2023-01-27; online 2023-01-27]
Bioinformatics Support for Computational Resources [Service] NGI Other [Service] NGI Short read [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Service]
PubMed DOI Crossref
High-density linkage maps and chromosome level genome assemblies unveil direction and frequency of extensive structural rearrangements in wood white butterflies (Leptidea spp.).
Höök L, Näsvall K, Vila R, Wiklund C, Backström N
Chromosome Res. 31 (1) 2 [2023-01-20; online 2023-01-20]
Bioinformatics Support for Computational Resources [Service] NGI Other [Service] NGI Short read [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Graphene oxide elicits microbiome-dependent type 2 immune responses via the aryl hydrocarbon receptor.
Peng G, Sinkko HM, Alenius H, ..., Bräutigam L, Fadeel B
Nat Nanotechnol 18 (1) 42-48 [2023-01-00; online 2022-12-12]
Bioinformatics Support for Computational Resources [Service] Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Short read [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Year 2022

PubMed DOI Crossref
An overlooked subset of Cx3cr1wt/wt microglia in the Cx3cr1CreER-Eyfp/wt mouse has a repopulation advantage over Cx3cr1CreER-Eyfp/wt microglia following microglial depletion
Zhou K, Han J, Lund H, ..., Harris RA, Blomgren K
J Neuroinflammation 19 (1) 20 [2022-12-00; online 2022-01-21]
Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Single cell [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Single-cell sequencing deconvolutes cellular responses to exercise in human skeletal muscle.
Lovrić A, Rassolie A, Alam S, ..., Gustafsson T, Rullman E
Commun Biol 5 (1) 1121 [2022-10-22; online 2022-10-22]
Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Short read [Service] NGI Single cell [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Linked-read whole-genome sequencing resolves common and private structural variants in multiple myeloma.
Peña-Pérez L, Frengen N, Hauenstein J, ..., Lindstrand A, Månsson R
Blood Adv 6 (17) 5009-5023 [2022-09-13; online 2022-06-09]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Other [Service] NGI Short read [Service] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Schwann cell precursors represent a neural crest-like state with biased multipotency.
Kastriti ME, Faure L, Von Ahsen D, ..., Fried K, Adameyko I
EMBO J. 41 (17) e108780 [2022-09-01; online 2022-07-11]
NGI Single cell [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
PRC2-mediated repression is essential to maintain identity and function of differentiated dopaminergic and serotonergic neurons.
Toskas K, Yaghmaeian-Salmani B, Skiteva O, ..., Perlmann T, Holmberg J
Sci Adv 8 (34) eabo1543 [2022-08-26; online 2022-08-26]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Single cell [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
A Genome for Edith's Checkerspot Butterfly: An Insect with Complex Host-Adaptive Suites and Rapid Evolutionary Responses to Environmental Changes.
Tunstrom K, Wheat CW, Parmesan C, Singer MC, Mikheyev AS
Genome Biol Evol 14 (8) - [2022-08-03; online 2022-07-26]
Bioinformatics Support for Computational Resources [Service] NGI Other [Service] NGI Short read [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Spatially resolved clonal copy number alterations in benign and malignant tissue.
Erickson A, He M, Berglund E, ..., Lamb AD, Lundeberg J
Nature 608 (7922) 360-367 [2022-08-00; online 2022-08-10]
NGI Short read [Service] NGI Spatial omics [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Claudin5 protects the peripheral endothelial barrier in an organ and vessel-type-specific manner.
Richards M, Nwadozi E, Pal S, ..., Nordling S, Claesson-Welsh L
Elife 11 (-) - [2022-07-21; online 2022-07-21]
Bioinformatics Support for Computational Resources [Service] Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Short read [Service] NGI Single cell [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Equilibrated evolution of the mixed auto-/allopolyploid haplotype-resolved genome of the invasive hexaploid Prussian carp.
Kuhl H, Du K, Schartl M, ..., Stöck M, Lamatsch DK
Nat Commun 13 (1) 4092 [2022-07-14; online 2022-07-14]
Bioinformatics Support for Computational Resources [Service] NGI Other [Service] NGI Short read [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Integrated single cell and spatial transcriptomics reveal autoreactive differentiated B cells in joints of early rheumatoid arthritis.
Hardt U, Carlberg K, Af Klint E, ..., Ståhl PL, Malmström V
Sci Rep 12 (1) 11876 [2022-07-13; online 2022-07-13]
Bioinformatics Support for Computational Resources [Service] Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Short read [Service] NGI Single cell [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Single-cell RNA-sequencing analysis of the developing mouse inner ear identifies molecular logic of auditory neuron diversification.
Petitpré C, Faure L, Uhl P, ..., Hadjab S, Lallemend F
Nat Commun 13 (1) 3878 [2022-07-05; online 2022-07-05]
Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Short read [Service] NGI Single cell [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Molecular profiling of stem cell-derived retinal pigment epithelial cell differentiation established for clinical translation.
Petrus-Reurer S, Lederer AR, Baqué-Vidal L, ..., La Manno G, Lanner F
Stem Cell Reports 17 (6) 1458-1475 [2022-06-14; online 2022-06-16]
Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Short read [Service] NGI Single cell [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The outcome of targeted NGS screening in patients with syndromic forms of sagittal and pansynostosis - IL11RA is an emerging core-gene for pansynostosis.
Topa A, Rohlin A, Andersson MK, ..., Stenman G, Kölby L
Eur J Med Genet 65 (5) 104476 [2022-05-00; online 2022-03-21]
Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Nutrient driven transcriptional changes during phage infection in an aquatic Gammaproteobacterium.
Nilsson E, Li K, Hoetzinger M, Holmfeldt K
Environ. Microbiol. 24 (5) 2270-2281 [2022-05-00; online 2022-01-26]
Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Epicardium-derived cells organize through tight junctions to replenish cardiac muscle in salamanders.
Eroglu E, Yen CYT, Tsoi YL, ..., Simon A, Chien KR
Nat Cell Biol 24 (5) 645-658 [2022-05-00; online 2022-05-12]
Bioinformatics Support for Computational Resources [Service] Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Short read [Service] NGI Single cell [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Epigenomic priming of immune genes implicates oligodendroglia in multiple sclerosis susceptibility.
Meijer M, Agirre E, Kabbe M, ..., Malhotra D, Castelo-Branco G
Neuron 110 (7) 1193-1210.e13 [2022-04-06; online 2022-01-31]
Bioinformatics Support for Computational Resources [Service] Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Single cell [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
Uterine fluid microRNAs are dysregulated in women with recurrent implantation failure.
von Grothusen C, Frisendahl C, Modhukur V, ..., Boggavarapu NR, Gemzell-Danielsson K
Hum. Reprod. 37 (4) 734-746 [2022-04-01; online 2022-02-12]
Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Single cell [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Target sequence capture of Barnadesioideae (Compositae) demonstrates the utility of low coverage loci in phylogenomic analyses.
Ferreira PdL, Batista R, Andermann T, ..., Bacon CD, Antonelli A
Mol. Phylogenet. Evol. 169 (-) 107432 [2022-04-00; online 2022-02-04]
NGI Short read [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
GBS-MeDIP: A protocol for parallel identification of genetic and epigenetic variation in the same reduced fraction of genomes across individuals.
Rezaei S, Uffenorde J, Gimm O, ..., Guerrero-Bosagna C, Pértille F
STAR Protoc 3 (1) 101202 [2022-03-18; online 2022-03-03]
NGI Short read [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Identification of a discrete subpopulation of spinal cord ependymal cells with neural stem cell properties.
Stenudd M, Sabelström H, Llorens-Bobadilla E, ..., Barnabé-Heider F, Frisén J
Cell Rep 38 (9) 110440 [2022-03-01; online 2022-03-03]
Bioinformatics Support for Computational Resources [Service] Integrated Microscopy Technologies Stockholm [Collaborative] NGI Short read [Service] NGI Single cell [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Utilizing museomics to trace the complex history and species boundaries in an avian-study system of conservation concern.
Ernst M, Jønsson KA, Ericson PGP, Blom MPK, Irestedt M
Heredity (Edinb) 128 (3) 159-168 [2022-03-00; online 2022-01-26]
Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Local selection signals in the genome of blue tits emphasize regulatory and neuronal evolution.
Mueller JC, Botero-Delgadillo E, Espíndola-Hernández P, ..., Gruselius J, Kempenaers B
Mol. Ecol. 31 (5) 1504-1514 [2022-03-00; online 2022-01-22]
NGI Short read [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Clonal relations in the mouse brain revealed by single-cell and spatial transcriptomics.
Ratz M, von Berlin L, Larsson L, ..., Lundeberg J, Frisén J
Nat. Neurosci. 25 (3) 285-294 [2022-03-00; online 2022-02-24]
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Widmark A, Sagredo EA, Karlström V, ..., Daniel C, Öhman M
J. Biol. Chem. 298 (3) 101682 [2022-03-00; online 2022-02-03]
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Int J Mol Sci 23 (4) - [2022-02-17; online 2022-02-17]
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Front Plant Sci 13 (-) 823019 [2022-02-17; online 2022-02-17]
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Three-dimensional spatial transcriptomics uncovers cell type localizations in the human rheumatoid arthritis synovium.
Vickovic S, Schapiro D, Carlberg K, ..., Regev A, Ståhl PL
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Hou XQ, Zhang DD, Powell D, ..., Andersson MN, Löfstedt C
BMC Biol. 20 (1) 34 [2022-02-07; online 2022-02-07]
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Partial Monosomy 21 Mirrors Gene Expression of Trisomy 21 in a Patient-Derived Neuroepithelial Stem Cell Model.
Schuy J, Eisfeldt J, Pettersson M, ..., Falk A, Lindstrand A
Front Genet 12 (-) 803683 [2022-02-04; online 2022-02-04]
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Genomic basis for skin phenotype and cold adaptation in the extinct Steller's sea cow.
Le Duc D, Velluva A, Cassatt-Johnstone M, ..., Shapiro B, Schöneberg T
Sci Adv 8 (5) eabl6496 [2022-02-04; online 2022-02-04]
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Population genomics and geographic dispersal in Chagas disease vectors: Landscape drivers and evidence of possible adaptation to the domestic setting.
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PLoS Genet. 18 (2) e1010019 [2022-02-00; online 2022-02-04]
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Christmas MJ, Jones JC, Olsson A, ..., Miller-Struttmann NE, Webster MT
Mol. Ecol. 31 (4) 1111-1127 [2022-02-00; online 2021-12-07]
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Occasional paternal inheritance of the germline-restricted chromosome in songbirds.
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Proc. Natl. Acad. Sci. U.S.A. 119 (4) - [2022-01-25; online 2022-01-22]
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Massive genome inversion drives coexistence of divergent morphs in common quails.
Sanchez-Donoso I, Ravagni S, Rodríguez-Teijeiro JD, ..., Leonard JA, Vilà C
Curr. Biol. 32 (2) 462-469.e6 [2022-01-24; online 2021-11-29]
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Fish Skin Microbiomes Are Highly Variable Among Individuals and Populations but Not Within Individuals.
Berggren H, Tibblin P, Yıldırım Y, ..., Lundin D, Forsman A
Front Microbiol 12 (-) 767770 [2022-01-21; online 2022-01-21]
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Transcriptome Analysis of an Aedes albopictus Cell Line Single- and Dual-Infected with Lammi Virus and WNV.
Öhlund P, Delhomme N, Hayer J, Hesson JC, Blomström AL
Int J Mol Sci 23 (2) - [2022-01-14; online 2022-01-14]
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Ghadamgahi F, Tarighi S, Taheri P, ..., Ortiz R, Vetukuri RR
Biology (Basel) 11 (1) - [2022-01-14; online 2022-01-14]
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Pujolar JM, Blom MPK, Reeve AH, ..., Irestedt M, Jønsson KA
Nat Commun 13 (1) 268 [2022-01-12; online 2022-01-12]
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Connectivity of Fennoscandian Shield terrestrial deep biosphere microbiomes with surface communities.
Westmeijer G, Mehrshad M, Turner S, ..., Bertilsson S, Dopson M
Commun Biol 5 (1) 37 [2022-01-11; online 2022-01-11]
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Canonical WNT signaling-dependent gating of MYC requires a noncanonical CTCF function at a distal binding site.
Chachoua I, Tzelepis I, Dai H, ..., Mehmood R, Göndör A
Nat Commun 13 (1) 204 [2022-01-11; online 2022-01-11]
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Land-use intensification differentially affects bacterial, fungal and protist communities and decreases microbiome network complexity.
Romdhane S, Spor A, Banerjee S, ..., Saghai A, Philippot L
Environ Microbiome 17 (1) 1 [2022-01-06; online 2022-01-06]
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Whole-genome resequencing confirms reproductive isolation between sympatric demes of brown trout (Salmo trutta) detected with allozymes.
Saha A, Andersson A, Kurland S, ..., Ryman N, Laikre L
Mol. Ecol. 31 (2) 498-511 [2022-01-00; online 2021-11-15]
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Proteome-scale mapping of binding sites in the unstructured regions of the human proteome.
Benz C, Ali M, Krystkowiak I, ..., Davey NE, Ivarsson Y
Mol. Syst. Biol. 18 (1) e10584 [2022-01-00; online 2022-01-20]
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Year 2021

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Biased TCR gene usage in citrullinated Tenascin C specific T-cells in rheumatoid arthritis.
Sharma RK, Boddul SV, Yoosuf N, ..., Klareskog L, Malmström V
Sci Rep 11 (1) 24512 [2021-12-31; online 2021-12-31]
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Pan-AMPK activator O304 prevents gene expression changes and remobilisation of histone marks in islets of diet-induced obese mice.
López-Pérez A, Norlin S, Steneberg P, ..., Edlund H, Hörnblad A
Sci Rep 11 (1) 24410 [2021-12-23; online 2021-12-23]
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Taxon-Specific Shifts in Bacterial and Archaeal Transcription of Dissolved Organic Matter Cycling Genes in a Stratified Fjord.
Pontiller B, Pérez-Martínez C, Bunse C, ..., Lundin D, Pinhassi J
mSystems 6 (6) e0057521 [2021-12-21; online 2021-12-14]
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Albert S, Hedberg P, Motwani NH, ..., Winder M, Nascimento FJA
Sci Rep 11 (1) 24033 [2021-12-15; online 2021-12-15]
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Interplay between eutrophication and climate warming on bacterial communities in coastal sediments differs depending on water depth and oxygen history.
Seidel L, Broman E, Turner S, Ståhle M, Dopson M
Sci Rep 11 (1) 23384 [2021-12-03; online 2021-12-03]
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Historical population declines prompted significant genomic erosion in the northern and southern white rhinoceros (Ceratotherium simum).
Sánchez-Barreiro F, Gopalakrishnan S, Ramos-Madrigal J, ..., Moodley Y, Gilbert MTP
Mol. Ecol. 30 (23) 6355-6369 [2021-12-00; online 2021-07-07]
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Evolutionary history of the extinct Sardinian dhole
Ciucani MM, Jensen JK, Sinding MHS, ..., Gilbert MTP, Gopalakrishnan S
Current Biology 31 (24) 5571-5579.e6 [2021-12-00; online 2021-12-00]
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An atlas of the Norway spruce needle seasonal transcriptome.
Bag P, Lihavainen J, Delhomme N, ..., Robinson KM, Jansson S
Plant J. 108 (6) 1815-1829 [2021-12-00; online 2021-10-21]
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Dredging and deposition of metal sulfide rich river sediments results in rapid conversion to acid sulfate soil materials.
Johnson A, Högfors-Rönnholm E, Engblom S, ..., Åström M, Dopson M
Sci. Total Environ. - (-) 151864 [2021-11-23; online 2021-11-23]
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Interplay between copy number alterations and immune profiles in the early breast cancer Scandinavian Breast Group 2004-1 randomized phase II trial: results from a feasibility study.
Zerdes I, Simonetti M, Matikas A, ..., Crosetto N, Foukakis T
NPJ Breast Cancer 7 (1) 144 [2021-11-19; online 2021-11-19]
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MapToCleave: High-throughput profiling of microRNA biogenesis in living cells.
Kang W, Fromm B, Houben AJ, ..., Biryukova I, Friedländer MR
Cell Rep 37 (7) 110015 [2021-11-16; online 2021-11-18]
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Tracing the evolution of aneuploid cancers by multiregional sequencing with CRUST.
Chattopadhyay S, Karlsson J, Valind A, Andersson N, Gisselsson D
Brief. Bioinformatics 22 (6) - [2021-11-05; online 2021-08-04]
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Small RNA Response to Infection of the Insect-Specific Lammi Virus and Hanko Virus in an Aedes albopictus Cell Line.
Öhlund P, Hayer J, Hesson JC, Blomström AL
Viruses 13 (11) - [2021-10-29; online 2021-10-29]
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Microbial Plankton Community Structure and Function Responses to Vitamin B12 and B1 Amendments in an Upwelling System.
Joglar V, Pontiller B, Martínez-García S, ..., Fernández E, Teira E
Appl. Environ. Microbiol. 87 (22) e0152521 [2021-10-28; online 2021-09-08]
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Massive parallel sequencing in individuals with multiple primary tumours reveals the benefit of re-analysis.
Wallander K, Thonberg H, Nilsson D, Tham E
Hered Cancer Clin Pract 19 (1) 46 [2021-10-28; online 2021-10-28]
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Adaptive Introgression Facilitates Adaptation to High Latitudes in European Aspen (Populus tremula L.).
Rendón-Anaya M, Wilson J, Sveinsson S, ..., Street NR, Ingvarsson PK
Mol. Biol. Evol. 38 (11) 5034-5050 [2021-10-27; online 2021-07-31]
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Seasonal migration patterns and the maintenance of evolutionary diversity in a cryptic bird radiation.
Tang Q, Burri R, Liu Y, ..., Heckel G, Schweizer M
Mol. Ecol. - (-) - [2021-10-21; online 2021-10-21]
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Transcriptome Analysis of Potato Infected with the Necrotrophic Pathogen Alternaria solani.
Brouwer SM, Brus-Szkalej M, Saripella GV, ..., Liljeroth E, Grenville-Briggs LJ
Plants (Basel) 10 (10) - [2021-10-18; online 2021-10-18]
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Spatial deconvolution of HER2-positive breast cancer delineates tumor-associated cell type interactions.
Andersson A, Larsson L, Stenbeck L, ..., Engblom C, Lundeberg J
Nat Commun 12 (1) 6012 [2021-10-14; online 2021-10-14]
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Inhibition of the ubiquitin-proteasome system by an NQO1-activatable compound.
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Cell Death Dis 12 (10) 914 [2021-10-06; online 2021-10-06]
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Sci Adv 7 (40) eabh4390 [2021-10-00; online 2021-10-01]
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Maternal genetic origin of the late and final Neolithic human populations from present-day Poland.
Juras A, Ehler E, Chyleński M, ..., Jakobsson M, Dabert M
Am. J. Phys. Anthropol. 176 (2) 223-236 [2021-10-00; online 2021-07-26]
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High diagnostic yield in skeletal ciliopathies using massively parallel genome sequencing, structural variant screening and RNA analyses.
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Ecologically coherent population structure of uncultivated bacterioplankton.
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Comparison of DNA and RNA sequencing of total nucleic acids from human cervix for metagenomics.
Arroyo Mühr LS, Dillner J, Ure AE, Sundström K, Hultin E
Sci Rep 11 (1) 18852 [2021-09-22; online 2021-09-22]
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Single-Cell Analysis Reveals Major Histocompatibility Complex II‒Expressing Keratinocytes in Pressure Ulcers with Worse Healing Outcomes.
Li D, Cheng S, Pei Y, ..., Deng Q, Xu Landén N
J. Invest. Dermatol. - (-) - [2021-09-16; online 2021-09-16]
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Ancient and modern genomes unravel the evolutionary history of the rhinoceros family.
Liu S, Westbury MV, Dussex N, ..., Dalén L, Gilbert MTP
Cell 184 (19) 4874-4885.e16 [2021-09-16; online 2021-08-24]
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Peona V, Palacios-Gimenez OM, Blommaert J, ..., Jern P, Suh A
Philos. Trans. R. Soc. Lond., B, Biol. Sci. 376 (1833) 20200186 [2021-09-13; online 2021-07-26]
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Commun Biol 4 (1) 1059 [2021-09-09; online 2021-09-09]
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Selection on accessible chromatin regions in Capsella grandiflora.
Horvath R, Josephs EB, Pesquet E, ..., Scofield D, Slotte T
Mol. Biol. Evol. - (-) - [2021-09-08; online 2021-09-08]
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Spatial mapping reveals human adipocyte subpopulations with distinct sensitivities to insulin.
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Nat Commun 12 (1) 5309 [2021-09-07; online 2021-09-07]
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Stop codon readthrough alters the activity of a POU/Oct transcription factor during Drosophila development.
Zhao Y, Lindberg BG, Esfahani SS, ..., Piazza S, Engström Y
BMC Biol. 19 (1) 185 [2021-09-03; online 2021-09-03]
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Regulatory T cells reduce endothelial neutral sphingomyelinase 2 to prevent T-cell migration into tumors.
Akeus P, Szeponik L, Langenes V, ..., Slusher BS, Quiding-Järbrink M
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Novel genome reveals susceptibility of popular gamebird, the red-legged partridge (Alectoris rufa, Phasianidae), to climate change.
Chattopadhyay B, Forcina G, Garg KM, ..., Barbanera F, Rheindt FE
Genomics 113 (5) 3430-3438 [2021-09-00; online 2021-08-13]
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Exploring the β-tubulin gene family in a benzimidazole-resistant Parascaris univalens population.
Martin F, Halvarsson P, Delhomme N, Höglund J, Tydén E
International Journal for Parasitology: Drugs and Drug Resistance 17 (-) 84-91 [2021-08-26; online 2021-08-26]
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Chromoanagenesis Event Underlies a de novo Pericentric and Multiple Paracentric Inversions in a Single Chromosome Causing Coffin-Siris Syndrome.
Grochowski CM, Krepischi ACV, Eisfeldt J, ..., Lindstrand A, Carvalho CMB
Front Genet 12 (-) 708348 [2021-08-26; online 2021-08-26]
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Amnion signals are essential for mesoderm formation in primates.
Yang R, Goedel A, Kang Y, ..., Niu Y, Chien KR
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Small-scale sequencing enables quality assessment of Ribo-Seq data: an example from Arabidopsis cell culture.
Mahboubi A, Delhomme N, Häggström S, Hanson J
Plant Methods 17 (1) 92 [2021-08-24; online 2021-08-24]
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Single-cell analysis pinpoints distinct populations of cytotoxic CD4+ T cells and an IL-10+CD109+ TH2 cell population in nasal polyps.
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Candidatus Methylumidiphilus Drives Peaks in Methanotrophic Relative Abundance in Stratified Lakes and Ponds Across Northern Landscapes.
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PopulusPtERF85 Balances Xylem Cell Expansion and Secondary Cell Wall Formation in Hybrid Aspen.
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Genome-wide estrogen receptor β chromatin binding in human colon cancer cells reveals its tumor suppressor activity.
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The exon-junction complex helicase eIF4A3 controls cell fate via coordinated regulation of ribosome biogenesis and translational output.
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Terrestrial dissolved organic matter inflow drives temporal dynamics of the bacterial community of a subarctic estuary (northern Baltic Sea).
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SFRP2 induces a mesenchymal subtype transition by suppression of SOX2 in glioblastoma.
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Dynamics of Baltic Sea phages driven by environmental changes.
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Genetic Barriers to Historical Gene Flow between Cryptic Species of Alpine Bumblebees Revealed by Comparative Population Genomics.
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Complex population structure of the Atlantic puffin revealed by whole genome analyses.
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Unraveling negative biotic interactions determining soil microbial community assembly and functioning.
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Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater.
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Genomic Predictions With Nonadditive Effects Improved Estimates of Additive Effects and Predictions of Total Genetic Values in Pinus sylvestris.
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High-Quality Genome Assembly and Comprehensive Transcriptome of the Painted Lady Butterfly Vanessa cardui.
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Candidate regulators and target genes of drought stress in needles and roots of Norway spruce.
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Gene Regulatory Network of Human GM-CSF-Secreting T Helper Cells.
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The genomics of phenotypically differentiated Asellus aquaticus cave, surface stream and lake ecotypes.
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Single-cell CUT&Tag profiles histone modifications and transcription factors in complex tissues.
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Mammuthus sp. (Early and Middle Pleistocene Mammoths).
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High throughput shotgun sequencing of eRNA reveals taxonomic and derived functional shifts across a benthic productivity gradient.
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FGFR1 overexpression in non-small cell lung cancer is mediated by genetic and epigenetic mechanisms and is a determinant of FGFR1 inhibitor response.
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Bifidobacteria-mediated immune system imprinting early in life
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Towards Bioleaching of a Vanadium Containing Magnetite for Metal Recovery.
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DNA metabarcoding reveals trophic niche diversity of micro and mesozooplankton species.
Novotny A, Zamora-Terol S, Winder M
Proc. Biol. Sci. 288 (1953) 20210908 [2021-06-30; online 2021-06-16]
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COVseq is a cost-effective workflow for mass-scale SARS-CoV-2 genomic surveillance.
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Nat Commun 12 (1) 3903 [2021-06-23; online 2021-06-23]
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Leveraging breeding programs and genomic data in Norway spruce (Picea abies L. Karst) for GWAS analysis.
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Variable kinship patterns in Neolithic Anatolia revealed by ancient genomes.
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Reinforcing one-carbon metabolism via folic acid/Folr1 promotes β-cell differentiation.
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Nat Commun 12 (1) 3362 [2021-06-07; online 2021-06-07]
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Low Energy Electron Irradiation Is a Potent Alternative to Gamma Irradiation for the Inactivation of (CAR-)NK-92 Cells in ATMP Manufacturing.
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Atg7 deficiency in microglia drives an altered transcriptomic profile associated with an impaired neuroinflammatory response.
Friess L, Cheray M, Keane L, Grabert K, Joseph B
Mol Brain 14 (1) 87 [2021-06-03; online 2021-06-03]
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RNA atlas of human bacterial pathogens uncovers stress dynamics linked to infection.
Avican K, Aldahdooh J, Togninalli M, ..., Rhen M, Fällman M
Nat Commun 12 (1) 3282 [2021-06-02; online 2021-06-02]
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Gene count from target sequence capture places three whole genome duplication events in Hibiscus L. (Malvaceae).
Eriksson JS, Bacon CD, Bennett DJ, ..., Oxelman B, Antonelli A
BMC Ecol Evol 21 (1) 107 [2021-06-02; online 2021-06-02]
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Genomic and fitness consequences of inbreeding in an endangered carnivore.
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Mol. Ecol. 30 (12) 2790-2799 [2021-06-00; online 2021-05-20]
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Genomic Characterization of the Barnacle Balanus improvisus Reveals Extreme Nucleotide Diversity in Coding Regions.
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Mar Biotechnol (NY) 23 (3) 402-416 [2021-06-00; online 2021-05-01]
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Divergent clonal differentiation trajectories establish CD8+ memory T cell heterogeneity during acute viral infections in humans.
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Cell Rep 35 (8) 109174 [2021-05-25; online 2021-05-27]
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Phage Biocontrol of Pseudomonas aeruginosa in Water.
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Viruses 13 (5) 928 [2021-05-17; online 2021-05-17]
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Ultralow amounts of DNA from long-term archived serum samples produce high-quality methylomes.
Wojewodzic MW, Leithaug M, Lauritzen M, ..., Grotmol T, Rounge TB
Clin Epigenetics 13 (1) 107 [2021-05-12; online 2021-05-12]
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Progesterone Dampens Immune Responses in In Vitro Activated CD4+ T Cells and Affects Genes Associated With Autoimmune Diseases That Improve During Pregnancy.
Hellberg S, Raffetseder J, Rundquist O, ..., Ernerudh J, Gustafsson M
Front Immunol 12 (-) 672168 [2021-05-12; online 2021-05-12]
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African and Asian leopards are highly differentiated at the genomic level.
Paijmans JLA, Barlow A, Becker MS, ..., Manica A, Hofreiter M
Curr. Biol. 31 (9) 1872-1882.e5 [2021-05-10; online 2021-04-12]
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The Effects of GC-Biased Gene Conversion on Patterns of Genetic Diversity among and across Butterfly Genomes.
Boman J, Mugal CF, Backström N
Genome Biol Evol 13 (5) - [2021-05-07; online 2021-03-25]
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Chromosome Level Assembly of the Comma Butterfly (Polygonia c-album).
Celorio-Mancera MP, Rastas P, Steward RA, Nylin S, Wheat CW
Genome Biol Evol 13 (5) - [2021-05-07; online 2021-03-23]
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Tissue-specific transcriptional imprinting and heterogeneity in human innate lymphoid cells revealed by full-length single-cell RNA-sequencing.
Mazzurana L, Czarnewski P, Jonsson V, ..., Almer S, Mjösberg J
Cell Res 31 (5) 554-568 [2021-05-00; online 2021-01-08]
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Novel form of rhizomelic skeletal dysplasia associated with a homozygous variant in GNPNAT1.
Ain NU, Baroncelli M, Costantini A, ..., Mäkitie O, Naz S
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In vivo screen identifies a SIK inhibitor that induces β cell proliferation through a transient UPR.
Charbord J, Ren L, Sharma RB, ..., Alonso LC, Andersson O
Nat Metab 3 (5) 682-700 [2021-05-00; online 2021-05-20]
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Hybrid sequencing resolves two germline ultra-complex chromosomal rearrangements consisting of 137 breakpoint junctions in a single carrier.
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Hum. Genet. 140 (5) 775-790 [2021-05-00; online 2020-12-14]
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Dual RNA-Seq transcriptome analysis of chicken macrophage-like cells (HD11) infected in vitro with Eimeria tenella.
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Parasitology 148 (6) 712-725 [2021-05-00; online 2021-02-04]
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Cyanophage Diversity and Community Structure in Dead Zone Sediments.
Broman E, Holmfeldt K, Bonaglia S, Hall POJ, Nascimento FJA
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Middle Pleistocene genome calibrates a revised evolutionary history of extinct cave bears.
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Genomic insights into the conservation status of the world's last remaining Sumatran rhinoceros populations.
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Nat Commun 12 (1) 2393 [2021-04-26; online 2021-04-26]
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Functional Diversity Facilitates Stability Under Environmental Changes in an Outdoor Microalgal Cultivation System.
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Active DNRA and denitrification in oxic hypereutrophic waters.
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A spinal organ of proprioception for integrated motor action feedback.
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Neuron 109 (7) 1188-1201.e7 [2021-04-07; online 2021-02-11]
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Severe congenital lactic acidosis and hypertrophic cardiomyopathy caused by an intronic variant in NDUFB7.
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Hum. Mutat. 42 (4) 378-384 [2021-04-00; online 2021-02-04]
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Novel Mutation m.10372A>G in MT-ND3 Causing Sensorimotor Axonal Polyneuropathy.
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Neurol Genet 7 (2) e566 [2021-04-00; online 2021-03-15]
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Experimental evidence of microbial inheritance in plants and transmission routes from seed to phyllosphere and root.
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Development of a highly efficient 50K single nucleotide polymorphism genotyping array for the large and complex genome of Norway spruce (Picea abies L. Karst) by whole genome resequencing and its transferability to other spruce species.
Bernhardsson C, Zan Y, Chen Z, Ingvarsson PK, Wu HX
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The evolution of ancestral and species-specific adaptations in snowfinches at the Qinghai-Tibet Plateau.
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Proc. Natl. Acad. Sci. U.S.A. 118 (13) e2012398118 [2021-03-30; online 2021-03-24]
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Estrogen Receptor Beta Influences the Inflammatory p65 Cistrome in Colon Cancer Cells.
Indukuri R, Hases L, Archer A, Williams C
Front Endocrinol (Lausanne) 12 (-) 650625 [2021-03-30; online 2021-03-30]
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PRDM16 regulates a temporal transcriptional program to promote progression of cortical neural progenitors.
He L, Jones J, He W, ..., Wen J, Dai Q
Development 148 (6) - [2021-03-17; online 2021-03-17]
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Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager.
Fellows Yates JA, Lamnidis TC, Borry M, ..., Neukamm J, Peltzer A
PeerJ 9 (-) e10947 [2021-03-16; online 2021-03-16]
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Expansions of adaptive-like NK cells with a tissue-resident phenotype in human lung and blood.
Brownlie D, Scharenberg M, Mold JE, ..., Marquardt N, Michaëlsson J
Proc. Natl. Acad. Sci. U.S.A. 118 (11) e2016580118 [2021-03-16; online 2021-04-11]
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The Fennoscandian Shield deep terrestrial virosphere suggests slow motion 'boom and burst' cycles.
Holmfeldt K, Nilsson E, Simone D, ..., Bertilsson S, Dopson M
Commun Biol 4 (1) 307 [2021-03-08; online 2021-03-08]
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Single cell transcriptomics of primate sensory neurons identifies cell types associated with chronic pain.
Kupari J, Usoskin D, Parisien M, ..., Diatchenko L, Ernfors P
Nat Commun 12 (1) 1510 [2021-03-08; online 2021-03-08]
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Heterogeneous Hunter-Gatherer and Steppe-Related Ancestries in Late Neolithic and Bell Beaker Genomes from Present-Day France.
Seguin-Orlando A, Donat R, Der Sarkissian C, ..., Guilaine J, Orlando L
Curr. Biol. 31 (5) 1072-1083.e10 [2021-03-08; online 2021-01-13]
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Divergence in Coding Sequence and Expression of Different Functional Categories of Immune Genes between Two Wild Rodent Species.
Zhong X, Lundberg M, Råberg L
Genome Biol Evol 13 (3) - [2021-03-01; online 2021-02-11]
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Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics.
Muus C, Luecken MD, Eraslan G, ..., NHLBI LungMap Consortium , Human Cell Atlas Lung Biological Network
Nat. Med. 27 (3) 546-559 [2021-03-00; online 2021-03-02]
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RNA transcript response by an Acidithiobacillus spp. mixed culture reveals adaptations to growth on arsenopyrite.
Barragán CE, Márquez MA, Dopson M, Montoya D
Extremophiles 25 (2) 143-158 [2021-03-00; online 2021-02-22]
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Million-year-old DNA sheds light on the genomic history of mammoths.
van der Valk T, Pečnerová P, Díez-Del-Molino D, ..., Götherström A, Dalén L
Nature 591 (7849) 265-269 [2021-03-00; online 2021-02-17]
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Cyclin A2 localises in the cytoplasm at the S/G2 transition to activate PLK1.
Silva Cascales H, Burdova K, Middleton A, ..., Macurek L, Lindqvist A
Life Sci. Alliance 4 (3) e202000980 [2021-03-00; online 2021-01-05]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Comparative Fungal Community Analyses Using Metatranscriptomics and Internal Transcribed Spacer Amplicon Sequencing from Norway Spruce.
Schneider AN, Sundh J, Sundström G, ..., Hurry V, Street NR
mSystems 6 (1) - [2021-02-16; online 2021-02-16]
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Distinct subtypes of proprioceptive dorsal root ganglion neurons regulate adaptive proprioception in mice.
Wu H, Petitpré C, Fontanet P, ..., Hadjab S, Lallemend F
Nat Commun 12 (1) 1026 [2021-02-15; online 2021-02-15]
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Asymmetric introgression reveals the genetic architecture of a plumage trait.
Semenov GA, Linck E, Enbody ED, ..., Andersson L, Taylor SA
Nat Commun 12 (1) 1019 [2021-02-15; online 2021-02-15]
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Temperature Stress Induces Shift From Co-Existence to Competition for Organic Carbon in Microalgae-Bacterial Photobioreactor Community - Enabling Continuous Production of Microalgal Biomass.
Sörenson E, Capo E, Farnelid H, Lindehoff E, Legrand C
Front Microbiol 12 (-) 607601 [2021-02-11; online 2021-02-11]
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PubMed DOI Crossref
The one-carbon pool controls mitochondrial energy metabolism via complex I and iron-sulfur clusters.
Schober FA, Moore D, Atanassov I, ..., Freyer C, Wredenberg A
Sci Adv 7 (8) - [2021-02-00; online 2021-02-19]
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Spatiotemporal dissection of the cell cycle with single-cell proteogenomics.
Mahdessian D, Cesnik AJ, Gnann C, ..., Sullivan DP, Lundberg E
Nature 590 (7847) 649-654 [2021-02-00; online 2021-02-24]
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A recently isolated human commensal Escherichia coli ST10 clone member mediates enhanced thermotolerance and tetrathionate respiration on a P1 phage-derived IncY plasmid.
Kamal SM, Cimdins-Ahne A, Lee C, ..., Mogk A, Römling U
Mol. Microbiol. 115 (2) 255-271 [2021-02-00; online 2020-10-12]
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The Importance of Sex in the Discovery of Colorectal Cancer Prognostic Biomarkers.
Hases L, Ibrahim A, Chen X, ..., Hartman J, Williams C
Int J Mol Sci 22 (3) 1354 [2021-01-29; online 2021-01-29]
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Endophilin A2 deficiency protects rodents from autoimmune arthritis by modulating T cell activation.
Norin U, Rintisch C, Meng L, ..., Bäckdahl L, Holmdahl R
Nat Commun 12 (1) 610 [2021-01-27; online 2021-01-27]
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Ecological adaptation in European eels is based on phenotypic plasticity.
Enbody ED, Pettersson ME, Sprehn CG, ..., Wickström H, Andersson L
Proc. Natl. Acad. Sci. U.S.A. 118 (4) e2022620118 [2021-01-26; online 2021-01-23]
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Sex-dimorphic genetic effects and novel loci for fasting glucose and insulin variability.
Lagou V, Mägi R, Hottenga JJ, ..., Prokopenko I, Meta-Analyses of Glucose and Insulin-related traits Consortium (MAGIC)
Nat Commun 12 (1) 24 [2021-01-05; online 2021-01-05]
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Severe congenital neutropenia-associated JAGN1 mutations unleash a calpain-dependent cell death programme in myeloid cells.
Khandagale A, Holmlund T, Entesarian M, ..., Nordenskjöld M, Fadeel B
Br. J. Haematol. 192 (1) 200-211 [2021-01-00; online 2020-11-18]
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Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird-of-paradise.
Peona V, Blom MPK, Xu L, ..., Irestedt M, Suh A
Mol Ecol Resour 21 (1) 263-286 [2021-01-00; online 2020-10-10]
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Human population dynamics and Yersinia pestis in ancient northeast Asia.
Kılınç GM, Kashuba N, Koptekin D, ..., Storå J, Götherström A
Sci Adv 7 (2) - [2021-01-00; online 2021-01-06]
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Host plant diet affects growth and induces altered gene expression and microbiome composition in the wood white (Leptidea sinapis) butterfly.
Näsvall K, Wiklund C, Mrazek V, ..., Vila R, Backström N
Mol. Ecol. 30 (2) 499-516 [2021-01-00; online 2020-12-14]
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Evaluating totipotency using criteria of increasing stringency.
Posfai E, Schell JP, Janiszewski A, ..., Lanner F, Rossant J
Nat Cell Biol 23 (1) 49-60 [2021-01-00; online 2021-01-08]
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Diversification of molecularly defined myenteric neuron classes revealed by single-cell RNA sequencing.
Morarach K, Mikhailova A, Knoflach V, ..., Ernfors P, Marklund U
Nat. Neurosci. 24 (1) 34-46 [2021-01-00; online 2020-12-07]
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Year 2020

PubMed DOI Crossref
Genomic Adaptations and Evolutionary History of the Extinct Scimitar-Toothed Cat, Homotherium latidens.
Barnett R, Westbury MV, Sandoval-Velasco M, ..., Yamaguchi N, Gilbert MTP
Curr. Biol. 30 (24) 5018-5025.e5 [2020-12-21; online 2020-10-15]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Moose genomes reveal past glacial demography and the origin of modern lineages.
Dussex N, Alberti F, Heino MT, ..., Dalén L, Díez-Del-Molino D
BMC Genomics 21 (1) 854 [2020-12-02; online 2020-12-02]
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Features of increased malignancy in eosinophilic clear cell renal cell carcinoma.
Nilsson H, Lindgren D, Axelson H, ..., Lundgren J, Johansson ME
J. Pathol. 252 (4) 384-397 [2020-12-00; online 2020-09-24]
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Effect of RNA silencing suppression activity of chrysanthemum virus B p12 protein on small RNA species.
Vetukuri RR, Kalyandurg PB, Saripella GV, ..., Grenville-Briggs LJ, Savenkov EI
Arch Virol 165 (12) 2953-2959 [2020-12-00; online 2020-10-10]
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PubMed DOI Crossref
Deep sequencing detects human papillomavirus (HPV) in cervical cancers negative for HPV by PCR.
Arroyo Mühr LS, Lagheden C, Lei J, ..., Sundström K, Dillner J
Br. J. Cancer 123 (12) 1790-1795 [2020-12-00; online 2020-10-06]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Competitive mapping allows for the identification and exclusion of human DNA contamination in ancient faunal genomic datasets.
Feuerborn TR, Palkopoulou E, van der Valk T, ..., Dalén L, Díez-Del-Molino D
BMC Genomics 21 (1) 844 [2020-11-30; online 2020-11-30]
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Immobilization of sulfate and thiosulfate-reducing biomass on sand under haloalkaline conditions.
Sousa JAB, Bolgár A, Christel S, ..., Stams AJM, Plugge CM
Sci. Total Environ. 745 (-) 141017 [2020-11-25; online 2020-07-22]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Genome-wide identification of Argonautes in Solanaceae with emphasis on potato.
Liao Z, Hodén KP, Singh RK, Dixelius C
Sci Rep 10 (1) 20577 [2020-11-25; online 2020-11-25]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Distinct oligodendrocyte populations have spatial preference and different responses to spinal cord injury
Floriddia EM, Lourenço T, Zhang S, ..., Nilsson M, Castelo-Branco G
Nat Commun 11 (1) 5860 [2020-11-17; online 2020-11-17]
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Evaluation of the efficiency of genomic versus pedigree predictions for growth and wood quality traits in Scots pine.
Calleja-Rodriguez A, Pan J, Funda T, ..., Abrahamsson S, Wu HX
BMC Genomics 21 (1) 796 [2020-11-16; online 2020-11-16]
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Genome-Scale Mapping Reveals Complex Regulatory Activities of RpoN in Yersinia pseudotuberculosis.
Mahmud AKMF, Nilsson K, Fahlgren A, ..., Avican K, Fällman M
mSystems 5 (6) - [2020-11-10; online 2020-11-10]
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Identification of candidate genetic variants and altered protein expression in neural stem and mature neural cells support altered microtubule function to be an essential component in bipolar disorder.
Truvé K, Parris TZ, Vizlin-Hodzic D, ..., Ågren H, Funa K
Transl Psychiatry 10 (1) 390 [2020-11-09; online 2020-11-09]
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Point-of-Care Approaches for Meningitis Diagnosis in a Low-Resource Setting (Southwestern Uganda): Observational Cohort Study Protocol of the "PI-POC" Trial.
Gaudenzi G, Kumbakumba E, Rasti R, ..., Mwanga-Amumpaire J, Alfvén T
JMIR Res Protoc 9 (11) e21430 [2020-11-04; online 2020-11-04]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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MYC as a driver of stochastic chromatin networks: implications for the fitness of cancer cells.
Sumida N, Sifakis EG, Kiani NA, ..., Göndör A, Ohlsson R
Nucleic Acids Res. 48 (19) 10867-10876 [2020-11-04; online 2020-10-15]
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Evolution from adherent to suspension: systems biology of HEK293 cell line development.
Malm M, Saghaleyni R, Lundqvist M, ..., Nielsen J, Rockberg J
Sci Rep 10 (1) 18996 [2020-11-04; online 2020-11-04]
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From Inquilines to Gall Inducers: Genomic Signature of a Life-Style Transition in Synergus Gall Wasps.
Gobbo E, Lartillot N, Hearn J, ..., Ide T, Ronquist F
Genome Biol Evol 12 (11) 2060-2073 [2020-11-03; online 2020-09-29]
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Putative Epigenetic Biomarkers of Stress in Red Blood Cells of Chickens Reared Across Different Biomes.
Pértille F, Ibelli AMG, Sharif ME, ..., Guerrero-Bosagna C, Coutinho LL
Front Genet 11 (-) 508809 [2020-11-02; online 2020-11-02]
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Interspecific Gene Flow and the Evolution of Specialization in Black and White Rhinoceros.
Moodley Y, Westbury MV, Russo IM, ..., Dalén L, Bruford MW
Mol. Biol. Evol. 37 (11) 3105-3117 [2020-11-01; online 2020-06-26]
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Leaf shape in Populus tremula is a complex, omnigenic trait.
Mähler N, Schiffthaler B, Robinson KM, ..., Hvidsten TR, Street NR
Ecol Evol 10 (21) 11922-11940 [2020-11-00; online 2020-10-13]
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Dense sampling of bird diversity increases power of comparative genomics.
Feng S, Stiller J, Deng Y, ..., Paten B, Zhang G
Nature 587 (7833) 252-257 [2020-11-00; online 2020-11-11]
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Cytogenetically visible inversions are formed by multiple molecular mechanisms.
Pettersson M, Grochowski CM, Wincent J, ..., Carvalho CMB, Lindstrand A
Hum. Mutat. 41 (11) 1979-1998 [2020-11-00; online 2020-10-01]
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PubMed DOI Crossref
Origins and genetic legacy of prehistoric dogs.
Bergström A, Frantz L, Schmidt R, ..., Larson G, Skoglund P
Science 370 (6516) 557-564 [2020-10-30; online 2020-10-29]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Horizontal Gene Transfer and Tandem Duplication Shape the Unique CAZyme Complement of the Mycoparasitic Oomycetes Pythium oligandrum and Pythium periplocum.
Liang D, Andersen CB, Vetukuri RR, Dou D, Grenville-Briggs LJ
Front Microbiol 11 (-) 581698 [2020-10-29; online 2020-10-29]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Population genomics reveals lack of greater white-fronted introgression into the Swedish lesser white-fronted goose.
Díez-Del-Molino D, von Seth J, Gyllenstrand N, ..., Sjögren-Gulve P, Dalén L
Sci Rep 10 (1) 18347 [2020-10-27; online 2020-10-27]
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Novel pathogenic genomic variants leading to autosomal dominant and recessive Robinow syndrome.
Zhang C, Mazzeu JF, Eisfeldt J, ..., Sutton VR, Carvalho CMB
Am. J. Med. Genet. A - (-) - [2020-10-13; online 2020-10-13]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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GeneSetCluster: a tool for summarizing and integrating gene-set analysis results.
Ewing E, Planell-Picola N, Jagodic M, Gomez-Cabrero D
BMC Bioinformatics 21 (1) 443 [2020-10-07; online 2020-10-07]
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Transcriptional responses in developing lesions of European common ash (Fraxinus excelsior) reveal genes responding to infection by Hymenoscyphus fraxineus.
Sahraei SE, Cleary M, Stenlid J, Brandström Durling M, Elfstrand M
BMC Plant Biol. 20 (1) 455 [2020-10-06; online 2020-10-06]
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PubMed DOI Crossref
Pre-extinction Demographic Stability and Genomic Signatures of Adaptation in the Woolly Rhinoceros.
Lord E, Dussex N, Kierczak M, ..., Götherström A, Dalén L
Curr. Biol. 30 (19) 3871-3879.e7 [2020-10-05; online 2020-08-13]
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Notch activation in the mouse mammary luminal lineage leads to ductal hyperplasia and altered partitioning of luminal cell subtypes.
Phoon YP, Chivukula IV, Tsoi YL, ..., Kuiper R, Lendahl U
Exp. Cell Res. 395 (1) 112156 [2020-10-01; online 2020-07-22]
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High-fat diet and estrogen impacts the colon and its transcriptome in a sex-dependent manner.
Hases L, Archer A, Indukuri R, ..., Korach-André M, Williams C
Sci Rep 10 (1) 16160 [2020-09-30; online 2020-09-30]
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Labile Dissolved Organic Matter Compound Characteristics Select for Divergence in Marine Bacterial Activity and Transcription.
Pontiller B, Martínez-García S, Lundin D, Pinhassi J
Front Microbiol 11 (-) 588778 [2020-09-25; online 2020-09-25]
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Generation of Sequencing Libraries for Structural Analysis of Bacterial 5' UTRs.
Ignatov D, Vaitkevicius K, Johansson J
STAR Protoc 1 (2) 100046 [2020-09-18; online 2020-06-06]
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Compositional and functional differences of the mucosal microbiota along the intestine of healthy individuals.
Vaga S, Lee S, Ji B, ..., Engstrand L, Shoaie S
Sci Rep 10 (1) 14977 [2020-09-11; online 2020-09-11]
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PubMed DOI Crossref
Parallel Evolution of Bower-Building Behavior in Two Groups of Bowerbirds Suggested by Phylogenomics.
Ericson PGP, Irestedt M, Nylander JAA, ..., Joseph L, Qu Y
Syst. Biol. 69 (5) 820-829 [2020-09-01; online 2020-05-18]
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The impact of damage-associated molecular patterns on the neurotransmitter release and gene expression in the ex vivo rat carotid body.
Mkrtchian S, Kåhlin J, Gómez-Galán M, ..., Erlandsson Harris H, Eriksson LI
Exp. Physiol. 105 (9) 1634-1647 [2020-09-00; online 2020-07-24]
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Reconstructing marine plankton food web interactions using DNA metabarcoding.
Zamora-Terol S, Novotny A, Winder M
Mol. Ecol. 29 (17) 3380-3395 [2020-09-00; online 2020-08-09]
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Linked-read sequencing enables haplotype-resolved resequencing at population scale.
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Mol Ecol Resour 20 (5) 1311-1322 [2020-09-00; online 2020-06-29]
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Index hopping on the Illumina HiseqX platform and its consequences for ancient DNA studies.
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Genetic association of gemcitabine/carboplatin-induced leukopenia and neutropenia in non-small cell lung cancer patients using whole-exome sequencing.
Svedberg A, Björn N, Sigurgeirsson B, ..., Lundeberg J, Gréen H
Lung Cancer 147 (-) 106-114 [2020-09-00; online 2020-07-12]
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DNA methylation variation in the brain of laying hens in relation to differential behavioral patterns.
Guerrero-Bosagna C, Pértille F, Gomez Y, ..., Voelkl B, Toscano MJ
Comp Biochem Physiol Part D Genomics Proteomics 35 (-) 100700 [2020-09-00; online 2020-06-02]
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A Shh/Gli-driven three-node timer motif controls temporal identity and fate of neural stem cells.
Dias JM, Alekseenko Z, Jeggari A, ..., Iber D, Ericson J
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Four SARS-CoV-2 Genome Sequences from Late April in Stockholm, Sweden, Reveal a Rare Mutation in the Spike Protein.
Soratto TAT, Darban H, Bjerkner A, ..., Allander T, Andersson B
Microbiol Resour Announc 9 (35) - [2020-08-27; online 2020-08-27]
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Whole-genome sequencing and gene network modules predict gemcitabine/carboplatin-induced myelosuppression in non-small cell lung cancer patients.
Björn N, Badam TVS, Spalinskas R, ..., Gustafsson M, Gréen H
npj Syst Biol Appl 6 (1) 25 [2020-08-24; online 2020-08-24]
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Rapid size change associated with intra-island evolutionary radiation in extinct Caribbean "island-shrews".
Woods R, Turvey ST, Brace S, ..., Brown MJF, Barnes I
BMC Evol. Biol. 20 (1) 106 [2020-08-18; online 2020-08-18]
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Gsta4 controls apoptosis of differentiating adult oligodendrocytes during homeostasis and remyelination via the mitochondria-associated Fas-Casp8-Bid-axis.
Carlström KE, Zhu K, Ewing E, ..., Castelo-Branco G, Piehl F
Nat Commun 11 (1) 4071 [2020-08-13; online 2020-08-13]
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Transcriptional mutagenesis dramatically alters genome-wide p53 transactivation landscape.
Liang S, Ezerskyte M, Wang J, Pelechano V, Dreij K
Sci Rep 10 (1) 13513 [2020-08-11; online 2020-08-11]
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Uncovering the hidden diversity of litter-decomposition mechanisms in mushroom-forming fungi.
Floudas D, Bentzer J, Ahrén D, ..., Persson P, Tunlid A
ISME J 14 (8) 2046-2059 [2020-08-00; online 2020-05-07]
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The compact genome of Giardia muris reveals important steps in the evolution of intestinal protozoan parasites.
Xu F, Jiménez-González A, Einarsson E, ..., Svärd SG, Jerlström-Hultqvist J
Microb Genom 6 (8) - [2020-08-00; online 2020-07-03]
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Preclinical safety studies of human embryonic stem cell-derived retinal pigment epithelial cells for the treatment of age-related macular degeneration.
Petrus-Reurer S, Kumar P, Padrell Sánchez S, ..., Kvanta A, Lanner F
Stem Cells Transl Med 9 (8) 936-953 [2020-08-00; online 2020-04-22]
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A 3D Cell Culture Model Identifies Wnt/β-Catenin Mediated Inhibition of p53 as a Critical Step during Human Hepatocyte Regeneration.
Oliva-Vilarnau N, Vorrink SU, Ingelman-Sundberg M, Lauschke VM
Adv Sci (Weinh) 7 (15) 2000248 [2020-08-00; online 2020-06-23]
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Early Pleistocene origin and extensive intra-species diversity of the extinct cave lion.
Stanton DWG, Alberti F, Plotnikov V, ..., Skoglund P, Dalén L
Sci Rep 10 (1) 12621 [2020-07-28; online 2020-07-28]
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Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma.
Ji AL, Rubin AJ, Thrane K, ..., Lundeberg J, Khavari PA
Cell 182 (2) 497-514.e22 [2020-07-23; online 2020-06-23]
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Translating GWAS-identified loci for cardiac rhythm and rate using an in vivo image- and CRISPR/Cas9-based approach
von der Heyde B, Emmanouilidou A, Mazzaferro E, ..., Brooke HL, den Hoed M
Sci Rep 10 (1) 11831 [2020-07-16; online 2020-07-16]
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Seamless integration of image and molecular analysis for spatial transcriptomics workflows.
Bergenstråhle J, Larsson L, Lundeberg J
BMC Genomics 21 (1) 482 [2020-07-14; online 2020-07-14]
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Systems biology of acidophile biofilms for efficient metal extraction.
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Sci Data 7 (1) 215 [2020-07-07; online 2020-07-07]
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Low Abundance of Methanotrophs in Sediments of Shallow Boreal Coastal Zones With High Water Methane Concentrations.
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Front Microbiol 11 (-) 1536 [2020-07-07; online 2020-07-07]
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Odorant receptor phylogeny confirms conserved channels for sex pheromone and host plant signals in tortricid moths.
Gonzalez F, Borrero-Echeverry F, Jósvai JK, ..., Bengtsson M, Walker WB
Ecol Evol 10 (14) 7334-7348 [2020-07-00; online 2020-06-30]
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Meiofauna improve oxygenation and accelerate sulfide removal in the seasonally hypoxic seabed.
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Mar Environ Res 159 (-) 104968 [2020-07-00; online 2020-03-29]
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Gastric Microbiota in a Low-Helicobacter pylori Prevalence General Population and Their Associations With Gastric Lesions.
Ndegwa N, Ploner A, Andersson AF, ..., Agreus L, Ye W
Clin Transl Gastroenterol 11 (7) e00191 [2020-07-00; online 2020-08-09]
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Comparison of spleen transcriptomes of two wild rodent species reveals differences in the immune response against Borrelia afzelii.
Zhong X, Lundberg M, Råberg L
Ecol Evol 10 (13) 6421-6434 [2020-07-00; online 2020-05-25]
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CAM-Delam: an in vivo approach to visualize and quantify the delamination and invasion capacity of human cancer cells.
Palaniappan TK, Šlekienė L, Jonasson AK, Gilthorpe J, Gunhaga L
Sci Rep 10 (1) 10472 [2020-06-26; online 2020-06-26]
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RNA-seq reveals altered gene expression levels in proximal tubular cell cultures compared to renal cortex but not during early glucotoxicity.
Nilsson LM, Castresana-Aguirre M, Scott L, Brismar H
Sci Rep 10 (1) 10390 [2020-06-25; online 2020-06-25]
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Skeletal Muscle Transcriptomic Comparison between Long-Term Trained and Untrained Men and Women.
Chapman MA, Arif M, Emanuelsson EB, ..., Mardinoglu A, Sundberg CJ
Cell Rep 31 (12) 107808 [2020-06-23; online 2020-06-25]
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Altered levels of CSF proteins in patients with FTD, presymptomatic mutation carriers and non-carriers.
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Transl Neurodegener 9 (1) 27 [2020-06-23; online 2020-06-23]
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CYCLIN-B1/2 and -D1 act in opposition to coordinate cortical progenitor self-renewal and lineage commitment.
Hagey DW, Topcic D, Kee N, ..., Perlmann T, Muhr J
Nat Commun 11 (1) 2898 [2020-06-09; online 2020-06-09]
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Size-Dependent Pulmonary Impact of Thin Graphene Oxide Sheets in Mice: Toward Safe-by-Design.
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Single-cell RNA counting at allele and isoform resolution using Smart-seq3.
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Nat. Biotechnol. 38 (6) 708-714 [2020-06-00; online 2020-05-04]
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Genome-wide CRISPR screen identifies ZIC2 as an essential gene that controls the cell fate of early mesodermal precursors to human heart progenitors.
Xu J, Zhou C, Foo KS, ..., Sahara M, Chien KR
Stem Cells 38 (6) 741-755 [2020-06-00; online 2020-03-10]
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Benchmarking single-cell RNA-sequencing protocols for cell atlas projects.
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Nat. Biotechnol. 38 (6) 747-755 [2020-06-00; online 2020-04-06]
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Balancing selection in Pattern Recognition Receptor signalling pathways is associated with gene function and pleiotropy in a wild rodent.
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Mol. Ecol. 29 (11) 1990-2003 [2020-06-00; online 2020-06-03]
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Activated carbon stimulates microbial diversity and PAH biodegradation under anaerobic conditions in oil-polluted sediments.
Bonaglia S, Broman E, Brindefalk B, ..., Udekwu K, Gunnarsson JS
Chemosphere 248 (-) 126023 [2020-06-00; online 2020-01-24]
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Myocardial micro-biopsy procedure for molecular characterization with increased precision and reduced trauma.
Grankvist R, Chireh A, Sandell M, ..., Daub CO, Holmin S
Sci Rep 10 (1) 8029 [2020-05-15; online 2020-05-15]
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Srebf1 Controls Midbrain Dopaminergic Neurogenesis.
Toledo EM, Yang S, Gyllborg D, ..., Linnarsson S, Arenas E
Cell Rep 31 (5) 107601 [2020-05-05; online 2020-05-07]
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Rare variants in dynein heavy chain genes in two individuals with situs inversus and developmental dyslexia: a case report.
Bieder A, Einarsdottir E, Matsson H, ..., Kere J, Tapia-Páez I
BMC Med. Genet. 21 (1) 87 [2020-05-01; online 2020-05-01]
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Differential Expression of Immune Genes between Two Closely Related Beetle Species with Different Immunocompetence following Attack by Asecodes parviclava.
Yang X, Fors L, Slotte T, ..., Wheat CW, Hambäck PA
Genome Biol Evol 12 (5) 522-534 [2020-05-01; online 2020-04-14]
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Whole-genome sequencing reveals complex chromosome rearrangement disrupting NIPBL in infant with Cornelia de Lange syndrome.
Plesser Duvdevani M, Pettersson M, Eisfeldt J, ..., Lindstrand A, Harel T
Am. J. Med. Genet. A 182 (5) 1143-1151 [2020-05-00; online 2020-03-03]
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Transcriptome profiling of Ewing sarcomas - treatment resistance pathways and IGF-dependency.
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Mol Oncol 14 (5) 1101-1117 [2020-05-00; online 2020-03-13]
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Next-Generation Sequencing Reveals Differential Responses to Acute versus Long-Term Exposures to Graphene Oxide in Human Lung Cells.
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Small 16 (21) e1907686 [2020-05-00; online 2020-03-29]
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Biodiversity between sand grains: Meiofauna composition across southern and western Sweden assessed by metabarcoding.
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Molecular profiling of driver events in metastatic uveal melanoma.
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Nat Commun 11 (1) 1894 [2020-04-20; online 2020-04-20]
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Genome-Scale Metabolic Modeling of Glioblastoma Reveals Promising Targets for Drug Development.
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Front Genet 11 (-) 381 [2020-04-17; online 2020-04-17]
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Whole-genome genotyping and resequencing reveal the association of a deletion in the complex interferon alpha gene cluster with hypothyroidism in dogs.
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BMC Genomics 21 (1) 307 [2020-04-16; online 2020-04-16]
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Automation of Spatial Transcriptomics library preparation to enable rapid and robust insights into spatial organization of tissues.
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BMC Genomics 21 (1) 298 [2020-04-15; online 2020-04-15]
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Generation of Retinal Pigment Epithelial Cells Derived from Human Embryonic Stem Cells Lacking Human Leukocyte Antigen Class I and II.
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Stem Cell Reports 14 (4) 648-662 [2020-04-14; online 2020-03-19]
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Draft Genome Sequence of the Urinary Catheter Isolate Enterobacter ludwigii CEB04 with High Biofilm Forming Capacity.
Shafeeq S, Wang X, Lünsdorf H, Brauner A, Römling U
Microorganisms 8 (4) 522 [2020-04-05; online 2020-04-05]
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Extensive Clonal Branching Shapes the Evolutionary History of High-Risk Pediatric Cancers.
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Cancer Res. 80 (7) 1512-1523 [2020-04-01; online 2020-02-10]
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Effects of whole-grain wheat, rye, and lignan supplementation on cardiometabolic risk factors in men with metabolic syndrome: a randomized crossover trial.
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Am. J. Clin. Nutr. 111 (4) 864-876 [2020-04-01; online 2020-02-26]
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Long-term application of Swedish sewage sludge on farmland does not cause clear changes in the soil bacterial resistome.
Rutgersson C, Ebmeyer S, Lassen SB, ..., Flach CF, Larsson DGJ
Environ Int 137 (-) 105339 [2020-04-00; online 2020-02-06]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Genes and variants in hematopoiesis-related pathways are associated with gemcitabine/carboplatin-induced thrombocytopenia.
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Pharmacogenomics J. 20 (2) 179-191 [2020-04-00; online 2019-10-15]
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Transcriptome Profiling and Toxicity Following Long-Term, Low Dose Exposure of Human Lung Cells to Ni and NiO Nanoparticles-Comparison with NiCl2.
Gliga AR, Di Bucchianico S, Åkerlund E, Karlsson HL
Nanomaterials (Basel) 10 (4) 649 [2020-03-31; online 2020-03-31]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Mutations in COL1A1/A2 and CREB3L1 are associated with oligodontia in osteogenesis imperfecta.
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Orphanet J Rare Dis 15 (1) 80 [2020-03-31; online 2020-03-31]
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An mRNA-mRNA Interaction Couples Expression of a Virulence Factor and Its Chaperone in Listeria monocytogenes.
Ignatov D, Vaitkevicius K, Durand S, ..., Condon C, Johansson J
Cell Rep 30 (12) 4027-4040.e7 [2020-03-24; online 2020-03-27]
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Inherited DNA Repair Gene Mutations in Men with Lethal Prostate Cancer.
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Genes 11 (3) 314 [2020-03-14; online 2020-03-14]
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Ecosystem-wide metagenomic binning enables prediction of ecological niches from genomes.
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Commun Biol 3 (1) 119 [2020-03-13; online 2020-03-13]
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Comparing the Performance of Microsatellites and RADseq in Population Genetic Studies: Analysis of Data for Pike (Esox lucius) and a Synthesis of Previous Studies.
Sunde J, Yıldırım Y, Tibblin P, Forsman A
Front Genet 11 (-) 218 [2020-03-13; online 2020-03-13]
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Uncovering diversity and metabolic spectrum of animals in dead zone sediments.
Broman E, Bonaglia S, Holovachov O, ..., Hall POJ, Nascimento FJA
Commun Biol 3 (1) 106 [2020-03-06; online 2020-03-06]
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An atlas of the protein-coding genes in the human, pig, and mouse brain.
Sjöstedt E, Zhong W, Fagerberg L, ..., Uhlén M, Mulder J
Science 367 (6482) eaay5947 [2020-03-06; online 2020-03-07]
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The Molecular Anatomy of Mouse Skin during Hair Growth and Rest.
Joost S, Annusver K, Jacob T, ..., Sandberg R, Kasper M
Cell Stem Cell 26 (3) 441-457.e7 [2020-03-05; online 2020-02-27]
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The nf-core framework for community-curated bioinformatics pipelines.
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Nat. Biotechnol. 38 (3) 276-278 [2020-03-00; online 2020-02-15]
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Hyena paleogenomes reveal a complex evolutionary history of cross-continental gene flow between spotted and cave hyena.
Westbury MV, Hartmann S, Barlow A, ..., Heller R, Hofreiter M
Sci Adv 6 (11) eaay0456 [2020-03-00; online 2020-03-13]
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Functionally distinct subgroups of oligodendrocyte precursor cells integrate neural activity and execute myelin formation.
Marisca R, Hoche T, Agirre E, ..., Castelo-Branco G, Czopka T
Nat. Neurosci. 23 (3) 363-374 [2020-03-00; online 2020-02-17]
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Evidence for widespread selection in shaping the genomic landscape during speciation of Populus.
Wang J, Street NR, Park EJ, Liu J, Ingvarsson PK
Mol. Ecol. 29 (6) 1120-1136 [2020-03-00; online 2020-03-09]
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Dominance of Mating Type A1 and Indication of Epigenetic Effects During Early Stages of Mating in Phytophthora infestans.
Tzelepis G, Hodén KP, Fogelqvist J, ..., Vetukuri RR, Dixelius C
Front Microbiol 11 (-) 252 [2020-02-21; online 2020-02-21]
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Biomolecular analyses reveal the age, sex and species identity of a near-intact Pleistocene bird carcass.
Dussex N, Stanton DWG, Sigeman H, ..., Hansson B, Dalén L
Commun Biol 3 (1) 84 [2020-02-21; online 2020-02-21]
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Validation of Novel Prognostic Biomarkers for Early-Stage Clear-Cell, Endometrioid and Mucinous Ovarian Carcinomas Using Immunohistochemistry.
Engqvist H, Parris TZ, Kovács A, ..., Karlsson P, Helou K
Front Oncol 10 (-) 162 [2020-02-18; online 2020-02-18]
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Whole genome sequencing unveils genetic heterogeneity in optic nerve hypoplasia.
Dahl S, Pettersson M, Eisfeldt J, ..., Anderlid BM, Lindstrand A
PLoS ONE 15 (2) e0228622 [2020-02-10; online 2020-02-10]
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Demography and Natural Selection Have Shaped Genetic Variation in the Widely Distributed Conifer Norway Spruce (Picea abies).
Wang X, Bernhardsson C, Ingvarsson PK
Genome Biol Evol 12 (2) 3803-3817 [2020-02-01; online 2020-01-21]
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The antimalarial drug amodiaquine stabilizes p53 through ribosome biogenesis stress, independently of its autophagy-inhibitory activity.
Espinoza JA, Zisi A, Kanellis DC, ..., Lindström MS, Bartek J
Cell Death Differ. 27 (2) 773-789 [2020-02-00; online 2019-07-08]
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Painting of Fourth and the X-Linked 1.688 Satellite in D. melanogaster is Involved in Chromosome-Wide Gene Regulation.
Ekhteraei-Tousi S, Lewerentz J, Larsson J
Cells 9 (2) 323 [2020-01-30; online 2020-01-30]
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Diversity and Host Interactions Among Virulent and Temperate Baltic Sea Flavobacterium Phages.
Nilsson E, Bayfield OW, Lundin D, Antson AA, Holmfeldt K
Viruses 12 (2) 158 [2020-01-30; online 2020-01-30]
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Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants.
Garcia M, Juhos S, Larsson M, ..., Käller M, Nystedt B
F1000Res 9 (-) 63 [2020-01-29; online 2020-01-29]
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Reverse engineering directed gene regulatory networks from transcriptomics and proteomics data of biomining bacterial communities with approximate Bayesian computation and steady-state signalling simulations.
Buetti-Dinh A, Herold M, Christel S, ..., Friedman R, Dopson M
BMC Bioinformatics 21 (1) 23 [2020-01-21; online 2020-01-21]
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A spontaneous mitonuclear epistasis converging on Rieske Fe-S protein exacerbates complex III deficiency in mice.
Purhonen J, Grigorjev V, Ekiert R, ..., Fellman V, Kallijärvi J
Nat Commun 11 (1) 322 [2020-01-16; online 2020-01-16]
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Gene regulatory response to hyposalinity in the brown seaweed Fucus vesiculosus.
Rugiu L, Panova M, Pereyra RT, Jormalainen V
BMC Genomics 21 (1) 42 [2020-01-13; online 2020-01-13]
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Development and characterization of an EMS-mutagenized wheat population and identification of salt-tolerant wheat lines.
Lethin J, Shakil SSM, Hassan S, ..., Olsson O, Aronsson H
BMC Plant Biol. 20 (1) 18 [2020-01-13; online 2020-01-13]
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A regulatory role for CHD2 in myelopoiesis.
Shahin Varnoosfaderani F, Palau A, Dong W, ..., Svensson JP, Lennartsson A
Epigenetics 15 (6-7) 702-714 [2020-01-10; online 2020-01-10]
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Evolutionary History, Genomic Adaptation to Toxic Diet, and Extinction of the Carolina Parakeet.
Gelabert P, Sandoval-Velasco M, Serres A, ..., Gilbert MTP, Lalueza-Fox C
Curr. Biol. 30 (1) 108-114.e5 [2020-01-06; online 2019-12-12]
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Discovery of Novel Sequences in 1,000 Swedish Genomes.
Eisfeldt J, Mårtensson G, Ameur A, Nilsson D, Lindstrand A
Mol. Biol. Evol. 37 (1) 18-30 [2020-01-01; online 2019-09-29]
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Genome-wide signatures of environmental adaptation in European aspen (Populus tremula) under current and future climate conditions.
Ingvarsson PK, Bernhardsson C
Evol Appl 13 (1) 132-142 [2020-01-00; online 2019-04-02]
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Year 2019

PubMed DOI Crossref
A Comprehensive Sequencing-Based Analysis of Allelic Methylation Patterns in Hemostatic Genes in Human Liver
Olsson Lindvall M, Davila Lopez M, Klasson S, ..., Stanne TM, Jern C
Thromb. Haemost. 120 (02) 229-242 [2019-12-30; online 2019-12-30]
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Consequences of past climate change and recent human persecution on mitogenomic diversity in the arctic fox.
Larsson P, von Seth J, Hagen IJ, ..., Stanton DWG, Dalén L
Philos. Trans. R. Soc. Lond., B, Biol. Sci. 374 (1788) 20190212 [2019-12-23; online 2019-11-04]
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Sequencing detects human papillomavirus in some apparently HPV-negative invasive cervical cancers.
Arroyo Mühr LS, Lagheden C, Eklund C, ..., Sundström K, Dillner J
J. Gen. Virol. - (-) - [2019-12-20; online 2019-12-20]
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A genome-wide transcriptomic analysis of protein-coding genes in human blood cells.
Uhlen M, Karlsson MJ, Zhong W, ..., Fagerberg L, Brodin P
Science 366 (6472) - [2019-12-20; online 2019-12-21]
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A transposable element insertion is associated with an alternative life history strategy.
Woronik A, Tunström K, Perry MW, ..., Käkelä R, Wheat CW
Nat Commun 10 (1) 5757 [2019-12-17; online 2019-12-17]
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NGS targeted screening of 100 Scandinavian patients with coronal synostosis.
Topa A, Rohlin A, Andersson MK, ..., Stenman G, Kölby L
Am. J. Med. Genet. A - (-) - [2019-12-14; online 2019-12-14]
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PubMed DOI Crossref
BEN-solo factors partition active chromatin to ensure proper gene activation in Drosophila.
Ueberschär M, Wang H, Zhang C, ..., Wen J, Dai Q
Nat Commun 10 (1) 5700 [2019-12-13; online 2019-12-13]
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A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart.
Asp M, Giacomello S, Larsson L, ..., Sylvén C, Lundeberg J
Cell 179 (7) 1647-1660.e19 [2019-12-12; online 2019-12-14]
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Cell Type-Specific Expression of Testis Elevated Genes Based on Transcriptomics and Antibody-Based Proteomics.
Pineau C, Hikmet F, Zhang C, ..., Uhlén M, Lindskog C
J. Proteome Res. 18 (12) 4215-4230 [2019-12-06; online 2019-08-29]
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PubMed DOI Crossref
Specialized sledge dogs accompanied Inuit dispersal across the North American Arctic.
Ameen C, Feuerborn TR, Brown SK, ..., Darwent CM, Evin A
Proc. Biol. Sci. 286 (1916) 20191929 [2019-12-04; online 2019-11-27]
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PubMed DOI Crossref
High throughput barcoding method for genome-scale phasing.
Redin D, Frick T, Aghelpasand H, ..., Olsen RA, Ahmadian A
Sci Rep 9 (1) 18116 [2019-12-02; online 2019-12-02]
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Whole genome DNA sequencing provides an atlas of somatic mutagenesis in healthy human cells and identifies a tumor-prone cell type
Franco I, Helgadottir HT, Moggio A, ..., Supek F, Eriksson M
Genome Biol. 20 (1) - [2019-12-00; online 2019-12-18]
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Sewage effluent from an Indian hospital harbors novel carbapenemases and integron-borne antibiotic resistance genes
Marathe NP, Berglund F, Razavi M, ..., Kristiansson E, Larsson DGJ
Microbiome 7 (1) - [2019-12-00; online 2019-06-27]
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PECTIN ACETYLESTERASE9 Affects the Transcriptome and Metabolome and Delays Aphid Feeding.
Kloth KJ, Abreu IN, Delhomme N, ..., Moritz T, Albrectsen BR
Plant Physiol. 181 (4) 1704-1720 [2019-12-00; online 2019-09-24]
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Improved power and precision with whole genome sequencing data in genome-wide association studies of inflammatory biomarkers
Höglund J, Rafati N, Rask-Andersen M, ..., Ek WE, Johansson Å
Sci Rep 9 (1) - [2019-12-00; online 2019-11-14]
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Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast.
Morales HE, Faria R, Johannesson K, ..., Westram AM, Butlin RK
Sci Adv 5 (12) eaav9963 [2019-12-00; online 2019-12-04]
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Conbase: a software for unsupervised discovery of clonal somatic mutations in single cells through read phasing
Hård J, Al Hakim E, Kindblom M, ..., Mold JE, Frisén J
Genome Biol. 20 (1) - [2019-12-00; online 2019-04-01]
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An AP2/ERF transcription factor ERF139 coordinates xylem cell expansion and secondary cell wall deposition.
Wessels B, Seyfferth C, Escamez S, ..., Felten J, Tuominen H
New Phytol. 224 (4) 1585-1599 [2019-12-00; online 2019-07-02]
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ATAC-seq reveals alterations in open chromatin in pancreatic islets from subjects with type 2 diabetes
Bysani M, Agren R, Davegårdh C, ..., Bacos K, Ling C
Sci Rep 9 (1) - [2019-12-00; online 2019-05-23]
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A cell fitness selection model for neuronal survival during development
Wang Y, Wu H, Fontanet P, ..., Hadjab S, Lallemend F
Nat Commun 10 (1) - [2019-12-00; online 2019-09-12]
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A Spatiomolecular Map of the Striatum
Märtin A, Calvigioni D, Tzortzi O, ..., Wärnberg E, Meletis K
Cell Rep 29 (13) 4320-4333.e5 [2019-12-00; online 2019-12-00]
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Programmed DNA elimination of germline development genes in songbirds.
Kinsella CM, Ruiz-Ruano FJ, Dion-Côté AM, ..., Forstmeier W, Suh A
Nat Commun 10 (1) 5468 [2019-11-29; online 2019-11-29]
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PubMed DOI Crossref
The human secretome
Uhlén M, Karlsson MJ, Hober A, ..., Fagerberg L, Sivertsson Å
Sci. Signal. 12 (609) eaaz0274 [2019-11-26; online 2019-11-26]
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Fast and Efficient Fc-Specific Photoaffinity Labeling To Produce Antibody-DNA Conjugates.
Stiller C, Aghelpasand H, Frick T, ..., Ahmadian A, Karlström AE
Bioconjug. Chem. 30 (11) 2790-2798 [2019-11-20; online 2019-10-25]
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Inferring the Genomic Landscape of Recombination Rate Variation in European Aspen ( Populus tremula).
Apuli RP, Bernhardsson C, Schiffthaler B, ..., Street NR, Ingvarsson PK
G3 (Bethesda) - (-) - [2019-11-19; online 2019-11-19]
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Human induced pluripotent stem cells from two azoospermic patients with Klinefelter syndrome show similar X chromosome inactivation behavior to female pluripotent stem cells.
Panula S, Kurek M, Kumar P, ..., Lanner F, Stukenborg JB
Hum. Reprod. - (-) - [2019-11-19; online 2019-11-19]
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Lithium treatment reverses irradiation-induced changes in rodent neural progenitors and rescues cognition.
Zanni G, Goto S, Fragopoulou AF, ..., Hermanson O, Blomgren K
Mol. Psychiatry - (-) - [2019-11-14; online 2019-11-14]
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Effects of the Antimicrobial Peptide LL-37 and Innate Effector Mechanisms in Colistin-Resistant Klebsiella pneumoniae With mgrB Insertions.
Al-Farsi HM, Al-Adwani S, Ahmed S, ..., Giske CG, Bergman P
Front Microbiol 10 (-) 2632 [2019-11-14; online 2019-11-14]
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PubMed DOI Crossref
Carnivores, competition and genetic connectivity in the Anthropocene.
Creel S, Spong G, Becker M, ..., Schiffthaler B, Chifunte C
Sci Rep 9 (1) 16339 [2019-11-08; online 2019-11-08]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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From cytogenetics to cytogenomics: whole-genome sequencing as a first-line test comprehensively captures the diverse spectrum of disease-causing genetic variation underlying intellectual disability.
Lindstrand A, Eisfeldt J, Pettersson M, ..., Lundin J, Nilsson D
Genome Med 11 (1) 68 [2019-11-07; online 2019-11-07]
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Distinct Coastal Microbiome Populations Associated With Autochthonous- and Allochthonous-Like Dissolved Organic Matter.
Broman E, Asmala E, Carstensen J, Pinhassi J, Dopson M
Front Microbiol 10 (-) 2579 [2019-11-07; online 2019-11-07]
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Establishing arthropod community composition using metabarcoding: Surprising inconsistencies between soil samples and preservative ethanol and homogenate from Malaise trap catches.
Marquina D, Esparza-Salas R, Roslin T, Ronquist F
Mol Ecol Resour 19 (6) 1516-1530 [2019-11-00; online 2019-09-18]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Puma genomes from North and South America provide insights into the genomic consequences of inbreeding.
Saremi NF, Supple MA, Byrne A, ..., Wilmers CC, Shapiro B
Nat Commun 10 (1) 4769 [2019-10-18; online 2019-10-18]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Whole-genome sequencing of synchronous thyroid carcinomas identifies aberrant DNA repair in thyroid cancer dedifferentiation
Paulsson JO, Backman S, Wang N, ..., Zedenius J, Juhlin CC
J. Pathol - (-) - [2019-10-17; online 2019-10-17]
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Microbe-host interplay in atopic dermatitis and psoriasis.
Fyhrquist N, Muirhead G, Prast-Nielsen S, ..., Andersson B, Alenius H
Nat Commun 10 (1) 4703 [2019-10-16; online 2019-10-16]
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Metagenomes and metatranscriptomes from boreal potential and actual acid sulfate soil materials.
Högfors-Rönnholm E, Lopez-Fernandez M, Christel S, ..., Engblom S, Dopson M
Sci Data 6 (1) 207 [2019-10-16; online 2019-10-16]
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PubMed DOI Crossref
Above-below surface interactions mediate effects of seagrass disturbance on meiobenthic diversity, nematode and polychaete trophic structure.
Nascimento FJA, Dahl M, Deyanova D, ..., Creer S, Gullström M
Commun Biol 2 (-) 362 [2019-10-04; online 2019-10-04]
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Extreme Differences in Recombination Rate between the Genomes of a Solitary and a Social Bee.
Jones JC, Wallberg A, Christmas MJ, Kapheim KM, Webster MT
Mol. Biol. Evol. 36 (10) 2277-2291 [2019-10-01; online 2019-05-31]
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PubMed DOI Crossref
Dissecting the Effects of Selection and Mutation on Genetic Diversity in Three Wood White (Leptidea) Butterfly Species.
Talla V, Soler L, Kawakami T, ..., Wiklund C, Backström N
Genome Biol Evol 11 (10) 2875-2886 [2019-10-01; online 2019-10-04]
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High-definition spatial transcriptomics for in situ tissue profiling.
Vickovic S, Eraslan G, Salmén F, ..., Regev A, Ståhl PL
Nat. Methods 16 (10) 987-990 [2019-10-00; online 2019-09-09]
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Genome-wide evidence supports mitochondrial relationships and pervasive parallel phenotypic evolution in open-habitat chats.
Schweizer M, Warmuth VM, Alaei Kakhki N, ..., Suh A, Burri R
Mol. Phylogenet. Evol. 139 (-) 106568 [2019-10-00; online 2019-07-23]
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Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny.
Cappellini E, Welker F, Pandolfi L, ..., Lordkipanidze D, Willerslev E
Nature 574 (7776) 103-107 [2019-10-00; online 2019-09-11]
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PubMed DOI Crossref
Clinical candidate and genistein analogue AXP107-11 has chemoenhancing functions in pancreatic adenocarcinoma through G protein-coupled estrogen receptor signaling.
Mesmar F, Dai B, Ibrahim A, ..., Fleming J, Williams C
Cancer Med - (-) - [2019-09-30; online 2019-09-30]
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Complete genomes of two extinct New Zealand passerines show responses to climate fluctuations but no evidence for genomic erosion prior to extinction.
Dussex N, von Seth J, Knapp M, ..., Robertson BC, Dalén L
Biol. Lett. 15 (9) 20190491 [2019-09-27; online 2019-09-04]
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Translational offsetting as a mode of estrogen receptor α-dependent regulation of gene expression.
Lorent J, Kusnadi EP, van Hoef V, ..., Larsson O, Furic L
EMBO J. - (-) e101323 [2019-09-26; online 2019-09-26]
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Ethylene Signaling Is Required for Fully Functional Tension Wood in Hybrid Aspen.
Seyfferth C, Wessels BA, Gorzsás A, ..., Sundberg B, Felten J
Front Plant Sci 10 (-) 1101 [2019-09-26; online 2019-09-26]
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Cytoplasmic protein misfolding titrates Hsp70 to activate nuclear Hsf1.
Masser AE, Kang W, Roy J, ..., Friedländer MR, Andréasson C
Elife 8 (-) - [2019-09-25; online 2019-09-25]
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Predisposition to childhood acute lymphoblastic leukemia caused by a constitutional translocation disrupting ETV6.
Järviaho T, Bang B, Zachariadis V, ..., Niinimäki R, Nordgren A
Blood Adv 3 (18) 2722-2731 [2019-09-24; online 2019-09-15]
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Ataxia in Patients With Bi-Allelic NFASC Mutations and Absence of Full-Length NF186.
Kvarnung M, Shahsavani M, Taylan F, ..., Lindstrand A, Falk A
Front Genet 10 (-) 896 [2019-09-24; online 2019-09-24]
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Genomic and Seasonal Variations among Aquatic Phages Infecting the Baltic Sea Gammaproteobacterium Rheinheimera sp. Strain BAL341.
Nilsson E, Li K, Fridlund J, ..., Pinhassi J, Holmfeldt K
Appl. Environ. Microbiol. 85 (18) - [2019-09-15; online 2019-08-29]
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A Single-Stranded Oligonucleotide Inhibits Toll-Like Receptor 3 Activation and Reduces Influenza A (H1N1) Infection.
Poux C, Dondalska A, Bergenstråhle J, ..., Tregoning JS, Spetz AL
Front Immunol 10 (-) 2161 [2019-09-12; online 2019-09-12]
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Combining ERBB family and MET inhibitors is an effective therapeutic strategy in cutaneous malignant melanoma independent of BRAF/NRAS mutation status.
Das I, Wilhelm M, Höiom V, ..., Tuominen R, Egyhàzi Brage S
Cell Death Dis 10 (9) 663 [2019-09-10; online 2019-09-10]
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Genome Sequencing of Pleurozium schreberi: The Assembled and Annotated Draft Genome of a Pleurocarpous Feather Moss.
Pederson ERA, Warshan D, Rasmussen U
G3 (Bethesda) 9 (9) 2791-2797 [2019-09-04; online 2019-09-04]
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Multilayered Tuning of Dosage Compensation and Z-Chromosome Masculinization in the Wood White (Leptidea sinapis) Butterfly.
Höök L, Leal L, Talla V, Backström N
Genome Biol Evol 11 (9) 2633-2652 [2019-09-01; online 2019-08-11]
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Effects of allochthonous dissolved organic matter input on microbial composition and nitrogen-cycling genes at two contrasting estuarine sites.
Happel EM, Markussen T, Teikari JE, ..., Kisand V, Riemann L
FEMS Microbiol. Ecol. 95 (9) - [2019-09-01; online 2019-08-10]
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Orthologous nuclear markers and new transcriptomes that broadly cover the phylogenetic diversity of Acanthaceae.
Morais EB, Schönenberger J, Conti E, Antonelli A, Szövényi P
Appl Plant Sci 7 (9) e11290 [2019-09-00; online 2019-09-25]
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Direct effects of organic pollutants on the growth and gene expression of the Baltic Sea model bacterium Rheinheimera sp. BAL341.
Karlsson CMG, Cerro-Gálvez E, Lundin D, ..., Vila-Costa M, Pinhassi J
Microb Biotechnol 12 (5) 892-906 [2019-09-00; online 2019-07-04]
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MiDRM pol: A High-Throughput Multiplexed Amplicon Sequencing Workflow to Quantify HIV-1 Drug Resistance Mutations against Protease, Reverse Transcriptase, and Integrase Inhibitors.
Aralaguppe SG, Ambikan AT, Ashokkumar M, ..., Sönnerborg A, Neogi U
Viruses 11 (9) - [2019-08-30; online 2019-08-30]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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DNA analysis of low- and high-density fractions defines heterogeneous subpopulations of small extracellular vesicles based on their DNA cargo and topology.
Lázaro-Ibáñez E, Lässer C, Shelke GV, ..., García-Rodríguez A, Lötvall J
J Extracell Vesicles 8 (1) 1656993 [2019-08-27; online 2019-08-27]
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Unique transcriptional and protein-expression signature in human lung tissue-resident NK cells.
Marquardt N, Kekäläinen E, Chen P, ..., Ljunggren HG, Michaëlsson J
Nat Commun 10 (1) 3841 [2019-08-26; online 2019-08-26]
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Non-parametric combination analysis of multiple data types enables detection of novel regulatory mechanisms in T cells of multiple sclerosis patients.
Fernandes SJ, Morikawa H, Ewing E, ..., Tegnér J, Gomez-Cabrero D
Sci Rep 9 (1) 11996 [2019-08-19; online 2019-08-19]
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Statistical Analysis of Community RNA Transcripts between Organic Carbon and Geogas-Fed Continental Deep Biosphere Groundwaters.
Lopez-Fernandez M, Broman E, Simone D, Bertilsson S, Dopson M
MBio 10 (4) - [2019-08-13; online 2019-08-13]
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PAK4 suppresses RELB to prevent senescence-like growth arrest in breast cancer.
Costa TDF, Zhuang T, Lorent J, ..., Defilippi P, Strömblad S
Nat Commun 10 (1) 3589 [2019-08-09; online 2019-08-09]
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Lack of gene flow: Narrow and dispersed differentiation islands in a triplet of Leptidea butterfly species
Talla V, Johansson A, Dincă V, ..., Wiklund C, Backström N
Mol Ecol 28 (6) 3756-3770 [2019-08-08; online 2019-08-08]
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Individual Physiological Adaptations Enable Selected Bacterial Taxa To Prevail during Long-Term Incubations.
Herlemann DPR, Markert S, Meeske C, ..., Jürgens K, Schweder T
Appl. Environ. Microbiol. 85 (15) - [2019-08-01; online 2019-07-18]
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Gene Flow in the Müllerian Mimicry Ring of a Poisonous Papuan Songbird Clade (Pitohui; Aves).
Garg KM, Sam K, Chattopadhyay B, ..., Ericson PGP, Rheindt FE
Genome Biol Evol 11 (8) 2332-2343 [2019-08-01; online 2019-08-17]
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Tobacco smoking induces changes in true DNA methylation, hydroxymethylation and gene expression in bronchoalveolar lavage cells.
Ringh MV, Hagemann-Jensen M, Needhamsen M, ..., Öckinger J, Ekström TJ
EBioMedicine 46 (-) 290-304 [2019-08-00; online 2019-07-12]
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Substantial Heritable Variation in Recombination Rate on Multiple Scales in Honeybees and Bumblebees.
Kawakami T, Wallberg A, Olsson A, ..., Rundlöf M, Webster MT
Genetics 212 (4) 1101-1119 [2019-08-00; online 2019-05-31]
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Salinity drives meiofaunal community structure dynamics across the Baltic ecosystem.
Broman E, Raymond C, Sommer C, ..., Creer S, Nascimento FJA
Mol. Ecol. 28 (16) 3813-3829 [2019-08-00; online 2019-09-05]
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Maintenance of High Genome Integrity over Vegetative Growth in the Fairy-Ring Mushroom Marasmius oreades
Hiltunen M, Grudzinska-Sterno M, Wallerman O, Ryberg M, Johannesson H
Current Biology 29 (16) 2758-2765.e6 [2019-08-00; online 2019-08-00]
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Linkage analysis revealed risk loci on 6p21 and 18p11.2-q11.2 in familial colon and rectal cancer, respectively.
von Holst S, Jiao X, Liu W, ..., Bryant P, Lindblom A
Eur. J. Hum. Genet. 27 (8) 1286-1295 [2019-08-00; online 2019-04-05]
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Interaction of Sox2 with RNA binding proteins in mouse embryonic stem cells
Samudyata , Amaral PP, Engström PG, ..., Kouzarides T, Castelo-Branco G
Experimental Cell Research 381 (1) 129-138 [2019-08-00; online 2019-08-00]
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Early activating somatic PIK3CA mutations promote ectopic muscle development and upper limb overgrowth.
Frisk S, Taylan F, Blaszczyk I, ..., Laurell T, Nordgren A
Clin. Genet. 96 (2) 118-125 [2019-08-00; online 2019-05-09]
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Complete subspecies-level phylogeny of the Oriolidae (Aves: Passeriformes): Out of Australasia and return.
Jønsson KA, Blom MPK, Marki PZ, ..., Ericson PGP, Irestedt M
Mol. Phylogenet. Evol. 137 (-) 200-209 [2019-08-00; online 2019-03-23]
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31° South: The physiology of adaptation to arid conditions in a passerine bird.
Ribeiro ÂM, Puetz L, Pattinson NB, ..., Smit B, Gilbert MTP
Mol. Ecol. 28 (16) 3709-3721 [2019-08-00; online 2019-08-06]
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Impact of vitamin D and vitamin D receptor TaqI polymorphism in primary human myoblasts.
Saini A, Björkhem-Bergman L, Boström J, ..., Rullman E, Gustafsson T
Endocr Connect 8 (7) 1070-1081 [2019-07-29; online 2019-07-29]
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Genomic differentiation tracks earth-historic isolation in an Indo-Australasian archipelagic pitta (Pittidae; Aves) complex.
Ericson PGP, Qu Y, Rasmussen PC, ..., Rheindt FE, Irestedt M
BMC Evol. Biol. 19 (1) 151 [2019-07-24; online 2019-07-24]
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Genetic analyses supporting colorectal, gastric, and prostate cancer syndromes.
Wallander K, Liu W, von Holst S, ..., Lindblom A, Lagerstedt-Robinson K
Genes Chromosomes Cancer - (-) - [2019-07-23; online 2019-07-23]
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Global gene expression analysis in etiolated and de-etiolated seedlings in conifers.
Ranade SS, Delhomme N, García-Gil MR
PLoS ONE 14 (7) e0219272 [2019-07-05; online 2019-07-05]
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Comparison of boreal acid sulfate soil microbial communities in oxidative and reductive environments.
Christel S, Yu C, Wu X, ..., Åström ME, Dopson M
Res. Microbiol. 170 (6-7) 288-295 [2019-07-03; online 2019-07-03]
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Efficient RNA silencing suppression activity of Potato Mop-Top Virus 8K protein is driven by variability and positive selection.
Kalyandurg PB, Tahmasebi A, Vetukuri RR, ..., Grenville-Briggs LJ, Savenkov EI
Virology 535 (-) 111-121 [2019-07-01; online 2019-07-01]
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Transcriptome analysis of shade avoidance and shade tolerance in conifers.
Ranade SS, Delhomme N, García-Gil MR
Planta 250 (1) 299-318 [2019-07-00; online 2019-04-26]
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Transcriptional and metabolic rewiring of colorectal cancer cells expressing the oncogenic KRASG13D mutation.
Charitou T, Srihari S, Lynn MA, ..., Kolch W, Lynn DJ
Br. J. Cancer 121 (1) 37-50 [2019-07-00; online 2019-05-28]
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Single cell analysis of autism patient with bi-allelic NRXN1-alpha deletion reveals skewed fate choice in neural progenitors and impaired neuronal functionality
Lam M, Moslem M, Bryois J, ..., Sullivan PF, Falk A
Experimental Cell Research 383 (1) 111469 [2019-07-00; online 2019-07-00]
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Hemostatic Genes Exhibit a High Degree of Allele-Specific Regulation in Liver.
Olsson Lindvall M, Hansson L, Klasson S, ..., Jern C, Stanne TM
Thromb. Haemost. 119 (7) 1072-1083 [2019-07-00; online 2019-04-29]
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Exploring Molecular Signs of Sex in the Marine Diatom Skeletonema marinoi.
Ferrante MI, Entrambasaguas L, Johansson M, ..., Montresor M, Godhe A
Genes 10 (7) - [2019-06-28; online 2019-06-28]
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Genomic Characterization of the Emerging Pathogen Streptococcus pseudopneumoniae.
Garriss G, Nannapaneni P, Simões AS, ..., de Lencastre H, Henriques-Normark B
MBio 10 (3) - [2019-06-25; online 2019-06-25]
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Identification of Salivary Microbiota and Its Association With Host Inflammatory Mediators in Periodontitis.
Lundmark A, Hu YOO, Huss M, ..., Andersson AF, Yucel-Lindberg T
Front. Cell. Infect. Microbiol. 9 (-) 216 [2019-06-21; online 2019-06-21]
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Improved phylogenomic sampling of free-living nematodes enhances resolution of higher-level nematode phylogeny.
Smythe AB, Holovachov O, Kocot KM
BMC Evol. Biol. 19 (1) 121 [2019-06-13; online 2019-06-13]
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Modeling Motor Neuron Resilience in ALS Using Stem Cells.
Allodi I, Nijssen J, Benitez JA, ..., Kiehn O, Hedlund E
Stem Cell Reports 12 (6) 1329-1341 [2019-06-11; online 2019-05-09]
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Spatiotemporal structure of cell fate decisions in murine neural crest
Soldatov R, Kaucka M, Kastriti ME, ..., Kharchenko PV, Adameyko I
Science 364 (6444) eaas9536 [2019-06-07; online 2019-06-07]
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Unprecedented reorganization of holocentric chromosomes provides insights into the enigma of lepidopteran chromosome evolution.
Hill J, Rastas P, Hornett EA, ..., Nylin S, Wheat CW
Sci Adv 5 (6) eaau3648 [2019-06-00; online 2019-06-12]
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Single-Cell RNA Sequencing of the T Helper Cell Response to House Dust Mites Defines a Distinct Gene Expression Signature in Airway Th2 Cells
Tibbitt CA, Stark JM, Martens L, ..., Saeys Y, Coquet JM
Immunity 51 (1) 169-184.e5 [2019-06-00; online 2019-06-00]
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Mutations in the mitochondrial tryptophanyl-tRNA synthetase cause growth retardation and progressive leukoencephalopathy.
Maffezzini C, Laine I, Dallabona C, ..., Wredenberg A, Wedell A
Mol Genet Genomic Med 7 (6) e654 [2019-06-00; online 2019-03-28]
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Further support linking the 22q11.2 microduplication to an increased risk of bladder exstrophy and highlighting LZTR1 as a candidate gene.
Lundin J, Markljung E, Baranowska Körberg I, ..., Lindstrand A, Nordenskjöld A
Mol Genet Genomic Med 7 (6) e666 [2019-06-00; online 2019-05-01]
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Ancient DNA from mastics solidifies connection between material culture and genetics of mesolithic hunter-gatherers in Scandinavia.
Kashuba N, Kırdök E, Damlien H, ..., Persson P, Götherström A
Commun Biol 2 (-) 185 [2019-05-15; online 2019-05-15]
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Adult Neural Progenitor Cells Transplanted into Spinal Cord Injury Differentiate into Oligodendrocytes, Enhance Myelination, and Contribute to Recovery.
Sankavaram SR, Hakim R, Covacu R, ..., Svensson M, Brundin L
Stem Cell Reports 12 (5) 950-966 [2019-05-14; online 2019-04-25]
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Periodontal Health and Oral Microbiota in Patients with Rheumatoid Arthritis.
Eriksson K, Fei G, Lundmark A, ..., Jansson L, Yucel-Lindberg T
J Clin Med 8 (5) - [2019-05-08; online 2019-05-08]
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Sensory receptor repertoire in cyprid antennules of the barnacle Balanus improvisus.
Abramova A, Alm Rosenblad M, Blomberg A, Larsson TA
PLoS ONE 14 (5) e0216294 [2019-05-02; online 2019-05-02]
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Comparative analyses identify genomic features potentially involved in the evolution of birds-of-paradise.
Prost S, Armstrong EE, Nylander J, ..., Ericson PGP, Irestedt M
Gigascience 8 (5) - [2019-05-01; online 2019-01-29]
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Chromosomal genome assembly of the ethanol production strain CBS 11270 indicates a highly dynamic genome structure in the yeast species Brettanomyces bruxellensis.
Tiukova IA, Pettersson ME, Hoeppner MP, ..., Söderberg J, Passoth V
PLoS ONE 14 (5) e0215077 [2019-05-01; online 2019-05-01]
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Gene expression profile of extraocular muscles following resection strabismus surgery.
Rodríguez MA, Sandgren Hochhard K, Vicente A, Liu JX, Pedrosa Domellöf F
Exp. Eye Res. 182 (-) 182-193 [2019-05-00; online 2019-04-03]
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Dynamic evolutionary history and gene content of sex chromosomes across diverse songbirds.
Xu L, Auer G, Peona V, ..., Irestedt M, Zhou Q
Nat Ecol Evol 3 (5) 834-844 [2019-05-00; online 2019-04-01]
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An Atlas of Vagal Sensory Neurons and Their Molecular Specialization
Kupari J, Häring M, Agirre E, Castelo-Branco G, Ernfors P
Cell Rep 27 (8) 2508-2523.e4 [2019-05-00; online 2019-05-00]
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Somatic mutation that affects transcription factor binding upstream of CD55 in the temporal cortex of a late-onset Alzheimer disease patient
Helgadottir HT, Lundin P, Wallén Arzt E, ..., Graff C, Eriksson M
Hum Mol Genet 28 (16) 2675-2685 [2019-04-24; online 2019-04-24]
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PAD2-Mediated Citrullination Contributes to Efficient Oligodendrocyte Differentiation and Myelination.
Falcão AM, Meijer M, Scaglione A, ..., Casaccia P, Castelo-Branco G
Cell Rep 27 (4) 1090-1102.e10 [2019-04-23; online 2019-04-25]
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The complex barnacle perfume: identification of waterborne pheromone homologues in Balanus improvisus and their differential expression during settlement
Abramova A, Lind U, Blomberg A, Rosenblad MA
Biofouling 35 (4) 416-428 [2019-04-21; online 2019-05-30]
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The Genome of Blue-Capped Cordon-Bleu Uncovers Hidden Diversity of LTR Retrotransposons in Zebra Finch.
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SQSTM1/p62-Directed Metabolic Reprogramming Is Essential for Normal Neurodifferentiation.
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SAMURAI (Solid-phase Assisted Mutagenesis by Uracil Restriction for Accurate Integration) for antibody affinity maturation and paratope mapping.
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Nucleic Acids Res. 47 (6) e34 [2019-04-08; online 2019-02-05]
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Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis.
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Science 364 (6435) 89-93 [2019-04-05; online 2019-04-06]
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Osteoporosis and skeletal dysplasia caused by pathogenic variants in SGMS2.
Pekkinen M, Terhal PA, Botto LD, ..., Holthuis JC, Mäkitie O
JCI Insight 4 (7) - [2019-04-04; online 2019-04-04]
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A TetR-family transcription factor regulates fatty acid metabolism in the archaeal model organism Sulfolobus acidocaldarius.
Wang K, Sybers D, Maklad HR, ..., Lindås AC, Peeters E
Nat Commun 10 (1) 1542 [2019-04-04; online 2019-04-04]
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Mesenchymal stem cells transplanted into spinal cord injury adopt immune cell-like characteristics.
Hakim R, Covacu R, Zachariadis V, ..., Brundin L, Svensson M
Stem Cell Res Ther 10 (1) 115 [2019-04-03; online 2019-04-03]
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Novel fibronectin mutations and expansion of the phenotype in spondylometaphyseal dysplasia with "corner fractures".
Costantini A, Valta H, Baratang NV, ..., Mäkitie O, Campeau PM
Bone 121 (-) 163-171 [2019-04-00; online 2018-12-30]
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Gain-of-function mutation of microRNA-140 in human skeletal dysplasia.
Grigelioniene G, Suzuki HI, Taylan F, ..., Sharp PA, Kobayashi T
Nat. Med. 25 (4) 583-590 [2019-04-00; online 2019-02-25]
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A geographically matched control population efficiently limits the number of candidate disease-causing variants in an unbiased whole-genome analysis
Rentoft M, Svensson D, Sjödin A, ..., Melin BS, Johansson E
PLoS ONE 14 (3) e0213350 [2019-03-27; online 2019-03-27]
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Ancient Mitochondrial Genomes Reveal the Absence of Maternal Kinship in the Burials of Çatalhöyük People and Their Genetic Affinities.
Chyleński M, Ehler E, Somel M, ..., Juras A, Marciniak A
Genes 10 (3) - [2019-03-11; online 2019-03-11]
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Single-Cell RNA-Seq Reveals Cellular Heterogeneity of Pluripotency Transition and X Chromosome Dynamics during Early Mouse Development.
Cheng S, Pei Y, He L, ..., Jing N, Deng Q
Cell Rep 26 (10) 2593-2607.e3 [2019-03-05; online 2019-03-07]
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Proteomic Analysis of Endothelial Cells Exposed to Ultrasmall Nanoparticles Reveals Disruption in Paracellular and Transcellular Transport.
Kuruvilla J, Bayat N, Cristobal S
Proteomics 19 (5) e1800228 [2019-03-00; online 2019-02-25]
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A radical switch in clonality reveals a stem cell niche in the epiphyseal growth plate.
Newton PT, Li L, Zhou B, ..., Sävendahl L, Chagin AS
Nature 567 (7747) 234-238 [2019-03-00; online 2019-02-27]
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Transcriptomics of cardiac biopsies reveals differences in patients with or without diagnostic parameters for heart failure with preserved ejection fraction.
Das S, Frisk C, Eriksson MJ, ..., Linde C, Persson B
Sci Rep 9 (1) 3179 [2019-02-28; online 2019-02-28]
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Population and Single-Cell Analysis of Human Cardiogenesis Reveals Unique LGR5 Ventricular Progenitors in Embryonic Outflow Tract.
Sahara M, Santoro F, Sohlmér J, ..., Gruber P, Chien KR
Dev. Cell 48 (4) 475-490.e7 [2019-02-25; online 2019-01-31]
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A deep proteome and transcriptome abundance atlas of 29 healthy human tissues.
Wang D, Eraslan B, Wieland T, ..., Hahne H, Kuster B
Mol. Syst. Biol. 15 (2) e8503 [2019-02-18; online 2019-02-18]
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Parental legacy, demography, and admixture influenced the evolution of the two subgenomes of the tetraploid Capsella bursa-pastoris (Brassicaceae).
Kryvokhyzha D, Salcedo A, Eriksson MC, ..., Wright SI, Lascoux M
PLoS Genet. 15 (2) e1007949 [2019-02-00; online 2019-02-15]
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Comprehensive structural variation genome map of individuals carrying complex chromosomal rearrangements.
Eisfeldt J, Pettersson M, Vezzi F, ..., Carvalho CMB, Lindstrand A
PLoS Genet. 15 (2) e1007858 [2019-02-00; online 2019-02-08]
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The ketogenic diet influences taxonomic and functional composition of the gut microbiota in children with severe epilepsy.
Lindefeldt M, Eng A, Darban H, ..., Dahlin M, Prast-Nielsen S
NPJ Biofilms Microbiomes 5 (-) 5 [2019-01-23; online 2019-01-23]
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Altered human oligodendrocyte heterogeneity in multiple sclerosis
Jäkel S, Agirre E, Falcão AM, ..., Williams A, Castelo-Branco G
Nature - (-) - [2019-01-23; online 2019-01-23]
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Fecal pollution can explain antibiotic resistance gene abundances in anthropogenically impacted environments.
Karkman A, Pärnänen K, Larsson DGJ
Nat Commun 10 (1) 80 [2019-01-08; online 2019-01-08]
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Historical Genomes Reveal the Genomic Consequences of Recent Population Decline in Eastern Gorillas.
van der Valk T, Díez-Del-Molino D, Marques-Bonet T, Guschanski K, Dalén L
Curr. Biol. 29 (1) 165-170.e6 [2019-01-07; online 2018-12-27]
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Near-complete phylogeny and taxonomic revision of the world's babblers (Aves: Passeriformes).
Cai T, Cibois A, Alström P, ..., Lei F, Fjeldså J
Mol. Phylogenet. Evol. 130 (-) 346-356 [2019-01-00; online 2018-10-12]
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Year 2018

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PRR14L mutations are associated with chromosome 22 acquired uniparental disomy, age-related clonal hematopoiesis and myeloid neoplasia.
Chase A, Pellagatti A, Singh S, ..., Boultwood J, Cross NCP
Leukemia - (-) - [2018-12-20; online 2018-12-20]
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Somatic Structural Alterations in Childhood Leukemia Can Be Backtracked in Neonatal Dried Blood Spots by Use of Whole-Genome Sequencing and Digital PCR.
Taylan F, Bang B, Öfverholm II, ..., Zachariadis V, Nordgren A
Clin. Chem. - (-) - [2018-12-05; online 2018-12-05]
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A Novel Inorganic Sulfur Compound Metabolizing Ferroplasma-Like Population Is Suggested to Mediate Extracellular Electron Transfer.
Ni G, Simone D, Palma D, ..., Turner S, Dopson M
Front Microbiol 9 (-) 2945 [2018-12-05; online 2018-12-05]
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Spatially and functionally distinct subclasses of breast cancer-associated fibroblasts revealed by single cell RNA sequencing.
Bartoschek M, Oskolkov N, Bocci M, ..., Björklund Å, Pietras K
Nat Commun 9 (1) 5150 [2018-12-04; online 2018-12-04]
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The Mutant p53-Targeting Compound APR-246 Induces ROS-Modulating Genes in Breast Cancer Cells.
Synnott NC, Madden SF, Bykov VJN, ..., Wiman KG, Duffy MJ
Transl Oncol 11 (6) 1343-1349 [2018-12-00; online 2018-09-06]
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Somatic mutagenesis in satellite cells associates with human skeletal muscle aging
Franco I, Johansson A, Olsson K, ..., Fischer H, Eriksson M
Nat Commun 9 (1) - [2018-12-00; online 2018-02-23]
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RNA-sequencing reveals long-term effects of silver nanoparticles on human lung cells
Gliga AR, Di Bucchianico S, Lindvall J, Fadeel B, Karlsson HL
Sci Rep 8 (1) - [2018-12-00; online 2018-04-27]
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Genomic screening in rare disorders: New mutations and phenotypes, highlighting ALG14 as a novel cause of severe intellectual disability.
Kvarnung M, Taylan F, Nilsson D, ..., Nordgren A, Lundberg ES
Clin. Genet. 94 (6) 528-537 [2018-12-00; online 2018-10-15]
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Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes
Alneberg J, Karlsson CMG, Divne AM, ..., Andersson AF, Pinhassi J
Microbiome 6 (1) - [2018-12-00; online 2018-09-28]
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A major locus controls local adaptation and adaptive life history variation in a perennial plant
Wang J, Ding J, Tan B, ..., Street NR, Ingvarsson PK
Genome Biol. 19 (1) - [2018-12-00; online 2018-06-04]
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A comprehensive map coupling histone modifications with gene regulation in adult dopaminergic and serotonergic neurons
Södersten E, Toskas K, Rraklli V, ..., Perlmann T, Holmberg J
Nat Commun 9 (1) - [2018-12-00; online 2018-03-26]
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Depth and Dissolved Organic Carbon Shape Microbial Communities in Surface Influenced but Not Ancient Saline Terrestrial Aquifers.
Lopez-Fernandez M, Åström M, Bertilsson S, Dopson M
Front Microbiol 9 (-) 2880 [2018-11-27; online 2018-11-27]
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Metatranscriptomes Reveal That All Three Domains of Life Are Active but Are Dominated by Bacteria in the Fennoscandian Crystalline Granitic Continental Deep Biosphere
Lopez-Fernandez M, Simone D, Wu X, ..., Bertilsson S, Dopson M
MBio 9 (6) - [2018-11-20; online 2018-11-20]
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Diazotrophs and N2-Fixation Associated With Particles in Coastal Estuarine Waters.
Pedersen JN, Bombar D, Paerl RW, Riemann L
Front Microbiol 9 (-) 2759 [2018-11-16; online 2018-11-16]
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Diet-dependent gene expression highlights the importance of Cytochrome P450 in detoxification of algal secondary metabolites in a marine isopod.
De Wit P, Yamada K, Panova M, André C, Johannesson K
Sci Rep 8 (1) 16824 [2018-11-14; online 2018-11-14]
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Comparative Analysis of the Nodule Transcriptomes of Ceanothus thyrsiflorus (Rhamnaceae, Rosales) and Datisca glomerata (Datiscaceae, Cucurbitales).
Salgado MG, van Velzen R, Nguyen TV, ..., Lundin D, Pawlowski K
Front Plant Sci 9 (-) 1629 [2018-11-14; online 2018-11-14]
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Parallel plumage colour evolution and introgressive hybridization in wheatears.
Schweizer M, Warmuth V, Alaei Kakhki N, ..., Suh A, Burri R
J. Evol. Biol. - (-) - [2018-11-12; online 2018-11-12]
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Disease-specific oligodendrocyte lineage cells arise in multiple sclerosis
Falcão AM, van Bruggen D, Marques S, ..., Guerreiro-Cacais AO, Castelo-Branco G
Nat Med - (-) - [2018-11-12; online 2018-11-12]
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Replicative and non-replicative mechanisms in the formation of clustered CNVs are indicated by whole genome characterization.
Nazaryan-Petersen L, Eisfeldt J, Pettersson M, ..., Tümer Z, Lindstrand A
PLoS Genet. 14 (11) e1007780 [2018-11-00; online 2018-11-12]
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Notch signaling promotes a HIF2α-driven hypoxic response in multiple tumor cell types.
Mutvei AP, Landor SK, Fox R, ..., Jin S, Lendahl U
Oncogene 37 (46) 6083-6095 [2018-11-00; online 2018-07-11]
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Barcoded solid-phase RNA capture for Spatial Transcriptomics profiling in mammalian tissue sections.
Salmén F, Ståhl PL, Mollbrink A, ..., Frisén J, Lundeberg J
Nat Protoc 13 (11) 2501-2534 [2018-11-00; online 2018-10-26]
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SMAD4 Is Essential for Human Cardiac Mesodermal Precursor Cell Formation.
Xu J, Gruber PJ, Chien KR
Stem Cells - (-) - [2018-10-30; online 2018-10-30]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen
Lin YC, Wang J, Delhomme N, ..., Ingvarsson PK, Street NR
Proc Natl Acad Sci USA - (-) 201801437 [2018-10-29; online 2018-10-29]
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Single-cell RNA-seq analysis reveals the platinum resistance gene COX7B and the surrogate marker CD63.
Tanaka N, Katayama S, Reddy A, ..., Oya M, Uhlén P
Cancer Med - (-) - [2018-10-26; online 2018-10-26]
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Single-Stranded Nucleic Acids Regulate TLR3/4/7 Activation through Interference with Clathrin-Mediated Endocytosis.
Järver P, Dondalska A, Poux C, ..., LeGrand R, Spetz AL
Sci Rep 8 (1) 15841 [2018-10-26; online 2018-10-26]
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Single-Cell Transcriptomics of Traced Epidermal and Hair Follicle Stem Cells Reveals Rapid Adaptations during Wound Healing.
Joost S, Jacob T, Sun X, ..., Sur I, Kasper M
Cell Rep 25 (3) 585-597.e7 [2018-10-16; online 2018-10-18]
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Spatially Resolved Transcriptomics Enables Dissection of Genetic Heterogeneity in Stage III Cutaneous Malignant Melanoma
Thrane K, Eriksson H, Maaskola J, Hansson J, Lundeberg J
Cancer Res 78 (20) 5970-5979 [2018-10-15; online 2018-10-15]
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Transcriptomic and genomic profiling of early-stage ovarian carcinomas associated with histotype and overall survival.
Engqvist H, Parris TZ, Rönnerman EW, ..., Karlsson P, Helou K
Oncotarget 9 (80) 35162-35180 [2018-10-12; online 2018-10-12]
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Enhanced validation of antibodies for research applications.
Edfors F, Hober A, Linderbäck K, ..., Forsström B, Uhlen M
Nat Commun 9 (1) 4130 [2018-10-08; online 2018-10-08]
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Partial genomic survival of cave bears in living brown bears.
Barlow A, Cahill JA, Hartmann S, ..., Shapiro B, Hofreiter M
Nat Ecol Evol 2 (10) 1563-1570 [2018-10-00; online 2018-08-27]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Ancient genomes suggest the eastern Pontic-Caspian steppe as the source of western Iron Age nomads.
Krzewińska M, Kılınç GM, Juras A, ..., Storå J, Götherström A
Sci Adv 4 (10) eaat4457 [2018-10-00; online 2018-10-03]
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Alu-Alu mediated intragenic duplications in IFT81 and MATN3 are associated with skeletal dysplasias.
Pettersson M, Vaz R, Hammarsjö A, ..., Grigelioniene G, Lindstrand A
Hum. Mutat. 39 (10) 1456-1467 [2018-10-00; online 2018-08-22]
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Microbial Community and Metabolic Activity in Thiocyanate Degrading Low Temperature Microbial Fuel Cells.
Ni G, Canizales S, Broman E, ..., Sleutels T, Dopson M
Front Microbiol 9 (-) 2308 [2018-09-28; online 2018-09-28]
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High-throughput metabarcoding reveals the effect of physicochemical soil properties on soil and litter biodiversity and community turnover across Amazonia.
Ritter CD, Zizka A, Roger F, ..., Nilsson RH, Antonelli A
PeerJ 6 (-) e5661 [2018-09-25; online 2018-09-25]
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SWI/SNF interacts with cleavage and polyadenylation factors and facilitates pre-mRNA 3' end processing.
Yu S, Jordán-Pla A, Gañez-Zapater A, ..., Östlund Farrants AK, Visa N
Nucleic Acids Res. 46 (16) 8557-8573 [2018-09-19; online 2018-06-04]
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Neuronal heterogeneity and stereotyped connectivity in the auditory afferent system.
Petitpré C, Wu H, Sharma A, ..., Hadjab S, Lallemend F
Nat Commun 9 (1) 3691 [2018-09-12; online 2018-09-12]
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Genomic and Strontium Isotope Variation Reveal Immigration Patterns in a Viking Age Town.
Krzewińska M, Kjellström A, Günther T, ..., Storå J, Götherström A
Curr. Biol. 28 (17) 2730-2738.e10 [2018-09-10; online 2018-08-23]
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Contribution of allelic imbalance to colorectal cancer.
Palin K, Pitkänen E, Turunen M, ..., Taipale J, Aaltonen LA
Nat Commun 9 (1) 3664 [2018-09-10; online 2018-09-10]
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Draft Genome Sequence for the Tree Pathogen Phytophthora plurivora.
Vetukuri RR, Tripathy S, Malar C M, ..., Grenville-Briggs LJ, Whisson SC
Genome Biol Evol 10 (9) 2432-2442 [2018-09-01; online 2018-09-01]
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The molecular genetic basis of herbivory between butterflies and their host plants.
Nallu S, Hill JA, Don K, ..., Wheat CW, Kronforst MR
Nat Ecol Evol 2 (9) 1418-1427 [2018-09-00; online 2018-08-03]
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The Protozoan Parasite Toxoplasma gondii Selectively Reprograms the Host Cell Translatome.
Leroux LP, Lorent J, Graber TE, ..., Larsson O, Jaramillo M
Infect. Immun. 86 (9) - [2018-09-00; online 2018-08-22]
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Phylogenetic relationships of rollers (Coraciidae) based on complete mitochondrial genomes and fifteen nuclear genes.
Johansson US, Irestedt M, Qu Y, Ericson PGP
Mol. Phylogenet. Evol. 126 (-) 17-22 [2018-09-00; online 2018-04-06]
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Genome Sequence Resource for the Oomycete Taro Pathogen Phytophthora colocasiae.
Vetukuri RR, Kushwaha SK, Sen D, ..., Lamour KH, Grenville-Briggs LJ
Mol. Plant Microbe Interact. 31 (9) 903-905 [2018-09-00; online 2018-08-03]
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Autosomal Recessive Osteogenesis Imperfecta Caused by a Novel Homozygous COL1A2 Mutation
Costantini A, Tournis S, Kämpe A, ..., Doulgeraki A, Mäkitie O
Calcif Tissue Int 103 (3) 353-358 [2018-09-00; online 2018-03-23]
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Novel genome and genome-wide SNPs reveal early fragmentation effects in an edge-tolerant songbird population across an urbanized tropical metropolis.
Tan DJX, Chattopadhyay B, Garg KM, ..., Irestedt M, Rheindt FE
Sci Rep 8 (1) 12804 [2018-08-24; online 2018-08-24]
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Reduced expression of PROX1 transitions glioblastoma cells into a mesenchymal gene expression subtype
Goudarzi KM, Espinoza JA, Guo M, ..., Lindström MS, Hägerstrand D
Cancer Res - (-) canres.0320.2018 [2018-08-22; online 2018-08-22]
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Single-cell RNA sequencing of mouse brain and lung vascular and vessel-associated cell types.
He L, Vanlandewijck M, Mäe MA, ..., Lendahl U, Betsholtz C
Sci Data 5 (1) 180160 [2018-08-21; online 2018-08-21]
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Transcriptional Convergence of Oligodendrocyte Lineage Progenitors during Development.
Marques S, van Bruggen D, Vanichkina DP, ..., Taft RJ, Castelo-Branco G
Dev. Cell 46 (4) 504-517.e7 [2018-08-20; online 2018-08-02]
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BtsCI and BseGI display sequence preference in the nucleotides flanking the recognition sequence
Rosa J, Fernandez-Gonzalez E, Ducani C, Högberg B
PLoS ONE 13 (8) e0202057 [2018-08-17; online 2018-08-17]
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Stationary and portable sequencing-based approaches for tracing wastewater contamination in urban stormwater systems.
Hu YOO, Ndegwa N, Alneberg J, ..., Fagerberg J, Andersson AF
Sci Rep 8 (1) 11907 [2018-08-09; online 2018-08-09]
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Molecular Architecture of the Mouse Nervous System.
Zeisel A, Hochgerner H, Lönnerberg P, ..., Marklund U, Linnarsson S
Cell 174 (4) 999-1014.e22 [2018-08-09; online 2018-08-11]
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Clonal relatedness in tumour pairs of breast cancer patients.
Biermann J, Parris TZ, Nemes S, ..., Karlsson P, Helou K
Breast Cancer Res. 20 (1) 96 [2018-08-09; online 2018-08-09]
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Huntingtin Aggregation Impairs Autophagy, Leading to Argonaute-2 Accumulation and Global MicroRNA Dysregulation.
Pircs K, Petri R, Madsen S, ..., Barker RA, Jakobsson J
Cell Rep 24 (6) 1397-1406 [2018-08-07; online 2018-08-09]
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Sample size effects on the assessment of eukaryotic diversity and community structure in aquatic sediments using high-throughput sequencing.
Nascimento FJA, Lallias D, Bik HM, Creer S
Sci Rep 8 (1) 11737 [2018-08-06; online 2018-08-06]
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Stereotypic Immune System Development in Newborn Children
Olin A, Henckel E, Chen Y, ..., Bohlin K, Brodin P
Cell 174 (5) 1277-1292.e14 [2018-08-00; online 2018-08-00]
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RNA velocity of single cells.
La Manno G, Soldatov R, Zeisel A, ..., Linnarsson S, Kharchenko PV
Nature 560 (7719) 494-498 [2018-08-00; online 2018-08-08]
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Data on the nucleotide composition of the first codons encoding the complementary determining region 3 (CDR3) in immunoglobulin heavy chains.
Thörnqvist L, Ohlin M
Data Brief 19 (-) 337-352 [2018-08-00; online 2018-05-04]
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Coupling biogeochemical process rates and metagenomic blueprints of coastal bacterial assemblages in the context of environmental change.
Markussen T, Happel EM, Teikari JE, ..., Middelboe M, Kisand V
Environ. Microbiol. 20 (8) 3083-3099 [2018-08-00; online 2018-09-19]
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Comprehensive RNA sequencing analysis in serum and muscle reveals novel small RNA signatures with biomarker potential for Duchenne Muscular Dystrophy
Coenen-Stass AML, Sork H, Gatto S, ..., Wood MJA, Roberts TC
Mol Ther Nucleic Acids - (-) - [2018-08-00; online 2018-08-00]
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Characterization of an activating R1353H insulin-like growth factor 1 receptor variant in a male with extreme tall height.
Lin Y, van Duyvenvoorde HA, Liu H, ..., Wit JM, Larsson O
Eur. J. Endocrinol. 179 (2) 85-95 [2018-08-00; online 2018-05-22]
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BARM and BalticMicrobeDB, a reference metagenome and interface to meta-omic data for the Baltic Sea.
Alneberg J, Sundh J, Bennke C, ..., Labrenz M, Andersson AF
Sci Data 5 (-) 180146 [2018-07-31; online 2018-07-31]
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Response of Microbial Communities to Changing Climate Conditions During Summer Cyanobacterial Blooms in the Baltic Sea.
Berner C, Bertos-Fortis M, Pinhassi J, Legrand C
Front Microbiol 9 (-) 1562 [2018-07-25; online 2018-07-25]
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A patient-derived xenograft pre-clinical trial reveals treatment responses and a resistance mechanism to karonudib in metastatic melanoma.
Einarsdottir BO, Karlsson J, Söderberg EMV, ..., Helleday T, Nilsson JA
Cell Death Dis 9 (8) 810 [2018-07-24; online 2018-07-24]
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Spring and Late Summer Phytoplankton Biomass Impact on the Coastal Sediment Microbial Community Structure.
Broman E, Li L, Fridlund J, ..., Legrand C, Dopson M
Microb. Ecol. - (-) - [2018-07-17; online 2018-07-17]
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Heterogeneity and interplay of the extracellular vesicle small RNA transcriptome and proteome.
Sork H, Corso G, Krjutskov K, ..., Mäger I, El Andaloussi S
Sci Rep 8 (1) 10813 [2018-07-17; online 2018-07-17]
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SECAPR—a bioinformatics pipeline for the rapid and user-friendly processing of targeted enriched Illumina sequences, from raw reads to alignments
Andermann T, Cano Á, Zizka A, Bacon C, Antonelli A
PeerJ 6 (-) e5175 [2018-07-13; online 2018-07-13]
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EviNet: a web platform for network enrichment analysis with flexible definition of gene sets.
Jeggari A, Alekseenko Z, Petrov I, ..., Ericson J, Alexeyenko A
Nucleic Acids Res. 46 (W1) W163-W170 [2018-07-02; online 2018-06-13]
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Detection of novel syntrophic acetate-oxidizing bacteria from biogas processes by continuous acetate enrichment approaches.
Westerholm M, Müller B, Singh A, Karlsson Lindsjö O, Schnürer A
Microb Biotechnol 11 (4) 680-693 [2018-07-00; online 2017-12-04]
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CRISPR-Cas9 genome editing induces a p53-mediated DNA damage response.
Haapaniemi E, Botla S, Persson J, Schmierer B, Taipale J
Nat. Med. 24 (7) 927-930 [2018-07-00; online 2018-06-11]
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Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity
Berglund E, Maaskola J, Schultz N, ..., Helleday T, Lundeberg J
Nat Commun 9 (1) 2419 [2018-06-20; online 2018-06-20]
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Gene expression profiling of periodontitis-affected gingival tissue by spatial transcriptomics.
Lundmark A, Gerasimcik N, Båge T, ..., Lundeberg J, Yucel-Lindberg T
Sci Rep 8 (1) 9370 [2018-06-19; online 2018-06-19]
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Investigating Holocene human population history in North Asia using ancient mitogenomes.
Kılınç GM, Kashuba N, Yaka R, ..., Storå J, Götherström A
Sci Rep 8 (1) 8969 [2018-06-12; online 2018-06-12]
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Neuronal atlas of the dorsal horn defines its architecture and links sensory input to transcriptional cell types.
Häring M, Zeisel A, Hochgerner H, ..., Linnarsson S, Ernfors P
Nat. Neurosci. 21 (6) 869-880 [2018-06-00; online 2018-04-23]
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Discovery of SNPs for individual identification by reduced representation sequencing of moose (Alces alces).
Blåhed IM, Königsson H, Ericsson G, Spong G
PLoS ONE 13 (5) e0197364 [2018-05-30; online 2018-05-30]
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SWI/SNF regulates half of its targets without the need of ATP-driven nucleosome remodeling by Brahma.
Jordán-Pla A, Yu S, Waldholm J, ..., Östlund Farrants AK, Visa N
BMC Genomics 19 (1) 367 [2018-05-18; online 2018-05-18]
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Transcriptomic analysis of the harvested endothelial cells in a swine model of mechanical thrombectomy.
Jaff N, Grankvist R, Muhl L, ..., Eriksson U, Holmin S
Neuroradiology - (-) - [2018-05-14; online 2018-05-14]
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Genome-wide multi-omics profiling of the 8p11-p12 amplicon in breast carcinoma.
Parris TZ, Rönnerman EW, Engqvist H, ..., Karlsson P, Helou K
Oncotarget 9 (35) 24140-24154 [2018-05-08; online 2018-05-08]
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O6-methylguanine–induced transcriptional mutagenesis reduces p53 tumor-suppressor function
Ezerskyte M, Paredes JA, Malvezzi S, ..., Scicchitano DA, Dreij K
Proc. Natl. Acad. Sci. U.S.A. 115 (18) 4731-4736 [2018-05-01; online 2018-04-17]
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Extended and Continuous Decline in Effective Population Size Results in Low Genomic Diversity in the World's Rarest Hyena Species, the Brown Hyena.
Westbury MV, Hartmann S, Barlow A, ..., Dalén L, Hofreiter M
Mol. Biol. Evol. 35 (5) 1225-1237 [2018-05-01; online 2018-03-13]
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Fatal demyelinating disease is induced by monocyte-derived macrophages in the absence of TGF-β signaling
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Nat. Immunol. 19 (5) 1-7 [2018-05-00; online 2018-04-16]
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Ethylene signaling induces gelatinous layers with typical features of tension wood in hybrid aspen.
Felten J, Vahala J, Love J, ..., Mellerowicz EJ, Sundberg B
New Phytol. 218 (3) 999-1014 [2018-05-00; online 2018-03-12]
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Full Mitogenomes in the Critically Endangered Kākāpō Reveal Major Post-Glacial and Anthropogenic Effects on Neutral Genetic Diversity.
Dussex N, von Seth J, Robertson BC, Dalén L
Genes 9 (4) 220 [2018-04-19; online 2018-04-19]
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Expression of scavenger receptor MARCO defines a targetable tumor-associated macrophage subset in non-small cell lung cancer.
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Int. J. Cancer - (-) - [2018-04-18; online 2018-04-18]
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Transcriptome profiling of the interconnection of pathways involved in malignant transformation and response to hypoxia.
Danielsson F, Fasterius E, Sullivan D, ..., Williams C, Lundberg E
Oncotarget 9 (28) 19730-19744 [2018-04-13; online 2018-04-13]
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Transcriptional Roadmap to Seasonal Variation in Wood Formation of Norway Spruce.
Jokipii-Lukkari S, Delhomme N, Schiffthaler B, ..., Street NR, Tuominen H
Plant Physiol. 176 (4) 2851-2870 [2018-04-00; online 2018-02-27]
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The functional 3'-end of immunoglobulin heavy chain variable (IGHV) genes.
Thörnqvist L, Ohlin M
Mol. Immunol. 96 (-) 61-68 [2018-04-00; online 2018-02-28]
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Long Non-Coding RNAs Associated with Metabolic Traits in Human White Adipose Tissue.
Gao H, Kerr A, Jiao H, ..., Dahlman I, Arner P
EBioMedicine 30 (-) 248-260 [2018-04-00; online 2018-03-15]
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Evaluation of the ISL1 gene in the pathogenesis of bladder exstrophy in a Swedish cohort.
Arkani S, Cao J, Lundin J, ..., Matsson H, Nordenskjöld A
Hum Genome Var 5 (-) 18009 [2018-03-29; online 2018-03-29]
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AMYCNE: Confident copy number assessment using whole genome sequencing data.
Eisfeldt J, Nilsson D, Andersson-Assarsson JC, Lindstrand A
PLoS ONE 13 (3) e0189710 [2018-03-26; online 2018-03-26]
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Multiscale patterns and drivers of arbuscular mycorrhizal fungal communities in the roots and root-associated soil of a wild perennial herb
Rasmussen PU, Hugerth LW, Blanchet FG, ..., Lindahl BD, Tack AJM
New Phytol - (-) - [2018-03-24; online 2018-03-24]
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Reducing Pericyte-Derived Scarring Promotes Recovery after Spinal Cord Injury.
Dias DO, Kim H, Holl D, ..., Göritz C, Frisén J
Cell 173 (1) 153-165.e22 [2018-03-22; online 2018-03-01]
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PubMed DOI Crossref
Ethylene-Related Gene Expression Networks in Wood Formation.
Seyfferth C, Wessels B, Jokipii-Lukkari S, ..., Felten J, Tuominen H
Front Plant Sci 9 (-) 272 [2018-03-14; online 2018-03-14]
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PubMed DOI Crossref
High-resolution detection of chromosomal rearrangements in leukemias through mate pair whole genome sequencing.
Tran AN, Taylan F, Zachariadis V, ..., Nilsson D, Barbany G
PLoS ONE 13 (3) e0193928 [2018-03-12; online 2018-03-12]
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PubMed DOI Crossref
Global analysis of A-to-I RNA editing reveals association with common disease variants
Franzén O, Ermel R, Sukhavasi K, ..., Schadt EE, Björkegren JLM
PeerJ 6 (-) e4466 [2018-03-06; online 2018-03-06]
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Transcriptome analysis of embryonic domains in Norway spruce reveals potential regulators of suspensor cell death.
Reza SH, Delhomme N, Street NR, ..., Minina EA, Bozhkov PV
PLoS ONE 13 (3) e0192945 [2018-03-02; online 2018-03-02]
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PubMed DOI Crossref
Impact of genetic risk loci for multiple sclerosis on expression of proximal genes in patients.
James T, Lindén M, Morikawa H, ..., Gomez-Cabrero D, Kockum I
Hum. Mol. Genet. 27 (5) 912-928 [2018-03-01; online 2018-01-13]
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Relicts of the lost arc: High-throughput sequencing of the Eutrichomyias rowleyi (Aves: Passeriformes) holotype uncovers an ancient biogeographic link between the Philippines and Fiji.
Jønsson KA, Blom MPK, Päckert M, Ericson PGP, Irestedt M
Mol. Phylogenet. Evol. 120 (-) 28-32 [2018-03-00; online 2017-12-02]
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PubMed DOI Crossref
First de novo whole genome sequencing and assembly of the pink-footed goose.
Pujolar JM, Dalén L, Olsen RA, Hansen MM, Madsen J
Genomics 110 (2) 75-79 [2018-03-00; online 2017-08-30]
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PubMed DOI Crossref
A molecular atlas of cell types and zonation in the brain vasculature.
Vanlandewijck M, He L, Mäe MA, ..., Lendahl U, Betsholtz C
Nature 554 (7693) 475-480 [2018-02-22; online 2018-02-14]
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Multi-omics Reveals the Lifestyle of the Acidophilic, Mineral-Oxidizing Model Species Leptospirillum ferriphilum T.
Christel S, Herold M, Bellenberg S, ..., Poetsch A, Dopson M
Appl. Environ. Microbiol. 84 (3) e02091-17 [2018-02-01; online 2018-01-17]
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PubMed DOI Crossref
T cells are influenced by a long non-coding RNA in the autoimmune associated PTPN2 locus
Houtman M, Shchetynsky K, Chemin K, ..., Malmström V, Padyukov L
Journal of Autoimmunity 90 (-) 28-38 [2018-02-00; online 2018-02-00]
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PubMed DOI Crossref
In situ protein detection with enhanced specificity using DNA-conjugated antibodies and proximity ligation.
Zieba A, Ponten F, Uhlén M, Landegren U
Mod. Pathol. 31 (2) 253-263 [2018-02-00; online 2017-09-22]
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Gene expression profiling across ontogenetic stages in the wood white (Leptidea sinapis) reveals pathways linked to butterfly diapause regulation.
Leal L, Talla V, Källman T, ..., Vila R, Backström N
Mol. Ecol. 27 (4) 935-948 [2018-02-00; online 2018-02-26]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Conserved properties of dentate gyrus neurogenesis across postnatal development revealed by single-cell RNA sequencing.
Hochgerner H, Zeisel A, Lönnerberg P, Linnarsson S
Nat. Neurosci. 21 (2) 290-299 [2018-02-00; online 2018-01-15]
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Activating FGFR1 Mutations in Sporadic Pheochromocytomas.
Welander J, Łysiak M, Brauckhoff M, ..., Söderkvist P, Gimm O
World J Surg 42 (2) 482-489 [2018-02-00; online 2017-11-22]
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Discovering viral genomes in human metagenomic data by predicting unknown protein families.
Barrientos-Somarribas M, Messina DN, Pou C, ..., Andersson B, Sonnhammer ELL
Sci Rep 8 (1) 28 [2018-01-08; online 2018-01-08]
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Analysis of the hybrid genomes of two field isolates of the soil-borne fungal species Verticillium longisporum.
Fogelqvist J, Tzelepis G, Bejai S, ..., Schwelm A, Dixelius C
BMC Genomics 19 (1) 14 [2018-01-03; online 2018-01-03]
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Urban landscape genomics identifies fine-scale gene flow patterns in an avian invasive.
Low GW, Chattopadhyay B, Garg KM, ..., Wu S, Rheindt FE
Heredity (Edinb) 120 (2) 138-153 [2018-01-00; online 2017-12-11]
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Population genomics of Mesolithic Scandinavia: Investigating early postglacial migration routes and high-latitude adaptation.
Günther T, Malmström H, Svensson EM, ..., Götherström A, Jakobsson M
PLoS Biol. 16 (1) e2003703 [2018-01-00; online 2018-01-09]
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Exome sequencing reveals NAA15 and PUF60 as candidate genes associated with intellectual disability.
Zhao JJ, Halvardson J, Zander CS, ..., Thuresson AC, Feuk L
Am. J. Med. Genet. B Neuropsychiatr. Genet. 177 (1) 10-20 [2018-01-00; online 2017-10-09]
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Year 2017

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Targeted copy number screening highlights an intragenic deletion of WDR63 as the likely cause of human occipital encephalocele and abnormal CNS development in zebrafish.
Hofmeister W, Pettersson M, Kurtoglu D, ..., Gustavsson P, Lindstrand A
Hum. Mutat. - (-) - [2017-12-28; online 2017-12-28]
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Chemical and microbiological evaluation of novel chemical treatment methods for acid sulfate soils.
Högfors-Rönnholm E, Christel S, Dalhem K, ..., Österholm P, Dopson M
Sci. Total Environ. 625 (-) 39-49 [2017-12-26; online 2017-12-26]
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Reading and editing the Pleurodeles waltl genome reveals novel features of tetrapod regeneration.
Elewa A, Wang H, Talavera-López C, ..., Andersson B, Simon A
Nat Commun 8 (1) 2286 [2017-12-22; online 2017-12-22]
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Discovery of the fourth mobile sulfonamide resistance gene.
Razavi M, Marathe NP, Gillings MR, ..., Kristiansson E, Joakim Larsson DG
Microbiome 5 (1) 160 [2017-12-15; online 2017-12-15]
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Transcriptomics and Targeted Proteomics Analysis to Gain Insights Into the Immune-control Mechanisms of HIV-1 Infected Elite Controllers.
Zhang W, Ambikan AT, Sperk M, ..., Sönnerborg A, Neogi U
EBioMedicine - (-) - [2017-12-12; online 2017-12-12]
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A Unique ISR Program Determines Cellular Responses to Chronic Stress.
Guan BJ, van Hoef V, Jobava R, ..., Larsson O, Hatzoglou M
Mol. Cell 68 (5) 885-900.e6 [2017-12-07; online 2017-12-09]
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Heterogeneous Patterns of Genetic Diversity and Differentiation in European and Siberian Chiffchaff ( Phylloscopus collybita abietinus/P. tristis).
Talla V, Kalsoom F, Shipilina D, Marova I, Backström N
G3 (Bethesda) 7 (12) 3983-3998 [2017-12-04; online 2017-12-04]
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Inflammatory infiltrates in parathyroid tumors.
Haglund F, Hallström BM, Nilsson IL, ..., Juhlin CC, Larsson C
Eur. J. Endocrinol. 177 (6) 445-453 [2017-12-00; online 2017-08-30]
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A female Viking warrior confirmed by genomics.
Hedenstierna-Jonson C, Kjellström A, Zachrisson T, ..., Götherström A, Storå J
Am. J. Phys. Anthropol. 164 (4) 853-860 [2017-12-00; online 2017-09-08]
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Intra-tumor heterogeneity in breast cancer has limited impact on transcriptomic-based molecular profiling.
Karthik GM, Rantalainen M, Stålhammar G, ..., Bergh J, Hartman J
BMC Cancer 17 (1) 802 [2017-11-29; online 2017-11-29]
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STRT-seq-2i: dual-index 5' single cell and nucleus RNA-seq on an addressable microwell array.
Hochgerner H, Lönnerberg P, Hodge R, ..., Zeisel A, Linnarsson S
Sci Rep 7 (1) 16327 [2017-11-27; online 2017-11-27]
Cellular Immunomonitoring [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Genome-Based Sexing Provides Clues about Behavior and Social Structure in the Woolly Mammoth.
Pečnerová P, Díez-Del-Molino D, Dussex N, ..., Vartanyan S, Dalén L
Curr. Biol. 27 (22) 3505-3510.e3 [2017-11-20; online 2017-11-02]
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Novel KIAA0753 mutations extend the phenotype of skeletal ciliopathies.
Hammarsjö A, Wang Z, Vaz R, ..., Grigelioniene G, Ikegawa S
Sci Rep 7 (1) 15585 [2017-11-14; online 2017-11-14]
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Genomic Analyses of Pre-European Conquest Human Remains from the Canary Islands Reveal Close Affinity to Modern North Africans.
Rodríguez-Varela R, Günther T, Krzewińska M, ..., Götherström A, Girdland-Flink L
Curr. Biol. 27 (21) 3396-3402.e5 [2017-11-06; online 2017-10-26]
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Unique case of cerebrotendinous xanthomatosis revisited: All the mutations responsible for this disease are present in the CYP27A1 gene.
Jiao H, Olin M, Hansson M, ..., Angelin B, Björkhem I
J. Intern. Med. - (-) - [2017-11-02; online 2017-11-02]
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Untreated urban waste contaminates Indian river sediments with resistance genes to last resort antibiotics.
Marathe NP, Pal C, Gaikwad SS, ..., Kristiansson E, Larsson DGJ
Water Res. 124 (-) 388-397 [2017-11-01; online 2017-07-25]
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Whole mitochondrial genome capture from faecal samples and museum-preserved specimens.
van der Valk T, Lona Durazo F, Dalén L, Guschanski K
Mol Ecol Resour 17 (6) e111-e121 [2017-11-00; online 2017-08-03]
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SweGen: a whole-genome data resource of genetic variability in a cross-section of the Swedish population.
Ameur A, Dahlberg J, Olason P, ..., Magnusson PK, Gyllensten U
Eur. J. Hum. Genet. 25 (11) 1253-1260 [2017-11-00; online 2017-08-23]
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Ninety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation.
Svartström O, Alneberg J, Terrapon N, ..., Aspeborg H, Andersson AF
ISME J 11 (11) 2538-2551 [2017-11-00; online 2017-07-21]
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High abundance and expression of transposases in bacteria from the Baltic Sea.
Vigil-Stenman T, Ininbergs K, Bergman B, Ekman M
ISME J 11 (11) 2611-2623 [2017-11-00; online 2017-07-21]
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Pujolar JM, Dalén L, Hansen MM, Madsen J
Mol. Ecol. 26 (22) 6270-6283 [2017-11-00; online 2017-11-03]
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Efficient protein production by yeast requires global tuning of metabolism.
Huang M, Bao J, Hallström BM, Petranovic D, Nielsen J
Nat Commun 8 (1) 1131 [2017-10-25; online 2017-10-25]
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Polysome-profiling in small tissue samples.
Liang S, Bellato HM, Lorent J, ..., Hajj GNM, Larsson O
Nucleic Acids Res. - (-) - [2017-10-23; online 2017-10-23]
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Spatial detection of fetal marker genes expressed at low level in adult human heart tissue.
Asp M, Salmén F, Ståhl PL, ..., Linde C, Lundeberg J
Sci Rep 7 (1) 12941 [2017-10-11; online 2017-10-11]
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Diatoms dominate the eukaryotic metatranscriptome during spring in coastal 'dead zone' sediments.
Broman E, Sachpazidou V, Dopson M, Hylander S
Proc. Biol. Sci. 284 (1864) - [2017-10-11; online 2017-10-06]
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Rapid Increase in Genome Size as a Consequence of Transposable Element Hyperactivity in Wood-White (Leptidea) Butterflies.
Talla V, Suh A, Kalsoom F, ..., Wiklund C, Backström N
Genome Biol Evol 9 (10) 2491-2505 [2017-10-01; online 2017-10-06]
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NorWood: a gene expression resource for evo-devo studies of conifer wood development.
Jokipii-Lukkari S, Sundell D, Nilsson O, ..., Street NR, Tuominen H
New Phytol. 216 (2) 482-494 [2017-10-00; online 2017-02-10]
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Conflicting results from mitochondrial genomic data challenge current views of Rubiaceae phylogeny
Rydin C, Wikström N, Bremer B
Am. J. Bot. 104 (10) 1522-1532 [2017-10-00; online 2017-10-18]
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Major transcriptional changes observed in the Fulani, an ethnic group less susceptible to malaria.
Quin JE, Bujila I, Chérif M, ..., Nebie I, Östlund Farrants AK
Elife 6 (-) - [2017-09-19; online 2017-09-19]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Acute doses of caffeine shift nervous system cell expression profiles toward promotion of neuronal projection growth.
Yu NY, Bieder A, Raman A, ..., Daub CO, Kere J
Sci Rep 7 (1) 11458 [2017-09-13; online 2017-09-13]
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Analysing Microbial Community Composition through Amplicon Sequencing: From Sampling to Hypothesis Testing.
Hugerth LW, Andersson AF
Front Microbiol 8 (-) 1561 [2017-09-04; online 2017-09-04]
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The Huperzia selago Shoot Tip Transcriptome Sheds New Light on the Evolution of Leaves.
Evkaikina AI, Berke L, Romanova MA, ..., Pawlowski K, Voitsekhovskaja OV
Genome Biol Evol 9 (9) 2444-2460 [2017-09-01; online 2017-09-29]
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Silencing FLI or targeting CD13/ANPEP lead to dephosphorylation of EPHA2, a mediator of BRAF inhibitor resistance, and induce growth arrest or apoptosis in melanoma cells.
Azimi A, Tuominen R, Costa Svedman F, ..., Hansson J, Egyhazi Brage S
Cell Death Dis 8 (8) e3029 [2017-08-31; online 2017-08-31]
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Identification of NCAN as a candidate gene for developmental dyslexia.
Einarsdottir E, Peyrard-Janvid M, Darki F, ..., Leinonen E, Kere J
Sci Rep 7 (1) 9294 [2017-08-24; online 2017-08-24]
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Cerium oxide nanoparticles inhibit differentiation of neural stem cells.
Gliga AR, Edoff K, Caputo F, ..., Ceccatelli S, Fadeel B
Sci Rep 7 (1) 9284 [2017-08-24; online 2017-08-24]
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Mitochondrial genome of the North African Sahara Honeybee, Apis mellifera sahariensis (Hymenoptera: Apidae).
Haddad N, Adjlane N, Loucif-Ayad W, ..., Al-Nakeeb K, Sicheritz-Ponten T
Mitochondrial DNA Part B 2 (2) 548-549 [2017-08-22; online 2017-08-22]
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A pathology atlas of the human cancer transcriptome.
Uhlen M, Zhang C, Lee S, ..., Mardinoglu A, Ponten F
Science 357 (6352) eaan2507 [2017-08-18; online 2017-08-19]
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Shifts in coastal sediment oxygenation cause pronounced changes in microbial community composition and associated metabolism.
Broman E, Sjöstedt J, Pinhassi J, Dopson M
Microbiome 5 (1) 96 [2017-08-09; online 2017-08-09]
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Rho-associated kinase is a therapeutic target in neuroblastoma.
Dyberg C, Fransson S, Andonova T, ..., Johnsen JI, Wickström M
Proc. Natl. Acad. Sci. U.S.A. 114 (32) E6603-E6612 [2017-08-08; online 2017-07-24]
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PLS3 Deletions Lead to Severe Spinal Osteoporosis and Disturbed Bone Matrix Mineralization.
Kämpe AJ, Costantini A, Levy-Shraga Y, ..., Grasemann C, Mäkitie O
J. Bone Miner. Res. - (-) - [2017-08-04; online 2017-08-04]
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Low temperature, autotrophic microbial denitrification using thiosulfate or thiocyanate as electron donor.
Broman E, Jawad A, Wu X, ..., Sundkvist JE, Dopson M
Biodegradation 28 (4) 287-301 [2017-08-00; online 2017-06-02]
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Genetic differences between willow warbler migratory phenotypes are few and cluster in large haplotype blocks
Lundberg M, Liedvogel M, Larson K, ..., Åkesson S, Bensch S
Evolution Letters 1 (3) 155-168 [2017-08-00; online 2017-06-16]
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Data on haplotype-supported immunoglobulin germline gene inference.
Kirik U, Greiff L, Levander F, Ohlin M
Data Brief 13 (-) 620-640 [2017-08-00; online 2017-06-27]
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A MUTYH germline mutation is associated with small intestinal neuroendocrine tumors.
Dumanski JP, Rasi C, Björklund P, ..., Hellman P, Tiensuu Janson E
Endocr. Relat. Cancer 24 (8) 427-443 [2017-08-00; online 2017-06-20]
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Droplet Barcode Sequencing for targeted linked-read haplotyping of single DNA molecules.
Redin D, Borgström E, He M, ..., Käller M, Ahmadian A
Nucleic Acids Res. 45 (13) e125 [2017-07-27; online 2017-05-20]
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PubMed DOI Crossref
PLS3 sequencing in childhood-onset primary osteoporosis identifies two novel disease-causing variants.
Kämpe AJ, Costantini A, Mäkitie RE, ..., Jiao H, Mäkitie O
Osteoporos Int - (-) - [2017-07-26; online 2017-07-26]
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Recent increased identification and transmission of HIV-1 unique recombinant forms in Sweden.
Neogi U, Siddik AB, Kalaghatgi P, ..., Marrone G, Sönnerborg A
Sci Rep 7 (1) 6371 [2017-07-25; online 2017-07-25]
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Combined epigenetic and differentiation-based treatment inhibits neuroblastoma tumor growth and links HIF2α to tumor suppression.
Westerlund I, Shi Y, Toskas K, ..., Schlisio S, Holmberg J
Proc. Natl. Acad. Sci. U.S.A. 114 (30) E6137-E6146 [2017-07-25; online 2017-07-10]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Transcriptional profiling of the rat nucleus accumbens after modest or high alcohol exposure.
Morud J, Ashouri A, Larsson E, Ericson M, Söderpalm B
PLoS ONE 12 (7) e0181084 [2017-07-17; online 2017-07-17]
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PubMed DOI Crossref
Analysis of aquaporins from the euryhaline barnacle Balanus improvisus reveals differential expression in response to changes in salinity.
Lind U, Järvå M, Alm Rosenblad M, ..., Hedfalk K, Blomberg A
PLoS ONE 12 (7) e0181192 [2017-07-17; online 2017-07-17]
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Does antifouling paint select for antibiotic resistance?
Flach CF, Pal C, Svensson CJ, ..., Tysklind M, Larsson DG
Sci. Total Environ. 590-591 (-) 461-468 [2017-07-15; online 2017-03-08]
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Niche-mediated depletion of the normal hematopoietic stem cell reservoir by Flt3-ITD-induced myeloproliferation.
Mead AJ, Neo WH, Barkas N, ..., Nerlov C, Jacobsen SEW
J. Exp. Med. 214 (7) 2005-2021 [2017-07-03; online 2017-06-21]
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Mineral Type Structures Soil Microbial Communities
Ahmed E, Hugerth LW, Logue JB, ..., Andersson AF, Holmström SJM
Geomicrobiology Journal 34 (6) 538-545 [2017-07-03; online 2016-11-22]
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Interspecific Plastome Recombination Reflects Ancient Reticulate Evolution in Picea (Pinaceae).
Sullivan AR, Schiffthaler B, Thompson SL, Street NR, Wang XR
Mol. Biol. Evol. 34 (7) 1689-1701 [2017-07-01; online 2017-04-07]
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Wholegrain oat diet changes the expression of genes associated with intestinal bile acid transport.
Andersson KE, Chawade A, Thuresson N, ..., Olsson O, Hellstrand P
Mol Nutr Food Res 61 (7) - [2017-07-00; online 2017-03-30]
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Primary familial brain calcification linked to deletion of 5' noncoding region of SLC20A2.
Pasanen P, Mäkinen J, Myllykangas L, ..., Pöyhönen M, Baumann P
Acta Neurol. Scand. 136 (1) 59-63 [2017-07-00; online 2016-10-10]
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Parallel antibody germline gene and haplotype analyses support the validity of immunoglobulin germline gene inference and discovery.
Kirik U, Greiff L, Levander F, Ohlin M
Mol. Immunol. 87 (-) 12-22 [2017-07-00; online 2017-04-04]
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Genomewide analysis of admixture and adaptation in the Africanized honeybee.
Nelson RM, Wallberg A, Simões ZLP, Lawson DJ, Webster MT
Mol. Ecol. 26 (14) 3603-3617 [2017-07-00; online 2017-04-24]
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2b-RAD genotyping for population genomic studies of Chagas disease vectors: Rhodnius ecuadoriensis in Ecuador.
Hernandez-Castro LE, Paterno M, Villacís AG, ..., Grijalva MJ, Llewellyn MS
PLoS Negl Trop Dis 11 (7) e0005710 [2017-07-00; online 2017-07-19]
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The wolf reference genome sequence (Canis lupus lupus) and its implications for Canis spp. population genomics.
Gopalakrishnan S, Samaniego Castruita JA, Sinding MS, ..., Dalén L, Gilbert MTP
BMC Genomics 18 (1) 495 [2017-06-29; online 2017-06-29]
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PubMed DOI Crossref
Leucine Biosynthesis Is Involved in Regulating High Lipid Accumulation in Yarrowia lipolytica.
Kerkhoven EJ, Kim YM, Wei S, ..., Metz TO, Nielsen J
MBio 8 (3) - [2017-06-20; online 2017-06-20]
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Microbial Community Structure in a Serpentine-Hosted Abiotic Gas Seepage at the Chimaera Ophiolite, Turkey.
Neubeck A, Sun L, Müller B, ..., Broman C, Schnürer A
Appl. Environ. Microbiol. 83 (12) - [2017-06-15; online 2017-05-31]
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PubMed DOI Crossref
Genome Sequence of Roseovarius mucosus Strain SMR3, Isolated from a Culture of the Diatom Skeletonema marinoi.
Töpel M, Pinder MIM, Johansson ON, ..., Godhe A, Clarke AK
Genome Announc 5 (22) - [2017-06-01; online 2017-06-01]
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DOI Crossref
Separating the effects of forage source and field microbiota on silage fermentation quality and aerobic stability
Mogodiniyai Kasmaei K, Dicksved J, Spörndly R, Udén P
Grass Forage Sci 72 (2) 281-289 [2017-06-00; online 2016-06-06]
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PubMed DOI Crossref
A subcellular map of the human proteome.
Thul PJ, Åkesson L, Wiking M, ..., Uhlén M, Lundberg E
Science 356 (6340) - [2017-05-26; online 2017-05-11]
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Type 2 diabetes and obesity induce similar transcriptional reprogramming in human myocytes.
Väremo L, Henriksen TI, Scheele C, ..., Pedersen BK, Nielsen J
Genome Med 9 (1) 47 [2017-05-25; online 2017-05-25]
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PubMed DOI Crossref
Draft Genome Sequence of the Mycoparasitic Oomycete Pythium oligandrum Strain CBS 530.74.
Kushwaha SK, Vetukuri RR, Grenville-Briggs LJ
Genome Announc 5 (21) - [2017-05-25; online 2017-05-25]
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TIDDIT, an efficient and comprehensive structural variant caller for massive parallel sequencing data.
Eisfeldt J, Vezzi F, Olason P, Nilsson D, Lindstrand A
F1000Res 6 (-) 664 [2017-05-10; online 2017-05-10]
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PubMed DOI Crossref
Spatially resolved transcriptome profiling in model plant species.
Giacomello S, Salmén F, Terebieniec BK, ..., Street NR, Lundeberg J
NPLANTS 3 (-) 17061 [2017-05-08; online 2017-05-08]
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Regulation of PfEMP1-VAR2CSA translation by a Plasmodium translation-enhancing factor.
Chan S, Frasch A, Mandava CS, ..., Sanyal S, Wahlgren M
Nat Microbiol 2 (-) 17068 [2017-05-08; online 2017-05-08]
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Two extended haplotype blocks are associated with adaptation to high altitude habitats in East African honey bees.
Wallberg A, Schöning C, Webster MT, Hasselmann M
PLoS Genet. 13 (5) e1006792 [2017-05-00; online 2017-05-25]
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Transcriptomics and methylomics of CD4-positive T cells in arsenic-exposed women.
Engström K, Wojdacz TK, Marabita F, ..., Vahter M, Broberg K
Arch. Toxicol. 91 (5) 2067-2078 [2017-05-00; online 2016-11-12]
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PubMed DOI Crossref
The chloroplast genome of Ephedra foeminea (Ephedraceae, Gnetales), an entomophilous gymnosperm endemic to the Mediterranean area.
Hou C, Wikström N, Rydin C
Mitochondrial DNA A DNA Mapp Seq Anal 28 (3) 330-331 [2017-05-00; online 2015-12-29]
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Induction of functional dopamine neurons from human astrocytes in vitro and mouse astrocytes in a Parkinson's disease model.
Rivetti di Val Cervo P, Romanov RA, Spigolon G, ..., Fisone G, Arenas E
Nat. Biotechnol. 35 (5) 444-452 [2017-05-00; online 2017-04-10]
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PubMed DOI Crossref
Further evidence for specific IFIH1 mutation as a cause of Singleton-Merten syndrome with phenotypic heterogeneity.
Pettersson M, Bergendal B, Norderyd J, ..., Nordgren A, Lindstrand A
Am. J. Med. Genet. A 173 (5) 1396-1399 [2017-05-00; online 2017-03-20]
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Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications.
Weissensteiner MH, Pang AWC, Bunikis I, ..., Suh A, Wolf JBW
Genome Res. 27 (5) 697-708 [2017-05-00; online 2017-03-30]
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PubMed DOI Crossref
Mitochondrial genome divergence between beluga whales in Baffin Bay and the Sea of Okhotsk.
Skovrind M, Samaniego Castruita JA, Heide-Jørgensen MP, Dalén L, Lorenzen E
Mitochondrial DNA Part B 2 (1) 257-258 [2017-04-28; online 2017-04-28]
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PubMed DOI Crossref
Draft Genome Sequences of Six Strains of Streptococcus pneumoniae from Serotypes 5, 6A, 6B, 18C, 19A, and 23F.
Jakobsson HE, Salvà-Serra F, Thorell K, ..., Kristiansson E, Moore ER
Genome Announc 5 (14) - [2017-04-06; online 2017-04-06]
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Genomic analysis reveals the presence of a class D beta-lactamase with broad substrate specificity in animal bite associated Capnocytophaga species.
Zangenah S, Andersson AF, Özenci V, Bergman P
Eur. J. Clin. Microbiol. Infect. Dis. 36 (4) 657-662 [2017-04-00; online 2016-12-03]
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PubMed DOI Crossref
Gene co-expression network connectivity is an important determinant of selective constraint.
Mähler N, Wang J, Terebieniec BK, ..., Street NR, Hvidsten TR
PLoS Genet. 13 (4) e1006402 [2017-04-00; online 2017-04-13]
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DOI Crossref
Effects of dietary inclusion of the yeasts Saccharomyces cerevisiae and Wickerhamomyces anomalus on gut microbiota of rainbow trout
Huyben D, Nyman A, Vidaković A, ..., Dicksved J, Lundh T
Aquaculture 473 (-) 528-537 [2017-04-00; online 2017-04-00]
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A Large Inversion Involving GNAS Exon A/B and All Exons Encoding Gsα Is Associated With Autosomal Dominant Pseudohypoparathyroidism Type Ib (PHP1B).
Grigelioniene G, Nevalainen PI, Reyes M, ..., Mäkitie O, Jüppner H
J. Bone Miner. Res. 32 (4) 776-783 [2017-04-00; online 2017-02-24]
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Improvement of identification methods for honeybee specific Lactic Acid Bacteria; future approaches.
Lamei S, Hu YO, Olofsson TC, ..., Forsgren E, Vásquez A
PLoS ONE 12 (3) e0174614 [2017-03-27; online 2017-03-27]
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Potential for hydrogen-oxidizing chemolithoautotrophic and diazotrophic populations to initiate biofilm formation in oligotrophic, deep terrestrial subsurface waters.
Wu X, Pedersen K, Edlund J, ..., Bertilsson S, Dopson M
Microbiome 5 (1) 37 [2017-03-23; online 2017-03-23]
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PubMed DOI Crossref
Draft Genome Sequence of the Mycoparasitic Oomycete Pythium periplocum Strain CBS 532.74.
Kushwaha SK, Vetukuri RR, Grenville-Briggs LJ
Genome Announc 5 (12) - [2017-03-23; online 2017-03-23]
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The evolutionary and phylogeographic history of woolly mammoths: a comprehensive mitogenomic analysis.
Chang D, Knapp M, Enk J, ..., Hofreiter M, Shapiro B
Sci Rep 7 (-) 44585 [2017-03-22; online 2017-03-22]
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PubMed DOI Crossref
Diverse origin of mitochondrial lineages in Iron Age Black Sea Scythians.
Juras A, Krzewińska M, Nikitin AG, ..., Dabert M, Götherström A
Sci Rep 7 (-) 43950 [2017-03-07; online 2017-03-07]
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PubMed DOI Crossref
Complete mitochondrial genome of the Oriental Hornet, Vespa orientalis F. (Hymenoptera: Vespidae).
Haddad NJ, Al-Nakeeb K, Petersen B, ..., Blom N, Sicheritz-Pontén T
Mitochondrial DNA Part B 2 (1) 139-140 [2017-03-01; online 2017-03-01]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Metapopulation theory identifies biogeographical patterns among core and satellite marine bacteria scaling from tens to thousands of kilometers.
Lindh MV, Sjöstedt J, Ekstam B, ..., Legrand C, Pinhassi J
Environ. Microbiol. 19 (3) 1222-1236 [2017-03-00; online 2017-02-06]
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PubMed DOI Crossref
Antibody-encoding repertoires of bone marrow and peripheral blood—a focus on IgE
Levin M, Levander F, Palmason R, Greiff L, Ohlin M
Journal of Allergy and Clinical Immunology 139 (3) 1026-1030 [2017-03-00; online 2017-03-00]
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Evaluating Variant Calling Tools for Non-Matched Next-Generation Sequencing Data.
Sandmann S, de Graaf AO, Karimi M, ..., Jansen JH, Dugas M
Sci Rep 7 (-) 43169 [2017-02-24; online 2017-02-24]
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PubMed DOI Crossref
Methane Production in Dairy Cows Correlates with Rumen Methanogenic and Bacterial Community Structure.
Danielsson R, Dicksved J, Sun L, ..., Schnürer A, Bertilsson J
Front Microbiol 8 (-) 226 [2017-02-17; online 2017-02-17]
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PubMed DOI Crossref
The mitochondrial genome sequences of the round goby and the sand goby reveal patterns of recent evolution in gobiid fish.
Adrian-Kalchhauser I, Svensson O, Kutschera VE, ..., Blomberg A, Burkhardt-Holm P
BMC Genomics 18 (1) 177 [2017-02-16; online 2017-02-16]
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Comparison of whole genome amplification techniques for human single cell exome sequencing.
Borgström E, Paterlini M, Mold JE, Frisen J, Lundeberg J
PLoS ONE 12 (2) e0171566 [2017-02-16; online 2017-02-16]
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PubMed DOI Crossref
The Baltic Sea Virome: Diversity and Transcriptional Activity of DNA and RNA Viruses.
Zeigler Allen L, McCrow JP, Ininbergs K, ..., Bergman B, Venter JC
mSystems 2 (1) - [2017-02-14; online 2017-02-14]
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PubMed DOI Crossref
A novel RNA sequencing data analysis method for cell line authentication.
Fasterius E, Raso C, Kennedy S, ..., Uhlén M, Al-Khalili Szigyarto C
PLoS ONE 12 (2) e0171435 [2017-02-13; online 2017-02-13]
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PubMed DOI Crossref
microRNAs with AAGUGC seed motif constitute an integral part of an oncogenic signaling network.
Zhou Y, Frings O, Branca RM, ..., Agami R, Orre LM
Oncogene 36 (6) 731-745 [2017-02-09; online 2016-08-01]
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The Human Adrenal Gland Proteome Defined by Transcriptomics and Antibody-Based Profiling.
Bergman J, Botling J, Fagerberg L, ..., Uhlén M, Pontén F
Endocrinology 158 (2) 239-251 [2017-02-01; online 2016-12-03]
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Whole-Genome Sequencing of Cytogenetically Balanced Chromosome Translocations Identifies Potentially Pathological Gene Disruptions and Highlights the Importance of Microhomology in the Mechanism of Formation.
Nilsson D, Pettersson M, Gustavsson P, ..., Carvalho CMB, Lindstrand A
Hum. Mutat. 38 (2) 180-192 [2017-02-00; online 2016-12-05]
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Meta-omic analyses of Baltic Sea cyanobacteria: diversity, community structure and salt acclimation.
Celepli N, Sundh J, Ekman M, ..., Bergman B, Ininbergs K
Environ. Microbiol. 19 (2) 673-686 [2017-02-00; online 2017-01-27]
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PubMed DOI Crossref
Massive parallel sequencing questions the pathogenic role of missense variants in dilated cardiomyopathy
Dalin MG, Engström PG, Ivarsson EG, ..., Andersson B, Bergo MO
International Journal of Cardiology 228 (-) 742-748 [2017-02-00; online 2017-02-00]
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Identification of new TRIP12 variants and detailed clinical evaluation of individuals with non-syndromic intellectual disability with or without autism.
Bramswig NC, Lüdecke HJ, Pettersson M, ..., Kleefstra T, Wieczorek D
Hum. Genet. 136 (2) 179-192 [2017-02-00; online 2016-11-15]
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Effects of microbe- and mussel-based diets on the gut microbiota in Arctic charr ( Salvelinus alpinus )
Nyman A, Huyben D, Lundh T, Dicksved J
Aquaculture Reports 5 (-) 34-40 [2017-02-00; online 2017-02-00]
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PubMed DOI Crossref
Draft Genome Sequences of Semiconstitutive Red, Dry, and Rough Biofilm-Forming Commensal and Uropathogenic Escherichia coli Isolates.
Cimdins A, Lüthje P, Li F, ..., Brauner A, Römling U
Genome Announc 5 (4) - [2017-01-26; online 2017-01-26]
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PubMed DOI Crossref
Comprehensive RNA sequencing of healthy human endometrium at two time points of the menstrual cycle.
Sigurgeirsson B, Åmark H, Jemt A, ..., Lundeberg J, Gidlöf S
Biol. Reprod. 96 (1) 24-33 [2017-01-01; online 2017-04-11]
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DOI Crossref
P1.02-063 Mutation Profiling by Targeted Next-Generation Sequencing of an Unselected NSCLC Cohort
La Fleur L, Falk-Sorqvist E, Smeds P, ..., Moens L, Botling J
Journal of Thoracic Oncology 12 (1) S526-S527 [2017-01-00; online 2017-01-00]
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PubMed DOI Crossref
Evolutionary engineering reveals divergent paths when yeast is adapted to different acidic environments.
Fletcher E, Feizi A, Bisschops MMM, ..., Siewers V, Nielsen J
Metab. Eng. 39 (-) 19-28 [2017-01-00; online 2016-11-02]
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Year 2016

PubMed DOI Crossref
Genetic Variants in CHIA and CHI3L1 Are Associated with the IgE Response to the Ascaris Resistance Marker ABA-1 and the Birch Pollen Allergen Bet v 1.
Acevedo N, Bornacelly A, Mercado D, ..., Scheynius A, Caraballo L
PLoS ONE 11 (12) e0167453 [2016-12-15; online 2016-12-15]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Collaborative] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Disentangling genetic and epigenetic determinants of ultrafast adaptation.
Gjuvsland AB, Zörgö E, Samy JK, ..., Omholt SW, Warringer J
Mol. Syst. Biol. 12 (12) 892 [2016-12-15; online 2016-12-15]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The In Vitro Stability of Circulating Tumour DNA.
Henao Diaz E, Yachnin J, Grönberg H, Lindberg J
PLoS ONE 11 (12) e0168153 [2016-12-13; online 2016-12-13]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Cluster Flow: A user-friendly bioinformatics workflow tool.
Ewels P, Krueger F, Käller M, Andrews S
F1000Res 5 (-) 2824 [2016-12-06; online 2016-12-06]
NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
Elucidating selection processes for antibiotic resistance in sewage treatment plants using metagenomics.
Bengtsson-Palme J, Hammarén R, Pal C, ..., Tysklind M, Larsson DG
Sci. Total Environ. 572 (-) 697-712 [2016-12-01; online 2016-08-21]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Evolutionary History of the Nesophontidae, the Last Unplaced Recent Mammal Family.
Brace S, Thomas JA, Dalén L, ..., Barnes I, Turvey ST
Mol. Biol. Evol. 33 (12) 3095-3103 [2016-12-00; online 2016-09-15]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Distribution and expression of microbial rhodopsins in the Baltic Sea and adjacent waters.
Brindefalk B, Ekman M, Ininbergs K, ..., Pinhassi J, Bergman B
Environ. Microbiol. 18 (12) 4442-4455 [2016-12-00; online 2016-06-17]
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PubMed DOI Crossref
Phylogenetic Signals of Salinity and Season in Bacterial Community Composition Across the Salinity Gradient of the Baltic Sea.
Herlemann DP, Lundin D, Andersson AF, Labrenz M, Jürgens K
Front Microbiol 7 (-) 1883 [2016-11-24; online 2016-11-24]
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PubMed DOI Crossref
A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism.
Hefzi H, Ang KS, Hanscho M, ..., Lee DY, Lewis NE
Cell Syst 3 (5) 434-443.e8 [2016-11-23; online 2016-11-25]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
An automated approach to prepare tissue-derived spatially barcoded RNA-sequencing libraries.
Jemt A, Salmén F, Lundmark A, ..., Yucel-Lindberg T, Lundeberg J
Sci Rep 6 (-) 37137 [2016-11-16; online 2016-11-16]
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PubMed DOI Crossref
Acidithiobacillus ferrivorans SS3 presents little RNA transcript response related to cold stress during growth at 8 °C suggesting it is a eurypsychrophile.
Christel S, Fridlund J, Watkin EL, Dopson M
Extremophiles 20 (6) 903-913 [2016-11-00; online 2016-10-25]
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PubMed DOI Crossref
Identification of mutations, gene expression changes and fusion transcripts by whole transcriptome RNAseq in docetaxel resistant prostate cancer cells.
Ma Y, Miao Y, Peng Z, ..., Nilsson S, Li C
Springerplus 5 (1) 1861 [2016-10-24; online 2016-10-24]
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Front Microbiol 7 (-) 1670 [2016-10-21; online 2016-10-21]
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PLoS ONE 11 (10) e0164548 [2016-10-19; online 2016-10-19]
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Vickovic S, Ståhl PL, Salmén F, ..., Frisén J, Lundeberg J
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Diabetes 65 (10) 2980-2989 [2016-10-00; online 2016-07-20]
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Conserved 33-kb haplotype in the MHC class III region regulates chronic arthritis.
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Draft Genome Sequence of Moraxella catarrhalis Type Strain CCUG 353T.
Jakobsson HE, Salvà-Serra F, Thorell K, ..., Kristiansson E, Moore ERB
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Marques S, Zeisel A, Codeluppi S, ..., Linnarsson S, Castelo-Branco G
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GPR44 is a pancreatic protein restricted to the human beta cell.
Hellström-Lindahl E, Danielsson A, Ponten F, ..., Johansson L, Eriksson O
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The POU/Oct Transcription Factor Pdm1/nub Is Necessary for a Beneficial Gut Microbiota and Normal Lifespan of Drosophila.
Dantoft W, Lundin D, Esfahani SS, Engström Y
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Thermotolerant yeasts selected by adaptive evolution express heat stress response at 30 °C.
Caspeta L, Chen Y, Nielsen J
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Metagenomic Analysis of the Indian Ocean Picocyanobacterial Community: Structure, Potential Function and Evolution.
Díez B, Nylander JA, Ininbergs K, ..., Rusch DB, Bergman B
PLoS ONE 11 (5) e0155757 [2016-05-19; online 2016-05-19]
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Minimal selective concentrations of tetracycline in complex aquatic bacterial biofilms.
Lundström SV, Östman M, Bengtsson-Palme J, ..., Flach CF, Larsson DG
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Wang M, Klevebring D, Lindberg J, ..., Grönberg H, Rantalainen M
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Unscrambling Cyanobacteria Community Dynamics Related to Environmental Factors.
Bertos-Fortis M, Farnelid HM, Lindh MV, ..., Pinhassi J, Legrand C
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Palkopoulou E, Baca M, Abramson NI, ..., Stankovic A, Dalén L
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Hytönen MK, Arumilli M, Lappalainen AK, ..., Drögemüller C, Lohi H
PLoS Genet. 12 (5) e1006037 [2016-05-00; online 2016-05-17]
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Mutations in histone modulators are associated with prolonged survival during azacitidine therapy.
Tobiasson M, McLornan DP, Karimi M, ..., Mufti GJ, Hellström-Lindberg E
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Cytosolic splice isoform of Hsp70 nucleotide exchange factor Fes1 is required for the degradation of misfolded proteins in yeast.
Gowda NK, Kaimal JM, Masser AE, ..., Friedländer MR, Andréasson C
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RNA transcript sequencing reveals inorganic sulfur compound oxidation pathways in the acidophile Acidithiobacillus ferrivorans.
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Global genome splicing analysis reveals an increased number of alternatively spliced genes with aging.
Rodríguez SA, Grochová D, McKenna T, ..., Erdos MR, Eriksson M
Aging Cell 15 (2) 267-278 [2016-04-00; online 2015-12-22]
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Digital image analysis outperforms manual biomarker assessment in breast cancer.
Stålhammar G, Fuentes Martinez N, Lippert M, ..., Grunkin M, Hartman J
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Draft Genome Sequence of Streptococcus gordonii Type Strain CCUG 33482T.
Salvà-Serra F, Jakobsson HE, Thorell K, ..., Kristiansson E, Moore ER
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The chemosensory receptors of codling moth Cydia pomonella-expression in larvae and adults.
Walker WB, Gonzalez F, Garczynski SF, Witzgall P
Sci Rep 6 (-) 23518 [2016-03-23; online 2016-03-23]
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Metagenomic analysis of bloodstream infections in patients with acute leukemia and therapy-induced neutropenia.
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Evolutionary history of host use, rather than plant phylogeny, determines gene expression in a generalist butterfly.
Celorio-Mancera Mde L, Wheat CW, Huss M, ..., Nylin S, Janz N
BMC Evol. Biol. 16 (-) 59 [2016-03-08; online 2016-03-08]
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Whole genome sequencing identifies a novel species of the genus Capnocytophaga isolated from dog and cat bite wounds in humans.
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Fast, accurate, and lightweight analysis of BS-treated reads with ERNE 2.
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Kryvokhyzha D, Holm K, Chen J, ..., Lagercrantz U, Lascoux M
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T-cell receptor-HLA-DRB1 associations suggest specific antigens in pulmonary sarcoidosis.
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Reclassification of Wolbachia persica as Francisella persica comb. nov. and emended description of the family Francisellaceae.
Larson MA, Nalbantoglu U, Sayood K, ..., Sjöstedt A, Hinrichs SH
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Natural Selection and Recombination Rate Variation Shape Nucleotide Polymorphism Across the Genomes of Three Related Populus Species.
Wang J, Street NR, Scofield DG, Ingvarsson PK
Genetics 202 (3) 1185-1200 [2016-03-00; online 2016-01-02]
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PubMed DOI Crossref
Estimation of copy number aberrations: Comparison of exome sequencing data with SNP microarrays identifies homozygous deletions of 19q13.2 and CIC in neuroblastoma.
Fransson S, Östensson M, Djos A, ..., Kogner P, Martinsson T
Int. J. Oncol. 48 (3) 1103-1116 [2016-03-00; online 2016-01-23]
Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Bacterial community composition and fhs profiles of low- and high-ammonia biogas digesters reveal novel syntrophic acetate-oxidising bacteria.
Müller B, Sun L, Westerholm M, Schnürer A
Biotechnol Biofuels 9 (-) 48 [2016-02-27; online 2016-02-27]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Xenacoelomorpha is the sister group to Nephrozoa.
Cannon JT, Vellutini BC, Smith J, ..., Jondelius U, Hejnol A
Nature 530 (7588) 89-93 [2016-02-04; online 2016-02-06]
Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Genomic sequencing of a dyslexia susceptibility haplotype encompassing ROBO1.
Massinen S, Wang J, Laivuori K, ..., Jiao H, Kere J
J Neurodev Disord 8 (-) 4 [2016-01-27; online 2016-01-27]
Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Reconstructing ecosystem functions of the active microbial community of the Baltic Sea oxygen depleted sediments.
Thureborn P, Franzetti A, Lundin D, Sjöling S
PeerJ 4 (-) e1593 [2016-01-19; online 2016-01-19]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Using Whole-Exome Sequencing to Identify Genetic Markers for Carboplatin and Gemcitabine-Induced Toxicities.
Gréen H, Hasmats J, Kupershmidt I, ..., Peterson C, Lundeberg J
Clin. Cancer Res. 22 (2) 366-373 [2016-01-15; online 2015-09-16]
Bioinformatics Support and Infrastructure [Service] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Pathogenenic variant in the COL2A1 gene is associated with Spondyloepiphyseal dysplasia type Stanescu.
Hammarsjö A, Nordgren A, Lagerstedt-Robinson K, ..., Nishimura G, Grigelioniene G
Am. J. Med. Genet. A 170A (1) 266-269 [2016-01-00; online 2015-10-01]
Bioinformatics Support for Computational Resources [Service] Clinical Genomics Stockholm [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Mutations in FLVCR2 associated with Fowler syndrome and survival beyond infancy.
Kvarnung M, Taylan F, Nilsson D, ..., Nordgren A, Syk Lundberg E
Clin. Genet. 89 (1) 99-103 [2016-01-00; online 2015-02-14]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Composition of human faecal microbiota in resistance to Campylobacter infection.
Kampmann C, Dicksved J, Engstrand L, Rautelin H
Clin. Microbiol. Infect. 22 (1) 61.e1-61.e8 [2016-01-00; online 2015-09-16]
Clinical Genomics Stockholm [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
DOI Crossref
Overexpression of Trypanosoma rangeli trypanothione reductase increases parasite survival under oxidative stress
BELTRAME-BOTELHO IT, STOCO PH, STEINDEL M, ..., GADELHA FR, GRISARD EC
Parasitology Open 2 (-) - [2016-00-00; online 2016-11-14]
NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Year 2015

PubMed DOI Crossref
The Urinary Bladder Transcriptome and Proteome Defined by Transcriptomics and Antibody-Based Profiling.
Habuka M, Fagerberg L, Hallström BM, ..., Yamamoto T, Uhlen M
PLoS ONE 10 (12) e0145301 [2015-12-22; online 2015-12-22]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Tissue Profiling [Collaborative]
PubMed DOI Crossref
Transcriptome analysis reveals mucin 4 to be highly associated with periodontitis and identifies pleckstrin as a link to systemic diseases.
Lundmark A, Davanian H, Båge T, ..., Lundeberg J, Yucel-Lindberg T
Sci Rep 5 (-) 18475 [2015-12-21; online 2015-12-21]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Metagenome-assembled genomes uncover a global brackish microbiome.
Hugerth LW, Larsson J, Alneberg J, ..., Pinhassi J, Andersson AF
Genome Biol. 16 (-) 279 [2015-12-14; online 2015-12-14]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Dietary Fiber-Induced Improvement in Glucose Metabolism Is Associated with Increased Abundance of Prevotella.
Kovatcheva-Datchary P, Nilsson A, Akrami R, ..., Björck I, Bäckhed F
Cell Metab. 22 (6) 971-982 [2015-12-01; online 2015-11-11]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
The Plant Genome Integrative Explorer Resource: PlantGenIE.org.
Sundell D, Mannapperuma C, Netotea S, ..., Hvidsten TR, Street NR
New Phytol. 208 (4) 1149-1156 [2015-12-00; online 2015-07-21]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Oral microbiota in patients with atherosclerosis.
Fåk F, Tremaroli V, Bergström G, Bäckhed F
Atherosclerosis 243 (2) 573-578 [2015-12-00; online 2015-11-05]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Experiences with workflows for automating data-intensive bioinformatics
Spjuth O, Bongcam-Rudloff E, Hernández GC, ..., Siretskiy A, Vassilev D
Biol. Direct 10 (1) - [2015-12-00; online 2015-08-19]
Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
De novo assembly of Dekkera bruxellensis: a multi technology approach using short and long-read sequencing and optical mapping.
Olsen RA, Bunikis I, Tiukova I, ..., Käller M, Vezzi F
Gigascience 4 (-) 56 [2015-11-26; online 2015-11-26]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure
DOI Crossref
A Conserved Odorant Receptor Detects the Same 1-Indanone Analogs in a Tortricid and a Noctuid Moth
Gonzalez F, Bengtsson JM, Walker WB, ..., Ignell R, Bengtsson M
Front. Ecol. Evol. 3 (-) - [2015-11-19; online 2015-11-19]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Single cell analysis of cancer cells using an improved RT-MLPA method has potential for cancer diagnosis and monitoring.
Kvastad L, Werne Solnestam B, Johansson E, ..., Latta D, Lundeberg J
Sci Rep 5 (-) 16519 [2015-11-12; online 2015-11-12]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Normalization of Host Intestinal Mucus Layers Requires Long-Term Microbial Colonization.
Johansson ME, Jakobsson HE, Holmén-Larsson J, ..., Bäckhed F, Hansson GC
Cell Host Microbe 18 (5) 582-592 [2015-11-11; online 2015-11-04]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Intra-mitochondrial Methylation Deficiency Due to Mutations in SLC25A26.
Kishita Y, Pajak A, Bolar NA, ..., Okazaki Y, Wedell A
Am. J. Hum. Genet. 97 (5) 761-768 [2015-11-05; online 2015-11-03]
Clinical Genomics Stockholm NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Variant Profiling of Candidate Genes in Pancreatic Ductal Adenocarcinoma.
Huang J, Löhr JM, Nilsson M, ..., Zheng Z, Ye W
Clin. Chem. 61 (11) 1408-1416 [2015-11-00; online 2015-09-16]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
The Human Endometrium-Specific Proteome Defined by Transcriptomics and Antibody-Based Profiling.
Zieba A, Sjöstedt E, Olovsson M, ..., Uhlen M, Ponten F
OMICS 19 (11) 659-668 [2015-11-00; online 2015-10-21]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Tissue Profiling [Technology development]
PubMed DOI Crossref
Rescue of primary ubiquinone deficiency due to a novel COQ7 defect using 2,4-dihydroxybensoic acid.
Freyer C, Stranneheim H, Naess K, ..., Wredenberg A, Wedell A
J. Med. Genet. 52 (11) 779-783 [2015-11-00; online 2015-06-19]
Clinical Genomics Stockholm NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Genus-Wide Comparative Genomics of Malassezia Delineates Its Phylogeny, Physiology, and Niche Adaptation on Human Skin.
Wu G, Zhao H, Li C, ..., Nagarajan N, Dawson TL
PLoS Genet. 11 (11) e1005614 [2015-11-00; online 2015-11-05]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Quinolone resistance mutations in the faecal microbiota of Swedish travellers to India.
Johnning A, Kristiansson E, Angelin M, ..., Johansson A, Larsson DG
BMC Microbiol. 15 (-) 235 [2015-10-24; online 2015-10-24]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Nurr1 and Retinoid X Receptor Ligands Stimulate Ret Signaling in Dopamine Neurons and Can Alleviate α-Synuclein Disrupted Gene Expression.
Volakakis N, Tiklova K, Decressac M, ..., Björklund A, Perlmann T
J. Neurosci. 35 (42) 14370-14385 [2015-10-21; online 2015-10-23]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Crosstalk between Gut Microbiota and Dietary Lipids Aggravates WAT Inflammation through TLR Signaling.
Caesar R, Tremaroli V, Kovatcheva-Datchary P, Cani PD, Bäckhed F
Cell Metab. 22 (4) 658-668 [2015-10-06; online 2015-09-01]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Candidate gene analysis and exome sequencing confirm LBX1 as a susceptibility gene for idiopathic scoliosis.
Grauers A, Wang J, Einarsdottir E, ..., Kere J, Gerdhem P
Spine J 15 (10) 2239-2246 [2015-10-01; online 2015-05-20]
Mutation Analysis Facility (MAF) NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Profound parental bias associated with chromosome 14 acquired uniparental disomy indicates targeting of an imprinted locus.
Chase A, Leung W, Tapper W, ..., Dumanski JP, Cross NC
Leukemia 29 (10) 2069-2074 [2015-10-00; online 2015-06-27]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Isolation of novel IncA/C and IncN fluoroquinolone resistance plasmids from an antibiotic-polluted lake.
Flach CF, Johnning A, Nilsson I, ..., Kristiansson E, Larsson DG
J. Antimicrob. Chemother. 70 (10) 2709-2717 [2015-10-00; online 2015-07-01]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Serendipitous Meta-Transcriptomics: The Fungal Community of Norway Spruce (Picea abies).
Delhomme N, Sundström G, Zamani N, ..., Grabherr MG, Street NR
PLoS ONE 10 (9) e0139080 [2015-09-28; online 2015-09-28]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Gene expression profiling of pre-eclamptic placentae by RNA sequencing.
Kaartokallio T, Cervera A, Kyllönen A, ..., Laivuori H, FINNPEC Core Investigator Group
Sci Rep 5 (-) 14107 [2015-09-21; online 2015-09-21]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Draft genome sequence of 'Treponema phagedenis' strain V1, isolated from bovine digital dermatitis.
Mushtaq M, Manzoor S, Pringle M, Rosander A, Bongcam-Rudloff E
Stand Genomic Sci 10 (-) 67 [2015-09-21; online 2015-09-21]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
PubMed DOI Crossref
PARP1- and CTCF-Mediated Interactions between Active and Repressed Chromatin at the Lamina Promote Oscillating Transcription.
Zhao H, Sifakis EG, Sumida N, ..., Imreh MP, Göndör A
Mol. Cell 59 (6) 984-997 [2015-09-17; online 2015-08-27]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
WNT3 involvement in human bladder exstrophy and cloaca development in zebrafish.
Baranowska Körberg I, Hofmeister W, Markljung E, ..., Lindstrand A, Nordenskjöld A
Hum. Mol. Genet. 24 (18) 5069-5078 [2015-09-15; online 2015-06-25]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
High cortisol in 5-year-old children causes loss of DNA methylation in SINE retrotransposons: a possible role for ZNF263 in stress-related diseases.
Nätt D, Johansson I, Faresjö T, Ludvigsson J, Thorsell A
Clin Epigenetics 7 (-) 91 [2015-09-04; online 2015-09-04]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Mutations in SLC12A5 in epilepsy of infancy with migrating focal seizures.
Stödberg T, McTague A, Ruiz AJ, ..., Wedell A, Kurian MA
Nat Commun 6 (-) 8038 [2015-09-03; online 2015-09-03]
Clinical Genomics Stockholm NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Transplanted Bone Marrow-Derived Cells Contribute to Human Adipogenesis.
Rydén M, Uzunel M, Hård JL, ..., Mattsson J, Arner P
Cell Metab. 22 (3) 408-417 [2015-09-01; online 2015-07-21]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Exome sequencing followed by genotyping suggests SYPL2 as a susceptibility gene for morbid obesity.
Jiao H, Arner P, Gerdhem P, ..., Kere J, Dahlman I
Eur. J. Hum. Genet. 23 (9) 1216-1222 [2015-09-00; online 2014-11-20]
Mutation Analysis Facility (MAF) NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
PubMed DOI Crossref
Altered serotonin (5-HT) 1D and 2A receptor expression may contribute to defective insulin and glucagon secretion in human type 2 diabetes.
Bennet H, Balhuizen A, Medina A, ..., Wierup N, Fex M
Peptides 71 (-) 113-120 [2015-09-00; online 2015-07-25]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Microfluidic screening and whole-genome sequencing identifies mutations associated with improved protein secretion by yeast.
Huang M, Bai Y, Sjostrom SL, ..., Andersson-Svahn H, Nielsen J
Proc. Natl. Acad. Sci. U.S.A. 112 (34) E4689-E4696 [2015-08-25; online 2015-08-12]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Complementing tissue characterization by integrating transcriptome profiling from the Human Protein Atlas and from the FANTOM5 consortium.
Yu NY, Hallström BM, Fagerberg L, ..., Uhlén M, Daub CO
Nucleic Acids Res. 43 (14) 6787-6798 [2015-08-18; online 2015-06-27]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Tissue Profiling [Collaborative]
PubMed DOI Crossref
Adaptive mutations in sugar metabolism restore growth on glucose in a pyruvate decarboxylase negative yeast strain.
Zhang Y, Liu G, Engqvist MK, ..., Siewers V, Nielsen J
Microb. Cell Fact. 14 (-) 116 [2015-08-08; online 2015-08-08]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Roux-en-Y Gastric Bypass and Vertical Banded Gastroplasty Induce Long-Term Changes on the Human Gut Microbiome Contributing to Fat Mass Regulation.
Tremaroli V, Karlsson F, Werling M, ..., Nielsen J, Bäckhed F
Cell Metab. 22 (2) 228-238 [2015-08-04; online 2015-08-06]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Genome-wide mapping of promoter-anchored interactions with close to single-enhancer resolution.
Sahlén P, Abdullayev I, Ramsköld D, ..., Lundeberg J, Sandberg R
Genome Biol. 16 (-) 156 [2015-08-03; online 2015-08-03]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Analysis of the Human Prostate-Specific Proteome Defined by Transcriptomics and Antibody-Based Profiling Identifies TMEM79 and ACOXL as Two Putative, Diagnostic Markers in Prostate Cancer.
O'Hurley G, Busch C, Fagerberg L, ..., Uhlén M, Pontén F
PLoS ONE 10 (8) e0133449 [2015-08-03; online 2015-08-03]
Affinity Proteomics Stockholm NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Spatial Proteomics Tissue Profiling [Technology development]
PubMed DOI Crossref
Whole-exome sequencing of Ethiopian patients with ichthyosis vulgaris and atopic dermatitis.
Taylan F, Nilsson D, Asad S, ..., Nordenskjöld M, Bradley M
J. Allergy Clin. Immunol. 136 (2) 507-9.e19 [2015-08-00; online 2015-03-31]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
SF3B1 mutation identifies a distinct subset of myelodysplastic syndrome with ring sideroblasts.
Malcovati L, Karimi M, Papaemmanuil E, ..., Cazzola M, Hellström Lindberg E
Blood 126 (2) 233-241 [2015-07-09; online 2015-05-10]
Clinical Genomics Uppsala NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Toward Rare Blood Cell Preservation for RNA Sequencing.
Vickovic S, Ahmadian A, Lewensohn R, Lundeberg J
J Mol Diagn 17 (4) 352-359 [2015-07-00; online 2015-05-16]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Polymorphisms in DCDC2 and S100B associate with developmental dyslexia.
Matsson H, Huss M, Persson H, ..., Peyrard-Janvid M, Kere J
J. Hum. Genet. 60 (7) 399-401 [2015-07-00; online 2015-04-17]
Mutation Analysis Facility (MAF) NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
The Plasmodiophora brassicae genome reveals insights in its life cycle and ancestry of chitin synthases.
Schwelm A, Fogelqvist J, Knaust A, ..., Ludwig-Müller J, Dixelius C
Sci Rep 5 (-) 11153 [2015-06-18; online 2015-06-18]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure
PubMed DOI Crossref
Defining the Human Brain Proteome Using Transcriptomics and Antibody-Based Profiling with a Focus on the Cerebral Cortex.
Sjöstedt E, Fagerberg L, Hallström BM, ..., Uhlén M, Mulder J
PLoS ONE 10 (6) e0130028 [2015-06-15; online 2015-06-15]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Tissue Profiling [Collaborative]
PubMed DOI Crossref
Phasing of single DNA molecules by massively parallel barcoding.
Borgström E, Redin D, Lundin S, ..., Andersson AF, Ahmadian A
Nat Commun 6 (-) 7173 [2015-06-09; online 2015-06-09]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Ancient wolf genome reveals an early divergence of domestic dog ancestors and admixture into high-latitude breeds.
Skoglund P, Ersmark E, Palkopoulou E, Dalén L
Curr. Biol. 25 (11) 1515-1519 [2015-06-01; online 2015-05-26]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed
Whole-genome Linkage Analysis and Sequence Analysis of Candidate Loci in Familial Breast Cancer.
Marikkannu R, Aravidis C, Rantala J, ..., Nilsson D, Lindblom A
Anticancer Res. 35 (6) 3155-3165 [2015-06-00; online 2015-05-31]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Microbial metagenomics in the Baltic Sea: Recent advancements and prospects for environmental monitoring.
Ininbergs K, Bergman B, Larsson J, Ekman M
Ambio 44 Suppl 3 (-) 439-450 [2015-06-00; online 2015-05-30]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
High-throughput mutational screening adds clinically important information in myelodysplastic syndromes and secondary or therapy-related acute myeloid leukemia.
Karimi M, Nilsson C, Dimitriou M, ..., Kere J, Hellström-Lindberg E
Haematologica 100 (6) e223-e225 [2015-06-00; online 2015-03-15]
Mutation Analysis Facility (MAF) NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Hemophagocytic lymphohistiocytosis in 2 patients with underlying IFN-γ receptor deficiency
Tesi B, Sieni E, Neves C, ..., Azzari C, Bryceson YT
Journal of Allergy and Clinical Immunology 135 (6) 1638-1641.e5 [2015-06-00; online 2015-06-00]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Exome sequencing of contralateral breast cancer identifies metastatic disease.
Klevebring D, Lindberg J, Rockberg J, ..., Sandberg M, Czene K
Breast Cancer Res. Treat. 151 (2) 319-324 [2015-06-00; online 2015-04-30]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Consequences of increased terrestrial dissolved organic matter and temperature on bacterioplankton community composition during a Baltic Sea mesocosm experiment.
Lindh MV, Lefébure R, Degerman R, ..., Andersson A, Pinhassi J
Ambio 44 Suppl 3 (-) 402-412 [2015-06-00; online 2015-05-30]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Complete genomes reveal signatures of demographic and genetic declines in the woolly mammoth.
Palkopoulou E, Mallick S, Skoglund P, ..., Reich D, Dalén L
Curr. Biol. 25 (10) 1395-1400 [2015-05-18; online 2015-04-23]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Complement inhibitor CD55 governs the integrity of membrane rafts in pancreatic beta cells, but plays no role in insulin secretion.
Nagaraj V, King B, Storm P, ..., Blom AM, Renström E
Biochem. Biophys. Res. Commun. 460 (3) 518-524 [2015-05-08; online 2015-03-24]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Intestinal dysbiosis in children with short bowel syndrome is associated with impaired outcome.
Engstrand Lilja H, Wefer H, Nyström N, Finkel Y, Engstrand L
Microbiome 3 (-) 18 [2015-05-04; online 2015-05-04]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Tracking the origin of metastatic prostate cancer.
Lindberg J, Kristiansen A, Wiklund P, Grönberg H, Egevad L
Eur. Urol. 67 (5) 819-822 [2015-05-00; online 2014-09-24]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Plant-mediated gene silencing restricts growth of the potato late blight pathogen Phytophthora infestans.
Jahan SN, Åsman AK, Corcoran P, ..., Vetukuri RR, Dixelius C
J. Exp. Bot. 66 (9) 2785-2794 [2015-05-00; online 2015-03-20]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Autosomal recessive mutations in the COL2A1 gene cause severe spondyloepiphyseal dysplasia.
Tham E, Nishimura G, Geiberger S, ..., Nordenskjöld M, Grigelioniene G
Clin. Genet. 87 (5) 496-498 [2015-05-00; online 2014-07-26]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Deep sequencing and SNP array analyses of pediatric T-cell acute lymphoblastic leukemia reveal NOTCH1 mutations in minor subclones and a high incidence of uniparental isodisomies affecting CDKN2A.
Karrman K, Castor A, Behrendtz M, ..., Paulsson K, Johansson B
J Hematol Oncol 8 (-) 42 [2015-04-24; online 2015-04-24]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Transplant experiments uncover Baltic Sea basin-specific responses in bacterioplankton community composition and metabolic activities.
Lindh MV, Figueroa D, Sjöstedt J, ..., Legrand C, Pinhassi J
Front Microbiol 6 (-) 223 [2015-04-01; online 2015-04-01]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Variations of gastric corpus microbiota are associated with early esophageal squamous cell carcinoma and squamous dysplasia.
Nasrollahzadeh D, Malekzadeh R, Ploner A, ..., Dawsey SM, Ye W
Sci Rep 5 (-) 8820 [2015-03-06; online 2015-03-06]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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The H1-receptor antagonist cetirizine ameliorates high-fat diet-induced glucose intolerance in male C57BL/6 mice, but not diabetes outcome in female non-obese diabetic (NOD) mice.
Anvari E, Wang X, Sandler S, Welsh N
Ups. J. Med. Sci. 120 (1) 40-46 [2015-03-00; online 2014-10-08]
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The Fun30 chromatin remodeler Fft3 controls nuclear organization and chromatin structure of insulators and subtelomeres in fission yeast.
Steglich B, Strålfors A, Khorosjutina O, ..., Javerzat JP, Ekwall K
PLoS Genet. 11 (3) e1005101 [2015-03-00; online 2015-03-23]
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Amplification-free sequencing of cell-free DNA for prenatal non-invasive diagnosis of chromosomal aberrations.
Karlsson K, Sahlin E, Iwarsson E, ..., Nordenskjöld M, Linnarsson S
Genomics 105 (3) 150-158 [2015-03-00; online 2014-12-30]
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The composition of the gut microbiota shapes the colon mucus barrier.
Jakobsson HE, Rodríguez-Piñeiro AM, Schütte A, ..., Hansson GC, Johansson ME
EMBO Rep. 16 (2) 164-177 [2015-02-00; online 2014-12-20]
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Genome and physiology of the ascomycete filamentous fungus Xeromyces bisporus, the most xerophilic organism isolated to date.
Leong SL, Lantz H, Pettersson OV, ..., Tellgren-Roth C, Schnürer J
Environ. Microbiol. 17 (2) 496-513 [2015-02-00; online 2014-08-22]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (SNP&SEQ Technology Platform) NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure
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Expression of human skin-specific genes defined by transcriptomics and antibody-based profiling.
Edqvist PH, Fagerberg L, Hallström BM, ..., Uhlén M, Pontén F
J. Histochem. Cytochem. 63 (2) 129-141 [2015-02-00; online 2014-11-19]
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CTNND2-a candidate gene for reading problems and mild intellectual disability.
Hofmeister W, Nilsson D, Topa A, ..., Syk Lundberg E, Lindstrand A
J. Med. Genet. 52 (2) 111-122 [2015-02-00; online 2014-12-05]
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Endonuclease specificity and sequence dependence of type IIS restriction enzymes.
Lundin S, Jemt A, Terje-Hegge F, ..., Lexow P, Lundeberg J
PLoS ONE 10 (1) e0117059 [2015-01-28; online 2015-01-28]
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Next-generation sequencing reveals low-dose effects of cationic dendrimers in primary human bronchial epithelial cells.
Feliu N, Kohonen P, Ji J, ..., Nyström A, Fadeel B
ACS Nano 9 (1) 146-163 [2015-01-27; online 2014-12-23]
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Proteomics. Tissue-based map of the human proteome.
Uhlén M, Fagerberg L, Hallström BM, ..., Nielsen J, Pontén F
Science 347 (6220) 1260419 [2015-01-23; online 2015-01-24]
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The human gastrointestinal tract-specific transcriptome and proteome as defined by RNA sequencing and antibody-based profiling.
Gremel G, Wanders A, Cedernaes J, ..., Uhlén M, Pontén F
J. Gastroenterol. 50 (1) 46-57 [2015-01-00; online 2014-05-03]
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Methylated RASSF1A in malignant peripheral nerve sheath tumors identifies neurofibromatosis type 1 patients with inferior prognosis.
Danielsen SA, Lind GE, Kolberg M, ..., Picci P, Lothe RA
Neuro-oncology 17 (1) 63-69 [2015-01-00; online 2014-07-20]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Year 2014

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The lung-specific proteome defined by integration of transcriptomics and antibody-based profiling.
Lindskog C, Fagerberg L, Hallström B, ..., Pontén F, Micke P
FASEB J. 28 (12) 5184-5196 [2014-12-00; online 2014-08-28]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Tissue Profiling [Collaborative]
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Intragenic duplication--a novel causative mechanism for SATB2-associated syndrome.
Liedén A, Kvarnung M, Nilssson D, Sahlin E, Lundberg ES
Am. J. Med. Genet. A 164A (12) 3083-3087 [2014-12-00; online 2014-09-25]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Insights into conifer giga-genomes.
De La Torre AR, Birol I, Bousquet J, ..., Zerbe P, Bohlmann J
Plant Physiol. 166 (4) 1724-1732 [2014-12-00; online 2014-10-29]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Donor or recipient origin of posttransplant lymphoproliferative disorders following solid organ transplantation.
Kinch A, Cavelier L, Bengtsson M, ..., Sundström C, Pauksens K
Am. J. Transplant. 14 (12) 2838-2845 [2014-12-00; online 2014-10-10]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Defining the human adipose tissue proteome to reveal metabolic alterations in obesity.
Mardinoglu A, Kampf C, Asplund A, ..., Uhlen M, Nielsen J
J. Proteome Res. 13 (11) 5106-5119 [2014-11-07; online 2014-09-16]
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Parallel barcoding of antibodies for DNA-assisted proteomics.
Dezfouli M, Vickovic S, Iglesias MJ, Schwenk JM, Ahmadian A
Proteomics 14 (21-22) 2432-2436 [2014-11-00; online 2014-09-30]
Affinity Proteomics Stockholm [Technology development] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Human isolates of Listeria monocytogenes in Sweden during half a century (1958-2010).
Lopez-Valladares G, Tham W, Parihar VS, ..., Henriques-Normark B, Danielsson-Tham ML
Epidemiol. Infect. 142 (11) 2251-2260 [2014-11-00; online 2014-02-01]
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Evolution reveals a glutathione-dependent mechanism of 3-hydroxypropionic acid tolerance.
Kildegaard KR, Hallström BM, Blicher TH, ..., Nielsen J, Borodina I
Metab. Eng. 26 (-) 57-66 [2014-11-00; online 2014-09-30]
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Defining the human gallbladder proteome by transcriptomics and affinity proteomics.
Kampf C, Mardinoglu A, Fagerberg L, ..., Pontén F, Uhlen M
Proteomics 14 (21-22) 2498-2507 [2014-11-00; online 2014-09-02]
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Bcl-2 maintains the mitochondrial membrane potential, but fails to affect production of reactive oxygen species and endoplasmic reticulum stress, in sodium palmitate-induced β-cell death.
Wang X, Welsh N
Ups. J. Med. Sci. 119 (4) 306-315 [2014-11-00; online 2014-10-01]
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Populus tremula (European aspen) shows no evidence of sexual dimorphism.
Robinson KM, Delhomme N, Mähler N, ..., Jansson S, Street NR
BMC Plant Biol. 14 (-) 276 [2014-10-16; online 2014-10-16]
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Human genetic evidence for involvement of CD137 in atherosclerosis.
Söderström LÅ, Gertow K, Folkersen L, ..., Hansson GK, Olofsson PS
Mol. Med. 20 (-) 456-465 [2014-10-14; online 2014-07-18]
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Gene and protein expression and cellular localisation of cytochrome P450 enzymes of the 1A, 2A, 2C, 2D and 2E subfamilies in equine intestine and liver.
Tydén E, Tjälve H, Larsson P
Acta Vet. Scand. 56 (-) 69 [2014-10-08; online 2014-10-08]
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Biofuels. Altered sterol composition renders yeast thermotolerant.
Caspeta L, Chen Y, Ghiaci P, ..., Petranovic D, Nielsen J
Science 346 (6205) 75-78 [2014-10-03; online 2014-10-02]
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Uneven distribution of human papillomavirus 16 in cervical carcinoma in situ and squamous cell carcinoma in older females: A retrospective database study.
Andersson S, Mints M, Gyllensten U, ..., Lambe M, Wilander E
Oncol Lett 8 (4) 1528-1532 [2014-10-00; online 2014-09-10]
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The DMRT3 'Gait keeper' mutation affects performance of Nordic and Standardbred trotters.
Jäderkvist K, Andersson LS, Johansson AM, ..., Andersson L, Lindgren G
J. Anim. Sci. 92 (10) 4279-4286 [2014-10-00; online 2014-08-03]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Signals that regulate the oncogenic fate of neural stem cells and progenitors.
Swartling FJ, Bolin S, Phillips JJ, Persson AI
Exp. Neurol. 260 (-) 56-68 [2014-10-00; online 2013-02-05]
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The Chironomus tentans genome sequence and the organization of the Balbiani ring genes.
Kutsenko A, Svensson T, Nystedt B, ..., Visa N, Wieslander L
BMC Genomics 15 (-) 819 [2014-09-27; online 2014-09-27]
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Plasmidome interchange between Clostridium botulinum, Clostridium novyi and Clostridium haemolyticum converts strains of independent lineages into distinctly different pathogens.
Skarin H, Segerman B
PLoS ONE 9 (9) e107777 [2014-09-25; online 2014-09-25]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
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Oncoprotein stabilization in brain tumors.
Hede SM, Savov V, Weishaupt H, Sangfelt O, Swartling FJ
Oncogene 33 (39) 4709-4721 [2014-09-25; online 2013-10-30]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Evidence that breast cancer risk at the 2q35 locus is mediated through IGFBP5 regulation.
Ghoussaini M, Edwards SL, Michailidou K, ..., Dunning AM, Australian Ovarian Cancer Management Group
Nat Commun 4 (1) 4999 [2014-09-23; online 2014-09-23]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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The DEK oncoprotein binds to highly and ubiquitously expressed genes with a dual role in their transcriptional regulation.
Sandén C, Järvstråt L, Lennartsson A, ..., Nilsson B, Gullberg U
Mol. Cancer 13 (-) 215 [2014-09-12; online 2014-09-12]
Bioinformatics and Expression Analysis (BEA) NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Neu-Laxova syndrome is a heterogeneous metabolic disorder caused by defects in enzymes of the L-serine biosynthesis pathway.
Acuna-Hidalgo R, Schanze D, Kariminejad A, ..., Hoischen A, Zenker M
Am. J. Hum. Genet. 95 (3) 285-293 [2014-09-04; online 2014-08-26]
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Recurrent GATA1 mutations in Diamond-Blackfan anaemia.
Klar J, Khalfallah A, Arzoo PS, Gazda HT, Dahl N
Br. J. Haematol. 166 (6) 949-951 [2014-09-00; online 2014-04-29]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Productivity and salinity structuring of the microplankton revealed by comparative freshwater metagenomics
Eiler A, Zaremba‐Niedzwiedzka K, Martínez‐García M, ..., Andersson SGE, Bertilsson S
Environ Microbiol 16 (9) 2682-2698 [2014-09-00; online 2013-11-12]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Picocyanobacteria containing a novel pigment gene cluster dominate the brackish water Baltic Sea.
Larsson J, Celepli N, Ininbergs K, ..., Bergman B, Ekman M
ISME J 8 (9) 1892-1903 [2014-09-00; online 2014-03-14]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Identification of three novel FGF16 mutations in X-linked recessive fusion of the fourth and fifth metacarpals and possible correlation with heart disease.
Laurell T, Nilsson D, Hofmeister W, ..., Grigelioniene G, Nordgren A
Mol Genet Genomic Med 2 (5) 402-411 [2014-09-00; online 2014-05-14]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Genome of the avirulent human-infective trypanosome--Trypanosoma rangeli.
Stoco PH, Wagner G, Talavera-Lopez C, ..., de Vasconcelos AT, Grisard EC
PLoS Negl Trop Dis 8 (9) e3176 [2014-09-00; online 2014-09-18]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Do the same genes underlie parallel phenotypic divergence in different Littorina saxatilis populations?
Westram AM, Galindo J, Alm Rosenblad M, ..., Panova M, Butlin RK
Mol. Ecol. 23 (18) 4603-4616 [2014-09-00; online 2014-08-13]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication.
Carneiro M, Rubin CJ, Di Palma F, ..., Lindblad-Toh K, Andersson L
Science 345 (6200) 1074-1079 [2014-08-29; online 2014-08-30]
Bioinformatics Support for Computational Resources NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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A multicentre hospital outbreak in Sweden caused by introduction of a vanB2 transposon into a stably maintained pRUM-plasmid in an Enterococcus faecium ST192 clone.
Sivertsen A, Billström H, Melefors Ö, ..., Sundsfjord A, Hegstad K
PLoS ONE 9 (8) e103274 [2014-08-25; online 2014-08-25]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Missing genes, multiple ORFs, and C-to-U type RNA editing in Acrasis kona (Heterolobosea, Excavata) mitochondrial DNA.
Fu CJ, Sheikh S, Miao W, Andersson SG, Baldauf SL
Genome Biol Evol 6 (9) 2240-2257 [2014-08-21; online 2014-08-21]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Winter bloom of a rare betaproteobacterium in the Arctic Ocean.
Alonso-Sáez L, Zeder M, Harding T, ..., Bertilsson S, Pedrós-Alió C
Front Microbiol 5 (-) 425 [2014-08-20; online 2014-08-20]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Species and gene divergence in Littorina snails detected by array comparative genomic hybridization.
Panova M, Johansson T, Canbäck B, ..., Tunlid A, André C
BMC Genomics 15 (-) 687 [2014-08-18; online 2014-08-18]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Evaluation of exome sequencing to estimate tumor burden in plasma.
Klevebring D, Neiman M, Sundling S, ..., Grönberg H, Lindberg J
PLoS ONE 9 (8) e104417 [2014-08-18; online 2014-08-18]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
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BESST--efficient scaffolding of large fragmented assemblies.
Sahlin K, Vezzi F, Nystedt B, Lundeberg J, Arvestad L
BMC Bioinformatics 15 (-) 281 [2014-08-15; online 2014-08-15]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Common genetic determinants of lung function, subclinical atherosclerosis and risk of coronary artery disease.
Sabater-Lleal M, Mälarstig A, Folkersen L, ..., Tobin MD, Hamsten A
PLoS ONE 9 (8) e104082 [2014-08-05; online 2014-08-05]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Differences in gene expression between mouse and human for dynamically regulated genes in early embryo.
Madissoon E, Töhönen V, Vesterlund L, ..., Hovatta O, Kere J
PLoS ONE 9 (8) e102949 [2014-08-04; online 2014-08-04]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Multifactorial analysis of changes in body mass index across the adult life course: a study with 65 years of follow-up.
Dahl AK, Reynolds CA, Fall T, Magnusson PK, Pedersen NL
Int J Obes (Lond) 38 (8) 1133-1141 [2014-08-00; online 2013-11-07]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Mechanisms of mRNA export.
Björk P, Wieslander L
Semin. Cell Dev. Biol. 32 (-) 47-54 [2014-08-00; online 2014-05-13]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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High risk of tobacco-related cancers in CDKN2A mutation-positive melanoma families.
Helgadottir H, Höiom V, Jönsson G, ..., Olsson H, Hansson J
J. Med. Genet. 51 (8) 545-552 [2014-08-00; online 2014-06-18]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Fusions involving protein kinase C and membrane-associated proteins in benign fibrous histiocytoma.
Płaszczyca A, Nilsson J, Magnusson L, ..., Nord KH, Mertens F
Int. J. Biochem. Cell Biol. 53 (-) 475-481 [2014-08-00; online 2014-04-08]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Differential methylation in CN-AML preferentially targets non-CGI regions and is dictated by DNMT3A mutational status and associated with predominant hypomethylation of HOX genes.
Qu Y, Lennartsson A, Gaidzik VI, ..., Döhner K, Lehmann S
Epigenetics 9 (8) 1108-1119 [2014-08-00; online 2014-05-29]
Bioinformatics and Expression Analysis (BEA) NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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DegePrime, a program for degenerate primer design for broad-taxonomic-range PCR in microbial ecology studies.
Hugerth LW, Wefer HA, Lundin S, ..., Engstrand L, Andersson AF
Appl. Environ. Microbiol. 80 (16) 5116-5123 [2014-08-00; online 2014-06-15]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Nuclease-assisted suppression of human DNA background in sepsis.
Song Y, Giske CG, Gille-Johnson P, ..., Lundeberg J, Gyarmati P
PLoS ONE 9 (7) e103610 [2014-07-30; online 2014-07-30]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Analysis of stranded information using an automated procedure for strand specific RNA sequencing.
Sigurgeirsson B, Emanuelsson O, Lundeberg J
BMC Genomics 15 (-) 631 [2014-07-28; online 2014-07-28]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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The archaeal legacy of eukaryotes: a phylogenomic perspective.
Guy L, Saw JH, Ettema TJ
Cold Spring Harb Perspect Biol 6 (10) a016022 [2014-07-03; online 2014-07-03]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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The human liver-specific proteome defined by transcriptomics and antibody-based profiling.
Kampf C, Mardinoglu A, Fagerberg L, ..., Nielsen J, Uhlen M
FASEB J. 28 (7) 2901-2914 [2014-07-00; online 2014-03-22]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Spatial Proteomics Tissue Profiling
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Autosomal dominant brachyolmia in a large Swedish family: phenotypic spectrum and natural course.
Grigelioniene G, Geiberger S, Horemuzova E, ..., Nordgren A, Mäkitie O
Am. J. Med. Genet. A 164A (7) 1635-1641 [2014-07-00; online 2014-03-29]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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'Geoarchaeote NAG1' is a deeply rooting lineage of the archaeal order Thermoproteales rather than a new phylum.
Guy L, Spang A, Saw JH, Ettema TJ
ISME J 8 (7) 1353-1357 [2014-07-00; online 2014-02-14]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Myelodysplastic syndromes are propagated by rare and distinct human cancer stem cells in vivo.
Woll PS, Kjällquist U, Chowdhury O, ..., Linnarsson S, Jacobsen SE
Cancer Cell 25 (6) 794-808 [2014-06-16; online 2014-05-15]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Mapping-by-sequencing accelerates forward genetics in barley.
Mascher M, Jost M, Kuon JE, ..., Graner A, Stein N
Genome Biol. 15 (6) R78 [2014-06-10; online 2014-06-10]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Efficient de novo assembly of large and complex genomes by massively parallel sequencing of Fosmid pools.
Alexeyenko A, Nystedt B, Vezzi F, ..., Wu CC, Lundeberg J
BMC Genomics 15 (-) 439 [2014-06-06; online 2014-06-06]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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p53 protein expression independently predicts outcome in patients with lower-risk myelodysplastic syndromes with del(5q).
Saft L, Karimi M, Ghaderi M, ..., MacBeth KJ, Hellström-Lindberg E
Haematologica 99 (6) 1041-1049 [2014-06-00; online 2014-04-01]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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microRNA-34b/c on chromosome 11q23 is aberrantly methylated in chronic lymphocytic leukemia.
Deneberg S, Kanduri M, Ali D, ..., Lennartsson A, Lehmann S
Epigenetics 9 (6) 910-917 [2014-06-00; online 2014-04-02]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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The human testis-specific proteome defined by transcriptomics and antibody-based profiling.
Djureinovic D, Fagerberg L, Hallström B, ..., Uhlén M, Pontén F
Mol. Hum. Reprod. 20 (6) 476-488 [2014-06-00; online 2014-03-07]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Tissue Profiling
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The age and genomic integrity of neurons after cortical stroke in humans.
Huttner HB, Bergmann O, Salehpour M, ..., Lundeberg J, Frisén J
Nat. Neurosci. 17 (6) 801-803 [2014-06-00; online 2014-04-20]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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SpliceVista, a tool for splice variant identification and visualization in shotgun proteomics data.
Zhu Y, Hultin-Rosenberg L, Forshed J, ..., Orre LM, Lehtiö J
Mol. Cell Proteomics 13 (6) 1552-1562 [2014-06-00; online 2014-04-01]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Simultaneous uptake of lignocellulose-based monosaccharides by Escherichia coli.
Jarmander J, Hallström BM, Larsson G
Biotechnol. Bioeng. 111 (6) 1108-1115 [2014-06-00; online 2014-01-03]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Recurrent activating mutation in PRKACA in cortisol-producing adrenal tumors.
Goh G, Scholl UI, Healy JM, ..., Carling T, Lifton RP
Nat. Genet. 46 (6) 613-617 [2014-06-00; online 2014-04-22]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Recurrent EWSR1-CREB3L1 gene fusions in sclerosing epithelioid fibrosarcoma.
Arbajian E, Puls F, Magnusson L, ..., Kindblom LG, Mertens F
Am. J. Surg. Pathol. 38 (6) 801-808 [2014-06-00; online 2014-01-21]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Genetic factors may play a prominent role in the development of coronary heart disease dependent on important environmental factors.
Song C, Chang Z, Magnusson PK, Ingelsson E, Pedersen NL
J. Intern. Med. 275 (6) 631-639 [2014-06-00; online 2013-12-18]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Diversity and abundance of aromatic catabolic genes in lake sediments in response to temperature change.
Osman OA, Gudasz C, Bertilsson S
FEMS Microbiol. Ecol. 88 (3) 468-481 [2014-06-00; online 2014-03-07]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Genetic architecture of main effect QTL for heading date in European winter wheat.
Zanke C, Ling J, Plieske J, ..., Ganal MW, Röder MS
Front Plant Sci 5 (-) 217 [2014-05-20; online 2014-05-20]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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The H1-receptor antagonist cetirizine protects partially against cytokine- and hydrogen peroxide-induced β-TC6 cell death in vitro.
Anvari E, Fred RG, Welsh N
Pancreas 43 (4) 624-629 [2014-05-00; online 2014-04-11]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Single cell genomics of deep ocean bacteria
Zhao W, Andersson SGE
Trends Microbiol. 22 (5) 233-234 [2014-05-00; online 2014-05-00]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
GRM1 is upregulated through gene fusion and promoter swapping in chondromyxoid fibroma.
Nord KH, Lilljebjörn H, Vezzi F, ..., Hogendoorn PC, Szuhai K
Nat. Genet. 46 (5) 474-477 [2014-05-00; online 2014-03-25]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
The complete genome of Blastobotrys (Arxula) adeninivorans LS3 - a yeast of biotechnological interest.
Kunze G, Gaillardin C, Czernicka M, ..., Scholz U, Neuvéglise C
Biotechnol Biofuels 7 (-) 66 [2014-04-24; online 2014-04-24]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Analysis of the DNA methylome and transcriptome in granulopoiesis reveals timed changes and dynamic enhancer methylation.
Rönnerblad M, Andersson R, Olofsson T, ..., Lennartsson A, FANTOM consortium
Blood 123 (17) e79-e89 [2014-04-24; online 2014-03-29]
Bioinformatics and Expression Analysis (BEA) NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Systematic design of 18S rRNA gene primers for determining eukaryotic diversity in microbial consortia.
Hugerth LW, Muller EE, Hu YO, ..., Wilmes P, Andersson AF
PLoS ONE 9 (4) e95567 [2014-04-22; online 2014-04-22]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Elucidating the interactions between the human gut microbiota and its host through metabolic modeling.
Shoaie S, Nielsen J
Front Genet 5 (-) 86 [2014-04-22; online 2014-04-22]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
A Drosophila immune response against Ras-induced overgrowth.
Hauling T, Krautz R, Markus R, ..., Kucerova L, Theopold U
Biol Open 3 (4) 250-260 [2014-04-15; online 2014-03-25]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Clinical and genetic features of pediatric acute lymphoblastic leukemia in Down syndrome in the Nordic countries.
Lundin C, Forestier E, Klarskov Andersen M, ..., Swedish Cytogenetic Leukemia Study Group (SCLSG) , NOPHO Leukemia Cytogenetic Study Group (NLCSG)
J Hematol Oncol 7 (-) 32 [2014-04-11; online 2014-04-11]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
RNA- and antibody-based profiling of the human proteome with focus on chromosome 19.
Stadler C, Fagerberg L, Sivertsson Å, ..., Lundberg E, Uhlén M
J. Proteome Res. 13 (4) 2019-2027 [2014-04-04; online 2014-03-04]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Spatial Proteomics
PubMed DOI Crossref
Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction.
El-Semman IE, Karlsson FH, Shoaie S, ..., Soliman TH, Nielsen J
BMC Syst Biol 8 (-) 41 [2014-04-03; online 2014-04-03]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Temporal profiling of cytokine-induced genes in pancreatic β-cells by meta-analysis and network inference.
Lopes M, Kutlu B, Miani M, ..., Bontempi G, Eizirik DL
Genomics 103 (4) 264-275 [2014-04-00; online 2014-01-28]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
A novel SERPINE1-FOSB fusion gene results in transcriptional up-regulation of FOSB in pseudomyogenic haemangioendothelioma.
Walther C, Tayebwa J, Lilljebjörn H, ..., Fletcher CD, Mertens F
J. Pathol. 232 (5) 534-540 [2014-04-00; online 2014-01-29]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge.
Brownstein CA, Beggs AH, Homer N, ..., Kohane IS, Margulies DM
Genome Biol. 15 (3) R53 [2014-03-25; online 2014-03-25]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Draft Genome Sequence of Pseudomonas aeruginosa SG17M, an Environmental Isolate Belonging to Clone C, Prevalent in Patients and Aquatic Habitats.
Lee C, Peters V, Melefors O, Römling U
Genome Announc 2 (2) - [2014-03-20; online 2014-03-20]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Genetic characterization of a novel Iflavirus associated with vomiting disease in the Chinese oak silkmoth Antheraea pernyi.
Geng P, Li W, Lin L, ..., An L, Terenius O
PLoS ONE 9 (3) e92107 [2014-03-17; online 2014-03-17]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Sequencing degraded RNA addressed by 3' tag counting.
Sigurgeirsson B, Emanuelsson O, Lundeberg J
PLoS ONE 9 (3) e91851 [2014-03-14; online 2014-03-14]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
The Dictyostelium discoideum RNA-dependent RNA polymerase RrpC silences the centromeric retrotransposon DIRS-1 post-transcriptionally and is required for the spreading of RNA silencing signals.
Wiegand S, Meier D, Seehafer C, ..., Söderbom F, Hammann C
Nucleic Acids Res. 42 (5) 3330-3345 [2014-03-00; online 2013-12-27]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
MAX mutations status in Swedish patients with pheochromocytoma and paraganglioma tumours.
Crona J, Maharjan R, Delgado Verdugo A, ..., Hellman P, Björklund P
Fam. Cancer 13 (1) 121-125 [2014-03-00; online 2013-06-08]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Investigation of a putative melanoma susceptibility locus at chromosome 3q29.
Tuominen R, Jönsson G, Enerbäck C, ..., Hansson J, Höiom V
Cancer Genet 207 (3) 70-74 [2014-03-00; online 2014-02-21]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Robust isolation of malignant plasma cells in multiple myeloma
Frigyesi I, Adolfsson J, Ali M, ..., Hansson M, Nilsson B
Blood 123 (9) 1336-1340 [2014-02-27; online 2014-02-27]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Functional tradeoffs underpin salinity-driven divergence in microbial community composition.
Dupont CL, Larsson J, Yooseph S, ..., Venter JC, Bergman B
PLoS ONE 9 (2) e89549 [2014-02-27; online 2014-02-27]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
An alternative root for the eukaryote tree of life.
He D, Fiz-Palacios O, Fu CJ, ..., Tsai CC, Baldauf SL
Curr. Biol. 24 (4) 465-470 [2014-02-17; online 2014-02-11]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Integrative genome and transcriptome analyses reveal two distinct types of ring chromosome in soft tissue sarcomas.
Nord KH, Macchia G, Tayebwa J, ..., Mandahl N, Mertens F
Hum. Mol. Genet. 23 (4) 878-888 [2014-02-15; online 2013-09-28]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
BET bromodomain inhibition of MYC-amplified medulloblastoma.
Bandopadhayay P, Bergthold G, Nguyen B, ..., Beroukhim R, Cho YJ
Clin. Cancer Res. 20 (4) 912-925 [2014-02-15; online 2013-12-04]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Microevolution during an Anthrax outbreak leading to clonal heterogeneity and penicillin resistance.
Ågren J, Finn M, Bengtsson B, Segerman B
PLoS ONE 9 (2) e89112 [2014-02-13; online 2014-02-13]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
PubMed DOI Crossref
Visual detection of DNA on paper chips.
Song Y, Gyarmati P, Araújo AC, ..., Brumer H, Ståhl PL
Anal. Chem. 86 (3) 1575-1582 [2014-02-04; online 2014-01-17]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Intraclonal variations among Streptococcus pneumoniae isolates influence the likelihood of invasive disease in children.
Browall S, Norman M, Tångrot J, ..., Normark S, Henriques-Normark B
J. Infect. Dis. 209 (3) 377-388 [2014-02-01; online 2013-09-07]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
WNT10A mutations account for ¼ of population-based isolated oligodontia and show phenotypic correlations.
Arzoo PS, Klar J, Bergendal B, Norderyd J, Dahl N
Am. J. Med. Genet. A 164A (2) 353-359 [2014-02-00; online 2014-01-23]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Rearrangements of chromosome bands 15q12-q21 are secondary to HMGA2 deregulation in conventional lipoma.
Macchia G, Nord KH, D'Alessandro G, ..., Storlazzi CT, Mertens F
Oncol. Rep. 31 (2) 807-811 [2014-02-00; online 2013-12-04]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Global DNA methylation patterns through an array-based approach in small intestinal neuroendocrine tumors.
Verdugo AD, Crona J, Starker L, ..., Hellman P, Björklund P
Endocr. Relat. Cancer 21 (1) L5-L7 [2014-02-00; online 2013-11-07]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Collecting and preserving biological samples from challenging environments for DNA analysis.
Buś MM, Allen M
Biopreserv Biobank 12 (1) 17-22 [2014-02-00; online 2014-03-14]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics.
Fagerberg L, Hallström BM, Oksvold P, ..., Ponten F, Uhlén M
Mol. Cell Proteomics 13 (2) 397-406 [2014-02-00; online 2013-12-07]
Affinity Proteomics Stockholm [Technology development] Autoimmunity and Serology Profiling [Technology development] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Spatial Proteomics Tissue Profiling
PubMed DOI Crossref
Trypanosoma cruzi Clone Dm28c Draft Genome Sequence.
Grisard EC, Teixeira SM, de Almeida LG, ..., Andersson B, de Vasconcelos AT
Genome Announc 2 (1) - [2014-01-30; online 2014-01-30]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Mycobacteria bypass mucosal NF-kB signalling to induce an epithelial anti-inflammatory IL-22 and IL-10 response.
Lutay N, Håkansson G, Alaridah N, ..., Westergren-Thorsson G, Godaly G
PLoS ONE 9 (1) e86466 [2014-01-28; online 2014-01-28]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
An N-Terminal Missense Mutation in STX11 Causative of FHL4 Abrogates Syntaxin-11 Binding to Munc18-2.
Müller ML, Chiang SC, Meeths M, ..., Naqvi A, Bryceson YT
Front Immunol 4 (-) 515 [2014-01-14; online 2014-01-14]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Assessment of whole genome amplification for sequence capture and massively parallel sequencing.
Hasmats J, Gréen H, Orear C, ..., Käller M, Lundeberg J
PLoS ONE 9 (1) e84785 [2014-01-07; online 2014-01-07]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Why time matters: codon evolution and the temporal dynamics of dN/dS.
Mugal CF, Wolf JB, Kaj I
Mol. Biol. Evol. 31 (1) 212-231 [2014-01-00; online 2013-10-17]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Magnetic bead assisted labeling of antibodies at nanogram scale.
Dezfouli M, Vickovic S, Iglesias MJ, ..., Schwenk JM, Ahmadian A
Proteomics 14 (1) 14-18 [2014-01-00; online 2013-12-07]
Affinity Proteomics Stockholm [Technology development] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics.
Branca RM, Orre LM, Johansson HJ, ..., Käll L, Lehtiö J
Nat. Methods 11 (1) 59-62 [2014-01-00; online 2013-11-17]
Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Different mutations in PDE4D associated with developmental disorders with mirror phenotypes.
Lindstrand A, Grigelioniene G, Nilsson D, ..., Mäkitie O, Nordgren A
J. Med. Genet. 51 (1) 45-54 [2014-01-00; online 2013-11-10]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Year 2013

PubMed DOI Crossref
Integrated molecular portrait of non-small cell lung cancers.
Lazar V, Suo C, Orear C, ..., Hansson J, Pawitan Y
BMC Med Genomics 6 (-) 53 [2013-12-03; online 2013-12-03]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Using transcriptomics to improve butanol tolerance of Synechocystis sp. strain PCC 6803.
Anfelt J, Hallström B, Nielsen J, Uhlén M, Hudson EP
Appl. Environ. Microbiol. 79 (23) 7419-7427 [2013-12-00; online 2013-09-24]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
High expression of glycolytic and pigment proteins is associated with worse clinical outcome in stage III melanoma.
Falkenius J, Lundeberg J, Johansson H, ..., Hansson J, Egyhazi Brage S
Melanoma Res. 23 (6) 452-460 [2013-12-00; online 2013-10-17]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Distinct loci in the CHRNA5/CHRNA3/CHRNB4 gene cluster are associated with onset of regular smoking.
Stephens SH, Hartz SM, Hoft NR, ..., Bierut LJ, Ehringer MA
Genet. Epidemiol. 37 (8) 846-859 [2013-12-00; online 2013-11-05]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Single-cell genomics reveal low recombination frequencies in freshwater bacteria of the SAR11 clade.
Zaremba-Niedzwiedzka K, Viklund J, Zhao W, ..., Stepanauskas R, Andersson SG
Genome Biol. 14 (11) R130 [2013-11-28; online 2013-11-28]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
De novo SNP discovery in the Scandinavian brown bear (Ursus arctos).
Norman AJ, Street NR, Spong G
PLoS ONE 8 (11) e81012 [2013-11-18; online 2013-11-18]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
miR-128 regulates non-myocyte hyperplasia, deposition of extracellular matrix and Islet1 expression during newt cardiac regeneration.
Witman N, Heigwer J, Thaler B, Lui WO, Morrison JI
Dev. Biol. 383 (2) 253-263 [2013-11-15; online 2013-09-24]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Disturbance induced decoupling between host genetics and composition of the associated microbiome.
Wegner KM, Volkenborn N, Peter H, Eiler A
BMC Microbiol. 13 (-) 252 [2013-11-09; online 2013-11-09]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Common variants associated with plasma triglycerides and risk for coronary artery disease.
Do R, Willer CJ, Schmidt EM, ..., Neale BM, Kathiresan S
Nat. Genet. 45 (11) 1345-1352 [2013-11-00; online 2013-10-08]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Chemical fragmentation for massively parallel sequencing library preparation.
Gyarmati P, Song Y, Hällman J, Käller M
J. Biotechnol. 168 (1) 95-100 [2013-10-10; online 2013-09-03]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Aneuploidy in neuroblastoma tumors is not associated with inactivating point mutations in the STAG2 gene.
Djos A, Fransson S, Kogner P, Martinsson T
BMC Med. Genet. 14 (-) 102 [2013-10-02; online 2013-10-02]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Recent advances in crayfish hematopoietic stem cell culture: a model for studies of hemocyte differentiation and immunity.
Söderhäll I
Cytotechnology 65 (5) 691-695 [2013-10-00; online 2013-05-21]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Determining indicator taxa across spatial and seasonal gradients in the Columbia River coastal margin.
Fortunato CS, Eiler A, Herfort L, ..., Peterson TD, Crump BC
ISME J 7 (10) 1899-1911 [2013-10-00; online 2013-05-31]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Comprehensive genetic analysis identifies a pathognomonic NAB2/STAT6 fusion gene, nonrandom secondary genomic imbalances, and a characteristic gene expression profile in solitary fibrous tumor.
Mohajeri A, Tayebwa J, Collin A, ..., Nord KH, Mertens F
Genes Chromosomes Cancer 52 (10) 873-886 [2013-10-00; online 2013-06-14]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
A metagenomics transect into the deepest point of the Baltic Sea reveals clear stratification of microbial functional capacities.
Thureborn P, Lundin D, Plathan J, ..., Sjöberg BM, Sjöling S
PLoS ONE 8 (9) e74983 [2013-09-23; online 2013-09-23]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Multiethnic meta-analysis of genome-wide association studies in >100 000 subjects identifies 23 fibrinogen-associated Loci but no strong evidence of a causal association between circulating fibrinogen and cardiovascular disease.
Sabater-Lleal M, Huang J, Chasman D, ..., Hamsten A, O'Donnell CJ
Circulation 128 (12) 1310-1324 [2013-09-17; online 2013-08-24]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
High modal number and triple trisomies are highly correlated favorable factors in childhood B-cell precursor high hyperdiploid acute lymphoblastic leukemia treated according to the NOPHO ALL 1992/2000 protocols.
Paulsson K, Forestier E, Andersen MK, ..., Swedish Cytogenetic Leukemia Study Group (SCLSG) , NOPHO Leukemia Cytogenetic Study Group (NLCSG)
Haematologica 98 (9) 1424-1432 [2013-09-00; online 2013-05-03]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Comparison of the nodule vs. root transcriptome of the actinorhizal plant Datisca glomerata: actinorhizal nodules contain a specific class of defensins.
Demina IV, Persson T, Santos P, Plaszczyca M, Pawlowski K
PLoS ONE 8 (8) e72442 [2013-08-29; online 2013-08-29]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Genome-wide transcriptional analysis of Drosophila larvae infected by entomopathogenic nematodes shows involvement of complement, recognition and extracellular matrix proteins.
Arefin B, Kucerova L, Dobes P, ..., Zurovec M, Theopold U
J Innate Immun 6 (2) 192-204 [2013-08-27; online 2013-08-27]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Genome-wide relatedness of Treponema pedis, from gingiva and necrotic skin lesions of pigs, with the human oral pathogen Treponema denticola.
Svartström O, Mushtaq M, Pringle M, Segerman B
PLoS ONE 8 (8) e71281 [2013-08-19; online 2013-08-19]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
A novel intellectual disability syndrome caused by GPI anchor deficiency due to homozygous mutations in PIGT.
Kvarnung M, Nilsson D, Lindstrand A, ..., Nordenskjöld M, Nordgren A
J. Med. Genet. 50 (8) 521-528 [2013-08-00; online 2013-05-03]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Clinical depression, antidepressant use and risk of future cardiovascular disease.
Rahman I, Humphreys K, Bennet AM, ..., Pedersen NL, Magnusson PK
Eur. J. Epidemiol. 28 (7) 589-595 [2013-07-00; online 2013-07-09]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Cenani-Lenz syndrome restricted to limb and kidney anomalies associated with a novel LRP4 missense mutation.
Khan TN, Klar J, Ali Z, ..., Baig SM, Dahl N
Eur J Med Genet 56 (7) 371-374 [2013-07-00; online 2013-05-15]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Active nitrogen-fixing heterotrophic bacteria at and below the chemocline of the central Baltic Sea.
Farnelid H, Bentzon-Tilia M, Andersson AF, ..., Jürgens K, Riemann L
ISME J 7 (7) 1413-1423 [2013-07-00; online 2013-03-01]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Unbiased approach for virus detection in skin lesions.
Bzhalava D, Johansson H, Ekström J, ..., Forslund O, Dillner J
PLoS ONE 8 (6) e65953 [2013-06-28; online 2013-06-28]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Molecular genetics and subjective well-being.
Rietveld CA, Cesarini D, Benjamin DJ, ..., Krueger RF, Bartels M
Proc. Natl. Acad. Sci. U.S.A. 110 (24) 9692-9697 [2013-06-11; online 2013-05-28]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Contribution of antibody-based protein profiling to the human Chromosome-centric Proteome Project (C-HPP).
Fagerberg L, Oksvold P, Skogs M, ..., von Feilitzen K, Uhlén M
J. Proteome Res. 12 (6) 2439-2448 [2013-06-07; online 2013-01-02]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Spatial Proteomics Tissue Profiling
PubMed DOI Crossref
Circadian regulation of melanization and prokineticin homologues is conserved in the brain of freshwater crayfish and zebrafish.
Noonin C, Watthanasurorot A, Winberg S, Söderhäll I
Dev. Comp. Immunol. 40 (2) 218-226 [2013-06-00; online 2013-03-19]
Genome Engineering Zebrafish NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
The Norway spruce genome sequence and conifer genome evolution.
Nystedt B, Street NR, Wetterbom A, ..., Lundeberg J, Jansson S
Nature 497 (7451) 579-584 [2013-05-30; online 2013-05-22]
Bioinformatics Support and Infrastructure Bioinformatics Support for Computational Resources Bioinformatics Support, Infrastructure and Training NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Metagenomic de novo assembly of an aquatic representative of the verrucomicrobial class Spartobacteria.
Herlemann DP, Lundin D, Labrenz M, ..., Aspeborg H, Andersson AF
MBio 4 (3) e00569-e00512 [2013-05-28; online 2013-05-28]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Age dependence of tumor genetics in unfavorable neuroblastoma: arrayCGH profiles of 34 consecutive cases, using a Swedish 25-year neuroblastoma cohort for validation.
Cetinkaya C, Martinsson T, Sandgren J, ..., Díaz de Ståhl T, Hedborg F
BMC Cancer 13 (-) 231 [2013-05-09; online 2013-05-09]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
The adenovirus VA RNA-derived miRNAs are not essential for lytic virus growth in tissue culture cells.
Kamel W, Segerman B, Öberg D, Punga T, Akusjärvi G
Nucleic Acids Res. 41 (9) 4802-4812 [2013-05-00; online 2013-03-26]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
SoxB1-driven transcriptional network underlies neural-specific interpretation of morphogen signals.
Oosterveen T, Kurdija S, Ensterö M, ..., Muhr J, Ericson J
Proc. Natl. Acad. Sci. U.S.A. 110 (18) 7330-7335 [2013-04-30; online 2013-04-15]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
β-thymosins and hemocyte homeostasis in a crustacean.
Saelee N, Noonin C, Nupan B, ..., Söderhäll K, Söderhäll I
PLoS ONE 8 (4) e60974 [2013-04-02; online 2013-04-02]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
The transporter ABCB7 is a mediator of the phenotype of acquired refractory anemia with ring sideroblasts.
Nikpour M, Scharenberg C, Liu A, ..., Grandien A, Hellström-Lindberg E
Leukemia 27 (4) 889-896 [2013-04-00; online 2012-10-17]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
The mitochondrial and autosomal mutation landscapes of prostate cancer.
Lindberg J, Mills IG, Klevebring D, ..., Egevad L, Grönberg H
Eur. Urol. 63 (4) 702-708 [2013-04-00; online 2012-12-26]
Karolinska High Throughput Center (KHTC) NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Identification of seven loci affecting mean telomere length and their association with disease.
Codd V, Nelson CP, Albrecht E, ..., van der Harst P, Samani NJ
Nat. Genet. 45 (4) 422-7, 427e1-2 [2013-04-00; online 2013-03-29]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Hereditary uveal melanoma: a report of a germline mutation in BAP1.
Höiom V, Edsgärd D, Helgadottir H, ..., Emanuelsson O, Hansson J
Genes Chromosomes Cancer 52 (4) 378-384 [2013-04-00; online 2013-01-23]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Comparative genomics of Wolbachia and the bacterial species concept.
Ellegaard KM, Klasson L, Näslund K, Bourtzis K, Andersson SG
PLoS Genet. 9 (4) e1003381 [2013-04-00; online 2013-04-04]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
PubMed DOI Crossref
Identification and verification of microRNAs by high-throughput sequencing.
Hällman J, Avesson L, Reimegård J, Käller M, Söderbom F
Methods Mol. Biol. 983 (-) 125-138 [2013-03-16; online 2013-03-16]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Hierarchical molecular tagging to resolve long continuous sequences by massively parallel sequencing.
Lundin S, Gruselius J, Nystedt B, ..., Käller M, Lundeberg J
Sci Rep 3 (-) 1186 [2013-03-09; online 2013-03-09]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
TagGD: fast and accurate software for DNA Tag generation and demultiplexing.
Costea PI, Lundeberg J, Akan P
PLoS ONE 8 (3) e57521 [2013-03-04; online 2013-03-04]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Genetic determinants of plasma β₂-glycoprotein I levels: a genome-wide association study in extended pedigrees from Spain.
Athanasiadis G, Sabater-Lleal M, Buil A, ..., Hamsten A, Soria JM
J. Thromb. Haemost. 11 (3) 521-528 [2013-03-00; online 2013-01-03]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Astakine 2--the dark knight linking melatonin to circadian regulation in crustaceans.
Watthanasurorot A, Saelee N, Phongdara A, ..., Söderhäll K, Söderhäll I
PLoS Genet. 9 (3) e1003361 [2013-03-00; online 2013-03-21]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
A genome-wide assessment of variability in human serum metabolism.
Hong MG, Karlsson R, Magnusson PK, ..., Wiklund F, Prince JA
Hum. Mutat. 34 (3) 515-524 [2013-03-00; online 2013-01-03]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
A gene transfer agent and a dynamic repertoire of secretion systems hold the keys to the explosive radiation of the emerging pathogen Bartonella.
Guy L, Nystedt B, Toft C, ..., Eriksson AS, Andersson SG
PLoS Genet. 9 (3) e1003393 [2013-03-00; online 2013-03-28]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
The synthetic progestin levonorgestrel is a potent androgen in the three-spined stickleback (Gasterosteus aculeatus).
Svensson J, Fick J, Brandt I, Brunström B
Environ. Sci. Technol. 47 (4) 2043-2051 [2013-02-19; online 2013-02-01]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure
PubMed DOI Crossref
Coastal bacterioplankton community dynamics in response to a natural disturbance.
Yeo SK, Huggett MJ, Eiler A, Rappé MS
PLoS ONE 8 (2) e56207 [2013-02-07; online 2013-02-07]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Causal relationship between obesity and vitamin D status: bi-directional Mendelian randomization analysis of multiple cohorts.
Vimaleswaran KS, Berry DJ, Lu C, ..., Hingorani AD, Hyppönen E
PLoS Med. 10 (2) e1001383 [2013-02-05; online 2013-02-05]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
The phylogeographic pattern of Francisella tularensis in Sweden indicates a Scandinavian origin of Eurosiberian tularaemia.
Karlsson E, Svensson K, Lindgren P, ..., Forsman M, Johansson A
Environ. Microbiol. 15 (2) 634-645 [2013-02-00; online 2012-12-16]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
PubMed DOI Crossref
Exome sequencing of prostate cancer supports the hypothesis of independent tumour origins.
Lindberg J, Klevebring D, Liu W, ..., Egevad L, Grönberg H
Eur. Urol. 63 (2) 347-353 [2013-02-00; online 2012-04-17]
Karolinska High Throughput Center (KHTC) NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Early cone setting in Picea abies acrocona is associated with increased transcriptional activity of a MADS box transcription factor.
Uddenberg D, Reimegård J, Clapham D, ..., Emanuelsson O, Sundström JF
Plant Physiol. 161 (2) 813-823 [2013-02-00; online 2012-12-12]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
An MBL-like protein may interfere with the activation of the proPO-system, an important innate immune reaction in invertebrates.
Wu C, Charoensapsri W, Nakamura S, ..., Söderhäll I, Söderhäll K
Immunobiology 218 (2) 159-168 [2013-02-00; online 2012-03-31]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Unveiling distribution patterns of freshwater phytoplankton by a next generation sequencing based approach.
Eiler A, Drakare S, Bertilsson S, ..., Znachor P, Lindström ES
PLoS ONE 8 (1) e53516 [2013-01-22; online 2013-01-22]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Genomic insights into the atopic eczema-associated skin commensal yeast Malassezia sympodialis.
Gioti A, Nystedt B, Li W, ..., Heitman J, Scheynius A
MBio 4 (1) e00572-e00512 [2013-01-22; online 2013-01-22]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Meta-analysis investigating associations between healthy diet and fasting glucose and insulin levels and modification by loci associated with glucose homeostasis in data from 15 cohorts.
Nettleton JA, Hivert MF, Lemaitre RN, ..., Meigs JB, Franks PW
Am. J. Epidemiol. 177 (2) 103-115 [2013-01-15; online 2012-12-21]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Year 2012

PubMed DOI Crossref
Novel missense mutation in the RSPO4 gene in congenital hyponychia and evidence for a polymorphic initiation codon (p.M1I).
Khan TN, Klar J, Nawaz S, ..., Baig SM, Dahl N
BMC Med. Genet. 13 (-) 120 [2012-12-13; online 2012-12-13]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Symptomatic atherosclerosis is associated with an altered gut metagenome.
Karlsson FH, Fåk F, Nookaew I, ..., Bäckhed F, Nielsen J
Nat Commun 3 (-) 1245 [2012-12-06; online 2012-12-06]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Comprehensive analysis of the genome transcriptome and proteome landscapes of three tumor cell lines.
Akan P, Alexeyenko A, Costea PI, ..., Uhlén M, Lundeberg J
Genome Med 4 (11) 86 [2012-11-18; online 2012-11-18]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Spatial Proteomics
PubMed DOI Crossref
Library preparation and multiplex capture for massive parallel sequencing applications made efficient and easy.
Neiman M, Sundling S, Grönberg H, ..., Lindberg J, Klevebring D
PLoS ONE 7 (11) e48616 [2012-11-05; online 2012-11-05]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae.
Nookaew I, Papini M, Pornputtapong N, ..., Uhlén M, Nielsen J
Nucleic Acids Res. 40 (20) 10084-10097 [2012-11-01; online 2012-09-12]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Comparison of total and cytoplasmic mRNA reveals global regulation by nuclear retention and miRNAs.
Solnestam BW, Stranneheim H, Hällman J, ..., Lundeberg J, Akan P
BMC Genomics 13 (-) 574 [2012-10-30; online 2012-10-30]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Spatial Proteomics
PubMed DOI Crossref
A novel mutation in the Lipase H gene underlies autosomal recessive hypotrichosis and woolly hair.
Tariq M, Azhar A, Baig SM, Dahl N, Klar J
Sci Rep 2 (-) 730 [2012-10-12; online 2012-10-12]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Scheffersomyces stipitis: a comparative systems biology study with the Crabtree positive yeast Saccharomyces cerevisiae.
Papini M, Nookaew I, Uhlén M, Nielsen J
Microb. Cell Fact. 11 (-) 136 [2012-10-09; online 2012-10-09]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Multiplex epitope mapping using bacterial surface display reveals both linear and conformational epitopes.
Hudson EP, Uhlen M, Rockberg J
Sci Rep 2 (-) 706 [2012-10-04; online 2012-10-04]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Gene expression profiles in paired gingival biopsies from periodontitis-affected and healthy tissues revealed by massively parallel sequencing.
Davanian H, Stranneheim H, Båge T, ..., Lundeberg J, Yucel-Lindberg T
PLoS ONE 7 (9) e46440 [2012-09-28; online 2012-09-28]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Identification of candidate SNPs for drug induced toxicity from differentially expressed genes in associated tissues.
Hasmats J, Kupershmidt I, Rodríguez-Antona C, ..., Lundeberg J, Green H
Gene 506 (1) 62-68 [2012-09-10; online 2012-07-01]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Improved gap size estimation for scaffolding algorithms.
Sahlin K, Street N, Lundeberg J, Arvestad L
Bioinformatics 28 (17) 2215-2222 [2012-09-01; online 2012-08-28]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Stepping stones in DNA sequencing.
Stranneheim H, Lundeberg J
Biotechnol J 7 (9) 1063-1073 [2012-09-00; online 2012-08-08]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Validation of whole genome amplification for analysis of the p53 tumor suppressor gene in limited amounts of tumor samples.
Hasmats J, Green H, Solnestam BW, ..., Bjursell M, Lundeberg J
Biochem. Biophys. Res. Commun. 425 (2) 379-383 [2012-08-24; online 2012-07-31]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Ichthyin/NIPAL4 localizes to keratins and desmosomes in epidermis and Ichthyin mutations affect epidermal lipid metabolism.
Dahlqvist J, Westermark GT, Vahlquist A, Dahl N
Arch. Dermatol. Res. 304 (5) 377-386 [2012-07-00; online 2012-01-20]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Freshwater bacterioplankton richness in oligotrophic lakes depends on nutrient availability rather than on species-area relationships.
Logue JB, Langenheder S, Andersson AF, ..., Lanzén A, Lindström ES
ISME J 6 (6) 1127-1136 [2012-06-00; online 2011-12-16]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
A novel variant in plakophilin-2 gene detected in a family with arrhythmogenic right ventricular cardiomyopathy.
Ostrowska Dahlgren B, Allen M, Lindström AC, Bjerke M, Blomström-Lundqvist C
J Interv Card Electrophysiol 34 (1) 11-18 [2012-06-00; online 2011-12-16]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
A novel mutation in lysophosphatidic acid receptor 6 gene in autosomal recessive hypotrichosis and evidence for a founder effect.
Azhar A, Tariq M, Baig SM, Dahl N, Klar J
Eur J Dermatol 22 (4) 464-466 [2012-04-26; online 2012-04-26]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Toward the single-hour high-quality genome.
Ståhl PL, Lundeberg J
Annu. Rev. Biochem. 81 (-) 359-378 [2012-03-20; online 2012-03-20]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Can silencing of transposons contribute to variation in effector gene expression in Phytophthora infestans?
Whisson S, Vetukuri R, Avrova A, Dixelius C
Mob Genet Elements 2 (2) 110-114 [2012-03-01; online 2012-08-31]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Signaling pathways involved in the regulation of TNFα-induced toll-like receptor 2 expression in human gingival fibroblasts.
Davanian H, Båge T, Lindberg J, ..., Sällberg Chen M, Yucel-Lindberg T
Cytokine 57 (3) 406-416 [2012-03-00; online 2012-01-10]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Low diversity of the gut microbiota in infants with atopic eczema.
Abrahamsson TR, Jakobsson HE, Andersson AF, ..., Engstrand L, Jenmalm MC
J. Allergy Clin. Immunol. 129 (2) 434-40, 440.e1-2 [2012-02-00; online 2011-12-14]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Non-bullous congentital ichthyosiform erythroderma associated with homozygosity for a novel missense mutation in an ATP binding domain of ABCA12.
Nawaz S, Tariq M, Ahmad I, ..., Dahl N, Klar J
Eur J Dermatol 22 (2) 178-181 [2012-01-20; online 2012-01-20]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Deregulation of the A-to-I RNA editing mechanism in psychiatric disorders.
Silberberg G, Lundin D, Navon R, Öhman M
Hum. Mol. Genet. 21 (2) 311-321 [2012-01-15; online 2011-10-11]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Combinations of histone modifications mark exon inclusion levels.
Enroth S, Bornelöv S, Wadelius C, Komorowski J
PLoS ONE 7 (1) e29911 [2012-01-05; online 2012-01-05]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
siRNA silencing of proteasome maturation protein (POMP) activates the unfolded protein response and constitutes a model for KLICK genodermatosis.
Dahlqvist J, Törmä H, Badhai J, Dahl N
PLoS ONE 7 (1) e29471 [2012-01-03; online 2012-01-03]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
High-throughput single-cell sequencing identifies photoheterotrophs and chemoautotrophs in freshwater bacterioplankton.
Martinez-Garcia M, Swan BK, Poulton NJ, ..., Sieracki ME, Stepanauskas R
ISME J 6 (1) 113-123 [2012-01-00; online 2011-07-01]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Year 2011

PubMed DOI Crossref
The inner nuclear membrane proteins Man1 and Ima1 link to two different types of chromatin at the nuclear periphery in S. pombe.
Steglich B, Filion GJ, van Steensel B, Ekwall K
Nucleus 3 (1) 77-87 [2011-12-14; online 2011-12-14]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Common variants of the BRCA1 wild-type allele modify the risk of breast cancer in BRCA1 mutation carriers.
Cox DG, Simard J, Sinnett D, ..., Sinilnikova OM, Consortium of Investigators of Modifiers of BRCA1/2
Hum. Mol. Genet. 20 (23) 4732-4747 [2011-12-01; online 2011-09-06]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Prognostic DNA methylation patterns in cytogenetically normal acute myeloid leukemia are predefined by stem cell chromatin marks.
Deneberg S, Guardiola P, Lennartsson A, ..., Döhner K, Lehmann S
Blood 118 (20) 5573-5582 [2011-11-17; online 2011-10-01]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Genome sequencing reveals a phage in Helicobacter pylori.
Lehours P, Vale FF, Bjursell MK, ..., Engstrand L, Andersson AF
MBio 2 (6) - [2011-11-15; online 2011-11-15]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Targeted enrichment of genomic DNA regions for next-generation sequencing.
Mertes F, Elsharawy A, Sauer S, ..., Lehrach H, Brookes AJ
Brief Funct Genomics 10 (6) 374-386 [2011-11-00; online 2011-11-26]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Adenosine kinase deficiency disrupts the methionine cycle and causes hypermethioninemia, encephalopathy, and abnormal liver function.
Bjursell MK, Blom HJ, Cayuela JA, ..., Lundeberg J, Wedell A
Am. J. Hum. Genet. 89 (4) 507-515 [2011-10-07; online 2011-10-04]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Evidence for involvement of Dicer-like, Argonaute and histone deacetylase proteins in gene silencing in Phytophthora infestans.
Vetukuri RR, Avrova AO, Grenville-Briggs LJ, ..., Whisson SC, Dixelius C
Mol. Plant Pathol. 12 (8) 772-785 [2011-10-00; online 2011-07-06]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Complete genome sequence of Brachyspira intermedia reveals unique genomic features in Brachyspira species and phage-mediated horizontal gene transfer.
Håfström T, Jansson DS, Segerman B
BMC Genomics 12 (-) 395 [2011-08-04; online 2011-08-04]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
The short non-coding transcriptome of the protozoan parasite Trypanosoma cruzi.
Franzén O, Arner E, Ferella M, ..., Andersson B, Daub CO
PLoS Negl Trop Dis 5 (8) e1283 [2011-08-00; online 2011-08-30]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure
PubMed DOI Crossref
Array-based genomic screening at diagnosis and during follow-up in chronic lymphocytic leukemia.
Gunnarsson R, Mansouri L, Isaksson A, ..., Juliusson G, Rosenquist R
Haematologica 96 (8) 1161-1169 [2011-08-00; online 2011-05-07]
Array and Analysis Facility NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Performance of ultra-deep pyrosequencing in analysis of HIV-1 pol gene variation.
Mild M, Hedskog C, Jernberg J, Albert J
PLoS ONE 6 (7) e22741 [2011-07-25; online 2011-07-25]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Scalable transcriptome preparation for massive parallel sequencing.
Stranneheim H, Werne B, Sherwood E, Lundeberg J
PLoS ONE 6 (7) e21910 [2011-07-07; online 2011-07-07]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Identification of noncoding transcripts from within CENP-A chromatin at fission yeast centromeres.
Choi ES, Strålfors A, Castillo AG, ..., Ekwall K, Allshire RC
J. Biol. Chem. 286 (26) 23600-23607 [2011-07-01; online 2011-05-03]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Species sorting and neutral processes are both important during the initial assembly of bacterial communities.
Langenheder S, Székely AJ
ISME J 5 (7) 1086-1094 [2011-07-00; online 2011-01-29]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Translational database selection and multiplexed sequence capture for up front filtering of reliable breast cancer biomarker candidates.
Ståhl PL, Bjursell MK, Mahdessian H, ..., Jirström K, Lundeberg J
PLoS ONE 6 (6) e20794 [2011-06-15; online 2011-06-15]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
KIT pathway alterations in mucosal melanomas of the vulva and other sites.
Omholt K, Grafström E, Kanter-Lewensohn L, Hansson J, Ragnarsson-Olding BK
Clin. Cancer Res. 17 (12) 3933-3942 [2011-06-15; online 2011-06-18]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Sequence and generation of mature ribosomal RNA transcripts in Dictyostelium discoideum.
Boesler C, Kruse J, Söderbom F, Hammann C
J. Biol. Chem. 286 (20) 17693-17703 [2011-05-20; online 2011-04-02]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Melanoma cells produce multiple laminin isoforms and strongly migrate on α5 laminin(s) via several integrin receptors.
Oikawa Y, Hansson J, Sasaki T, ..., Tryggvason K, Patarroyo M
Exp. Cell Res. 317 (8) 1119-1133 [2011-05-01; online 2011-01-05]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Nitrogenase gene amplicons from global marine surface waters are dominated by genes of non-cyanobacteria.
Farnelid H, Andersson AF, Bertilsson S, ..., Hagström Å, Riemann L
PLoS ONE 6 (4) e19223 [2011-04-29; online 2011-04-29]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Large scale library generation for high throughput sequencing.
Borgström E, Lundin S, Lundeberg J
PLoS ONE 6 (4) e19119 [2011-04-27; online 2011-04-27]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Clostridium botulinum group III: a group with dual identity shaped by plasmids, phages and mobile elements.
Skarin H, Håfström T, Westerberg J, Segerman B
BMC Genomics 12 (-) 185 [2011-04-12; online 2011-04-12]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Human oral, gut, and plaque microbiota in patients with atherosclerosis.
Koren O, Spor A, Felin J, ..., Ley RE, Bäckhed F
Proc. Natl. Acad. Sci. U.S.A. 108 Suppl 1 (-) 4592-4598 [2011-03-15; online 2010-10-13]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Decoding a substantial set of samples in parallel by massive sequencing.
Neiman M, Lundin S, Savolainen P, Ahmadian A
PLoS ONE 6 (3) e17785 [2011-03-09; online 2011-03-09]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Bioinformatic tools for using whole genome sequencing as a rapid high resolution diagnostic typing tool when tracing bioterror organisms in the food and feed chain.
Segerman B, De Medici D, Ehling Schulz M, ..., Van Rotterdam B, Knutsson R
Int. J. Food Microbiol. 145 Suppl 1 (-) S167-S176 [2011-03-01; online 2010-09-10]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
The Swedish new variant of Chlamydia trachomatis.
Unemo M, Clarke IN
Curr. Opin. Infect. Dis. 24 (1) 62-69 [2011-02-00; online 2010-12-16]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Sun-induced nonsynonymous p53 mutations are extensively accumulated and tolerated in normal appearing human skin.
Ståhl PL, Stranneheim H, Asplund A, ..., Pontén F, Lundeberg J
J. Invest. Dermatol. 131 (2) 504-508 [2011-02-00; online 2010-10-15]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
High-resolution genomic screening in mantle cell lymphoma--specific changes correlate with genomic complexity, the proliferation signature and survival.
Halldórsdóttir AM, Sander B, Göransson H, ..., Rosenquist R, Ehrencrona H
Genes Chromosomes Cancer 50 (2) 113-121 [2011-02-00; online 2010-12-01]
Array and Analysis Facility NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
A systems biology model of the regulatory network in Populus leaves reveals interacting regulators and conserved regulation.
Street NR, Jansson S, Hvidsten TR
BMC Plant Biol. 11 (-) 13 [2011-01-13; online 2011-01-13]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Year 2010

PubMed DOI Crossref
Defining the transcriptome and proteome in three functionally different human cell lines.
Lundberg E, Fagerberg L, Klevebring D, ..., Mann M, Uhlen M
Mol. Syst. Biol. 6 (-) 450 [2010-12-21; online 2010-12-24]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Spatial Proteomics
PubMed DOI Crossref
High frequency of p16(INK4A) promoter methylation in NRAS-mutated cutaneous melanoma.
Jonsson A, Tuominen R, Grafström E, Hansson J, Egyhazi S
J. Invest. Dermatol. 130 (12) 2809-2817 [2010-12-00; online 2010-08-13]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
A pyrosequencing study in twins shows that gastrointestinal microbial profiles vary with inflammatory bowel disease phenotypes.
Willing BP, Dicksved J, Halfvarson J, ..., Jansson JK, Engstrand L
Gastroenterology 139 (6) 1844-1854.e1 [2010-12-00; online 2010-09-08]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Production of ectomycorrhizal mycelium peaks during canopy closure in Norway spruce forests.
Wallander H, Johansson U, Sterkenburg E, Brandström Durling M, Lindahl BD
New Phytol. 187 (4) 1124-1134 [2010-09-00; online 2010-06-22]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Familial cutaneous melanoma.
Hansson J
Adv. Exp. Med. Biol. 685 (-) 134-145 [2010-08-07; online 2010-08-07]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Dynamics of HIV-1 quasispecies during antiviral treatment dissected using ultra-deep pyrosequencing.
Hedskog C, Mild M, Jernberg J, ..., Andersson B, Albert J
PLoS ONE 5 (7) e11345 [2010-07-07; online 2010-07-07]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Classification of DNA sequences using Bloom filters.
Stranneheim H, Käller M, Allander T, ..., Arvestad L, Lundeberg J
Bioinformatics 26 (13) 1595-1600 [2010-07-01; online 2010-05-18]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Revolutionizing membrane protein overexpression in bacteria.
Schlegel S, Klepsch M, Gialama D, ..., Slotboom DJ, de Gier JW
Microb Biotechnol 3 (4) 403-411 [2010-07-00; online 2009-09-04]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Increased throughput by parallelization of library preparation for massive sequencing.
Lundin S, Stranneheim H, Pettersson E, Klevebring D, Lundeberg J
PLoS ONE 5 (4) e10029 [2010-04-06; online 2010-04-06]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Short-term antibiotic treatment has differing long-term impacts on the human throat and gut microbiome.
Jakobsson HE, Jernberg C, Andersson AF, ..., Jansson JK, Engstrand L
PLoS ONE 5 (3) e9836 [2010-03-24; online 2010-03-24]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species.
Künstner A, Wolf JB, Backström N, ..., Warren WC, Ellegren H
Mol. Ecol. 19 Suppl 1 (Suppl 1) 266-276 [2010-03-00; online 2010-04-02]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Gene-specific FACS sorting method for target selection in high-throughput amplicon sequencing.
Sandberg J, Neiman M, Ahmadian A, Lundeberg J
BMC Genomics 11 (-) 140 [2010-02-26; online 2010-02-26]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Coexisting NRAS and BRAF mutations in primary familial melanomas with specific CDKN2A germline alterations.
Jovanovic B, Egyhazi S, Eskandarpour M, ..., Hayward NK, Hansson J
J. Invest. Dermatol. 130 (2) 618-620 [2010-02-00; online 2009-09-18]
NGI Short read [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure [Service]
PubMed DOI Crossref
A computational screen for site selective A-to-I editing detects novel sites in neuron specific Hu proteins.
Ensterö M, Akerborg O, Lundin D, ..., Ohman M, Lagergren J
BMC Bioinformatics 11 (-) 6 [2010-01-04; online 2010-01-04]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
SciLifeLab Data Centre
Publications 9.5.1