NGI Stockholm (Genomics Production)

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Publications

2021 (265)

2020 (592)

2019 (720)

2018 (635)

2017 (677)

2016 (656)

2015 (427)

2014 (376)

2013 (320)

2012 (243)

2011 (163)

2010 (139)

All (5213)


Infrastructure Units

Journals

SciLifeLab Infrastructure Unit 2013–2019.

Started: 2013

Ended: 2019

907 publications

Year 2021

PubMed DOI Crossref
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 [2021-12-00; online 2021-01-27]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Chemical Biology Consortium Sweden (CBCS) [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Genome-wide estrogen receptor β chromatin binding in human colon cancer cells reveals its tumor suppressor activity.
Indukuri R, Jafferali MH, Song D, ..., Archer A, Williams C
Int. J. Cancer 149 (3) 692-706 [2021-08-01; online 2021-04-05]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
FGFR1 overexpression in non-small cell lung cancer is mediated by genetic and epigenetic mechanisms and is a determinant of FGFR1 inhibitor response.
Bogatyrova O, Mattsson JSM, Ross EM, ..., Esdar C, Micke P
Eur. J. Cancer 151 (-) 136-149 [2021-07-00; online 2021-05-10]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Mammuthus sp. (Early and Middle Pleistocene Mammoths).
Pečnerová P, Díez-Del-Molino D, van der Valk T, ..., Götherström A, Dalén L
Trends Genet. 37 (7) 682-683 [2021-07-00; online 2021-05-11]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Variable kinship patterns in Neolithic Anatolia revealed by ancient genomes.
Yaka R, Mapelli I, Kaptan D, ..., Özer F, Somel M
Curr. Biol. 31 (11) 2455-2468.e18 [2021-06-07; online 2021-04-14]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Genomic and fitness consequences of inbreeding in an endangered carnivore.
Hasselgren M, Dussex N, von Seth J, ..., Dalén L, Norén K
Mol. Ecol. 30 (12) 2790-2799 [2021-06-00; online 2021-05-20]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Genomic Characterization of the Barnacle Balanus improvisus Reveals Extreme Nucleotide Diversity in Coding Regions
Alm Rosenblad M, Abramova A, Lind U, ..., Nystedt B, Blomberg A
Mar Biotechnol - (-) - [2021-05-01; online 2021-05-01]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Hybrid sequencing resolves two germline ultra-complex chromosomal rearrangements consisting of 137 breakpoint junctions in a single carrier.
Eisfeldt J, Pettersson M, Petri A, ..., Feuk L, Lindstrand A
Hum. Genet. 140 (5) 775-790 [2021-05-00; online 2020-12-14]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Dual RNA-Seq transcriptome analysis of chicken macrophage-like cells (HD11) infected in vitro with Eimeria tenella.
Sandholt AKS, Xu F, Söderlund R, ..., Svärd SG, Wattrang E
Parasitology 148 (6) 712-725 [2021-05-00; online 2021-02-04]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Cyanophage Diversity and Community Structure in Dead Zone Sediments.
Broman E, Holmfeldt K, Bonaglia S, Hall POJ, Nascimento FJA
mSphere 6 (2) - [2021-04-28; online 2021-04-28]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Middle Pleistocene genome calibrates a revised evolutionary history of extinct cave bears.
Barlow A, Paijmans JLA, Alberti F, ..., Baryshnikov G, Hofreiter M
Curr. Biol. 31 (8) 1771-1779.e7 [2021-04-26; online 2021-02-15]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Genomic insights into the conservation status of the world's last remaining Sumatran rhinoceros populations.
von Seth J, Dussex N, Díez-Del-Molino D, ..., Götherström A, Dalén L
Nat Commun 12 (1) 2393 [2021-04-26; online 2021-04-26]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Functional Diversity Facilitates Stability Under Environmental Changes in an Outdoor Microalgal Cultivation System.
Mattsson L, Sörenson E, Capo E, ..., Lindehoff E, Legrand C
Front Bioeng Biotechnol 9 (-) 651895 [2021-04-22; online 2021-04-22]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
High diagnostic yield in skeletal ciliopathies using massively parallel genome sequencing, structural variant screening and RNA analyses.
Hammarsjö A, Pettersson M, Chitayat D, ..., Lindstrand A, Grigelioniene G
J. Hum. Genet. - (-) - [2021-04-20; online 2021-04-20]
Clinical Genomics Stockholm [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Active DNRA and denitrification in oxic hypereutrophic waters.
Broman E, Zilius M, Samuiloviene A, ..., Nascimento FJA, Bonaglia S
Water Res. 194 (-) 116954 [2021-04-15; online 2021-02-21]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Single-cell CUT&Tag profiles histone modifications and transcription factors in complex tissues
Bartosovic M, Kabbe M, Castelo-Branco G
Nat Biotechnol - (-) - [2021-04-12; online 2021-04-12]
Eukaryotic Single Cell Genomics (ESCG) [Collaborative] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
A spinal organ of proprioception for integrated motor action feedback.
Picton LD, Bertuzzi M, Pallucchi I, ..., Shearing PR, El Manira A
Neuron 109 (7) 1188-1201.e7 [2021-04-07; online 2021-02-11]
Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Genetic barriers to historical gene flow between cryptic species of alpine bumblebees revealed by comparative population genomics.
Christmas MJ, Jones JC, Olsson A, ..., Geib JC, Webster MT
Mol. Biol. Evol. - (-) - [2021-04-06; online 2021-04-06]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure
PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
The evolution of ancestral and species-specific adaptations in snowfinches at the Qinghai-Tibet Plateau.
Qu Y, Chen C, Chen X, ..., Zhang YE, Lei F
Proc. Natl. Acad. Sci. U.S.A. 118 (13) - [2021-03-30; online 2021-03-24]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
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) - [2021-03-16; online 2021-04-11]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
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) - [2021-03-00; online 2021-01-05]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
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]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Spatial Proteomics [Collaborative]
PubMed DOI Crossref
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) - [2021-01-29; online 2021-01-29]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
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) - [2021-01-26; online 2021-01-23]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Candidate regulators and target genes of drought stress in needles and roots of Norway spruce.
Haas JC, Vergara A, Serrano AR, ..., Hurry V, Street NR
Tree Physiol - (-) - [2021-01-08; online 2021-01-08]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
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 [2021-01-08; online 2021-01-08]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

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]
PubMed DOI Crossref
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 [2020-12-07; online 2020-12-07]
Bioinformatics Compute and Storage [Service] Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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 [2020-12-00; online 2020-11-16]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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) - [2020-12-00; online 2020-01-16]
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
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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 [2020-11-20; online 2020-11-20]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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. - (-) - [2020-11-18; online 2020-11-18]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] Eukaryotic Single Cell Genomics (ESCG) [Service] In Situ Sequencing (ISS) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Development of a highly efficient 50K SNP genotyping array for the large and complex genome of Norway spruce (Picea abies L. Karst) by whole genome re-sequencing and its transferability to other spruce species.
Bernhardsson C, Zan Y, Chen Z, Ingvarsson PK, Wu HX
Mol Ecol Resour - (-) - [2020-11-11; online 2020-11-11]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Systems Biology [Collaborative]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Leaf shape in Populus tremula is a complex, omnigenic trait.
Mähler N, Schiffthaler B, Robinson KM, ..., Hvidsten TR, Street NR
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Horizontal Gene Transfer and Tandem Duplication Shape the Unique CAZyme Complement of the Mycoparasitic Oomycetes Pythium oligandrum and Pythium periplocum.
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Population genomics reveals lack of greater white-fronted introgression into the Swedish lesser white-fronted goose.
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Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird‐of‐paradise
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Mol Ecol Resour 21 (1) 263-286 [2020-10-10; online 2020-10-10]
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GeneSetCluster: a tool for summarizing and integrating gene-set analysis results.
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BMC Bioinformatics 21 (1) 443 [2020-10-07; online 2020-10-07]
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Deep sequencing detects human papillomavirus (HPV) in cervical cancers negative for HPV by PCR.
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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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Pre-extinction Demographic Stability and Genomic Signatures of Adaptation in the Woolly Rhinoceros.
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Notch activation in the mouse mammary luminal lineage leads to ductal hyperplasia and altered partitioning of luminal cell subtypes.
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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.
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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.
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Labile Dissolved Organic Matter Compound Characteristics Select for Divergence in Marine Bacterial Activity and Transcription.
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Generation of Sequencing Libraries for Structural Analysis of Bacterial 5' UTRs.
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Compositional and functional differences of the mucosal microbiota along the intestine of healthy individuals.
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Sci Rep 10 (1) 14977 [2020-09-11; online 2020-09-11]
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Genetic association of gemcitabine/carboplatin-induced leukopenia and neutropenia in non-small cell lung cancer patients using whole-exome sequencing.
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Lung Cancer 147 (-) 106-114 [2020-09-00; online 2020-07-12]
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A Shh/Gli-driven three-node timer motif controls temporal identity and fate of neural stem cells.
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Sci Adv 6 (38) - [2020-09-00; online 2020-09-16]
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DNA methylation variation in the brain of laying hens in relation to differential behavioral patterns.
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Comp Biochem Physiol Part D Genomics Proteomics 35 (-) 100700 [2020-09-00; online 2020-06-02]
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Reconstructing marine plankton food web interactions using DNA metabarcoding.
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Mol. Ecol. 29 (17) 3380-3395 [2020-09-00; online 2020-08-09]
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Index hopping on the Illumina HiseqX platform and its consequences for ancient DNA studies.
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Mol Ecol Resour 20 (5) 1171-1181 [2020-09-00; online 2019-05-05]
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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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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.
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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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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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The compact genome of Giardia muris reveals important steps in the evolution of intestinal protozoan parasites.
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Microb Genom 6 (8) - [2020-08-00; online 2020-07-03]
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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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High throughput shotgun sequencing of eRNA reveals taxonomic and derived functional shifts across a benthic productivity gradient.
Broman E, Bonaglia S, Norkko A, Creer S, Nascimento FJA
Mol. Ecol. - (-) - [2020-07-24; online 2020-07-24]
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Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma.
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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.
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Sci Rep 10 (1) 11831 [2020-07-16; online 2020-07-16]
BioImage Informatics Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Genome Engineering Zebrafish [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]
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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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Low Abundance of Methanotrophs in Sediments of Shallow Boreal Coastal Zones With High Water Methane Concentrations.
Broman E, Sun X, Stranne C, ..., Humborg C, Nascimento FJA
Front Microbiol 11 (-) 1536 [2020-07-07; online 2020-07-07]
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Systems biology of acidophile biofilms for efficient metal extraction.
Buetti-Dinh A, Herold M, Christel S, ..., Pivkin IV, Dopson M
Sci Data 7 (1) 215 [2020-07-07; online 2020-07-07]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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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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Novel form of rhizomelic skeletal dysplasia associated with a homozygous variant in GNPNAT1.
Ain NU, Baroncelli M, Costantini A, ..., Mäkitie O, Naz S
J. Med. Genet. - (-) jmedgenet-2020-106929 [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.
Remnestål J, Öijerstedt L, Ullgren A, ..., Graff C, Nilsson P
Transl Neurodegener 9 (1) 27 [2020-06-23; online 2020-06-23]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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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.
Rodrigues AF, Newman L, Jasim D, ..., Kostarelos K, Bussy C
Adv Sci (Weinh) 7 (12) 1903200 [2020-06-00; online 2020-05-07]
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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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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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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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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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Linked-read sequencing enables haplotype-resolved resequencing at population scale.
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Mol Ecol Resour 20 (5) 1311-1322 [2020-05-18; online 2020-05-18]
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Parallel Evolution of Bower-Building Behavior in Two Groups of Bowerbirds Suggested by Phylogenomics.
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Syst. Biol. 69 (5) 820-829 [2020-05-16; online 2020-05-16]
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Myocardial micro-biopsy procedure for molecular characterization with increased precision and reduced trauma.
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Sci Rep 10 (1) 8029 [2020-05-15; online 2020-05-15]
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Uncovering the hidden diversity of litter-decomposition mechanisms in mushroom-forming fungi.
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ISME J - (-) - [2020-05-07; online 2020-05-07]
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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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Srebf1 Controls Midbrain Dopaminergic Neurogenesis.
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Cell Rep 31 (5) 107601 [2020-05-05; online 2020-05-07]
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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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Rare variants in dynein heavy chain genes in two individuals with situs inversus and developmental dyslexia: a case report.
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BMC Med. Genet. 21 (1) 87 [2020-05-01; online 2020-05-01]
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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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Whole-genome sequencing reveals complex chromosome rearrangement disrupting NIPBL in infant with Cornelia de Lange syndrome.
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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.
Atherton S, Jondelius U
Biodivers Data J 8 (-) e51813 [2020-04-27; online 2020-04-27]
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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.
Bianchi M, Rafati N, Karlsson Å, ..., Lindblad-Toh K, Rosengren Pielberg G
BMC Genomics 21 (1) 307 [2020-04-16; online 2020-04-16]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Automation of Spatial Transcriptomics library preparation to enable rapid and robust insights into spatial organization of tissues.
Berglund E, Saarenpää S, Jemt A, ..., Lundeberg J, Giacomello S
BMC Genomics 21 (1) 298 [2020-04-15; online 2020-04-15]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Generation of Retinal Pigment Epithelial Cells Derived from Human Embryonic Stem Cells Lacking Human Leukocyte Antigen Class I and II.
Petrus-Reurer S, Winblad N, Kumar P, ..., Kvanta A, Lanner F
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
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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.
Eriksen AK, Brunius C, Mazidi M, ..., Dicksved J, Landberg R
Am. J. Clin. Nutr. 111 (4) 864-876 [2020-04-01; online 2020-02-26]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Extensive Clonal Branching Shapes the Evolutionary History of High-Risk Pediatric Cancers.
Andersson N, Bakker B, Karlsson J, ..., Foijer F, Gisselsson D
Cancer Res. 80 (7) 1512-1523 [2020-04-01; online 2020-02-10]
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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]
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Genes and variants in hematopoiesis-related pathways are associated with gemcitabine/carboplatin-induced thrombocytopenia.
Björn N, Sigurgeirsson B, Svedberg A, ..., Lundeberg J, Gréen H
Pharmacogenomics J. 20 (2) 179-191 [2020-04-00; online 2019-10-15]
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]
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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 NiCl 2.
Gliga AR, Di Bucchianico S, Åkerlund E, Karlsson HL
Nanomaterials (Basel) 10 (4) - [2020-03-31; online 2020-03-31]
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Mutations in COL1A1/A2 and CREB3L1 are associated with oligodontia in osteogenesis imperfecta.
Andersson K, Malmgren B, Åström E, ..., Taylan F, Dahllöf G
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.
Rantapero T, Wahlfors T, Kähler A, ..., Schleutker J, Wiklund F
Genes 11 (3) 314 [2020-03-14; online 2020-03-14]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Ecosystem-wide metagenomic binning enables prediction of ecological niches from genomes.
Alneberg J, Bennke C, Beier S, ..., Pinhassi J, Andersson AF
Commun Biol 3 (1) 119 [2020-03-13; online 2020-03-13]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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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
Ewels PA, Peltzer A, Fillinger S, ..., Di Tommaso P, Nahnsen S
Nat Biotechnol 38 (3) 276-278 [2020-03-00; online 2020-02-13]
NGI Stockholm (Genomics Applications) [Technology development] NGI Stockholm (Genomics Production) [Technology development] National Genomics Infrastructure [Technology development]
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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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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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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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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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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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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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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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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]
Chemical Biology Consortium Sweden (CBCS) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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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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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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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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) 1-13 [2020-01-10; online 2020-01-10]
Bioinformatics Compute and Storage [Service] CRISPR Functional Genomics [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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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]
NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Collaborative] National Genomics Infrastructure [Collaborative]
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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]
Bioinformatics Compute and Storage [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 [Collaborative]
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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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]
Bioinformatics Compute and Storage [Service] 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] Systems Biology [Collaborative]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] Cellular Immunomonitoring [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Eukaryotic Single Cell Genomics (ESCG) [Service] In Situ Sequencing (ISS) [Technology development] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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]
NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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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PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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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PubMed DOI Crossref
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]
Cryo-EM [Service] Integrated Microscopy Technologies Umeå [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] 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 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]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Swedish Metabolomics Centre (SMC) [Service]
PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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]
Affinity Proteomics Stockholm [Collaborative] Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Spatial Proteomics [Collaborative]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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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Front Microbiol 10 (-) 2632 [2019-11-14; online 2019-11-14]
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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]
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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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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.
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Genome Med 11 (1) 68 [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]
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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]
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Whole-genome sequencing of synchronous thyroid carcinomas identifies aberrant DNA repair in thyroid cancer dedifferentiation
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J. Pathol - (-) - [2019-10-17; online 2019-10-17]
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PubMed DOI Crossref
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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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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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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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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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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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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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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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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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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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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Translational offsetting as a mode of estrogen receptor α-dependent regulation of gene expression.
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EMBO J. - (-) e101323 [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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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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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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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]
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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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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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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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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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PubMed DOI Crossref
Complete subspecies-level phylogeny of the Oriolidae (Aves: Passeriformes): Out of Australasia and return.
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Mol. Phylogenet. Evol. 137 (-) 200-209 [2019-08-00; online 2019-03-23]
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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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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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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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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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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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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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PubMed DOI Crossref
Transcriptional and metabolic rewiring of colorectal cancer cells expressing the oncogenic KRAS G13D 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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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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PubMed DOI Crossref
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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Mutations in the mitochondrial tryptophanyl-tRNA synthetase cause growth retardation and progressive leukoencephalopathy.
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Mol Genet Genomic Med 7 (6) e654 [2019-06-00; online 2019-03-28]
Clinical Genomics Stockholm [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Unprecedented reorganization of holocentric chromosomes provides insights into the enigma of lepidopteran chromosome evolution.
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Sci Adv 5 (6) eaau3648 [2019-06-00; online 2019-06-12]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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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.
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Mol Genet Genomic Med 7 (6) e666 [2019-06-00; online 2019-05-01]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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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
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Immunity 51 (1) 169-184.e5 [2019-06-00; online 2019-06-00]
Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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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.
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Stem Cell Reports 12 (5) 950-966 [2019-05-14; online 2019-04-25]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Chromosomal genome assembly of the ethanol production strain CBS 11270 indicates a highly dynamic genome structure in the yeast species Brettanomyces bruxellensis.
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PLoS ONE 14 (5) e0215077 [2019-05-01; online 2019-05-01]
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PubMed DOI Crossref
Comparative analyses identify genomic features potentially involved in the evolution of birds-of-paradise.
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Gigascience 8 (5) - [2019-05-01; online 2019-01-29]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Gene expression profile of extraocular muscles following resection strabismus surgery.
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Exp. Eye Res. 182 (-) 182-193 [2019-05-00; online 2019-04-03]
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]
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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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PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The Genome of Blue-Capped Cordon-Bleu Uncovers Hidden Diversity of LTR Retrotransposons in Zebra Finch.
Boman J, Frankl-Vilches C, da Silva Dos Santos M, ..., Gahr M, Suh A
Genes 10 (4) - [2019-04-13; online 2019-04-13]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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SQSTM1/p62-Directed Metabolic Reprogramming Is Essential for Normal Neurodifferentiation.
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Stem Cell Reports 12 (4) 696-711 [2019-04-09; online 2019-02-28]
Bioinformatics Compute and Storage [Service] Clinical Genomics Stockholm [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
SAMURAI (Solid-phase Assisted Mutagenesis by Uracil Restriction for Accurate Integration) for antibody affinity maturation and paratope mapping.
Hu FJ, Lundqvist M, Uhlén M, Rockberg J
Nucleic Acids Res. 47 (6) e34 [2019-04-08; online 2019-02-05]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis.
Maniatis S, Äijö T, Vickovic S, ..., Bonneau R, Phatnani H
Science 364 (6435) 89-93 [2019-04-05; online 2019-04-06]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The repertoire of maternal anti-viral antibodies in human newborns.
Pou C, Nkulikiyimfura D, Henckel E, ..., Bohlin K, Brodin P
Nat. Med. 25 (4) 591-596 [2019-04-00; online 2019-03-18]
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PubMed DOI Crossref
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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PubMed DOI Crossref
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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PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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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PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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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PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] Clinical Genomics Stockholm [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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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]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Year 2018

PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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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PubMed DOI Crossref
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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PubMed DOI Crossref
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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PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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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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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PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] Clinical Genomics Stockholm [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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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PubMed DOI Crossref
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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PubMed DOI Crossref
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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PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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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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PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Service] Bioinformatics Support, Infrastructure and Training [Service] Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] 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
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]
Global Proteomics and Proteogenomics [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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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]
Bioinformatics Compute and Storage [Service] Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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 2018-08-28]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Support, Infrastructure and Training [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Systems Biology [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] Clinical Genomics Stockholm [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] CRISPR Functional Genomics [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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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PubMed DOI Crossref
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]
Bioinformatics Long-term Support WABI [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Stereotypic Immune System Development in Newborn Children.
Olin A, Henckel E, Chen Y, ..., Bohlin K, Brodin P
Cell 174 (5) 1277-1292.e14 [2018-08-23; online 2018-08-25]
Affinity Proteomics Stockholm [Service] Bioinformatics Compute and Storage [Service] Cellular Immunomonitoring [Technology development] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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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PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Protein Science Facility (PSF) [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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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PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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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PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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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PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Notch signaling promotes a HIF2α-driven hypoxic response in multiple tumor cell types.
Mutvei AP, Landor SK, Fox R, ..., Jin S, Lendahl U
Oncogene - (-) - [2018-07-11; online 2018-07-11]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] 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
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]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
CRISPR Functional Genomics [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Protein Science Facility (PSF) [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] 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
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]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] 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
Fatal demyelinating disease is induced by monocyte-derived macrophages in the absence of TGF-β signaling.
Lund H, Pieber M, Parsa R, ..., Zhang XM, Harris RA
Nat. Immunol. 19 (5) 1-7 [2018-05-00; online 2018-04-16]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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) - [2018-04-19; online 2018-04-19]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Expression of scavenger receptor MARCO defines a targetable tumor-associated macrophage subset in non-small cell lung cancer.
La Fleur L, Boura VF, Alexeyenko A, ..., Karlsson MCI, Botling J
Int. J. Cancer - (-) - [2018-04-18; online 2018-04-18]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] Clinical Genomics Uppsala [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] 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
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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]
Bioinformatics Compute and Storage [Service] Clinical Genomics Stockholm [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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]
Bioinformatics Compute and Storage [Service] Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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]
Affinity Proteomics Uppsala [Technology development] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Tissue Profiling [Collaborative]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Year 2017

PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
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
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]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Long-term Support WABI [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Demographic inference from whole-genome and RAD sequencing data suggests alternating human impacts on goose populations since the last ice age.
Pujolar JM, Dalén L, Hansen MM, Madsen J
Mol. Ecol. 26 (22) 6270-6283 [2017-11-00; online 2017-11-03]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] 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] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] 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
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]
Clinical Proteomics Mass spectrometry [Service] Global Proteomics and Proteogenomics [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Integrated Microscopy Technologies Stockholm [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Tissue Profiling [Technology development]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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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PubMed DOI Crossref
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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PubMed DOI Crossref
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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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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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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]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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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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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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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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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]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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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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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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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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PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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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]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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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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PubMed DOI Crossref
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]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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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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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Spatial Proteomics [Collaborative]
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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PubMed DOI Crossref
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
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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PubMed DOI Crossref
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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PubMed DOI Crossref
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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PubMed DOI Crossref
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
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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PubMed DOI Crossref
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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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
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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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]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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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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]
Bioinformatics Compute and Storage [Service] Clinical Genomics Stockholm [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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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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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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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]
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]
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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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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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]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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
Antibody-encoding repertoires of bone marrow and peripheral blood-a focus on IgE.
Levin M, Levander F, Palmason R, Greiff L, Ohlin M
J. Allergy Clin. Immunol. 139 (3) 1026-1030 [2017-03-00; online 2016-08-09]
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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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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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]
Clinical Genomics Uppsala [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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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
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 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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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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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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]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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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PubMed DOI Crossref
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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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]
Bioinformatics Compute and Storage [Service] 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]
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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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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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]
Bioinformatics Compute and Storage [Service] Clinical Genomics Stockholm [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] Clinical Genomics Stockholm [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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
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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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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Year 2016

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
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
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
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]
Bioinformatics Compute and Storage [Service] 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
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]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Prokaryotic Responses to Ammonium and Organic Carbon Reveal Alternative CO2 Fixation Pathways and Importance of Alkaline Phosphatase in the Mesopelagic North Atlantic.
Baltar F, Lundin D, Palovaara J, ..., Herndl GJ, Pinhassi J
Front Microbiol 7 (-) 1670 [2016-10-21; online 2016-10-21]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Over Expression of NANOS3 and DAZL in Human Embryonic Stem Cells.
Panula S, Reda A, Stukenborg JB, ..., Reijo Pera RA, Hovatta O
PLoS ONE 11 (10) e0165268 [2016-10-21; online 2016-10-21]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Gene-specific correlation of RNA and protein levels in human cells and tissues.
Edfors F, Danielsson F, Hallström BM, ..., Forsström B, Uhlén M
Mol. Syst. Biol. 12 (10) 883 [2016-10-20; online 2016-10-20]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Tissue Profiling [Collaborative]
PubMed DOI Crossref
The Transcriptome of Rhabdomyosarcoma Cells Infected with Cytolytic and Non-Cytolytic Variants of Coxsackievirus B2 Ohio-1.
Sävneby A, Luthman J, Nordenskjöld F, Andersson B, Lindberg AM
PLoS ONE 11 (10) e0164548 [2016-10-19; online 2016-10-19]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Massive and parallel expression profiling using microarrayed single-cell sequencing.
Vickovic S, Ståhl PL, Salmén F, ..., Frisén J, Lundeberg J
Nat Commun 7 (-) 13182 [2016-10-14; online 2016-10-14]
Bioinformatics Compute and Storage [Service] 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
Penicillium arizonense, a new, genome sequenced fungal species, reveals a high chemical diversity in secreted metabolites.
Grijseels S, Nielsen JC, Randelovic M, ..., Workman M, Frisvad JC
Sci Rep 6 (-) 35112 [2016-10-14; online 2016-10-14]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Virome characterisation from Guthrie cards in children who later developed acute lymphoblastic leukaemia.
Bogdanovic G, Pou C, Barrientos-Somarribas M, ..., Andersson B, Gustafsson B
Br. J. Cancer 115 (8) 1008-1014 [2016-10-11; online 2016-08-24]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The structure and diversity of human, animal and environmental resistomes.
Pal C, Bengtsson-Palme J, Kristiansson E, Larsson DG
Microbiome 4 (1) 54 [2016-10-07; online 2016-10-07]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Molecular Diversity of Midbrain Development in Mouse, Human, and Stem Cells.
La Manno G, Gyllborg D, Codeluppi S, ..., Arenas E, Linnarsson S
Cell 167 (2) 566-580.e19 [2016-10-06; online 2016-10-08]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
MultiQC: summarize analysis results for multiple tools and samples in a single report.
Ewels P, Magnusson M, Lundin S, Käller M
Bioinformatics 32 (19) 3047-3048 [2016-10-01; online 2016-06-16]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Technology development] NGI Stockholm (Genomics Production) [Technology development] National Genomics Infrastructure [Technology development]
PubMed DOI Crossref
Whole-Exome Sequencing Suggests LAMB3 as a Susceptibility Gene for Morbid Obesity.
Jiao H, Kulyté A, Näslund E, ..., Arner P, Dahlman I
Diabetes 65 (10) 2980-2989 [2016-10-00; online 2016-07-20]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Towards integration of population and comparative genomics in forest trees.
Ingvarsson PK, Hvidsten TR, Street NR
New Phytol. 212 (2) 338-344 [2016-10-00; online 2016-08-31]
NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Investigation of rare and low-frequency variants using high-throughput sequencing with pooled DNA samples.
Wang J, Skoog T, Einarsdottir E, ..., Kere J, Jiao H
Sci Rep 6 (-) 33256 [2016-09-16; online 2016-09-16]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Absence of the Autophagy Adaptor SQSTM1/p62 Causes Childhood-Onset Neurodegeneration with Ataxia, Dystonia, and Gaze Palsy.
Haack TB, Ignatius E, Calvo-Garrido J, ..., Carroll CJ, Klopstock T
Am. J. Hum. Genet. 99 (3) 735-743 [2016-09-01; online 2016-08-23]
Clinical Genomics Stockholm [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The Impact of Endurance Training on Human Skeletal Muscle Memory, Global Isoform Expression and Novel Transcripts.
Lindholm ME, Giacomello S, Werne Solnestam B, ..., Kjellqvist S, Sundberg CJ
PLoS Genet. 12 (9) e1006294 [2016-09-00; online 2016-09-22]
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
Electricity generation from an inorganic sulfur compound containing mining wastewater by acidophilic microorganisms.
Ni G, Christel S, Roman P, ..., Bijmans MF, Dopson M
Res. Microbiol. 167 (7) 568-575 [2016-09-00; online 2016-05-08]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The Adipose Transcriptional Response to Insulin Is Determined by Obesity, Not Insulin Sensitivity.
Rydén M, Hrydziuszko O, Mileti E, ..., Daub CO, Arner P
Cell Rep 16 (9) 2317-2326 [2016-08-30; online 2016-08-23]
Bioinformatics Compute and Storage [Service] 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
Oxidation and cyclization of casbene in the biosynthesis of Euphorbia factors from mature seeds of Euphorbia lathyris L.
Luo D, Callari R, Hamberger B, ..., Staerk D, Hamberger B
Proc. Natl. Acad. Sci. U.S.A. 113 (34) E5082-E5089 [2016-08-23; online 2016-08-11]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
DOI Crossref
Effects of wastewater treatment plant effluent inputs on planktonic metabolic rates and microbial community composition in the Baltic Sea
Vaquer-Sunyer R, Reader HE, Muthusamy S, ..., Conley DJ, Kritzberg ES
Biogeosciences 13 (16) 4751-4765 [2016-08-23; online 2016-08-23]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Cardiometabolic risk loci share downstream cis- and trans-gene regulation across tissues and diseases.
Franzén O, Ermel R, Cohain A, ..., Schadt EE, Björkegren JL
Science 353 (6301) 827-830 [2016-08-19; online 2016-08-20]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Single base resolution analysis of 5-hydroxymethylcytosine in 188 human genes: implications for hepatic gene expression.
Ivanov M, Kals M, Lauschke V, ..., Milani L, Ingelman-Sundberg M
Nucleic Acids Res. 44 (14) 6756-6769 [2016-08-19; online 2016-04-29]
Bioinformatics Compute and Storage [Service] Clinical Proteomics Mass spectrometry [Collaborative] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
The genome-scale DNA-binding profile of BarR, a β-alanine responsive transcription factor in the archaeon Sulfolobus acidocaldarius.
Liu H, Wang K, Lindås AC, Peeters E
BMC Genomics 17 (-) 569 [2016-08-08; online 2016-08-08]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Adaptation to different types of stress converge on mitochondrial metabolism.
Lahtvee PJ, Kumar R, Hallström BM, Nielsen J
Mol. Biol. Cell 27 (15) 2505-2514 [2016-08-01; online 2016-06-17]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Spondyloocular Syndrome: Novel Mutations in XYLT2 Gene and Expansion of the Phenotypic Spectrum.
Taylan F, Costantini A, Coles N, ..., Tüysüz B, Mäkitie O
J. Bone Miner. Res. 31 (8) 1577-1585 [2016-08-00; online 2016-03-19]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Profiling cancer testis antigens in non-small-cell lung cancer.
Djureinovic D, Hallström BM, Horie M, ..., Uhlén M, Micke P
JCI Insight 1 (10) e86837 [2016-07-07; online 2016-07-07]
Bioinformatics Compute and Storage [Service] Clinical Genomics Uppsala [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Tissue Profiling [Collaborative]
PubMed DOI Crossref
Exome sequencing in pooled DNA samples to identify maternal pre-eclampsia risk variants.
Kaartokallio T, Wang J, Heinonen S, ..., Kere J, Laivuori H
Sci Rep 6 (-) 29085 [2016-07-07; online 2016-07-07]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Diversity and Expression of Bacterial Metacaspases in an Aquatic Ecosystem.
Asplund-Samuelsson J, Sundh J, Dupont CL, ..., Ininbergs K, Ekman M
Front Microbiol 7 (-) 1043 [2016-07-06; online 2016-07-06]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Visualization and analysis of gene expression in tissue sections by spatial transcriptomics.
Ståhl PL, Salmén F, Vickovic S, ..., Lundeberg J, Frisén J
Science 353 (6294) 78-82 [2016-07-01; online 2016-07-02]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Fluorescence Tissue Profiling [Collaborative] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Tissue Profiling [Collaborative]
PubMed DOI Crossref
Variation in Linked Selection and Recombination Drive Genomic Divergence during Allopatric Speciation of European and American Aspens.
Wang J, Street NR, Scofield DG, Ingvarsson PK
Mol. Biol. Evol. 33 (7) 1754-1767 [2016-07-00; online 2016-03-18]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The genetic landscape of paediatric de novo acute myeloid leukaemia as defined by single nucleotide polymorphism array and exon sequencing of 100 candidate genes.
Olsson L, Zettermark S, Biloglav A, ..., Paulsson K, Johansson B
Br. J. Haematol. 174 (2) 292-301 [2016-07-00; online 2016-03-31]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Whole genome duplication in coast redwood (Sequoia sempervirens) and its implications for explaining the rarity of polyploidy in conifers.
Scott AD, Stenz NW, Ingvarsson PK, Baum DA
New Phytol. 211 (1) 186-193 [2016-07-00; online 2016-03-22]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The role of germline alterations in the DNA damage response genes BRIP1 and BRCA2 in melanoma susceptibility.
Tuominen R, Engström PG, Helgadottir H, ..., Hansson J, Höiom V
Genes Chromosomes Cancer 55 (7) 601-611 [2016-07-00; online 2016-04-14]
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
Conserved 33-kb haplotype in the MHC class III region regulates chronic arthritis.
Yau AC, Tuncel J, Haag S, ..., Padyukov L, Holmdahl R
Proc. Natl. Acad. Sci. U.S.A. 113 (26) E3716-E3724 [2016-06-28; online 2016-06-16]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Draft Genome Sequence of Moraxella catarrhalis Type Strain CCUG 353T.
Jakobsson HE, Salvà-Serra F, Thorell K, ..., Kristiansson E, Moore ER
Genome Announc 4 (3) e00552-16 [2016-06-16; online 2016-06-16]
Clinical Genomics Gothenburg [Service] Clinical Genomics Stockholm [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Oligodendrocyte heterogeneity in the mouse juvenile and adult central nervous system.
Marques S, Zeisel A, Codeluppi S, ..., Linnarsson S, Castelo-Branco G
Science 352 (6291) 1326-1329 [2016-06-10; online 2016-06-11]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
GPR44 is a pancreatic protein restricted to the human beta cell.
Hellström-Lindahl E, Danielsson A, Ponten F, ..., Johansson L, Eriksson O
Acta Diabetol 53 (3) 413-421 [2016-06-00; online 2015-10-14]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Tissue Profiling [Collaborative]
PubMed DOI Crossref
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
J Innate Immun 8 (4) 412-426 [2016-05-28; online 2016-05-28]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Thermotolerant yeasts selected by adaptive evolution express heat stress response at 30 °C.
Caspeta L, Chen Y, Nielsen J
Sci Rep 6 (-) 27003 [2016-05-27; online 2016-05-27]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
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
Minimal selective concentrations of tetracycline in complex aquatic bacterial biofilms.
Lundström SV, Östman M, Bengtsson-Palme J, ..., Flach CF, Larsson DG
Sci. Total Environ. 553 (-) 587-595 [2016-05-15; online 2016-03-05]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Diversity of Pico- to Mesoplankton along the 2000 km Salinity Gradient of the Baltic Sea.
Hu YO, Karlson B, Charvet S, Andersson AF
Front Microbiol 7 (-) 679 [2016-05-12; online 2016-05-12]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Determining breast cancer histological grade from RNA-sequencing data.
Wang M, Klevebring D, Lindberg J, ..., Grönberg H, Rantalainen M
Breast Cancer Res. 18 (1) 48 [2016-05-10; online 2016-05-10]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Unscrambling Cyanobacteria Community Dynamics Related to Environmental Factors.
Bertos-Fortis M, Farnelid HM, Lindh MV, ..., Pinhassi J, Legrand C
Front Microbiol 7 (-) 625 [2016-05-09; online 2016-05-09]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Synchronous genetic turnovers across Western Eurasia in Late Pleistocene collared lemmings.
Palkopoulou E, Baca M, Abramson NI, ..., Stankovic A, Dalén L
Glob Chang Biol 22 (5) 1710-1721 [2016-05-00; online 2016-02-27]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Molecular Characterization of Three Canine Models of Human Rare Bone Diseases: Caffey, van den Ende-Gupta, and Raine Syndromes.
Hytönen MK, Arumilli M, Lappalainen AK, ..., Drögemüller C, Lohi H
PLoS Genet. 12 (5) e1006037 [2016-05-00; online 2016-05-17]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Microbial metagenomes from three aquifers in the Fennoscandian shield terrestrial deep biosphere reveal metabolic partitioning among populations.
Wu X, Holmfeldt K, Hubalek V, ..., Bertilsson S, Dopson M
ISME J 10 (5) 1192-1203 [2016-05-00; online 2015-10-21]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Biotin and Thiamine Responsive Basal Ganglia Disease--A vital differential diagnosis in infants with severe encephalopathy.
Ygberg S, Naess K, Eriksson M, ..., Wedell A, Wickström R
Eur. J. Paediatr. Neurol. 20 (3) 457-461 [2016-05-00; online 2016-03-16]
Bioinformatics Compute and Storage [Service] Clinical Genomics Stockholm [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
nanoCAGE reveals 5' UTR features that define specific modes of translation of functionally related MTOR-sensitive mRNAs.
Gandin V, Masvidal L, Hulea L, ..., Larsson O, Topisirovic I
Genome Res. 26 (5) 636-648 [2016-05-00; online 2016-03-18]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Spatio-Temporal Interdependence of Bacteria and Phytoplankton during a Baltic Sea Spring Bloom.
Bunse C, Bertos-Fortis M, Sassenhagen I, ..., Pinhassi J, Legrand C
Front Microbiol 7 (-) 517 [2016-04-21; online 2016-04-21]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Mutations in histone modulators are associated with prolonged survival during azacitidine therapy.
Tobiasson M, McLornan DP, Karimi M, ..., Mufti GJ, Hellström-Lindberg E
Oncotarget 7 (16) 22103-22115 [2016-04-19; online 2016-03-10]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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
Mol. Biol. Cell 27 (8) 1210-1219 [2016-04-15; online 2016-02-26]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Transcriptomics resources of human tissues and organs.
Uhlén M, Hallström BM, Lindskog C, ..., Pontén F, Nielsen J
Mol. Syst. Biol. 12 (4) 862 [2016-04-04; online 2016-04-04]
Bioinformatics Support, Infrastructure and Training [Technology development] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Systems Biology [Technology development] Tissue Profiling [Collaborative]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Digital image analysis outperforms manual biomarker assessment in breast cancer.
Stålhammar G, Fuentes Martinez N, Lippert M, ..., Grunkin M, Hartman J
Mod. Pathol. 29 (4) 318-329 [2016-04-00; online 2016-02-27]
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PubMed DOI Crossref
RNA transcript sequencing reveals inorganic sulfur compound oxidation pathways in the acidophile Acidithiobacillus ferrivorans.
Christel S, Fridlund J, Buetti-Dinh A, ..., Watkin EL, Dopson M
FEMS Microbiol. Lett. 363 (7) - [2016-04-00; online 2016-03-10]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Draft Genome Sequence of Streptococcus gordonii Type Strain CCUG 33482T.
Salvà-Serra F, Jakobsson HE, Thorell K, ..., Kristiansson E, Moore ER
Genome Announc 4 (2) e00175-16 [2016-03-24; online 2016-03-24]
Bioinformatics Compute and Storage [Service] Clinical Genomics Gothenburg [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Metagenomic analysis of bloodstream infections in patients with acute leukemia and therapy-induced neutropenia.
Gyarmati P, Kjellander C, Aust C, ..., Öhrmalm L, Giske CG
Sci Rep 6 (-) 23532 [2016-03-21; online 2016-03-21]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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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PubMed DOI Crossref
Whole genome sequencing identifies a novel species of the genus Capnocytophaga isolated from dog and cat bite wounds in humans.
Zangenah S, Abbasi N, Andersson AF, Bergman P
Sci Rep 6 (-) 22919 [2016-03-07; online 2016-03-07]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Fast, accurate, and lightweight analysis of BS-treated reads with ERNE 2.
Prezza N, Vezzi F, Käller M, Policriti A
BMC Bioinformatics 17 Suppl 4 (-) 69 [2016-03-02; online 2016-03-02]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Collaborative] National Genomics Infrastructure [Service]
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 Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The influence of population structure on gene expression and flowering time variation in the ubiquitous weed Capsella bursa-pastoris (Brassicaceae).
Kryvokhyzha D, Holm K, Chen J, ..., Lagercrantz U, Lascoux M
Mol. Ecol. 25 (5) 1106-1121 [2016-03-00; online 2016-01-23]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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
Int. J. Syst. Evol. Microbiol. 66 (3) 1200-1205 [2016-03-00; online 2016-01-10]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
T-cell receptor-HLA-DRB1 associations suggest specific antigens in pulmonary sarcoidosis.
Grunewald J, Kaiser Y, Ostadkarampour M, ..., Ronninger M, Eklund A
Eur. Respir. J. 47 (3) 898-909 [2016-03-00; online 2015-11-19]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Collaborative] National Genomics Infrastructure [Collaborative]
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 Compute and Storage [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 Compute and Storage [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 Compute and Storage [Service] 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]
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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
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 Compute and Storage [Service] Clinical Genomics Stockholm [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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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
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]