Bioinformatics Compute and Storage

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Publications

2022 (8)

2021 (761)

2020 (595)

2019 (722)

2018 (638)

2017 (678)

2016 (656)

2015 (427)

2014 (376)

2013 (320)

2012 (243)

2011 (163)

2010 (139)

All (5726)


Infrastructure Units

Journals

SciLifeLab Infrastructure Unit since 2013.

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

Started: 2013

Ended: Current

Year 2021

PubMed DOI Crossref
The SEQC2 epigenomics quality control (EpiQC) study.
Foox J, Nordlund J, Lalancette C, ..., Deng Y, Mason CE
Genome Biol. 22 (1) 332 [2021-12-06; online 2021-12-06]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
Insights into the changes in the proteome of Alzheimer disease elucidated by a meta-analysis.
Haytural H, Benfeitas R, Schedin-Weiss S, ..., Frykman S, Tjernberg LO
Sci Data 8 (1) 312 [2021-12-03; online 2021-12-03]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Global similarity, and some key differences, in the metagenomes of Swedish varroa-surviving and varroa-susceptible honeybees.
Thaduri S, Marupakula S, Terenius O, ..., Locke B, de Miranda JR
Sci Rep 11 (1) 23214 [2021-12-01; online 2021-12-01]
Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
DOI Crossref
Long-term agricultural management impacts arbuscular mycorrhizal fungi more than short-term experimental drought
Kozjek K, Kundel D, Kushwaha SK, ..., Birkhofer K, Hedlund K
Applied Soil Ecology 168 (-) 104140 [2021-12-00; online 2021-12-00]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
A genomic and morphometric analysis of alpine bumblebees: Ongoing reductions in tongue length but no clear genetic component.
Christmas MJ, Jones JC, Olsson A, ..., Miller-Struttmann NE, Webster MT
Mol. Ecol. - (-) - [2021-11-27; online 2021-11-27]
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] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Dredging and deposition of metal sulfide rich river sediments results in rapid conversion to acid sulfate soil materials.
Johnson A, Högfors-Rönnholm E, Engblom S, ..., Åström M, Dopson M
Sci. Total Environ. - (-) 151864 [2021-11-23; online 2021-11-23]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Interplay between copy number alterations and immune profiles in the early breast cancer Scandinavian Breast Group 2004-1 randomized phase II trial: results from a feasibility study.
Zerdes I, Simonetti M, Matikas A, ..., Crosetto N, Foukakis T
NPJ Breast Cancer 7 (1) 144 [2021-11-19; online 2021-11-19]
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 Genetic Architecture of Obsessive-Compulsive Disorder: Contribution of Liability to OCD From Alleles Across the Frequency Spectrum.
Mahjani B, Klei L, Mattheisen M, ..., Devlin B, Grice DE
Am J Psychiatry - (-) appiajp202121010101 [2021-11-18; online 2021-11-18]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Single cell genomics reveals plastid-lacking Picozoa are close relatives of red algae.
Schön ME, Zlatogursky VV, Singh RP, ..., Wideman JG, Burki F
Nat Commun 12 (1) 6651 [2021-11-17; online 2021-11-17]
Bioinformatics Compute and Storage [Service] Microbial Single Cell Genomics [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Novel loss-of-function variant in DENND5A impedes melanosomal cargo transport and predisposes to familial cutaneous melanoma.
Yang M, Johnsson P, Bräutigam L, ..., Cao Y, Höiom V
Genet Med - (-) - [2021-11-17; online 2021-11-17]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
MapToCleave: High-throughput profiling of microRNA biogenesis in living cells.
Kang W, Fromm B, Houben AJ, ..., Biryukova I, Friedländer MR
Cell Rep 37 (7) 110015 [2021-11-16; online 2021-11-18]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Identification and characterization of distinct cell cycle stages in cardiomyocytes using the FUCCI transgenic system.
Baniol M, Murganti F, Smialowska A, ..., Derks W, Bergmann O
Exp. Cell Res. 408 (2) 112880 [2021-11-15; online 2021-10-14]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Plasma proteins elevated in severe asthma despite oral steroid use and unrelated to Type-2 inflammation.
Mikus MS, Kolmert J, Andersson LI, ..., U–BIOPRED (Unbiased Biomarkers for the Prediction of Respiratory Disease outcome) Study Group , BIOAIR (Longitudinal Assessment of Clinical Course and Biomarkers in Severe Chronic Airway Disease) Consortium
Eur. Respir. J. - (-) 2100142 [2021-11-04; online 2021-11-04]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Loss of Y and clonal hematopoiesis in blood-two sides of the same coin?
Ljungström V, Mattisson J, Halvardson J, ..., Baliakas P, Forsberg LA
Leukemia - (-) - [2021-11-01; online 2021-11-01]
Bioinformatics Compute and Storage [Service] Clinical Genomics Uppsala [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Small RNA Response to Infection of the Insect-Specific Lammi Virus and Hanko Virus in an Aedes albopictus Cell Line.
Öhlund P, Hayer J, Hesson JC, Blomström AL
Viruses 13 (11) - [2021-10-29; online 2021-10-29]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Massive parallel sequencing in individuals with multiple primary tumours reveals the benefit of re-analysis.
Wallander K, Thonberg H, Nilsson D, Tham E
Hered Cancer Clin Pract 19 (1) 46 [2021-10-28; online 2021-10-28]
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
Adaptive Introgression Facilitates Adaptation to High Latitudes in European Aspen (Populus tremula L.).
Rendón-Anaya M, Wilson J, Sveinsson S, ..., Street NR, Ingvarsson PK
Mol. Biol. Evol. 38 (11) 5034-5050 [2021-10-27; online 2021-07-31]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Whole-genome resequencing confirms reproductive isolation between sympatric demes of brown trout (Salmo trutta) detected with allozymes.
Saha A, Andersson A, Kurland S, ..., Ryman N, Laikre L
Mol. Ecol. - (-) - [2021-10-26; online 2021-10-26]
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
The oral microbiota of wild bears in Sweden reflects the history of antibiotic use by humans.
Brealey JC, Leitão HG, Hofstede T, Kalthoff DC, Guschanski K
Curr. Biol. 31 (20) 4650-4658.e6 [2021-10-25; online 2021-08-25]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Whole-genome Sequencing of Follicular Thyroid Carcinomas Reveal Recurrent Mutations in MicroRNA Processing Subunit DGCR8.
Paulsson JO, Rafati N, DiLorenzo S, ..., Zedenius J, Juhlin CC
J. Clin. Endocrinol. Metab. 106 (11) 3265-3282 [2021-10-21; online 2021-06-26]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Seasonal migration patterns and the maintenance of evolutionary diversity in a cryptic bird radiation.
Tang Q, Burri R, Liu Y, ..., Heckel G, Schweizer M
Mol. Ecol. - (-) - [2021-10-21; online 2021-10-21]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Transcriptome Analysis of Potato Infected with the Necrotrophic Pathogen Alternaria solani.
Brouwer SM, Brus-Szkalej M, Saripella GV, ..., Liljeroth E, Grenville-Briggs LJ
Plants (Basel) 10 (10) - [2021-10-18; online 2021-10-18]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Frailty and the risk of dementia: is the association explained by shared environmental and genetic factors?
Bai G, Wang Y, Kuja-Halkola R, ..., Hägg S, Jylhävä J
BMC Med 19 (1) 248 [2021-10-18; online 2021-10-18]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
DOI Crossref
scSPLAT, a scalable plate-based protocol for single cell WGBS library preparation
Raine A, Lundmark A, Annett A, ..., Bergin C, Nordlund J
- - (-) - [2021-10-15; online 2021-10-15]
Bioinformatics Compute and Storage [Service] Microbial Single Cell Genomics [Technology development] NGI Uppsala (SNP&SEQ Technology Platform) [Technology development] National Genomics Infrastructure [Technology development]
PubMed DOI Crossref
Spatial deconvolution of HER2-positive breast cancer delineates tumor-associated cell type interactions.
Andersson A, Larsson L, Stenbeck L, ..., Engblom C, Lundeberg J
Nat Commun 12 (1) 6012 [2021-10-14; online 2021-10-14]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Philippine Ayta possess the highest level of Denisovan ancestry in the world.
Larena M, McKenna J, Sanchez-Quinto F, ..., Endicott P, Jakobsson M
Curr. Biol. 31 (19) 4219-4230.e10 [2021-10-11; online 2021-08-12]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
HPA axis dysregulation is associated with differential methylation of CpG-sites in related genes.
Chatzittofis A, Boström ADE, Ciuculete DM, ..., Schiöth HB, Jokinen J
Sci Rep 11 (1) 20134 [2021-10-11; online 2021-10-11]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Comparison of sequencing data processing pipelines and application to underrepresented African human populations.
Breton G, Johansson ACV, Sjödin P, Schlebusch CM, Jakobsson M
BMC Bioinformatics 22 (1) 488 [2021-10-09; online 2021-10-09]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
An atlas of the Norway spruce needle seasonal transcriptome.
Bag P, Lihavainen J, Delhomme N, ..., Robinson KM, Jansson S
Plant J. - (-) - [2021-10-08; online 2021-10-08]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Transcriptomic analysis reveals pro-inflammatory signatures associated with acute myeloid leukemia progression.
Stratmann S, Yones SA, Garbulowski M, ..., Komorowski J, Holmfeldt L
Blood Adv - (-) - [2021-10-07; online 2021-10-07]
Bioinformatics Compute and Storage [Service] Clinical Genomics Uppsala [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Genome-wide association mapping uncovers sex-associated copy number variation markers and female hemizygous regions on the W chromosome in Salix viminalis.
Hallingbäck HR, Pucholt P, Ingvarsson PK, Rönnberg-Wästljung AC, Berlin S
BMC Genomics 22 (1) 710 [2021-10-02; online 2021-10-02]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Service] Bioinformatics Support, Infrastructure and Training [Service]
PubMed DOI Crossref
A cis-acting structural variation at the ZNF558 locus controls a gene regulatory network in human brain development.
Johansson PA, Brattås PL, Douse CH, ..., Eichler EE, Jakobsson J
Cell Stem Cell - (-) - [2021-10-01; online 2021-10-01]
Bioinformatics Compute and Storage [Service] Clinical Genomics Lund [Service]
PubMed DOI Crossref
The role of H3K36 methylation and associated methyltransferases in chromosome-specific gene regulation.
Lindehell H, Glotov A, Dorafshan E, Schwartz YB, Larsson J
Sci Adv 7 (40) eabh4390 [2021-10-00; online 2021-10-01]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Pregnancy-related hormones and COMT genotype: Associations with maternal working memory.
Amiel Castro R, Kunovac Kallak T, Sundström Poromaa I, ..., Ehlert U, Skalkidou A
Psychoneuroendocrinology 132 (-) 105361 [2021-10-00; online 2021-07-17]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Maternal genetic origin of the late and final Neolithic human populations from present-day Poland.
Juras A, Ehler E, Chyleński M, ..., Jakobsson M, Dabert M
Am. J. Phys. Anthropol. 176 (2) 223-236 [2021-10-00; online 2021-07-26]
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
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. 66 (10) 995-1008 [2021-10-00; online 2021-04-20]
Bioinformatics Compute and Storage [Service] Clinical Genomics Stockholm [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Genome-wide association study of liver enzyme elevation in rheumatoid arthritis patients starting methotrexate.
Sundbaum JK, Baecklund E, Eriksson N, ..., Wadelius M, Hallberg P
Pharmacogenomics 22 (15) 973-982 [2021-10-00; online 2021-09-15]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Ecologically coherent population structure of uncultivated bacterioplankton.
Sjöqvist C, Delgado LF, Alneberg J, Andersson AF
ISME J 15 (10) 3034-3049 [2021-10-00; online 2021-05-05]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
DOI Crossref
In-depth Phylogenomic Analysis of Arbuscular Mycorrhizal Fungi Based on a Comprehensive Set of de novo Genome Assemblies
Montoliu-Nerin M, Sánchez-García M, Bergin C, ..., Bever JD, Rosling A
Front. Fungal Biol. 2 (-) - [2021-09-29; online 2021-09-29]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Microbial Single Cell Genomics [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Composition and Seasonality of Membrane Transporters in Marine Picoplankton.
Hagström Å, Zweifel UL, Sundh J, ..., Müller-Karulis B, Pinhassi J
Front Microbiol 12 (-) 714732 [2021-09-28; online 2021-09-28]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Saturation mutagenesis charts the functional landscape of Salmonella ProQ and reveals a gene regulatory function of its C-terminal domain.
Rizvanovic A, Kjellin J, Söderbom F, Holmqvist E
Nucleic Acids Res. 49 (17) 9992-10006 [2021-09-27; online 2021-08-28]
Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Metabolic drift in the aging nervous system is reflected in human cerebrospinal fluid.
Peters K, Herman S, Khoonsari PE, ..., Neumann S, Kultima K
Sci Rep 11 (1) 18822 [2021-09-22; online 2021-09-22]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Avian neo-sex chromosomes reveal dynamics of recombination suppression and W degeneration.
Sigeman H, Strandh M, Proux-Wéra E, ..., Westerdahl H, Hansson B
Mol. Biol. Evol. - (-) - [2021-09-20; online 2021-09-20]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
Single-Cell Analysis Reveals Major Histocompatibility Complex II‒Expressing Keratinocytes in Pressure Ulcers with Worse Healing Outcomes.
Li D, Cheng S, Pei Y, ..., Deng Q, Xu Landén N
J. Invest. Dermatol. - (-) - [2021-09-16; online 2021-09-16]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Ancient and modern genomes unravel the evolutionary history of the rhinoceros family.
Liu S, Westbury MV, Dussex N, ..., Dalén L, Gilbert MTP
Cell 184 (19) 4874-4885.e16 [2021-09-16; online 2021-08-24]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Limited access to antigen drives generation of early B cell memory while restraining the plasmablast response.
Glaros V, Rauschmeier R, Artemov AV, ..., Busslinger M, Kreslavsky T
Immunity 54 (9) 2005-2023.e10 [2021-09-14; online 2021-09-16]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Dual RNA-seq transcriptome analysis of caecal tissue during primary Eimeria tenella infection in chickens.
Sandholt AKS, Wattrang E, Lilja T, ..., Svärd SG, Söderlund R
BMC Genomics 22 (1) 660 [2021-09-14; online 2021-09-14]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities.
Peona V, Palacios-Gimenez OM, Blommaert J, ..., Jern P, Suh A
Philos. Trans. R. Soc. Lond., B, Biol. Sci. 376 (1833) 20200186 [2021-09-13; online 2021-07-26]
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 highly-contiguous genome assembly of the Eurasian spruce bark beetle, Ips typographus, provides insight into a major forest pest.
Powell D, Groβe-Wilde E, Krokene P, ..., Andersson MN, Schlyter F
Commun Biol 4 (1) 1059 [2021-09-09; online 2021-09-09]
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
Selection on accessible chromatin regions in Capsella grandiflora.
Horvath R, Josephs EB, Pesquet E, ..., Scofield D, Slotte T
Mol. Biol. Evol. - (-) - [2021-09-08; online 2021-09-08]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Single-nuclei transcriptomes from human adrenal gland reveal distinct cellular identities of low and high-risk neuroblastoma tumors.
Bedoya-Reina OC, Li W, Arceo M, ..., Kogner P, Schlisio S
Nat Commun 12 (1) 5309 [2021-09-07; online 2021-09-07]
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
Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing.
Xiao W, Ren L, Chen Z, ..., Wang C, Shi L
Nat. Biotechnol. 39 (9) 1141-1150 [2021-09-00; online 2021-09-09]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
The genetic consequences of dog breed formation-Accumulation of deleterious genetic variation and fixation of mutations associated with myxomatous mitral valve disease in cavalier King Charles spaniels.
Axelsson E, Ljungvall I, Bhoumik P, ..., Häggström J, Lindblad-Toh K
PLoS Genet. 17 (9) e1009726 [2021-09-00; online 2021-09-02]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Positive selection plays a major role in shaping signatures of differentiation across the genomic landscape of two independent Ficedula flycatcher species pairs.
Chase MA, Ellegren H, Mugal CF
Evolution 75 (9) 2179-2196 [2021-09-00; online 2021-05-03]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Interaction between the STAT4 rs11889341(T) risk allele and smoking confers increased risk of myocardial infarction and nephritis in patients with systemic lupus erythematosus.
Reid S, Hagberg N, Sandling JK, ..., Rönnblom L, Leonard D
Ann. Rheum. Dis. 80 (9) 1183-1189 [2021-09-00; online 2021-03-25]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Genomic and transcriptomic characterization of desmoplastic small round cell tumors.
Sydow S, Versleijen-Jonkers YMH, Hansson M, ..., Flucke UE, Mertens F
Genes Chromosomes Cancer 60 (9) 595-603 [2021-09-00; online 2021-05-17]
Bioinformatics Compute and Storage [Service] Clinical Genomics Lund [Service]
DOI Crossref
Drought legacy affects microbial community trait distributions related to moisture along a savannah grassland precipitation gradient
Leizeaga A, Hicks LC, Manoharan L, Hawkes CV, Rousk J
J Ecol 109 (9) 3195-3210 [2021-09-00; online 2020-11-26]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Exploring the β-tubulin gene family in a benzimidazole-resistant Parascaris univalens population.
Martin F, Halvarsson P, Delhomme N, Höglund J, Tydén E
International Journal for Parasitology: Drugs and Drug Resistance 17 (-) 84-91 [2021-08-26; online 2021-08-26]
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
Chromoanagenesis Event Underlies a de novo Pericentric and Multiple Paracentric Inversions in a Single Chromosome Causing Coffin-Siris Syndrome.
Grochowski CM, Krepischi ACV, Eisfeldt J, ..., Lindstrand A, Carvalho CMB
Front Genet 12 (-) 708348 [2021-08-26; online 2021-08-26]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Amnion signals are essential for mesoderm formation in primates.
Yang R, Goedel A, Kang Y, ..., Niu Y, Chien KR
Nat Commun 12 (1) 5126 [2021-08-26; online 2021-08-26]
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
Pulmonary and blood dendritic cells from sarcoidosis patients more potently induce IFNγ-producing Th1 cells compared with monocytes.
Lepzien R, Nie M, Czarnewski P, ..., Grunewald J, Smed-Sörensen A
J Leukoc Biol - (-) - [2021-08-25; online 2021-08-25]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Small-scale sequencing enables quality assessment of Ribo-Seq data: an example from Arabidopsis cell culture.
Mahboubi A, Delhomme N, Häggström S, Hanson J
Plant Methods 17 (1) 92 [2021-08-24; online 2021-08-24]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Community composition of aquatic fungi across the thawing Arctic.
Kluge M, Wurzbacher C, Wauthy M, ..., Stenlid J, Peura S
Sci Data 8 (1) 221 [2021-08-19; online 2021-08-19]
Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Haplotype-Specific Expression Analysis of MHC Class II Genes in Healthy Individuals and Rheumatoid Arthritis Patients.
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Front Immunol 12 (-) 707217 [2021-08-17; online 2021-08-17]
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Microbiological Surveillance of Biogas Plants: Targeting Acetogenic Community.
Singh A, Moestedt J, Berg A, Schnürer A
Front Microbiol 12 (-) 700256 [2021-08-16; online 2021-08-16]
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Transcriptome Analysis of Post-Mortem Brain Tissue Reveals Up-Regulation of the Complement Cascade in a Subgroup of Schizophrenia Patients.
Lindholm Carlström E, Niazi A, Etemadikhah M, ..., Nilsson B, Feuk L
Genes 12 (8) - [2021-08-13; online 2021-08-13]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
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Single-cell analysis pinpoints distinct populations of cytotoxic CD4+ T cells and an IL-10+CD109+ TH2 cell population in nasal polyps.
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Sci Immunol 6 (62) - [2021-08-13; online 2021-08-15]
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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Candidatus Methylumidiphilus Drives Peaks in Methanotrophic Relative Abundance in Stratified Lakes and Ponds Across Northern Landscapes.
Martin G, Rissanen AJ, Garcia SL, ..., Buck M, Peura S
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Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Diffusible signal factor signaling controls bioleaching activity and niche protection in the acidophilic, mineral-oxidizing leptospirilli.
Bellenberg S, Salas B, Ganji S, ..., Dopson M, Vera M
Sci Rep 11 (1) 16275 [2021-08-11; online 2021-08-11]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Genomic profile - a possible diagnostic and prognostic marker in upper tract urothelial carcinoma.
Grahn A, Eisfeldt J, Malm C, ..., Tham E, Brehmer M
BJU Int. - (-) - [2021-08-10; online 2021-08-10]
Bioinformatics Compute and Storage [Service] Clinical Genomics Stockholm [Service]
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Mutational patterns and clonal evolution from diagnosis to relapse in pediatric acute lymphoblastic leukemia.
Sayyab S, Lundmark A, Larsson M, ..., Nordlund J, Syvänen A
Sci Rep 11 (1) 15988 [2021-08-06; online 2021-08-06]
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Complete Genome Sequence and Methylome of the Type Strain of Shewanella algae.
Tellgren-Roth C, Thorell K, Galperin MY, ..., Sjöling Å, Martín-Rodríguez AJ
Microbiol Resour Announc 10 (31) e0055921 [2021-08-05; online 2021-08-05]
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Single-cell multimodal analysis in a case with reduced penetrance of Progranulin-Frontotemporal Dementia.
Natarajan K, Eisfeldt J, Hammond M, ..., Öijerstedt L, Graff C
Acta Neuropathol Commun 9 (1) 132 [2021-08-03; online 2021-08-03]
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PopulusPtERF85 Balances Xylem Cell Expansion and Secondary Cell Wall Formation in Hybrid Aspen.
Seyfferth C, Wessels BA, Vahala J, ..., Tuominen H, Lundberg-Felten J
Cells 10 (8) 1971 [2021-08-03; online 2021-08-03]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Terrestrial dissolved organic matter inflow drives temporal dynamics of the bacterial community of a subarctic estuary (northern Baltic Sea).
Figueroa D, Capo E, Lindh MV, ..., Pinhassi J, Andersson A
Environ. Microbiol. 23 (8) 4200-4213 [2021-08-00; online 2021-06-01]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Long- and short-read metabarcoding technologies reveal similar spatiotemporal structures in fungal communities.
Furneaux B, Bahram M, Rosling A, Yorou NS, Ryberg M
Mol Ecol Resour 21 (6) 1833-1849 [2021-08-00; online 2021-05-06]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
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Genomic inference of contemporary effective population size in a large island population of collared flycatchers (Ficedula albicollis).
Nadachowska-Brzyska K, Dutoit L, Smeds L, ..., Gustafsson L, Ellegren H
Mol. Ecol. 30 (16) 3965-3973 [2021-08-00; online 2021-07-01]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Dynamics of Baltic Sea phages driven by environmental changes.
Hoetzinger M, Nilsson E, Arabi R, ..., Middelboe M, Holmfeldt K
Environ. Microbiol. 23 (8) 4576-4594 [2021-08-00; online 2021-07-07]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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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. 38 (8) 3126-3143 [2021-07-29; online 2021-04-07]
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Single-cell analysis of mosquito hemocytes identifies signatures of immune cell subtypes and cell differentiation.
Kwon H, Mohammed M, Franzén O, Ankarklev J, Smith RC
Elife 10 (-) - [2021-07-28; online 2021-07-28]
Bioinformatics Compute and Storage [Service] Eukaryotic Single Cell Genomics (ESCG) [Service] Microbial Single Cell Genomics NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Genome-scale metabolic network reconstruction of model animals as a platform for translational research.
Wang H, Robinson JL, Kocabas P, ..., Zetterberg H, Nielsen J
Proc. Natl. Acad. Sci. U.S.A. 118 (30) e2102344118 [2021-07-27; online 2021-07-21]
Bioinformatics Compute and Storage [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] Systems Biology [Technology development]
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Genome of Peştera Muierii skull shows high diversity and low mutational load in pre-glacial Europe.
Svensson E, Günther T, Hoischen A, ..., Netea MG, Jakobsson M
Curr. Biol. 31 (14) 2973-2983.e9 [2021-07-26; online 2021-05-18]
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Bifidobacteria-mediated immune system imprinting early in life.
Henrick BM, Rodriguez L, Lakshmikanth T, ..., Frese SA, Brodin P
Cell 184 (15) 3884-3898.e11 [2021-07-22; online 2021-06-17]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] Cellular Immunomonitoring [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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A search for modifying genetic factors in CHEK2:c.1100delC breast cancer patients.
Wendt C, Muranen TA, Mielikäinen L, ..., Borg Å, Lindblom A
Sci Rep 11 (1) 14763 [2021-07-20; online 2021-07-20]
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DNA Methylation-Based Interferon Scores Associate With Sub-Phenotypes in Primary Sjögren's Syndrome.
Imgenberg-Kreuz J, Sandling JK, Norheim KB, ..., Eloranta ML, Nordmark G
Front Immunol 12 (-) 702037 [2021-07-16; online 2021-07-16]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]
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Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater.
Mehrshad M, Lopez-Fernandez M, Sundh J, ..., Bertilsson S, Dopson M
Nat Commun 12 (1) 4253 [2021-07-12; online 2021-07-12]
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Genomic Predictions With Nonadditive Effects Improved Estimates of Additive Effects and Predictions of Total Genetic Values in Pinus sylvestris.
Calleja-Rodriguez A, Chen Z, Suontama M, Pan J, Wu HX
Front Plant Sci 12 (-) 666820 [2021-07-07; online 2021-07-07]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Common and mutation specific phenotypes of KRAS and BRAF mutations in colorectal cancer cells revealed by integrative -omics analysis.
Kundu S, Ali MA, Handin N, ..., Globisch D, Sjöblom T
J. Exp. Clin. Cancer Res. 40 (1) 225 [2021-07-07; online 2021-07-07]
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High-Quality Genome Assembly and Comprehensive Transcriptome of the Painted Lady Butterfly Vanessa cardui.
Zhang L, Steward RA, Wheat CW, Reed RD
Genome Biol Evol 13 (7) - [2021-07-06; online 2021-07-21]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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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 41 (7) 1230-1246 [2021-07-05; online 2021-01-09]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Whole genome sequencing reveals high differentiation, low levels of genetic diversity and short runs of homozygosity among Swedish wels catfish.
Jensen A, Lillie M, Bergström K, Larsson P, Höglund J
Heredity (Edinb) 127 (1) 79-91 [2021-07-00; online 2021-05-07]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Variants in BANK1 are associated with lupus nephritis of European ancestry.
Bolin K, Imgenberg-Kreuz J, Leonard D, ..., Rönnblom L, Nordmark G
Genes Immun. 22 (3) 194-202 [2021-07-00; online 2021-06-14]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]
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The genomics of phenotypically differentiated Asellus aquaticus cave, surface stream and lake ecotypes.
Bakovic V, Martin Cerezo ML, Höglund A, ..., Hargeby A, Wright D
Mol. Ecol. 30 (14) 3530-3547 [2021-07-00; online 2021-06-08]
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 CUT&Tag profiles histone modifications and transcription factors in complex tissues.
Bartosovic M, Kabbe M, Castelo-Branco G
Nat. Biotechnol. 39 (7) 825-835 [2021-07-00; online 2021-04-12]
Bioinformatics Compute and Storage [Service] Eukaryotic Single Cell Genomics (ESCG) [Collaborative] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Severe COVID-19 in an APS1 patient with interferon autoantibodies treated with plasmapheresis.
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J. Allergy Clin. Immunol. 148 (1) 96-98 [2021-07-00; online 2021-04-16]
Autoimmunity and Serology Profiling [Service] Bioinformatics Compute and Storage [Service] Cellular Immunomonitoring [Collaborative]
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Quality of phytoplankton deposition structures bacterial communities at the water-sediment interface.
Izabel-Shen D, Albert S, Winder M, Farnelid H, Nascimento FJA
Mol. Ecol. 30 (14) 3515-3529 [2021-07-00; online 2021-06-11]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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On the origin of the widespread self-compatible allotetraploid Capsella bursa-pastoris (Brassicaceae).
Bachmann JA, Tedder A, Fracassetti M, ..., Köhler C, Slotte T
Heredity (Edinb) 127 (1) 124-134 [2021-07-00; online 2021-04-19]
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) [Service] National Genomics Infrastructure [Service]
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Monocytes in sarcoidosis are potent tumour necrosis factor producers and predict disease outcome.
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Eur. Respir. J. 58 (1) 2003468 [2021-07-00; online 2021-07-22]
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Molecular evaluation of five different isolation methods for extracellular vesicles reveals different clinical applicability and subcellular origin.
Veerman RE, Teeuwen L, Czarnewski P, ..., Gabrielsson S, Eldh M
J Extracell Vesicles 10 (9) e12128 [2021-07-00; online 2021-07-22]
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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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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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. 30 (13) 3023-3039 [2021-07-00; online 2020-08-19]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Genomic signatures of rapid adaptive divergence in a tropical montane species.
Ericson PGP, Irestedt M, She H, Qu Y
Biol. Lett. 17 (7) 20210089 [2021-07-00; online 2021-07-28]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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A single-cell type transcriptomics map of human tissues.
Karlsson M, Zhang C, Méar L, ..., Uhlén M, Lindskog C
Sci Adv 7 (31) eabh2169 [2021-07-00; online 2021-07-28]
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Towards Bioleaching of a Vanadium Containing Magnetite for Metal Recovery.
Bellenberg S, Turner S, Seidel L, ..., Leiviskä T, Dopson M
Front Microbiol 12 (-) 693615 [2021-06-30; online 2021-06-30]
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DNA metabarcoding reveals trophic niche diversity of micro and mesozooplankton species.
Novotny A, Zamora-Terol S, Winder M
Proc. Biol. Sci. 288 (1953) 20210908 [2021-06-30; online 2021-06-16]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Genomic and Phenotypic Evolution of Achromobacter xylosoxidans during Chronic Airway Infections of Patients with Cystic Fibrosis.
Khademi SMH, Gabrielaite M, Paulsson M, ..., Marvig RL, Påhlman LI
mSystems - (-) e0052321 [2021-06-29; online 2021-06-29]
Bioinformatics Compute and Storage [Service] Clinical Genomics Lund [Service]
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Whole-Genome Metagenomic Analysis of the Gut Microbiome in HIV-1-Infected Individuals on Antiretroviral Therapy.
Bai X, Narayanan A, Nowak P, ..., Neogi U, Sönnerborg A
Front Microbiol 12 (-) 667718 [2021-06-25; online 2021-06-25]
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Functional differences between TSHR alleles associate with variation in spawning season in Atlantic herring.
Chen J, Bi H, Pettersson ME, ..., Scheerer P, Andersson L
Commun Biol 4 (1) 795 [2021-06-25; online 2021-06-25]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Toll-like receptor 4 methylation grade is linked to depressive symptom severity.
Rasmusson AJ, Gallwitz M, Soltanabadi B, ..., Schiöth HB, Cunningham JL
Transl Psychiatry 11 (1) 371 [2021-06-24; online 2021-06-24]
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Profiling temporal dynamics of acetogenic communities in anaerobic digesters using next-generation sequencing and T-RFLP.
Singh A, Müller B, Schnürer A
Sci Rep 11 (1) 13298 [2021-06-24; online 2021-06-24]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Differential DNA Methylation of the Genes for Amyloid Precursor Protein, Tau, and Neurofilaments in Human Traumatic Brain Injury.
Abu Hamdeh S, Ciuculete DM, Sarkisyan D, ..., Schiöth HB, Marklund N
J. Neurotrauma 38 (12) 1679-1688 [2021-06-15; online 2021-01-08]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Leveraging breeding programs and genomic data in Norway spruce (Picea abies L. Karst) for GWAS analysis.
Chen ZQ, Zan Y, Milesi P, ..., Lascoux M, Wu HX
Genome Biol. 22 (1) 179 [2021-06-13; online 2021-06-13]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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DNA Methylation Signatures Predict Cytogenetic Subtype and Outcome in Pediatric Acute Myeloid Leukemia (AML).
Krali O, Palle J, Bäcklin CL, ..., Zeller B, Nordlund J
Genes 12 (6) 895 [2021-06-10; online 2021-06-10]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]
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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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Reinforcing one-carbon metabolism via folic acid/Folr1 promotes β-cell differentiation.
Karampelias C, Rezanejad H, Rosko M, ..., Korbutt GS, Andersson O
Nat Commun 12 (1) 3362 [2021-06-07; online 2021-06-07]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Atg7 deficiency in microglia drives an altered transcriptomic profile associated with an impaired neuroinflammatory response.
Friess L, Cheray M, Keane L, Grabert K, Joseph B
Mol Brain 14 (1) 87 [2021-06-03; online 2021-06-03]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Methylome and transcriptome signature of bronchoalveolar cells from multiple sclerosis patients in relation to smoking.
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Mult. Scler. 27 (7) 1014-1026 [2021-06-00; online 2020-07-30]
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Large-scale identification of protein histidine methylation in human cells.
Kapell S, Jakobsson ME
NAR Genom Bioinform 3 (2) lqab045 [2021-06-00; online 2021-05-22]
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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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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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 (NY) 23 (3) 402-416 [2021-06-00; online 2021-05-01]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Divergent clonal differentiation trajectories establish CD8+ memory T cell heterogeneity during acute viral infections in humans.
Mold JE, Modolo L, Hård J, ..., Michaëlsson J, Frisén J
Cell Rep 35 (8) 109174 [2021-05-25; online 2021-05-27]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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A combined approach for single-cell mRNA and intracellular protein expression analysis.
Reimegård J, Tarbier M, Danielsson M, ..., Friedländer MR, Gallant CJ
Commun Biol 4 (1) 624 [2021-05-25; online 2021-05-25]
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Stromal Heterogeneity in the Human Proliferative Endometrium-A Single-Cell RNA Sequencing Study.
Queckbörner S, von Grothusen C, Boggavarapu NR, ..., Davies LC, Gemzell-Danielsson K
J Pers Med 11 (6) - [2021-05-22; online 2021-05-22]
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Virus Diversity and Loads in Crickets Reared for Feed: Implications for Husbandry.
de Miranda JR, Granberg F, Low M, ..., Jansson A, Berggren Å
Front Vet Sci 8 (-) 642085 [2021-05-20; online 2021-05-20]
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Size Variation of the Nonrecombining Region on the Mating-Type Chromosomes in the Fungal Podospora anserina Species Complex.
Hartmann FE, Ament-Velásquez SL, Vogan AA, ..., Silar P, Giraud T
Mol. Biol. Evol. 38 (6) 2475-2492 [2021-05-19; online 2021-02-09]
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X-chromosome variants are associated with aldosterone producing adenomas.
Dutta RK, Larsson M, Arnesen T, ..., Gimm O, Söderkvist P
Sci Rep 11 (1) 10562 [2021-05-18; online 2021-05-18]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Clinical Genomics Linköping [Service]
PubMed DOI Crossref
Pulmonary fibrosis in relation to genetic loci in an inception cohort of patients with early rheumatoid arthritis from northern Sweden.
Jönsson E, Ljung L, Norrman E, ..., Dahlqvist J, Dahlqvist SR
Rheumatology (Oxford) - (-) - [2021-05-16; online 2021-05-16]
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Comprehensive dataset of shotgun metagenomes from oxygen stratified freshwater lakes and ponds.
Buck M, Garcia SL, Fernandez L, ..., Bertilsson S, Peura S
Sci Data 8 (1) 131 [2021-05-14; online 2021-05-14]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Freshwater Chlorobia Exhibit Metabolic Specialization among Cosmopolitan and Endemic Populations.
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mSystems 6 (3) - [2021-05-11; online 2021-05-11]
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The Genetic Variation of Lactase Persistence Alleles in Sudan and South Sudan.
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Genome Biol Evol 13 (5) - [2021-05-07; online 2021-03-25]
Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
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The Effects of GC-Biased Gene Conversion on Patterns of Genetic Diversity among and across Butterfly Genomes.
Boman J, Mugal CF, Backström N
Genome Biol Evol 13 (5) - [2021-05-07; online 2021-03-25]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
How to Make a Rodent Giant: Genomic Basis and Tradeoffs of Gigantism in the Capybara, the World's Largest Rodent.
Herrera-Álvarez S, Karlsson E, Ryder OA, Lindblad-Toh K, Crawford AJ
Mol. Biol. Evol. 38 (5) 1715-1730 [2021-05-04; online 2020-11-11]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Activation of endogenous retroviruses during brain development causes an inflammatory response.
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EMBO J. 40 (9) e106423 [2021-05-03; online 2021-03-01]
Bioinformatics Compute and Storage [Service] Clinical Genomics Lund [Service]
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Tissue-specific transcriptional imprinting and heterogeneity in human innate lymphoid cells revealed by full-length single-cell RNA-sequencing.
Mazzurana L, Czarnewski P, Jonsson V, ..., Almer S, Mjösberg J
Cell Res 31 (5) 554-568 [2021-05-00; online 2021-01-08]
Bioinformatics Compute and Storage [Service] 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
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The Enterprise, a massive transposon carrying Spok meiotic drive genes.
Vogan AA, Ament-Velásquez SL, Bastiaans E, ..., Suh A, Johannesson H
Genome Res. 31 (5) 789-798 [2021-05-00; online 2021-04-19]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Stem girdling affects the onset of autumn senescence in aspen in interaction with metabolic signals.
Lihavainen J, Edlund E, Björkén L, ..., Robinson KM, Jansson S
Physiol Plantarum 172 (1) 201-217 [2021-05-00; online 2021-01-07]
Bioinformatics Compute and Storage [Service] Swedish Metabolomics Centre (SMC) [Service]
PubMed DOI Crossref
Single-cell transcriptomics of human embryos identifies multiple sympathoblast lineages with potential implications for neuroblastoma origin.
Kameneva P, Artemov AV, Kastriti ME, ..., Kharchenko PV, Adameyko I
Nat. Genet. 53 (5) 694-706 [2021-05-00; online 2021-04-08]
Bioinformatics Compute and Storage [Service] Eukaryotic Single Cell Genomics (ESCG)
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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. 58 (5) 351-356 [2021-05-00; online 2020-06-26]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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In vivo screen identifies a SIK inhibitor that induces β cell proliferation through a transient UPR.
Charbord J, Ren L, Sharma RB, ..., Alonso LC, Andersson O
Nat Metab 3 (5) 682-700 [2021-05-00; online 2021-05-20]
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Hybrid sequencing resolves two germline ultra-complex chromosomal rearrangements consisting of 137 breakpoint junctions in a single carrier.
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]
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Histological and transcriptional characterization of the pancreatic acinar tissue in type 1 diabetes.
Granlund L, Hedin A, Wahlhütter M, ..., Skog O, Lundberg M
BMJ Open Diabetes Res Care 9 (1) - [2021-05-00; online 2021-05-26]
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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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Comparison of DNA Methylation Profiles of Hemostatic Genes between Liver Tissue and Peripheral Blood within Individuals.
Olsson Lindvall M, Angerfors A, Andersson B, ..., Stanne TM, Jern C
Thromb. Haemost. 121 (5) 573-583 [2021-05-00; online 2020-11-17]
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Complete Genome Sequence of an Antimicrobial-Producing Bacillus velezensis Sam8H1 Isolate from the Makgadikgadi Saltpans of Botswana.
Modikwe G, Manoharan L, Mabutho G, ..., Lebogang L, Zhou N
Microbiol Resour Announc 10 (17) - [2021-04-29; online 2021-04-29]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Small noncoding RNA profiling across cellular and biofluid compartments and their implications for multiple sclerosis immunopathology.
Zheleznyakova GY, Piket E, Needhamsen M, ..., Piehl F, Jagodic M
Proc. Natl. Acad. Sci. U.S.A. 118 (17) e2011574118 [2021-04-27; online 2021-04-22]
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PubMed DOI Crossref
An introgressed gene causes meiotic drive in Neurospora sitophila.
Svedberg J, Vogan AA, Rhoades NA, ..., Hammond TM, Johannesson H
Proc. Natl. Acad. Sci. U.S.A. 118 (17) e2026605118 [2021-04-27; online 2021-04-21]
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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]
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Divergent airway microbiomes in lung transplant recipients with or without pulmonary infection.
Påhlman LI, Manoharan L, Aspelund AS
Respir. Res. 22 (1) 118 [2021-04-23; online 2021-04-23]
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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]
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Epigenome-wide association study of level and change in cognitive abilities from midlife through late life.
Karlsson IK, Ericsson M, Wang Y, ..., Reynolds CA, Pedersen NL
Clin Epigenetics 13 (1) 85 [2021-04-21; online 2021-04-21]
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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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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A QTL for conformation of back and croup influences lateral gait quality in Icelandic horses.
Rosengren MK, Sigurðardóttir H, Eriksson S, ..., Solé M, Lindgren G
BMC Genomics 22 (1) 267 [2021-04-14; online 2021-04-14]
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DNA methylation in cord blood in association with prenatal depressive symptoms.
Kallak TK, Bränn E, Fransson E, ..., Lyle R, Skalkidou A
Clin Epigenetics 13 (1) 78 [2021-04-12; online 2021-04-12]
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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]
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Monoallelic and bi-allelic variants in NCDN cause neurodevelopmental delay, intellectual disability, and epilepsy.
Fatima A, Hoeber J, Schuster J, ..., Klar J, Dahl N
Am. J. Hum. Genet. 108 (4) 739-748 [2021-04-01; online 2021-03-11]
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The heart microbiome of insectivorous bats from Central and South Eastern Europe.
Corduneanu A, Mihalca AD, Sándor AD, ..., Viso NP, Bongcam-Rudloff E
Comp Immunol Microbiol Infect Dis 75 (-) 101605 [2021-04-00; online 2021-01-07]
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The effects of drift and selection on latitudinal genetic variation in Scandinavian common toads (Bufo bufo) following postglacial recolonisation.
Thörn F, Rödin-Mörch P, Cortazar-Chinarro M, ..., Laurila A, Höglund J
Heredity (Edinb) 126 (4) 656-667 [2021-04-00; online 2021-02-09]
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Novel Mutation m.10372A>G in MT-ND3 Causing Sensorimotor Axonal Polyneuropathy.
Bruhn H, Samuelsson K, Schober FA, ..., Wedell A, Wredenberg A
Neurol Genet 7 (2) e566 [2021-04-00; online 2021-03-15]
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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Life-Time Covariation of Major Cardiovascular Diseases: A 40-Year Longitudinal Study and Genetic Studies.
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Circ Genom Precis Med 14 (2) e002963 [2021-04-00; online 2021-02-26]
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Immune cells lacking Y chromosome show dysregulation of autosomal gene expression.
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Cell. Mol. Life Sci. 78 (8) 4019-4033 [2021-04-00; online 2021-04-10]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
Development of a highly efficient 50K single nucleotide polymorphism genotyping array for the large and complex genome of Norway spruce (Picea abies L. Karst) by whole genome resequencing and its transferability to other spruce species.
Bernhardsson C, Zan Y, Chen Z, Ingvarsson PK, Wu HX
Mol Ecol Resour 21 (3) 880-896 [2021-04-00; online 2020-12-02]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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A modified protein marker panel to identify four consensus molecular subtypes in colorectal cancer using immunohistochemistry.
Li X, Larsson P, Ljuslinder I, ..., Edin S, Palmqvist R
Pathol Res Pract 220 (-) 153379 [2021-04-00; online 2021-03-05]
Bioinformatics Compute and Storage [Service] Clinical Genomics Umeå [Collaborative]
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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) e2012398118 [2021-03-30; online 2021-03-24]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Estrogen Receptor Beta Influences the Inflammatory p65 Cistrome in Colon Cancer Cells.
Indukuri R, Hases L, Archer A, Williams C
Front Endocrinol (Lausanne) 12 (-) 650625 [2021-03-30; online 2021-03-30]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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High-Throughput and Automated Acoustic Trapping of Extracellular Vesicles to Identify microRNAs With Diagnostic Potential for Prostate Cancer.
Ku A, Fredsøe J, Sørensen KD, ..., Lilja H, Ceder Y
Front Oncol 11 (-) 631021 [2021-03-25; online 2021-03-25]
Bioinformatics Compute and Storage [Service] Clinical Genomics Lund [Service]
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PRDM16 regulates a temporal transcriptional program to promote progression of cortical neural progenitors.
He L, Jones J, He W, ..., Wen J, Dai Q
Development 148 (6) - [2021-03-17; online 2021-03-17]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Transcriptional analysis of islets of Langerhans from organ donors of different ages.
Seiron P, Stenwall A, Hedin A, ..., Lundberg M, Skog O
PLoS ONE 16 (3) e0247888 [2021-03-12; online 2021-03-12]
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The Fennoscandian Shield deep terrestrial virosphere suggests slow motion 'boom and burst' cycles.
Holmfeldt K, Nilsson E, Simone D, ..., Bertilsson S, Dopson M
Commun Biol 4 (1) 307 [2021-03-08; online 2021-03-08]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Single cell transcriptomics of primate sensory neurons identifies cell types associated with chronic pain.
Kupari J, Usoskin D, Parisien M, ..., Diatchenko L, Ernfors P
Nat Commun 12 (1) 1510 [2021-03-08; online 2021-03-08]
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PubMed DOI Crossref
Effluent solids recirculation to municipal sludge digesters enhances long-chain fatty acids degradation capacity.
Shakeri Yekta S, Liu T, Mendes Anacleto T, ..., Björn A, Schnürer A
Biotechnol Biofuels 14 (1) 56 [2021-03-04; online 2021-03-04]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Divergence in Coding Sequence and Expression of Different Functional Categories of Immune Genes between Two Wild Rodent Species.
Zhong X, Lundberg M, Råberg L
Genome Biol Evol 13 (3) - [2021-03-01; online 2021-02-11]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Whole-genome analyses provide no evidence for dog introgression in Fennoscandian wolf populations.
Smeds L, Aspi J, Berglund J, ..., Tirronen K, Ellegren H
Evol Appl 14 (3) 721-734 [2021-03-00; online 2020-11-09]
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RNA transcript response by an Acidithiobacillus spp. mixed culture reveals adaptations to growth on arsenopyrite.
Barragán CE, Márquez MA, Dopson M, Montoya D
Extremophiles 25 (2) 143-158 [2021-03-00; online 2021-02-22]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Plasma metabolomics of presymptomatic PSEN1-H163Y mutation carriers: a pilot study.
Natarajan K, Ullgren A, Khoshnood B, ..., Blennow K, Graff C
Ann Clin Transl Neurol 8 (3) 579-591 [2021-03-00; online 2021-01-21]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] Swedish Metabolomics Centre (SMC) [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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Escherichia coli EC93 deploys two plasmid-encoded class I contact-dependent growth inhibition systems for antagonistic bacterial interactions.
Wäneskog M, Halvorsen T, Filek K, ..., Poole SJ, Koskiniemi S
Microb Genom 7 (3) - [2021-03-00; online 2021-03-01]
Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
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Challenging conventional karyotyping by next-generation karyotyping in 281 intensively treated patients with AML.
Mareschal S, Palau A, Lindberg J, ..., Grönberg H, Lehmann S
Blood Adv 5 (4) 1003-1016 [2021-02-23; online 2021-02-17]
Bioinformatics Compute and Storage [Service] Clinical Genomics Uppsala [Collaborative]
PubMed DOI Crossref
Sheep nemabiome diversity and its response to anthelmintic treatment in Swedish sheep herds.
Halvarsson P, Höglund J
Parasit Vectors 14 (1) 114 [2021-02-18; online 2021-02-18]
Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Characterization of the nuclear and cytosolic transcriptomes in human brain tissue reveals new insights into the subcellular distribution of RNA transcripts.
Zaghlool A, Niazi A, Björklund ÅK, ..., Ameur A, Feuk L
Sci Rep 11 (1) 4076 [2021-02-18; online 2021-02-18]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
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 Compute and Storage [Service] 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
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]
Bioinformatics Compute and Storage [Service] Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Combined removal of organic micropollutants and ammonium in reactive barriers developed for managed aquifer recharge.
Modrzyński JJ, Aamand J, Wittorf L, ..., Hallin S, Albers CN
Water Res. 190 (-) 116669 [2021-02-15; online 2020-11-25]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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]
Bioinformatics Compute and Storage [Service] 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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
A novel canine reference genome resolves genomic architecture and uncovers transcript complexity.
Wang C, Wallerman O, Arendt ML, ..., Meadows JRS, Lindblad-Toh K
Commun Biol 4 (1) 185 [2021-02-10; online 2021-02-10]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
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Genomic characterization of relapsed acute myeloid leukemia reveals novel putative therapeutic targets.
Stratmann S, Yones SA, Mayrhofer M, ..., Cavelier L, Holmfeldt L
Blood Adv 5 (3) 900-912 [2021-02-09; online 2021-02-10]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Clinical Genomics Uppsala [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
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Cell-free tumour DNA analysis detects copy number alterations in gastro-oesophageal cancer patients.
Wallander K, Eisfeldt J, Lindblad M, ..., Liedén A, Tham E
PLoS ONE 16 (2) e0245488 [2021-02-04; online 2021-02-04]
Bioinformatics Compute and Storage [Service] Clinical Genomics Stockholm [Service]
PubMed DOI Crossref
Genomic Evidence of an Ancient East Asian Divergence Event in Wild Saccharomyces cerevisiae.
Bendixsen DP, Gettle N, Gilchrist C, Zhang Z, Stelkens R
Genome Biol Evol 13 (2) - [2021-02-03; online 2021-01-13]
Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
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Isolation of high-yield and -quality RNA from human precision-cut lung slices for RNA-sequencing and computational integration with larger patient cohorts.
Stegmayr J, Alsafadi HN, Langwiński W, ..., Leigh ND, Wagner DE
Am J Physiol Lung Cell Mol Physiol 320 (2) L232-L240 [2021-02-01; online 2020-10-28]
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PubMed DOI Crossref
The one-carbon pool controls mitochondrial energy metabolism via complex I and iron-sulfur clusters.
Schober FA, Moore D, Atanassov I, ..., Freyer C, Wredenberg A
Sci Adv 7 (8) - [2021-02-00; online 2021-02-19]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Taste perception and lifestyle: insights from phenotype and genome data among Africans and Asians.
Sjöstrand AE, Sjödin P, Hegay T, ..., Heyer E, Jakobsson M
Eur. J. Hum. Genet. 29 (2) 325-337 [2021-02-00; online 2020-10-01]
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PubMed DOI Crossref
Small-scale population divergence is driven by local larval environment in a temperate amphibian.
Rödin-Mörch P, Palejowski H, Cortazar-Chinarro M, ..., Höglund J, Laurila A
Heredity (Edinb) 126 (2) 279-292 [2021-02-00; online 2020-09-21]
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PubMed DOI Crossref
Single nucleus transcriptomics data integration recapitulates the major cell types in human liver.
Diamanti K, Inda Díaz JS, Raine A, ..., Wadelius C, Cavalli M
Hepatol Res 51 (2) 233-238 [2021-02-00; online 2020-11-28]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
Hybrid seed incompatibility in Capsella is connected to chromatin condensation defects in the endosperm.
Dziasek K, Simon L, Lafon-Placette C, ..., Slotte T, Köhler C
PLoS Genet. 17 (2) e1009370 [2021-02-00; online 2021-02-11]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Genome-wide single nucleotide polymorphism markers reveal population structure and dispersal direction of an expanding nuisance algal bloom species.
Rengefors K, Gollnisch R, Sassenhagen I, ..., Bassham S, Ahrén D
Mol. Ecol. 30 (4) 912-925 [2021-02-00; online 2021-01-20]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Comparative genomics highlights the importance of drug efflux transporters during evolution of mycoparasitism in Clonostachys subgenus Bionectria (Fungi, Ascomycota, Hypocreales).
Broberg M, Dubey M, Iqbal M, ..., Brandström Durling M, Karlsson M
Evol Appl 14 (2) 476-497 [2021-02-00; online 2020-09-28]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
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A recently isolated human commensal Escherichia coli ST10 clone member mediates enhanced thermotolerance and tetrathionate respiration on a P1 phage-derived IncY plasmid.
Kamal SM, Cimdins-Ahne A, Lee C, ..., Mogk A, Römling U
Mol. Microbiol. 115 (2) 255-271 [2021-02-00; online 2020-10-12]
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 heterozygous variant in FGF9 associated with previously unreported features of multiple synostosis syndrome 3.
Thuresson AC, Croft B, Hailer YD, ..., Harley VR, Stattin EL
Clin. Genet. 99 (2) 325-329 [2021-02-00; online 2020-11-12]
Bioinformatics Compute and Storage [Service] Clinical Genomics Uppsala [Service]
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) 1354 [2021-01-29; online 2021-01-29]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Ecological adaptation in European eels is based on phenotypic plasticity.
Enbody ED, Pettersson ME, Sprehn CG, ..., Wickström H, Andersson L
Proc. Natl. Acad. Sci. U.S.A. 118 (4) e2022620118 [2021-01-26; online 2021-01-23]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Temporal changes in DNA methylation and RNA expression in a small song bird: within- and between-tissue comparisons.
Lindner M, Verhagen I, Viitaniemi HM, ..., Husby A, van Oers K
BMC Genomics 22 (1) 36 [2021-01-07; online 2021-01-07]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Post-treatment of dewatered digested sewage sludge by thermophilic high-solid digestion for pasteurization with positive energy output.
Nordell E, Moestedt J, Österman J, ..., Sun L, Schnürer A
Waste Management 119 (-) 11-21 [2021-01-01; online 2020-10-05]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Variable degree of mosaicism for tetrasomy 18p in phenotypically discordant monozygotic twins-Diagnostic implications.
Rydzanicz M, Olszewski P, Kedra D, ..., Dumanski JP, Płoski R
Mol Genet Genomic Med 9 (1) e1526 [2021-01-00; online 2020-12-14]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
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Urbanization is associated with modifications in DNA methylation in a small passerine bird.
Watson H, Powell D, Salmón P, Jacobs A, Isaksson C
Evol Appl 14 (1) 85-98 [2021-01-00; online 2020-11-13]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Severe congenital neutropenia-associated JAGN1 mutations unleash a calpain-dependent cell death programme in myeloid cells.
Khandagale A, Holmlund T, Entesarian M, ..., Nordenskjöld M, Fadeel B
Br. J. Haematol. 192 (1) 200-211 [2021-01-00; online 2020-11-18]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Molecular pathways in patients with systemic lupus erythematosus revealed by gene-centred DNA sequencing.
Sandling JK, Pucholt P, Hultin Rosenberg L, ..., Lindblad-Toh K, Rönnblom L
Ann. Rheum. Dis. 80 (1) 109-117 [2021-01-00; online 2020-10-09]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]
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Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird-of-paradise.
Peona V, Blom MPK, Xu L, ..., Irestedt M, Suh A
Mol Ecol Resour 21 (1) 263-286 [2021-01-00; online 2020-10-10]
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 (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
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Human population dynamics and Yersinia pestis in ancient northeast Asia.
Kılınç GM, Kashuba N, Koptekin D, ..., Storå J, Götherström A
Sci Adv 7 (2) - [2021-01-00; online 2021-01-06]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Host plant diet affects growth and induces altered gene expression and microbiome composition in the wood white (Leptidea sinapis) butterfly.
Näsvall K, Wiklund C, Mrazek V, ..., Vila R, Backström N
Mol. Ecol. 30 (2) 499-516 [2021-01-00; online 2020-12-14]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Evaluating totipotency using criteria of increasing stringency.
Posfai E, Schell JP, Janiszewski A, ..., Lanner F, Rossant J
Nat Cell Biol 23 (1) 49-60 [2021-01-00; online 2021-01-08]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Diversification of molecularly defined myenteric neuron classes revealed by single-cell RNA sequencing.
Morarach K, Mikhailova A, Knoflach V, ..., Ernfors P, Marklund U
Nat. Neurosci. 24 (1) 34-46 [2021-01-00; online 2020-12-07]
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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Crown‐fire severity is more important than ground‐fire severity in determining soil fungal community development in the boreal forest
Pérez‐Izquierdo L, Clemmensen KE, Strengbom J, ..., Nilsson M, Lindahl BD
J Ecol 109 (1) 504-518 [2021-01-00; online 2020-11-00]
Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
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BL1391: an established cell line from a human malignant peripheral nerve sheath tumor with unique genomic features.
Tolomeo D, Agostini A, Macchia G, ..., Mertens F, Storlazzi CT
Hum Cell 34 (1) 238-245 [2021-01-00; online 2020-08-27]
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A Tribute to Professor Per Artursson - Scientist, Explorer, Mentor, Innovator, and Giant in Pharmaceutical Research.
Matsson P, Baranczewski P, Giacomini KM, ..., Charman WN, Bergström CAS
J Pharm Sci 110 (1) 2-11 [2021-01-00; online 2020-10-21]
Bioinformatics Compute and Storage [Service] Drug Discovery and Development (DDD) [Collaborative]

Year 2020

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Defining eligible patients for allele-selective chemotherapies targeting NAT2 in colorectal cancer.
Rendo V, Kundu S, Rameika N, ..., Stoimenov I, Sjöblom T
Sci Rep 10 (1) 22436 [2020-12-31; online 2020-12-31]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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The Bactericidal Fatty Acid Mimetic 2CCA-1 Selectively Targets Pneumococcal Extracellular Polyunsaturated Fatty Acid Metabolism.
Reithuber E, Nannapaneni P, Rzhepishevska O, ..., Henriques-Normark B, Mellroth P
MBio 11 (6) e03027-20 [2020-12-15; online 2020-12-15]
Bioinformatics Compute and Storage [Service] Swedish Metabolomics Centre (SMC) [Service]
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Hodgkin Lymphoma Monozygotic Triplets Reveal Divergences in DNA Methylation Signatures.
Xia C, Olsen TK, Zirakzadeh AA, ..., Björkholm M, Strååt K
Front Oncol 10 (-) 598872 [2020-12-09; online 2020-12-09]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Capillary leakage provides nutrients and antioxidants for rapid pneumococcal proliferation in influenza-infected lower airways.
Sender V, Hentrich K, Pathak A, ..., Normark S, Henriques-Normark B
Proc. Natl. Acad. Sci. U.S.A. 117 (49) 31386-31397 [2020-12-08; online 2020-11-23]
Bioinformatics Compute and Storage [Service] Chemical Proteomics [Collaborative]
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A shotgun metagenomic investigation of the microbiota of udder cleft dermatitis in comparison to healthy skin in dairy cows.
Ekman L, Bagge E, Nyman A, ..., Pringle M, Segerman B
PLoS ONE 15 (12) e0242880 [2020-12-02; online 2020-12-02]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Amplification-free long-read sequencing reveals unforeseen CRISPR-Cas9 off-target activity.
Höijer I, Johansson J, Gudmundsson S, ..., Gyllensten U, Ameur A
Genome Biol. 21 (1) 290 [2020-12-01; online 2020-12-01]
Bioinformatics Compute and Storage [Service] Clinical Genomics Uppsala [Collaborative] NGI Uppsala (Uppsala Genome Center) [Technology development] National Genomics Infrastructure [Technology development]
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Tissue-specific patterns of regulatory changes underlying gene expression differences among Ficedula flycatchers and their naturally occurring F1 hybrids.
Mugal CF, Wang M, Backström N, ..., Qvarnström A, Ellegren H
Genome Res. 30 (12) 1727-1739 [2020-12-00; online 2020-11-03]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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The methylation landscape and its role in domestication and gene regulation in the chicken.
Höglund A, Henriksen R, Fogelholm J, ..., Jensen P, Wright D
Nat Ecol Evol 4 (12) 1713-1724 [2020-12-00; online 2020-09-21]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
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Metagenome assembled-genomes reveal similar functional profiles of CPR/Patescibacteria phyla in soils.
Nascimento Lemos L, Manoharan L, William Mendes L, ..., Satler Pylro V, Tsai SM
Environ Microbiol Rep 12 (6) 651-655 [2020-12-00; online 2020-09-07]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
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Genome-wide association study of angioedema induced by angiotensin-converting enzyme inhibitor and angiotensin receptor blocker treatment.
Rasmussen ER, Hallberg P, Baranova EV, ..., Palmer CNA, Wadelius M
Pharmacogenomics J. 20 (6) 770-783 [2020-12-00; online 2020-02-21]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Features of increased malignancy in eosinophilic clear cell renal cell carcinoma.
Nilsson H, Lindgren D, Axelson H, ..., Lundgren J, Johansson ME
J. Pathol. 252 (4) 384-397 [2020-12-00; online 2020-09-24]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Dysregulation in Akt/mTOR/HIF-1 signaling identified by proteo-transcriptomics of SARS-CoV-2 infected cells.
Appelberg S, Gupta S, Svensson Akusjärvi S, ..., Mirazimi A, Neogi U
Emerg Microbes Infect 9 (1) 1748-1760 [2020-12-00; online 2020-07-22]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]
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A metabolite roadmap of the wood-forming tissue in Populus tremula.
Abreu IN, Johansson AI, Sokołowska K, ..., Street NR, Moritz T
New Phytol. 228 (5) 1559-1572 [2020-12-00; online 2020-08-27]
Bioinformatics Compute and Storage [Service] Swedish Metabolomics Centre (SMC) [Collaborative]
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Evaluation of Single-Molecule Sequencing Technologies for Structural Variant Detection in Two Swedish Human Genomes.
Fatima N, Petri A, Gyllensten U, Feuk L, Ameur A
Genes 11 (12) 1444 [2020-11-30; online 2020-11-30]
Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Technology development] National Genomics Infrastructure [Technology development]
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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]
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New Insights into the Microbial Profiles of Infected Root Canals in Traumatized Teeth.
Manoharan L, Brundin M, Rakhimova O, Chávez de Paz L, Romani Vestman N
J Clin Med 9 (12) 3877 [2020-11-28; online 2020-11-28]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
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High CD45 expression of CD8+ and CD4+ T cells correlates with the size of HIV-1 reservoir in blood.
Petkov S, Bekele Y, Lakshmikanth T, ..., Brodin P, Chiodi F
Sci Rep 10 (1) 20425 [2020-11-24; online 2020-11-24]
Bioinformatics Compute and Storage [Service] Cellular Immunomonitoring [Collaborative]
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Distinct oligodendrocyte populations have spatial preference and different responses to spinal cord injury.
Floriddia EM, Lourenço T, Zhang S, ..., Nilsson M, Castelo-Branco G
Nat Commun 11 (1) 5860 [2020-11-17; online 2020-11-17]
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]
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Evaluation of the efficiency of genomic versus pedigree predictions for growth and wood quality traits in Scots pine.
Calleja-Rodriguez A, Pan J, Funda T, ..., Abrahamsson S, Wu HX
BMC Genomics 21 (1) 796 [2020-11-16; online 2020-11-16]
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]
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A ribonucleotide reductase from Clostridium botulinum reveals distinct evolutionary pathways to regulation via the overall activity site.
Martínez-Carranza M, Jonna VR, Lundin D, ..., Stenmark P, Hofer A
J. Biol. Chem. 295 (46) 15576-15587 [2020-11-13; online 2020-09-03]
Bioinformatics Compute and Storage [Service] Protein Science Facility (PSF) [Service]
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The Immunology of Multisystem Inflammatory Syndrome in Children with COVID-19.
Consiglio CR, Cotugno N, Sardh F, ..., Palma P, Brodin P
Cell 183 (4) 968-981.e7 [2020-11-12; online 2020-09-06]
Affinity Proteomics Stockholm [Service] Autoimmunity and Serology Profiling [Service] Bioinformatics Compute and Storage [Service] Cellular Immunomonitoring [Collaborative]
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Identification of Pre-Diagnostic Metabolic Patterns for Glioma Using Subset Analysis of Matched Repeated Time Points.
Jonsson P, Antti H, Späth F, Melin B, Björkblom B
Cancers (Basel) 12 (11) 3349 [2020-11-12; online 2020-11-12]
Bioinformatics Compute and Storage [Service] Swedish Metabolomics Centre (SMC) [Service]
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Association of aberrant ASNS imprinting with asparaginase sensitivity and chromosomal abnormality in childhood BCP-ALL.
Watanabe A, Miyake K, Nordlund J, ..., Sugita K, Inukai T
Blood 136 (20) 2319-2333 [2020-11-12; online 2020-06-24]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Genome-Scale Mapping Reveals Complex Regulatory Activities of RpoN in Yersinia pseudotuberculosis.
Mahmud AKMF, Nilsson K, Fahlgren A, ..., Avican K, Fällman M
mSystems 5 (6) - [2020-11-10; online 2020-11-10]
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]
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Targeted sequencing reveals the somatic mutation landscape in a Swedish breast cancer cohort.
Mathioudaki A, Ljungström V, Melin M, ..., Sjöblom T, Lindblad-Toh K
Sci Rep 10 (1) 19304 [2020-11-09; online 2020-11-09]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Identification of candidate genetic variants and altered protein expression in neural stem and mature neural cells support altered microtubule function to be an essential component in bipolar disorder.
Truvé K, Parris TZ, Vizlin-Hodzic D, ..., Ågren H, Funa K
Transl Psychiatry 10 (1) 390 [2020-11-09; online 2020-11-09]
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]
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Lysine-specific demethylase 1A restricts ex vivo propagation of human HSCs and is a target of UM171.
Subramaniam A, Žemaitis K, Talkhoncheh MS, ..., Zubarev RA, Larsson J
Blood 136 (19) 2151-2161 [2020-11-05; online 2020-06-26]
Bioinformatics Compute and Storage [Service] Chemical Proteomics [Collaborative]
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Draft Genome Assembly of the Freshwater Apex Predator Wels Catfish (Silurus glanis) Using Linked-Read Sequencing.
Ozerov MY, Flajšhans M, Noreikiene K, Vasemägi A, Gross R
G3 (Bethesda) 10 (11) 3897-3906 [2020-11-05; online 2020-11-05]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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MYC as a driver of stochastic chromatin networks: implications for the fitness of cancer cells.
Sumida N, Sifakis EG, Kiani NA, ..., Göndör A, Ohlsson R
Nucleic Acids Res. 48 (19) 10867-10876 [2020-11-04; online 2020-10-15]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Hybridization-based in situ sequencing (HybISS) for spatially resolved transcriptomics in human and mouse brain tissue.
Gyllborg D, Langseth CM, Qian X, ..., Lein ES, Nilsson M
Nucleic Acids Res. 48 (19) e112 [2020-11-04; online 2020-09-30]
Bioinformatics Compute and Storage [Service] In Situ Sequencing (ISS) [Technology development]
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Naming the untouchable - environmental sequences and niche partitioning as taxonomical evidence in fungi.
Kalsoom Khan F, Kluting K, Tångrot J, ..., Ryberg M, Rosling A
IMA Fungus 11 (1) 23 [2020-11-03; online 2020-11-03]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
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From Inquilines to Gall Inducers: Genomic Signature of a Life-Style Transition in Synergus Gall Wasps.
Gobbo E, Lartillot N, Hearn J, ..., Ide T, Ronquist F
Genome Biol Evol 12 (11) 2060-2073 [2020-11-03; online 2020-09-29]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Pericyte dysfunction due to Shb gene deficiency increases B16F10 melanoma lung metastasis.
He Q, Li X, He L, ..., Betsholtz C, Welsh M
Int. J. Cancer 147 (9) 2634-2644 [2020-11-01; online 2020-05-30]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Sahelian pastoralism from the perspective of variants associated with lactase persistence.
Priehodová E, Austerlitz F, Čížková M, ..., Schlebusch CM, Černý V
Am. J. Phys. Anthropol. 173 (3) 423-436 [2020-11-00; online 2020-08-19]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Leaf shape in Populus tremula is a complex, omnigenic trait.
Mähler N, Schiffthaler B, Robinson KM, ..., Hvidsten TR, Street NR
Ecol Evol 10 (21) 11922-11940 [2020-11-00; online 2020-10-13]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Identification and rescue of a tRNA wobble inosine deficiency causing intellectual disability disorder.
Ramos J, Proven M, Halvardson J, ..., Thuresson AC, Fu D
RNA 26 (11) 1654-1666 [2020-11-00; online 2020-08-06]
Bioinformatics Compute and Storage [Service] Clinical Genomics Uppsala [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
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Cytogenetically visible inversions are formed by multiple molecular mechanisms.
Pettersson M, Grochowski CM, Wincent J, ..., Carvalho CMB, Lindstrand A
Hum. Mutat. 41 (11) 1979-1998 [2020-11-00; online 2020-10-01]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Intra-Individual Behavioural Variability: A Trait under Genetic Control.
Henriksen R, Höglund A, Fogelholm J, ..., Dingemanse NJ, Wright D
Int J Mol Sci 21 (21) 8069 [2020-10-29; online 2020-10-29]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Activation of RAS Signalling is Associated with Altered Cell Adhesion in Phaeochromocytoma.
Rossitti HM, Dutta RK, Larsson C, ..., Söderkvist P, Gimm O
Int J Mol Sci 21 (21) 8072 [2020-10-29; online 2020-10-29]
Bioinformatics Compute and Storage [Service] Clinical Genomics Linköping [Service]
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Nuclear gene proximity and protein interactions shape transcript covariations in mammalian single cells.
Tarbier M, Mackowiak SD, Frade J, ..., Gallant CJ, Friedländer MR
Nat Commun 11 (1) 5445 [2020-10-28; online 2020-10-28]
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Population genomics reveals lack of greater white-fronted introgression into the Swedish lesser white-fronted goose.
Díez-Del-Molino D, von Seth J, Gyllenstrand N, ..., Sjögren-Gulve P, Dalén L
Sci Rep 10 (1) 18347 [2020-10-27; online 2020-10-27]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Epigenetic alterations in skin homing CD4+CLA+ T cells of atopic dermatitis patients.
Acevedo N, Benfeitas R, Katayama S, ..., Söderhäll C, Scheynius A
Sci Rep 10 (1) 18020 [2020-10-22; online 2020-10-22]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training
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Automated identification of the mouse brain's spatial compartments from in situ sequencing data.
Partel G, Hilscher MM, Milli G, ..., Nilsson M, Wählby C
BMC Biol. 18 (1) 144 [2020-10-19; online 2020-10-19]
BioImage Informatics [Collaborative] Bioinformatics Compute and Storage [Service]
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The influence of common polygenic risk and gene sets on social skills group training response in autism spectrum disorder.
Li D, Choque-Olsson N, Jiao H, ..., Bölte S, Tammimies K
npj Genom. Med. 5 (1) 45 [2020-10-12; online 2020-10-12]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
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Temporal changes in the vaginal microbiota in self-samples and its association with persistent HPV16 infection and CIN2.
Berggrund M, Gustavsson I, Aarnio R, ..., Olovsson M, Gyllensten U
Virol J 17 (1) 147 [2020-10-07; online 2020-10-07]
Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
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GeneSetCluster: a tool for summarizing and integrating gene-set analysis results.
Ewing E, Planell-Picola N, Jagodic M, Gomez-Cabrero D
BMC Bioinformatics 21 (1) 443 [2020-10-07; online 2020-10-07]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Transcriptional responses in developing lesions of European common ash (Fraxinus excelsior) reveal genes responding to infection by Hymenoscyphus fraxineus.
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Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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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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Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Brain Transcriptomics of Wild and Domestic Rabbits Suggests That Changes in Dopamine Signaling and Ciliary Function Contributed to Evolution of Tameness.
Sato DX, Rafati N, Ring H, ..., Carneiro M, Andersson L
Genome Biol Evol 12 (10) 1918-1928 [2020-10-01; online 2020-08-25]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
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Rodriguez L, Brodin P
J Clin Immunol 40 (7) 958-959 [2020-10-00; online 2020-08-22]
Bioinformatics Compute and Storage [Service] Cellular Immunomonitoring [Collaborative]
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Hong MG, Dodig-Crnković T, Chen X, ..., Magnusson PK, Schwenk JM
Life Sci. Alliance 3 (10) e202000817 [2020-10-00; online 2020-07-31]
Affinity Proteomics Stockholm [Collaborative] Autoimmunity and Serology Profiling [Service] Bioinformatics Compute and Storage [Service]
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Mitigation of the replication of SARS-CoV-2 by nitric oxide in vitro.
Akaberi D, Krambrich J, Ling J, ..., Lennerstrand J, Lundkvist Å
Redox Biol 37 (-) 101734 [2020-10-00; online 2020-09-21]
Bioinformatics Compute and Storage [Service] Drug Discovery and Development (DDD) [Service]
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Al-Kass Z, Guo Y, Vinnere Pettersson O, Niazi A, Morrell JM
Animal Reproduction Science 221 (-) 106568 [2020-10-00; online 2020-08-01]
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Function of multiple sclerosis-protective HLA class I alleles revealed by genome-wide protein-quantitative trait loci mapping of interferon signalling.
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PLoS Genet. 16 (10) e1009199 [2020-10-00; online 2020-10-26]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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High-fat diet and estrogen impacts the colon and its transcriptome in a sex-dependent manner.
Hases L, Archer A, Indukuri R, ..., Korach-André M, Williams C
Sci Rep 10 (1) 16160 [2020-09-30; online 2020-09-30]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Streamlined and Abundant Bacterioplankton Thrive in Functional Cohorts.
Mondav R, Bertilsson S, Buck M, ..., Lindström ES, Garcia SL
mSystems 5 (5) - [2020-09-29; online 2020-09-29]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Reconstruction of the birth of a male sex chromosome present in Atlantic herring.
Rafati N, Chen J, Herpin A, ..., Schartl M, Andersson L
Proc. Natl. Acad. Sci. U.S.A. 117 (39) 24359-24368 [2020-09-29; online 2020-09-16]
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Labile Dissolved Organic Matter Compound Characteristics Select for Divergence in Marine Bacterial Activity and Transcription.
Pontiller B, Martínez-García S, Lundin D, Pinhassi J
Front Microbiol 11 (-) 588778 [2020-09-25; online 2020-09-25]
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 Sequencing Libraries for Structural Analysis of Bacterial 5' UTRs.
Ignatov D, Vaitkevicius K, Johansson J
STAR Protoc 1 (2) 100046 [2020-09-18; online 2020-06-06]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Presynaptic dysfunction in CASK-related neurodevelopmental disorders.
Becker M, Mastropasqua F, Reising JP, ..., Bölte S, Tammimies K
Transl Psychiatry 10 (1) 312 [2020-09-14; online 2020-09-14]
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Diversity and Abundance of Microbial Communities in UASB Reactors during Methane Production from Hydrolyzed Wheat Straw and Lucerne.
Liu T, Schnürer A, Björkmalm J, Willquist K, Kreuger E
Microorganisms 8 (9) 1394 [2020-09-11; online 2020-09-11]
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Compositional and functional differences of the mucosal microbiota along the intestine of healthy individuals.
Vaga S, Lee S, Ji B, ..., Engstrand L, Shoaie S
Sci Rep 10 (1) 14977 [2020-09-11; online 2020-09-11]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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A whole-genome sequenced control population in northern Sweden reveals subregional genetic differences.
Svensson D, Rentoft M, Dahlin AM, ..., Trygg J, Johansson E
PLoS ONE 15 (9) e0237721 [2020-09-11; online 2020-09-11]
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Integration of molecular profiles in a longitudinal wellness profiling cohort.
Tebani A, Gummesson A, Zhong W, ..., Uhlen M, Fagerberg L
Nat Commun 11 (1) 4487 [2020-09-08; online 2020-09-08]
Affinity Proteomics Stockholm [Collaborative] Autoimmunity and Serology Profiling [Collaborative] Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Cellular Immunomonitoring [Collaborative] Swedish Metabolomics Centre (SMC) [Collaborative]
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Genome sequence of segmented filamentous bacteria present in the human intestine.
Jonsson H, Hugerth LW, Sundh J, Lundin E, Andersson AF
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Hanke L, Vidakovics Perez L, Sheward DJ, ..., Murrell B, McInerney GM
Nat Commun 11 (1) 4420 [2020-09-04; online 2020-09-04]
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River biofilms adapted to anthropogenic disturbances are more resistant to WWTP inputs.
Freixa A, Perujo N, Langenheder S, Romaní AM
FEMS Microbiol. Ecol. 96 (9) - [2020-09-01; online 2020-08-09]
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Parallel Evolution of Bower-Building Behavior in Two Groups of Bowerbirds Suggested by Phylogenomics.
Ericson PGP, Irestedt M, Nylander JAA, ..., Joseph L, Qu Y
Syst. Biol. 69 (5) 820-829 [2020-09-01; online 2020-05-18]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Evolutionary Remodeling of the Cell Envelope in Bacteria of the Planctomycetes Phylum.
Mahajan M, Seeger C, Yee B, Andersson SGE
Genome Biol Evol 12 (9) 1528-1548 [2020-09-01; online 2020-08-08]
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Xdrop: Targeted sequencing of long DNA molecules from low input samples using droplet sorting.
Madsen EB, Höijer I, Kvist T, Ameur A, Mikkelsen MJ
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Reconstructing marine plankton food web interactions using DNA metabarcoding.
Zamora-Terol S, Novotny A, Winder M
Mol. Ecol. 29 (17) 3380-3395 [2020-09-00; online 2020-08-09]
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Linked-read sequencing enables haplotype-resolved resequencing at population scale.
Lutgen D, Ritter R, Olsen RA, ..., Suh A, Burri R
Mol Ecol Resour 20 (5) 1311-1322 [2020-09-00; online 2020-06-29]
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van der Valk T, Vezzi F, Ormestad M, Dalén L, Guschanski K
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Comparative analysis of genome-wide DNA methylation in Neurospora.
Hosseini S, Meunier C, Nguyen D, Reimegård J, Johannesson H
Epigenetics 15 (9) 972-987 [2020-09-00; online 2020-03-31]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
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A Shh/Gli-driven three-node timer motif controls temporal identity and fate of neural stem cells.
Dias JM, Alekseenko Z, Jeggari A, ..., Iber D, Ericson J
Sci Adv 6 (38) - [2020-09-00; online 2020-09-16]
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]
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High-Throughput Sequencing and Unsupervised Analysis of Formyltetrahydrofolate Synthetase (FTHFS) Gene Amplicons to Estimate Acetogenic Community Structure.
Singh A, Nylander JAA, Schnürer A, Bongcam-Rudloff E, Müller B
Front Microbiol 11 (-) 2066 [2020-08-27; online 2020-08-27]
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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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Systems-Level Immunomonitoring from Acute to Recovery Phase of Severe COVID-19.
Rodriguez L, Pekkarinen PT, Lakshmikanth T, ..., Kekäläinen E, Brodin P
Cell Reports Medicine 1 (5) 100078 [2020-08-25; online 2020-08-05]
Affinity Proteomics Stockholm [Service] Bioinformatics Compute and Storage [Service] Cellular Immunomonitoring [Collaborative]
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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]
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 identifies early diversity of sensory neurons forming via bi-potential intermediates.
Faure L, Wang Y, Kastriti ME, ..., Adameyko I, Hadjab S
Nat Commun 11 (1) 4175 [2020-08-21; online 2020-08-21]
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Natural killer cell immunotypes related to COVID-19 disease severity.
Maucourant C, Filipovic I, Ponzetta A, ..., Björkström NK, Karolinska COVID-19 Study Group
Sci Immunol 5 (50) eabd6832 [2020-08-21; online 2020-08-23]
Affinity Proteomics Stockholm [Service] Bioinformatics Compute and Storage [Service]
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Designing custom CRISPR libraries for hypothesis-driven drug target discovery.
Iyer VS, Jiang L, Shen Y, ..., Schmierer B, Wermeling F
Computational and Structural Biotechnology Journal 18 (-) 2237-2246 [2020-08-18; online 2020-08-18]
Bioinformatics Compute and Storage [Service] CRISPR Functional Genomics [Collaborative]
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Gsta4 controls apoptosis of differentiating adult oligodendrocytes during homeostasis and remyelination via the mitochondria-associated Fas-Casp8-Bid-axis.
Carlström KE, Zhu K, Ewing E, ..., Castelo-Branco G, Piehl F
Nat Commun 11 (1) 4071 [2020-08-13; online 2020-08-13]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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zOPT: an open source optical projection tomography system and methods for rapid 3D zebrafish imaging.
Zhang H, Waldmann L, Manuel R, ..., Haitina T, Allalou A
Biomed. Opt. Express 11 (8) 4290-4305 [2020-08-01; online 2020-07-15]
BioImage Informatics Bioinformatics Compute and Storage [Service] Genome Engineering Zebrafish [Service]
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The importance of the ZBED6-IGF2 axis for metabolic regulation in mouse myoblast cells.
Younis S, Naboulsi R, Wang X, ..., Welsh N, Andersson L
FASEB J. 34 (8) 10250-10266 [2020-08-00; online 2020-06-19]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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The Neolithic Pitted Ware culture foragers were culturally but not genetically influenced by the Battle Axe culture herders.
Coutinho A, Günther T, Munters AR, ..., Malmström H, Jakobsson M
Am. J. Phys. Anthropol. 172 (4) 638-649 [2020-08-00; online 2020-06-04]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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SWEDEGENE-a Swedish nation-wide DNA sample collection for pharmacogenomic studies of serious adverse drug reactions.
Hallberg P, Yue QY, Eliasson E, ..., Ås J, Wadelius M
Pharmacogenomics J. 20 (4) 579-585 [2020-08-00; online 2020-01-17]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Recent introgression between Taiga Bean Goose and Tundra Bean Goose results in a largely homogeneous landscape of genetic differentiation.
Ottenburghs J, Honka J, Müskens GJDM, Ellegren H
Heredity (Edinb) 125 (1-2) 73-84 [2020-08-00; online 2020-05-26]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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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]
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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Management of an outbreak of postpartum Streptococcus pyogenes emm75 infections.
Trell K, Jörgensen J, Rasmussen M, Senneby E
J. Hosp. Infect. 105 (4) 752-756 [2020-08-00; online 2020-06-01]
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Joint impact of common risk factors on incident dementia: A cohort study of the Swedish Twin Registry.
Tomata Y, Li X, Karlsson IK, ..., Pedersen NL, Hägg S
J. Intern. Med. 288 (2) 234-247 [2020-08-00; online 2020-05-03]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Higher host plant specialization of root-associated endophytes than mycorrhizal fungi along an arctic elevational gradient.
Abrego N, Huotari T, Tack AJM, ..., Ovaskainen O, Roslin T
Ecol Evol 10 (16) 8989-9002 [2020-08-00; online 2020-08-06]
Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
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Evolutionary genetics of canine respiratory coronavirus and recent introduction into Swedish dogs.
Wille M, Wensman JJ, Larsson S, ..., Hayer J, Malmberg M
Infection, Genetics and Evolution 82 (-) 104290 [2020-08-00; online 2020-03-20]
Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
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Determinants of genetic variation across eco-evolutionary scales in pinnipeds.
Peart CR, Tusso S, Pophaly SD, ..., Shafer ABA, Wolf JBW
Nat Ecol Evol 4 (8) 1095-1104 [2020-08-00; online 2020-06-08]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Association between proteomics and obstructive sleep apnea phenotypes in a community-based cohort of women.
Ljunggren M, Theorell-Haglöw J, Freyhult E, ..., Janson C, Lindberg E
J Sleep Res 29 (4) e13041 [2020-08-00; online 2020-04-08]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
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Archaea in boreal Swedish lakes are diverse, dominated by Woesearchaeota and follow deterministic community assembly.
Juottonen H, Fontaine L, Wurzbacher C, ..., Peura S, Eiler A
Environ. Microbiol. 22 (8) 3158-3171 [2020-08-00; online 2020-06-03]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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A decade of epigenetic change in aging twins: Genetic and environmental contributions to longitudinal DNA methylation.
Reynolds CA, Tan Q, Munoz E, ..., Hägg S, Pedersen NL
Aging Cell 19 (8) e13197 [2020-08-00; online 2020-07-24]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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The genetic regulation of size variation in the transcriptome of the cerebrum in the chicken and its role in domestication and brain size evolution.
Höglund A, Strempfl K, Fogelholm J, Wright D, Henriksen R
BMC Genomics 21 (1) 518 [2020-07-29; online 2020-07-29]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Combining transcriptomics and genetic linkage based information to identify candidate genes associated with Heterobasidion-resistance in Norway spruce.
Chaudhary R, Lundén K, Dalman K, ..., Stenlid J, Elfstrand M
Sci Rep 10 (1) 12711 [2020-07-29; online 2020-07-29]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Prototypical pacemaker neurons interact with the resident microbiota.
Klimovich A, Giacomello S, Björklund Å, ..., Adameyko I, Bosch TCG
Proc. Natl. Acad. Sci. U.S.A. 117 (30) 17854-17863 [2020-07-28; online 2020-07-09]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
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Human Immune System Variation during 1 Year.
Lakshmikanth T, Muhammad SA, Olin A, ..., Uhlen M, Brodin P
Cell Rep 32 (3) 107923 [2020-07-21; online 2020-07-23]
Affinity Proteomics Stockholm [Service] Bioinformatics Compute and Storage [Service] Cellular Immunomonitoring [Collaborative]
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Descriptive Proteome Analysis to Investigate Context-Dependent Treatment Responses to OXPHOS Inhibition in Colon Carcinoma Cells Grown as Monolayer and Multicellular Tumor Spheroids.
Steinmetz J, Senkowski W, Lengqvist J, ..., Fryknäs M, Kultima K
ACS Omega 5 (28) 17242-17254 [2020-07-21; online 2020-07-06]
Bioinformatics Compute and Storage [Service] Drug Discovery and Development (DDD) [Service]
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Translating GWAS-identified loci for cardiac rhythm and rate using an in vivo image- and CRISPR/Cas9-based approach.
von der Heyde B, Emmanouilidou A, Mazzaferro E, ..., Brooke HL, den Hoed M
Sci Rep 10 (1) 11831 [2020-07-16; online 2020-07-16]
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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A Patient-Derived Cell Atlas Informs Precision Targeting of Glioblastoma.
Johansson P, Krona C, Kundu S, ..., Marino S, Nelander S
Cell Rep 32 (2) 107897 [2020-07-14; online 2020-07-16]
Bioinformatics Compute and Storage [Service] Drug Discovery and Development (DDD) [Service]
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Transcriptional responses in Parascaris univalens after in vitro exposure to ivermectin, pyrantel citrate and thiabendazole.
Martin F, Dube F, Karlsson Lindsjö O, ..., Bergström TF, Tydén E
Parasit Vectors 13 (1) 342 [2020-07-09; online 2020-07-09]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Disturbance history can increase functional stability in the face of both repeated disturbances of the same type and novel disturbances.
Renes SE, Sjöstedt J, Fetzer I, Langenheder S
Sci Rep 10 (1) 11333 [2020-07-09; online 2020-07-09]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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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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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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Discovery and population genomics of structural variation in a songbird genus.
Weissensteiner MH, Bunikis I, Catalán A, ..., Warmuth VM, Wolf JBW
Nat Commun 11 (1) 3403 [2020-07-07; online 2020-07-07]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
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Spatio-molecular domains identified in the mouse subthalamic nucleus and neighboring glutamatergic and GABAergic brain structures.
Wallén-Mackenzie Å, Dumas S, Papathanou M, ..., König N, Björklund ÅK
Commun Biol 3 (1) 338 [2020-07-03; online 2020-07-03]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Eukaryotic Single Cell Genomics (ESCG) [Service]
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meQTL and ncRNA functional analyses of 102 GWAS-SNPs associated with depression implicate HACE1 and SHANK2 genes.
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Clin Epigenetics 12 (1) 99 [2020-07-02; online 2020-07-02]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Y-Chromosome Variation in Southern African Khoe-San Populations Based on Whole-Genome Sequences.
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Genome Biol Evol 12 (7) 1031-1039 [2020-07-01; online 2020-07-23]
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BMC Bioinformatics 21 (1) 273 [2020-07-01; online 2020-07-01]
Bioinformatics Compute and Storage [Service] Clinical Genomics Stockholm [Technology development]
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Transcriptomes from German shepherd dogs reveal differences in immune activity between atopic dermatitis affected and control skin.
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Immunogenetics 72 (5) 315-323 [2020-07-00; online 2020-06-18]
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Support systems to guide clinical decision-making in precision oncology: The Cancer Core Europe Molecular Tumor Board Portal.
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Pre- and postnatal Lactobacillus reuteri treatment alters DNA methylation of infant T helper cells.
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Pediatr Allergy Immunol 31 (5) 544-553 [2020-07-00; online 2020-04-03]
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Odorant receptor phylogeny confirms conserved channels for sex pheromone and host plant signals in tortricid moths.
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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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Inflammatory markers in women with postpartum depressive symptoms.
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Growth-Inhibitory Activity of Bone Morphogenetic Protein 4 in Human Glioblastoma Cell Lines Is Heterogeneous and Dependent on Reduced SOX2 Expression.
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Mol Cancer Res 18 (7) 981-991 [2020-07-00; online 2020-03-31]
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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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Female-biased gene flow between two species of Darwin's finches.
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Nat Ecol Evol 4 (7) 979-986 [2020-07-00; online 2020-05-04]
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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]
PubMed DOI Crossref
Whole genome sequencing of familial isolated oesophagus atresia uncover shared structural variants.
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BMC Med Genomics 13 (1) 85 [2020-06-26; online 2020-06-26]
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Evolutionary History of the Marchantia polymorpha Complex.
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Front Plant Sci 11 (-) 829 [2020-06-26; online 2020-06-26]
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Whole-genome sequence association analysis of blood proteins in a longitudinal wellness cohort.
Zhong W, Gummesson A, Tebani A, ..., Fagerberg L, Uhlén M
Genome Med 12 (1) 53 [2020-06-23; online 2020-06-23]
Affinity Proteomics Stockholm [Collaborative] Bioinformatics Compute and Storage [Service]
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Skeletal Muscle Transcriptomic Comparison between Long-Term Trained and Untrained Men and Women.
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Cell Rep 31 (12) 107808 [2020-06-23; online 2020-06-25]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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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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Illuminating Genetic Mysteries of the Dead Sea Scrolls.
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Cell 181 (6) 1218-1231.e27 [2020-06-11; online 2020-06-02]
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Whole-genome sequencing of glioblastoma reveals enrichment of non-coding constraint mutations in known and novel genes.
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Genome Biol. 21 (1) 127 [2020-06-09; online 2020-06-09]
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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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The regulation and pharmacological modulation of immune complex induced type III IFN production by plasmacytoid dendritic cells.
Hjorton K, Hagberg N, Pucholt P, Eloranta ML, Rönnblom L
Arthritis Res. Ther. 22 (1) 130 [2020-06-05; online 2020-06-05]
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LPS-treatment of bovine endometrial epithelial cells causes differential DNA methylation of genes associated with inflammation and endometrial function.
Jhamat N, Niazi A, Guo Y, ..., Andersson G, Humblot P
BMC Genomics 21 (1) 385 [2020-06-03; online 2020-06-03]
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Cell Rep 31 (9) 107699 [2020-06-02; online 2020-06-04]
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Mol Omics 16 (3) 185-194 [2020-06-01; online 2020-03-19]
Bioinformatics Compute and Storage [Service] Genome Engineering Zebrafish [Service]
PubMed DOI Crossref
Mitochondrial genomes from Bronze Age Poland reveal genetic continuity from the Late Neolithic and additional genetic affinities with the steppe populations.
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Am. J. Phys. Anthropol. 172 (2) 176-188 [2020-06-00; online 2020-04-15]
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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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Balancing selection in Pattern Recognition Receptor signalling pathways is associated with gene function and pleiotropy in a wild rodent.
Lundberg M, Zhong X, Konrad A, Olsen RA, Råberg L
Mol. Ecol. 29 (11) 1990-2003 [2020-06-00; online 2020-06-03]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Collaborative] National Genomics Infrastructure [Collaborative]
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An immune gene expression signature distinguishes central nervous system metastases from primary tumours in non-small-cell lung cancer.
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Eur. J. Cancer 132 (-) 24-34 [2020-06-00; online 2020-04-20]
Bioinformatics Compute and Storage [Service] Clinical Genomics Uppsala [Collaborative]
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Activated carbon stimulates microbial diversity and PAH biodegradation under anaerobic conditions in oil-polluted sediments.
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Chemosphere 248 (-) 126023 [2020-06-00; online 2020-01-24]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Restoration of KMT2C/MLL3 in human colorectal cancer cells reinforces genome-wide H3K4me1 profiles and influences cell growth and gene expression.
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Clin Epigenetics 12 (1) 74 [2020-05-29; online 2020-05-29]
Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
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Integration of whole-body [18F]FDG PET/MRI with non-targeted metabolomics can provide new insights on tissue-specific insulin resistance in type 2 diabetes.
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Sci Rep 10 (1) 8343 [2020-05-20; online 2020-05-20]
Bioinformatics Compute and Storage [Service] Swedish Metabolomics Centre (SMC) [Service]
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Behavioral Characterization of dmrt3a Mutant Zebrafish Reveals Crucial Aspects of Vertebrate Locomotion through Phenotypes Related to Acceleration.
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BioImage Informatics Bioinformatics Compute and Storage [Service] Genome Engineering Zebrafish [Service]
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Single cell transcriptomics identifies stem cell-derived graft composition in a model of Parkinson's disease.
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Nat Commun 11 (1) 2434 [2020-05-15; online 2020-05-15]
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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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Integrative genomics approach identifies molecular features associated with early-stage ovarian carcinoma histotypes.
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Sci Rep 10 (1) 7946 [2020-05-14; online 2020-05-14]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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In Situ Sequencing: A High-Throughput, Multi-Targeted Gene Expression Profiling Technique for Cell Typing in Tissue Sections.
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Methods Mol. Biol. 2148 (-) 313-329 [2020-05-13; online 2020-05-13]
Bioinformatics Compute and Storage [Service] In Situ Sequencing (ISS) [Collaborative]
PubMed DOI Crossref
Srebf1 Controls Midbrain Dopaminergic Neurogenesis.
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Cell Rep 31 (5) 107601 [2020-05-05; online 2020-05-07]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
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 reveals complex chromosome rearrangement disrupting NIPBL in infant with Cornelia de Lange syndrome.
Plesser Duvdevani M, Pettersson M, Eisfeldt J, ..., Lindstrand A, Harel T
Am. J. Med. Genet. A 182 (5) 1143-1151 [2020-05-00; online 2020-03-03]
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 human remains to enable genealogy DNA database searches - A case report.
Tillmar A, Sjölund P, Lundqvist B, ..., Älgenäs C, Green H
Forensic Sci Int Genet 46 (-) 102233 [2020-05-00; online 2020-01-17]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Transcriptome profiling of Ewing sarcomas - treatment resistance pathways and IGF-dependency.
Chen Y, Hesla AC, Lin Y, ..., Larsson O, Haglund F
Mol Oncol 14 (5) 1101-1117 [2020-05-00; 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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Recurrent Fusions Between YAP1 and KMT2A in Morphologically Distinct Neoplasms Within the Spectrum of Low-grade Fibromyxoid Sarcoma and Sclerosing Epithelioid Fibrosarcoma.
Puls F, Agaimy A, Flucke U, ..., Arbajian E, Mertens F
Am. J. Surg. Pathol. 44 (5) 594-606 [2020-05-00; online 2020-01-09]
Bioinformatics Compute and Storage [Service] Clinical Genomics Lund [Service]
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Genetic identification of cell types underlying brain complex traits yields insights into the etiology of Parkinson's disease.
Bryois J, Skene NG, Hansen TF, ..., Hjerling-Leffler J, Sullivan PF
Nat. Genet. 52 (5) 482-493 [2020-05-00; online 2020-04-27]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Analysis of DNA methylation patterns in the tumor immune microenvironment of metastatic melanoma.
Mitra S, Lauss M, Cabrita R, ..., Brown KM, Jönsson G
Mol Oncol 14 (5) 933-950 [2020-05-00; online 2020-03-21]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Trade-off between somatic and germline repair in a vertebrate supports the expensive germ line hypothesis.
Chen HY, Jolly C, Bublys K, Marcu D, Immler S
Proc. Natl. Acad. Sci. U.S.A. 117 (16) 8973-8979 [2020-04-21; online 2020-04-03]
Bioinformatics Compute and Storage [Service] Genome Engineering Zebrafish [Service]
PubMed DOI Crossref
Molecular profiling of driver events in metastatic uveal melanoma.
Karlsson J, Nilsson LM, Mitra S, ..., Olofsson Bagge R, Nilsson JA
Nat Commun 11 (1) 1894 [2020-04-20; online 2020-04-20]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Genome-Scale Metabolic Modeling of Glioblastoma Reveals Promising Targets for Drug Development.
Larsson I, Uhlén M, Zhang C, Mardinoglu A
Front Genet 11 (-) 381 [2020-04-17; online 2020-04-17]
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 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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Increased burden of ultra-rare structural variants localizing to boundaries of topologically associated domains in schizophrenia.
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Nat Commun 11 (1) 1842 [2020-04-15; online 2020-04-15]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Service] Systems Biology [Collaborative]
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Automation of Spatial Transcriptomics library preparation to enable rapid and robust insights into spatial organization of tissues.
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BMC Genomics 21 (1) 298 [2020-04-15; online 2020-04-15]
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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The honeybee (Apis mellifera) developmental state shapes the genetic composition of the deformed wing virus-A quasispecies during serial transmission.
Yañez O, Chávez-Galarza J, Tellgren-Roth C, ..., Neumann P, de Miranda JR
Sci Rep 10 (1) 5956 [2020-04-06; online 2020-04-06]
Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
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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The conifer root rot pathogens Heterobasidion irregulare and Heterobasidion occidentale employ different strategies to infect Norway spruce.
Hu Y, Elfstrand M, Stenlid J, Durling MB, Olson Å
Sci Rep 10 (1) 5884 [2020-04-03; online 2020-04-03]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Paralogization and New Protein Architectures in Planctomycetes Bacteria with Complex Cell Structures.
Mahajan M, Yee B, Hägglund E, ..., Fuerst JA, Andersson SGE
Mol. Biol. Evol. 37 (4) 1020-1040 [2020-04-01; online 2019-12-07]
Bioinformatics Compute and Storage [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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The acute effect of metabolic cofactor supplementation: a potential therapeutic strategy against non-alcoholic fatty liver disease.
Zhang C, Bjornson E, Arif M, ..., Borén J, Mardinoglu A
Mol. Syst. Biol. 16 (4) e9495 [2020-04-00; online 2020-04-28]
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Screening for autoantibody targets in post-vaccination narcolepsy using proteome arrays.
Lind A, Eriksson D, Akel O, ..., Elding Larsson H, Landegren N
Scand. J. Immunol. 91 (4) e12864 [2020-04-00; online 2020-02-13]
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Molecular characterization of a large unselected cohort of metastatic colorectal cancers in relation to primary tumor location, rare metastatic sites and prognosis.
Nunes L, Aasebø K, Mathot L, ..., Sjöblom T, Glimelius B
Acta Oncol 59 (4) 417-426 [2020-04-00; online 2020-01-10]
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ABCB1 single-nucleotide variants and survival in patients with glioblastoma treated with radiotherapy concomitant with temozolomide.
Malmström A, Łysiak M, Åkesson L, ..., Green H, Söderkvist P
Pharmacogenomics J. 20 (2) 213-219 [2020-04-00; online 2019-10-17]
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A Multi-Omics Approach to Liver Diseases: Integration of Single Nuclei Transcriptomics with Proteomics and HiCap Bulk Data in Human Liver.
Cavalli M, Diamanti K, Pan G, ..., Komorowski J, Wadelius C
OMICS 24 (4) 180-194 [2020-04-00; online 2020-03-16]
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Identification of cell surface markers and establishment of monolayer differentiation to retinal pigment epithelial cells.
Plaza Reyes A, Petrus-Reurer S, Padrell Sánchez S, ..., Kvanta A, Lanner F
Nat Commun 11 (1) 1609 [2020-03-30; online 2020-03-30]
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Antimicrobial peptide and sequence variation along a latitudinal gradient in two anurans.
Cortázar-Chinarro M, Meyer-Lucht Y, Van der Valk T, ..., Laurila A, Höglund J
BMC Genet. 21 (1) 38 [2020-03-30; online 2020-03-30]
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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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PubMed DOI Crossref
Marine Sediments Illuminate Chlamydiae Diversity and Evolution.
Dharamshi JE, Tamarit D, Eme L, ..., Spang A, Ettema TJG
Curr. Biol. 30 (6) 1032-1048.e7 [2020-03-23; online 2020-03-05]
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Effects of acute sleep loss on diurnal plasma dynamics of CNS health biomarkers in young men.
Benedict C, Blennow K, Zetterberg H, Cedernaes J
Neurology 94 (11) e1181-e1189 [2020-03-17; online 2020-01-08]
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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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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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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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Exploiting loss of heterozygosity for allele-selective colorectal cancer chemotherapy.
Rendo V, Stoimenov I, Mateus A, ..., Cheong I, Sjöblom T
Nat Commun 11 (1) 1308 [2020-03-11; online 2020-03-11]
Bioinformatics Compute and Storage [Service] Chemical Biology Consortium Sweden (CBCS) [Collaborative] Drug Discovery and Development (DDD) [Service]
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Footprints of natural selection at the mannose-6-phosphate isomerase locus in barnacles.
Nunez JCB, Flight PA, Neil KB, ..., Blomberg A, Rand DM
Proc. Natl. Acad. Sci. U.S.A. 117 (10) 5376-5385 [2020-03-10; online 2020-02-25]
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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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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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]
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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Stressful Beginnings with Long-Term Consequences.
Consiglio CR, Brodin P
Cell 180 (5) 820-821 [2020-03-05; online 2020-03-07]
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Single-cell analysis of human ovarian cortex identifies distinct cell populations but no oogonial stem cells.
Wagner M, Yoshihara M, Douagi I, ..., Lanner F, Damdimopoulou P
Nat Commun 11 (1) 1147 [2020-03-02; online 2020-03-02]
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Epigenome-wide meta-analysis of blood DNA methylation in newborns and children identifies numerous loci related to gestational age.
Merid SK, Novoloaca A, Sharp GC, ..., London SJ, Melén E
Genome Med 12 (1) 25 [2020-03-02; online 2020-03-02]
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Overexpression of chromatin remodeling and tyrosine kinase genes in iAMP21-positive acute lymphoblastic leukemia.
Ivanov Öfverholm I, Zachariadis V, Taylan F, ..., Nordlund J, Barbany G
Leuk. Lymphoma 61 (3) 604-613 [2020-03-00; online 2019-10-22]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]
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Longitudinal changes in the frequency of mosaic chromosome Y loss in peripheral blood cells of aging men varies profoundly between individuals.
Danielsson M, Halvardson J, Davies H, ..., Dumanski JP, Forsberg LA
Eur. J. Hum. Genet. 28 (3) 349-357 [2020-03-00; online 2019-10-25]
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High genetic risk score is associated with early disease onset, damage accrual and decreased survival in systemic lupus erythematosus.
Reid S, Alexsson A, Frodlund M, ..., Rönnblom L, Leonard D
Ann. Rheum. Dis. 79 (3) 363-369 [2020-03-00; online 2019-12-11]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]
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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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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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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A link between the newly described colistin resistance gene mcr-9 and clinical Enterobacteriaceae isolates carrying blaSHV-12 from horses in Sweden.
Börjesson S, Greko C, Myrenås M, ..., Nilsson O, Pedersen K
J Glob Antimicrob Resist 20 (-) 285-289 [2020-03-00; online 2019-09-05]
Bioinformatics Compute and Storage [Service] Clinical Genomics Stockholm [Service]
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Patterns of African and Asian admixture in the Afrikaner population of South Africa.
Hollfelder N, Erasmus JC, Hammaren R, ..., Greeff JM, Schlebusch CM
BMC Biol. 18 (1) 16 [2020-02-24; online 2020-02-24]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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rs953413 Regulates Polyunsaturated Fatty Acid Metabolism by Modulating ELOVL2 Expression.
Pan G, Cavalli M, Carlsson B, ..., Kumar C, Wadelius C
iScience 23 (2) 100808 [2020-02-21; online 2020-01-09]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Achieving symptom relief in patients with Myalgic encephalomyelitis by targeting the neuro-immune interface and inducing disease tolerance
Rodriguez LST, Pou C, Lakshmikanth T, ..., Julin P, Brodin P
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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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Refined detection and phasing of structural aberrations in pediatric acute lymphoblastic leukemia by linked-read whole-genome sequencing.
Nordlund J, Marincevic-Zuniga Y, Cavelier L, ..., Lönnerholm G, Syvänen AC
Sci Rep 10 (1) 2512 [2020-02-13; online 2020-02-13]
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Using null models to compare bacterial and microeukaryotic metacommunity assembly under shifting environmental conditions.
Vass M, Székely AJ, Lindström ES, Langenheder S
Sci Rep 10 (1) 2455 [2020-02-12; online 2020-02-12]
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Longitudinal trajectories, correlations and mortality associations of nine biological ages across 20-years follow-up.
Li X, Ploner A, Wang Y, ..., Jylhävä J, Hägg S
Elife 9 (-) - [2020-02-11; online 2020-02-11]
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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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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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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Plasma Lipidome and Prediction of Type 2 Diabetes in the Population-Based Malmö Diet and Cancer Cohort.
Fernandez C, Surma MA, Klose C, ..., Simons K, Melander O
Diabetes Care 43 (2) 366-373 [2020-02-00; online 2019-12-08]
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Genomic and transcriptomic features of dermatofibrosarcoma protuberans: Unusual chromosomal origin of the COL1A1-PDGFB fusion gene and synergistic effects of amplified regions in tumor development.
Köster J, Arbajian E, Viklund B, ..., Mandahl N, Mertens F
Cancer Genet 241 (-) 34-41 [2020-02-00; online 2019-12-10]
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Artificial intelligence for diagnosis and grading of prostate cancer in biopsies: a population-based, diagnostic study.
Ström P, Kartasalo K, Olsson H, ..., Egevad L, Eklund M
Lancet Oncol 21 (2) 222-232 [2020-02-00; online 2020-01-08]
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Painting of Fourth and the X-Linked 1.688 Satellite in D. melanogaster is Involved in Chromosome-Wide Gene Regulation.
Ekhteraei-Tousi S, Lewerentz J, Larsson J
Cells 9 (2) 323 [2020-01-30; online 2020-01-30]
Bioinformatics Compute and Storage [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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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]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Technology development] Bioinformatics Support and Infrastructure [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development] Clinical Genomics Stockholm [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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The round goby genome provides insights into mechanisms that may facilitate biological invasions.
Adrian-Kalchhauser I, Blomberg A, Larsson T, ..., Schloissnig S, Winkler S
BMC Biol. 18 (1) 11 [2020-01-28; online 2020-01-28]
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Building de novo reference genome assemblies of complex eukaryotic microorganisms from single nuclei.
Montoliu-Nerin M, Sánchez-García M, Bergin C, ..., Johannesson H, Rosling A
Sci Rep 10 (1) 1303 [2020-01-28; online 2020-01-28]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Microbial Single Cell Genomics [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Extracellular Vesicles Released From the Skin Commensal Yeast Malassezia sympodialis Activate Human Primary Keratinocytes.
Vallhov H, Johansson C, Veerman RE, Scheynius A
Front. Cell. Infect. Microbiol. 10 (-) 6 [2020-01-24; online 2020-01-24]
Bioinformatics Compute and Storage [Service] Integrated Microscopy Technologies Stockholm [Service]
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CREBBP and WDR 24 Identified as Candidate Genes for Quantitative Variation in Red-Brown Plumage Colouration in the Chicken.
Fogelholm J, Henriksen R, Höglund A, ..., Jensen P, Wright D
Sci Rep 10 (1) 1161 [2020-01-24; online 2020-01-24]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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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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Transcriptome analysis of fibroblasts from schizophrenia patients reveals differential expression of schizophrenia-related genes.
Etemadikhah M, Niazi A, Wetterberg L, Feuk L
Sci Rep 10 (1) 630 [2020-01-20; online 2020-01-20]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [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) 702-714 [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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DAF-16/FOXO requires Protein Phosphatase 4 to initiate transcription of stress resistance and longevity promoting genes.
Sen I, Zhou X, Chernobrovkin A, ..., Zubarev RA, Riedel CG
Nat Commun 11 (1) 138 [2020-01-09; online 2020-01-09]
Bioinformatics Compute and Storage [Service] Chemical Proteomics [Service]
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The Mitogenome of Norway Spruce and a Reappraisal of Mitochondrial Recombination in Plants.
Sullivan AR, Eldfjell Y, Schiffthaler B, ..., Street NR, Wang XR
Genome Biol Evol 12 (1) 3586-3598 [2020-01-01; online 2019-11-28]
Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
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The Genome of the Endangered Dryas Monkey Provides New Insights into the Evolutionary History of the Vervets.
van der Valk T, Gonda CM, Silegowa H, ..., Detwiler KM, Guschanski K
Mol. Biol. Evol. 37 (1) 183-194 [2020-01-01; online 2019-09-19]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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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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Whole genome sequencing of apparently mutation-negative MEN1 patients.
Backman S, Bajic D, Crona J, ..., Skogseid B, Stålberg P
Eur. J. Endocrinol. 182 (1) 35-45 [2020-01-00; online 2019-10-29]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Variable neurodevelopmental and morphological phenotypes of carriers with 12q12 duplications.
Myers L, Blyth M, Moradkhani K, ..., Anderlid BM, Tammimies K
Mol Genet Genomic Med 8 (1) e1013 [2020-01-00; online 2019-11-15]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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The Proteome of the Dentate Terminal Zone of the Perforant Path Indicates Presynaptic Impairment in Alzheimer Disease.
Haytural H, Mermelekas G, Emre C, ..., Tjernberg LO, Frykman S
Mol. Cell Proteomics 19 (1) 128-141 [2020-01-00; online 2019-11-07]
Bioinformatics Compute and Storage [Service] Global Proteomics and Proteogenomics [Collaborative]
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Protein and DNA methylation-based scores as surrogate markers for interferon system activation in patients with primary Sjögren's syndrome.
Björk A, Richardsdotter Andersson E, Imgenberg-Kreuz J, ..., Nordmark G, Wahren-Herlenius M
RMD Open 6 (1) e000995 [2020-01-00; online 2020-01-21]
Bioinformatics Compute and Storage [Service] Clinical Biomarkers [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service] PLA and Single Cell Proteomics [Service]
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Probabilistic cell typing enables fine mapping of closely related cell types in situ.
Qian X, Harris KD, Hauling T, ..., Hjerling-Leffler J, Nilsson M
Nat. Methods 17 (1) 101-106 [2020-01-00; online 2019-11-18]
Bioinformatics Compute and Storage [Service] In Situ Sequencing (ISS) [Service]
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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]
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Cell-of-origin determined by both gene expression profiling and immunohistochemistry is the strongest predictor of survival in patients with diffuse large B-cell lymphoma.
Abdulla M, Hollander P, Pandzic T, ..., Rosenquist R, Amini RM
Am. J. Hematol. 95 (1) 57-67 [2020-01-00; online 2019-11-07]
Bioinformatics Compute and Storage [Service] Clinical Genomics Uppsala [Collaborative]
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Association of genetic variants related to plasma fatty acids with type 2 diabetes mellitus and glycaemic traits: a Mendelian randomisation study.
Yuan S, Larsson SC
Diabetologia 63 (1) 116-123 [2020-01-00; online 2019-11-05]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [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
Gene transfer across species boundaries in bryophytes: evidence from major life cycle stages in Homalothecium lutescens and H. sericeum.
Sawangproh W, Hedenäs L, Lang AS, Hansson B, Cronberg N
Ann. Bot. - (-) - [2019-12-24; online 2019-12-24]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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]
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Genetic Screening of Plasticity Regulating Nogo-Type Signaling Genes in Migraine.
Smedfors G, Liesecke F, Ran C, ..., Karlsson TE, Carmine Belin A
Brain Sci 10 (1) - [2019-12-20; online 2019-12-20]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [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
Longitudinal DNA methylation changes at MET may alter HGF/c-MET signalling in adolescents at risk for depression.
Ciuculete DM, Voisin S, Kular L, ..., Mwinyi J, Schiöth HB
Epigenetics 15 (6-7) 646-663 [2019-12-19; online 2019-12-19]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [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]
Advanced FISH Technologies 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
Comprehensive longitudinal study of epigenetic mutations in aging.
Wang Y, Karlsson R, Jylhävä J, ..., Almgren M, Hägg S
Clin Epigenetics 11 (1) 187 [2019-12-09; online 2019-12-09]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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A Gene-Environment Interaction Between Smoking and Gene polymorphisms Provides a High Risk of Two Subgroups of Sarcoidosis.
Rivera NV, Patasova K, Kullberg S, ..., Grunewald J, Padyukov L
Sci Rep 9 (1) 18633 [2019-12-09; online 2019-12-09]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Epigenome-wide meta-analysis of blood DNA methylation and its association with subcortical volumes: findings from the ENIGMA Epigenetics Working Group.
Jia T, Chu C, Liu Y, ..., Schumann G, Desrivières S
Mol. Psychiatry - (-) - [2019-12-06; online 2019-12-06]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Humanized Stem Cell Models of Pediatric Medulloblastoma Reveal an Oct4/mTOR Axis that Promotes Malignancy.
Čančer M, Hutter S, Holmberg KO, ..., Weishaupt H, Swartling FJ
Cell Stem Cell 25 (6) 855-870.e11 [2019-12-05; online 2019-11-27]
Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
GLUL Ablation Can Confer Drug Resistance to Cancer Cells via a Malate-Aspartate Shuttle-Mediated Mechanism.
Muthu M, Kumar R, Syed Khaja AS, ..., Persson JL, Nordström A
Cancers (Basel) 11 (12) 1945 [2019-12-05; online 2019-12-05]
Bioinformatics Compute and Storage [Service] Swedish Metabolomics Centre (SMC) [Service]
PubMed DOI Crossref
Dinucleotide Degradation by REXO2 Maintains Promoter Specificity in Mammalian Mitochondria.
Nicholls TJ, Spåhr H, Jiang S, ..., Larsson NG, Gustafsson CM
Mol. Cell 76 (5) 784-796.e6 [2019-12-05; online 2019-10-03]
Bioinformatics Compute and Storage [Service] Protein Science Facility (PSF) [Service]
PubMed DOI Crossref
Replicating associations between DNA methylation and body mass index in a longitudinal sample of older twins.
Karlsson IK, Ericsson M, Wang Y, ..., Reynolds CA, Dahl Aslan AK
Int J Obes (Lond) - (-) - [2019-12-04; online 2019-12-04]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Population history and genetic adaptation of the Fulani nomads: inferences from genome-wide data and the lactase persistence trait.
Vicente M, Priehodová E, Diallo I, ..., Černý V, Schlebusch CM
BMC Genomics 20 (1) 915 [2019-12-02; online 2019-12-02]
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PECTIN ACETYLESTERASE9 Affects the Transcriptome and Metabolome and Delays Aphid Feeding.
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Intra- and inter-individual metabolic profiling highlights carnitine and lysophosphatidylcholine pathways as key molecular defects in type 2 diabetes
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Improved power and precision with whole genome sequencing data in genome-wide association studies of inflammatory biomarkers
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Genome expansion of an obligate parthenogenesis-associated Wolbachia poses an exception to the symbiont reduction model
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Genetic Prediction of Serum 25-Hydroxyvitamin D, Calcium, and Parathyroid Hormone Levels in Relation to Development of Type 2 Diabetes: A Mendelian Randomization Study.
Yuan S, Jiang X, Michaëlsson K, Larsson SC
Diabetes Care 42 (12) 2197-2203 [2019-12-00; online 2019-09-23]
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Conbase: a software for unsupervised discovery of clonal somatic mutations in single cells through read phasing
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A cell fitness selection model for neuronal survival during development
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Nat Commun 10 (1) - [2019-12-00; online 2019-09-12]
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MYCN-enhanced Oxidative and Glycolytic Metabolism Reveals Vulnerabilities for Targeting Neuroblastoma.
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The Swedish Twin Registry: Content and Management as a Research Infrastructure.
Zagai U, Lichtenstein P, Pedersen NL, Magnusson PKE
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Evidence that genes involved in hedgehog signaling are associated with both bipolar disorder and high BMI.
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Transl Psychiatry 9 (1) 315 [2019-11-21; online 2019-11-21]
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BET and Aurora Kinase A inhibitors synergize against MYCN-positive human glioblastoma cells.
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Cell Death Dis 10 (12) 881 [2019-11-21; online 2019-11-21]
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Fast and Efficient Fc-Specific Photoaffinity Labeling To Produce Antibody-DNA Conjugates.
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Bioconjug. Chem. 30 (11) 2790-2798 [2019-11-20; online 2019-10-25]
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Inferring the Genomic Landscape of Recombination Rate Variation in European Aspen ( Populus tremula).
Apuli RP, Bernhardsson C, Schiffthaler B, ..., Street NR, Ingvarsson PK
G3 (Bethesda) - (-) - [2019-11-19; online 2019-11-19]
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Human induced pluripotent stem cells from two azoospermic patients with Klinefelter syndrome show similar X chromosome inactivation behavior to female pluripotent stem cells.
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Hum. Reprod. - (-) - [2019-11-19; online 2019-11-19]
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Genotype-dependent epigenetic regulation of DLGAP2 in alcohol use and dependence.
Meng W, Sjöholm LK, Kononenko O, ..., Rüegg J, Liu Y
Mol. Psychiatry - (-) - [2019-11-19; online 2019-11-19]
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Lithium treatment reverses irradiation-induced changes in rodent neural progenitors and rescues cognition.
Zanni G, Goto S, Fragopoulou AF, ..., Hermanson O, Blomgren K
Mol. Psychiatry - (-) - [2019-11-14; online 2019-11-14]
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On-demand virtual research environments using microservices.
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PeerJ Comput Sci 5 (-) e232 [2019-11-11; online 2019-11-11]
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Long-read metabarcoding of the eukaryotic rDNA operon to phylogenetically and taxonomically resolve environmental diversity
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Mol Ecol Resour - (-) - [2019-11-09; online 2019-11-09]
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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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Linkage and exome analysis implicate multiple genes in non-syndromic intellectual disability in a large Swedish family.
Lindholm Carlström E, Halvardson J, Etemadikhah M, ..., Gustavson KH, Feuk L
BMC Med Genomics 12 (1) 156 [2019-11-06; online 2019-11-06]
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Viromics Reveal a Number of Novel RNA Viruses in Swedish Mosquitoes.
Öhlund P, Hayer J, Lundén H, Hesson JC, Blomström AL
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Serum Parathyroid Hormone and Risk of Coronary Artery Disease: Exploring Causality Using Mendelian Randomization.
Melhus H, Michaëlsson K, Larsson SC
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Lindqvist HM, Gjertsson I, Andersson S, Calder PC, Bärebring L
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Diabetologia 62 (11) 1998-2006 [2019-11-00; online 2019-08-24]
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EZH2 upregulates the PI3K/AKT pathway through IGF1R and MYC in clinically aggressive chronic lymphocytic leukaemia.
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Characterization of Bacterial Communities in Breeding Waters of Anopheles darlingi in Manaus in the Amazon Basin Malaria-Endemic Area.
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A rapid and accurate method to quantify neurite outgrowth from cell and tissue cultures: Two image analytic approaches using adaptive thresholds or machine learning
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High-grade progression confers poor survival in pancreatic neuroendocrine tumors.
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Inhibition of translation termination by small molecules targeting ribosomal release factors.
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Sci Rep 9 (1) 15424 [2019-10-28; online 2019-10-28]
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A chromosome-level assembly of the Atlantic herring genome-detection of a supergene and other signals of selection.
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Genome Res. - (-) - [2019-10-24; online 2019-10-24]
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Considerations and Implications in the Purification of Extracellular Vesicles - A Cautionary Tale.
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Whole-genome sequencing of synchronous thyroid carcinomas identifies aberrant DNA repair in thyroid cancer dedifferentiation
Paulsson JO, Backman S, Wang N, ..., Zedenius J, Juhlin CC
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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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doepipeline: a systematic approach to optimizing multi-level and multi-step data processing workflows.
Svensson D, Sjögren R, Sundell D, Sjödin A, Trygg J
BMC Bioinformatics 20 (1) 498 [2019-10-15; online 2019-10-15]
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Along the Indian Ocean coast: genomic variation in Mozambique provides new insights into the Bantu expansion.
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Above-below surface interactions mediate effects of seagrass disturbance on meiobenthic diversity, nematode and polychaete trophic structure.
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Commun Biol 2 (-) 362 [2019-10-04; online 2019-10-04]
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Skeletal Mineralization in Association with Type X Collagen Expression Is an Ancestral Feature for Jawed Vertebrates.
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Interoperable and scalable data analysis with microservices: applications in metabolomics.
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Dissecting the Effects of Selection and Mutation on Genetic Diversity in Three Wood White (Leptidea) Butterfly Species.
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Genome Biol Evol 11 (10) 2875-2886 [2019-10-01; online 2019-10-04]
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Transcriptome and Proteome Profiling of Neural Induced Pluripotent Stem Cells from Individuals with Down Syndrome Disclose Dynamic Dysregulations of Key Pathways and Cellular Functions.
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High-definition spatial transcriptomics for in situ tissue profiling.
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Nat. Methods 16 (10) 987-990 [2019-10-00; online 2019-09-09]
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Genome-wide evidence supports mitochondrial relationships and pervasive parallel phenotypic evolution in open-habitat chats.
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Mol. Phylogenet. Evol. 139 (-) 106568 [2019-10-00; online 2019-07-23]
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Genetic basis and timing of a major mating system shift in Capsella.
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Kurland S, Wheat CW, de la Paz Celorio Mancera M, ..., Ryman N, Laikre L
Ecol Evol 9 (19) 11448-11463 [2019-10-00; online 2019-09-26]
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Distribution of bacteria between different milk fractions, investigated using culture-dependent methods and molecular-based and fluorescent microscopy approaches.
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J Appl Microbiol 127 (4) 1028-1037 [2019-10-00; online 2019-07-22]
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Cell generation dynamics underlying naive T-cell homeostasis in adult humans.
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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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Leaf metabolic signatures induced by real and simulated herbivory in black mustard (Brassica nigra).
Papazian S, Girdwood T, Wessels BA, ..., Moritz T, Albrectsen BR
Metabolomics 15 (10) 130 [2019-09-28; online 2019-09-28]
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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.
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Cytoplasmic protein misfolding titrates Hsp70 to activate nuclear Hsf1.
Masser AE, Kang W, Roy J, ..., Friedländer MR, Andréasson C
Elife 8 (-) - [2019-09-25; online 2019-09-25]
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Predisposition to childhood acute lymphoblastic leukemia caused by a constitutional translocation disrupting ETV6.
Järviaho T, Bang B, Zachariadis V, ..., Niinimäki R, Nordgren A
Blood Adv 3 (18) 2722-2731 [2019-09-24; online 2019-09-15]
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Novel Y-Chromosome Long Non-Coding RNAs Expressed in Human Male CNS During Early Development.
Johansson MM, Pottmeier P, Suciu P, ..., Peuckert C, Jazin E
Front Genet 10 (-) 891 [2019-09-24; online 2019-09-24]
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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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Hypermethylation-associated downregulation of microRNA-4456 in hypersexual disorder with putative influence on oxytocin signalling: A DNA methylation analysis of miRNA genes.
Boström AE, Chatzittofis A, Ciuculete DM, ..., Schiöth HB, Jokinen J
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Model System for the Formation of Tick-Borne Encephalitis Virus Replication Compartments without Viral RNA Replication.
Yau WL, Nguyen-Dinh V, Larsson E, ..., Överby AK, Lundmark R
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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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Recurrent convergent evolution at amino acid residue 261 in fish rhodopsin.
Hill J, Enbody ED, Pettersson ME, ..., Scheerer P, Andersson L
Proc. Natl. Acad. Sci. U.S.A. 116 (37) 18473-18478 [2019-09-10; online 2019-08-26]
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Metagenomes from Coastal Marine Sediments Give Insights into the Ecological Role and Cellular Features of Loki- and Thorarchaeota.
Manoharan L, Kozlowski JA, Murdoch RW, ..., Sousa FL, Schleper C
MBio 10 (5) - [2019-09-10; online 2019-09-10]
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Associations of Smoking and Alcohol and Coffee Intake with Fracture and Bone Mineral Density: A Mendelian Randomization Study.
Yuan S, Michaëlsson K, Wan Z, Larsson SC
Calcif. Tissue Int. - (-) - [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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Genetic Affinities among Southern Africa Hunter-Gatherers and the Impact of Admixing Farmer and Herder Populations.
Vicente M, Jakobsson M, Ebbesen P, Schlebusch CM
Mol. Biol. Evol. 36 (9) 1849-1861 [2019-09-01; online 2019-07-10]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Ancestral Admixture Is the Main Determinant of Global Biodiversity in Fission Yeast.
Tusso S, Nieuwenhuis BPS, Sedlazeck FJ, ..., Jeffares DC, Wolf JBW
Mol. Biol. Evol. 36 (9) 1975-1989 [2019-09-01; online 2019-06-22]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Impact of demography on linked selection in two outcrossing Brassicaceae species.
Mattila TM, Laenen B, Horvath R, ..., Savolainen O, Slotte T
Ecol Evol 9 (17) 9532-9545 [2019-09-00; online 2019-08-13]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Copy number variation and neuropsychiatric problems in females and males in the general population.
Martin J, Tammimies K, Karlsson R, ..., Lichtenstein P, Magnusson PKE
Am. J. Med. Genet. B Neuropsychiatr. Genet. 180 (6) 341-350 [2019-09-00; online 2018-10-11]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Large-scale GWAS reveals insights into the genetic architecture of same-sex sexual behavior.
Ganna A, Verweij KJH, Nivard MG, ..., Neale BM, Zietsch BP
Science 365 (6456) - [2019-08-30; online 2019-08-31]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Neuroticism as a predictor of frailty in old age: a genetically informative approach.
Danielsdottir HB, Jylhävä J, Hägg S, ..., Mosing MA, Lehto K
Psychosom Med - (-) - [2019-08-28; online 2019-08-28]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Profiling surface proteins on individual exosomes using a proximity barcoding assay.
Wu D, Yan J, Shen X, ..., Landegren U, Kamali-Moghaddam M
Nat Commun 10 (1) 3854 [2019-08-26; online 2019-08-26]
Bioinformatics Compute and Storage [Service] PLA and Single Cell Proteomics [Technology development]
PubMed DOI Crossref
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]
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] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
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
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
DOI Crossref
Microbial utilization of simple carbon substrates in boreal peat soils at low temperatures
Segura JH, Nilsson MB, Schleucher J, ..., Bertilsson S, Öquist MG
Soil Biology and Biochemistry 135 (-) 438-448 [2019-08-00; online 2019-08-00]
Bioinformatics Compute and Storage [Service] Swedish NMR Centre (SNC) [Collaborative]
PubMed DOI Crossref
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]
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) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
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
Goodbye reference, hello genome graphs.
Ameur A
Nat. Biotechnol. 37 (8) 866-868 [2019-08-00; online 2019-08-04]
Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
Complete subspecies-level phylogeny of the Oriolidae (Aves: Passeriformes): Out of Australasia and return.
Jønsson KA, Blom MPK, Marki PZ, ..., Ericson PGP, Irestedt M
Mol. Phylogenet. Evol. 137 (-) 200-209 [2019-08-00; online 2019-03-23]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
DOI Crossref
Boreal tree species affect soil organic matter composition and saprotrophic mineralization rates
Segura JH, Nilsson MB, Sparrman T, ..., Tolu J, Öquist MG
Plant Soil 441 (1-2) 173-190 [2019-08-00; online 2019-05-24]
Bioinformatics Compute and Storage [Service] Swedish NMR Centre (SNC) [Collaborative]
PubMed DOI Crossref
Shared and Unique Patterns of DNA Methylation in Systemic Lupus Erythematosus and Primary Sjögren's Syndrome.
Imgenberg-Kreuz J, Almlöf JC, Leonard D, ..., Sandling JK, Nordmark G
Front Immunol 10 (-) 1686 [2019-07-30; online 2019-07-30]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Multiplex plasma protein profiling identifies novel markers to discriminate patients with adenocarcinoma of the lung.
Djureinovic D, Pontén V, Landelius P, ..., Micke P, Ståhle E
BMC Cancer 19 (1) 741 [2019-07-29; online 2019-07-29]
Bioinformatics Compute and Storage [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Collaborative]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Combinations of Spok genes create multiple meiotic drivers in Podospora.
Vogan AA, Ament-Velásquez SL, Granger-Farbos A, ..., Saupe SJ, Johannesson H
Elife 8 (-) - [2019-07-26; online 2019-07-26]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
TAF1, associated with intellectual disability in humans, is essential for embryogenesis and regulates neurodevelopmental processes in zebrafish.
Gudmundsson S, Wilbe M, Filipek-Górniok B, ..., Annerén G, Bondeson ML
Sci Rep 9 (1) 10730 [2019-07-24; online 2019-07-24]
BioImage Informatics [Collaborative] Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] Clinical Genomics Uppsala [Collaborative] Genome Engineering Zebrafish [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
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
Genome and plasmid diversity of Extended-Spectrum β-Lactamase-producing Escherichia coli ST131 - tracking phylogenetic trajectories with Bayesian inference.
Ny S, Sandegren L, Salemi M, Giske CG
Sci Rep 9 (1) 10291 [2019-07-16; online 2019-07-16]
Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Association between Copy Number Variation and Response to Social Skills Training in Autism Spectrum Disorder.
Tammimies K, Li D, Rabkina I, ..., Choque-Olsson N, Bölte S
Sci Rep 9 (1) 9810 [2019-07-08; online 2019-07-08]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Service] Bioinformatics Support, Infrastructure and Training [Service]
DOI Crossref
GUESSmyLT: Software to guess the RNA-Seq library type of paired and single end read files
Wik E, Olin H, Haughey C, Klasson L, Dainat J
JOSS 4 (39) 1344 [2019-07-07; online 2019-07-07]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] 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
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
DOI Crossref
Surface activated polyethylene separator promoting Li+ ion transport in gel polymer electrolytes and cycling stability of Li-metal anode
Qiu Z, Shi L, Wang Z, ..., Zhao Y, Yuan S
Chemical Engineering Journal 368 (-) 321-330 [2019-07-00; online 2019-07-00]
Bioinformatics Compute and Storage [Service] Swedish NMR Centre (SNC) [Service]
PubMed DOI Crossref
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]
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
Seeking the ultimate challenge.
Brodin P
Nat. Med. 25 (7) 1026 [2019-07-00; online 2019-07-05]
Bioinformatics Compute and Storage [Service] Cellular Immunomonitoring [Technology development]
PubMed DOI Crossref
Leucocytosis is associated with retinopathy of prematurity in extremely preterm infants.
Lundgren P, Klevebro S, Brodin P, ..., Hallberg B, Hellström A
Acta Paediatr. 108 (7) 1357-1358 [2019-07-00; online 2019-04-12]
Bioinformatics Compute and Storage [Service] Cellular Immunomonitoring [Collaborative]
PubMed DOI Crossref
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]
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
Expanding the phenotypic spectrum of osteogenesis imperfecta type V including heterotopic ossification of muscle origins and attachments.
Clewemar P, Hailer NP, Hailer Y, ..., Ljunggren Ö, Stattin EL
Mol Genet Genomic Med 7 (7) e00723 [2019-07-00; online 2019-05-16]
Bioinformatics Compute and Storage [Service] Clinical Genomics Uppsala [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Analyzing DNA methylation patterns in subjects diagnosed with schizophrenia using machine learning methods.
Torabi Moghadam B, Etemadikhah M, Rajkowska G, ..., Feuk L, Carlström EL
J Psychiatr Res 114 (-) 41-47 [2019-07-00; online 2019-04-02]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
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]
DOI Crossref
Shotgun Environmental DNA, Pollen, and Macrofossil Analysis of Lateglacial Lake Sediments From Southern Sweden
Parducci L, Alsos IG, Unneberg P, ..., Slotte T, Wohlfarth B
Front. Ecol. Evol. 7 (-) 189 [2019-06-20; online 2019-06-20]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Comparative genomics of Mycobacterium mucogenicum and Mycobacterium neoaurum clade members emphasizing tRNA and non-coding RNA.
Behra PRK, Pettersson BMF, Das S, Dasgupta S, Kirsebom LA
BMC Evol. Biol. 19 (1) 124 [2019-06-18; online 2019-06-18]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
A Call for Blood-In Human Immunology.
Brodin P, Duffy D, Quintana-Murci L
Immunity 50 (6) 1335-1336 [2019-06-18; online 2019-06-20]
Bioinformatics Compute and Storage [Service] Cellular Immunomonitoring [Technology development]
PubMed DOI Crossref
Ouabain-regulated phosphoproteome reveals molecular mechanisms for Na+, K+–ATPase control of cell adhesion, proliferation, and survival
Panizza E, Zhang L, Fontana JM, ..., Lehtiö J, Aperia A
The FASEB Journal - (-) fj.201900445R [2019-06-14; online 2019-06-14]
Bioinformatics Compute and Storage [Service] Global Proteomics and Proteogenomics [Technology development] Integrated Microscopy Technologies Stockholm [Collaborative]
PubMed DOI Crossref
Systematic assessment of antibody selectivity in plasma based on a resource of enrichment profiles.
Fredolini C, Byström S, Sanchez-Rivera L, ..., Lehtiö J, Schwenk JM
Sci Rep 9 (1) 8324 [2019-06-06; online 2019-06-06]
Affinity Proteomics Stockholm [Technology development] Autoimmunity and Serology Profiling [Technology development] Bioinformatics Compute and Storage [Service] Global Proteomics and Proteogenomics [Technology development]
PubMed DOI Crossref
Identification of DNA methylation patterns predisposing for an efficient response to BCG vaccination in healthy BCG-naïve subjects.
Das J, Verma D, Gustafsson M, Lerm M
Epigenetics 14 (6) 589-601 [2019-06-00; online 2019-04-22]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Gene fusion involving the insulin-like growth factor 1 receptor in an ALK-negative inflammatory myofibroblastic tumour.
Piarulli G, Puls F, Wängberg B, ..., Arbajian E, Mertens F
Histopathology 74 (7) 1098-1102 [2019-06-00; online 2019-04-24]
Bioinformatics Compute and Storage [Service] Clinical Genomics Lund [Service]
PubMed DOI Crossref
Further support linking the 22q11.2 microduplication to an increased risk of bladder exstrophy and highlighting LZTR1 as a candidate gene.
Lundin J, Markljung E, Baranowska Körberg I, ..., Lindstrand A, Nordenskjöld A
Mol Genet Genomic Med 7 (6) e666 [2019-06-00; online 2019-05-01]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Crystal structure of the catalytic domain of the Weissella oryzae botulinum‐like toxin
Košenina S, Masuyer G, Zhang S, Dong M, Stenmark P
FEBS Lett 593 (12) 1403-1410 [2019-06-00; online 2019-05-31]
Bioinformatics Compute and Storage [Service] Protein Science Facility (PSF) [Service]
PubMed DOI Crossref
Can markers of biological age predict dependency in old age?
Jylhävä J, Jiang M, Foebel AD, Pedersen NL, Hägg S
Biogerontology 20 (3) 321-329 [2019-06-00; online 2019-01-21]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
A targeted proteomics approach reveals a serum protein signature as diagnostic biomarker for resectable gastric cancer.
Shen Q, Polom K, Williams C, ..., Roviello F, Kamali-Moghaddam M
EBioMedicine 44 (-) 322-333 [2019-06-00; online 2019-05-28]
Bioinformatics Compute and Storage [Service] Clinical Biomarkers [Service] Glycoproteomics [Collaborative] PLA and Single Cell Proteomics [Technology development]
PubMed DOI Crossref
A novel RAD21 p.(Gln592del) variant expands the clinical description of Cornelia de Lange syndrome type 4 - Review of the literature.
Gudmundsson S, Annerén G, Marcos-Alcalde Í, ..., Gómez-Puertas P, Bondeson ML
Eur J Med Genet 62 (6) 103526 [2019-06-00; online 2018-08-17]
Bioinformatics Compute and Storage [Service] Clinical Genomics Uppsala [Collaborative]
PubMed DOI Crossref
Serum Metabolite Markers of Dementia Through Quantitative NMR Analysis: The Importance of Threonine-Linked Metabolic Pathways.
Figueira J, Adolfsson R, Nordin Adolfsson A, Nyberg L, Öhman A
J. Alzheimers Dis. 69 (3) 763-774 [2019-05-28; online 2019-05-28]
Bioinformatics Compute and Storage [Service] Swedish NMR Centre (SNC) [Collaborative]
PubMed DOI Crossref
The viral protein corona directs viral pathogenesis and amyloid aggregation.
Ezzat K, Pernemalm M, Pålsson S, ..., Spetz AL, El Andaloussi S
Nat Commun 10 (1) 2331 [2019-05-27; online 2019-05-27]
Bioinformatics Compute and Storage [Service] Global Proteomics and Proteogenomics [Technology development]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Automated Cell Processing for Mass Cytometry Experiments.
Mikes J, Olin A, Lakshmikanth T, Chen Y, Brodin P
Methods Mol. Biol. 1989 (-) 111-123 [2019-05-12; online 2019-05-12]
Bioinformatics Compute and Storage [Service] Cellular Immunomonitoring [Technology development]
PubMed DOI Crossref
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
Genetical Genomics of Tonic Immobility in the Chicken.
Fogelholm J, Inkabi S, Höglund A, ..., Henriksen R, Wright D
Genes 10 (5) - [2019-05-07; online 2019-05-07]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [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
SciPipe: A workflow library for agile development of complex and dynamic bioinformatics pipelines.
Lampa S, Dahlö M, Alvarsson J, Spjuth O
Gigascience 8 (5) - [2019-05-01; online 2019-04-28]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development]
PubMed DOI Crossref
Prompt apoptotic response to high glucose in SGLT-expressing renal cells.
Nilsson LM, Zhang L, Bondar A, ..., Scott L, Aperia A
Am. J. Physiol. Renal Physiol. 316 (5) F1078-F1089 [2019-05-01; online 2019-03-13]
Bioinformatics Compute and Storage [Service] Integrated Microscopy Technologies Stockholm [Service]
PubMed DOI Crossref
How Linked Selection Shapes the Diversity Landscape in Ficedula Flycatchers
Rettelbach A, Nater A, Ellegren H
Genetics 212 (1) 277-285 [2019-05-01; online 2019-03-14]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Comparative analyses identify genomic features potentially involved in the evolution of birds-of-paradise.
Prost S, Armstrong EE, Nylander J, ..., Ericson PGP, Irestedt M
Gigascience 8 (5) - [2019-05-01; online 2019-01-29]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Genotype-free estimation of allele frequencies reduces bias and improves demographic inference from RADSeq data.
Warmuth VM, Ellegren H
Mol Ecol Resour 19 (3) 586-596 [2019-05-00; online 2019-04-17]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Footprints of adaptive evolution revealed by whole Z chromosomes haplotypes in flycatchers.
Nadachowska-Brzyska K, Burri R, Ellegren H
Mol. Ecol. 28 (9) 2290-2304 [2019-05-00; online 2019-05-29]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Exome sequencing in 51 early onset non-familial CRC cases.
Thutkawkorapin J, Lindblom A, Tham E
Mol Genet Genomic Med 7 (5) e605 [2019-05-00; online 2019-02-27]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [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
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]
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
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]
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
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
A Genome-Wide Association Study of Bisphosphonate-Associated Atypical Femoral Fracture.
Kharazmi M, Michaëlsson K, Schilcher J, ..., Wadelius M, Hallberg P
Calcif. Tissue Int. - (-) - [2019-04-20; online 2019-04-20]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
RNA Sequencing Provides Novel Insights into the Transcriptome of Aldosterone Producing Adenomas.
Backman S, Åkerström T, Maharjan R, ..., Hellman P, Björklund P
Sci Rep 9 (1) 6269 [2019-04-18; online 2019-04-18]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [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]
PubMed DOI Crossref
SQSTM1/p62-Directed Metabolic Reprogramming Is Essential for Normal Neurodifferentiation.
Calvo-Garrido J, Maffezzini C, Schober FA, ..., Freyer C, Wredenberg A
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
Breast cancer quantitative proteome and proteogenomic landscape.
Johansson HJ, Socciarelli F, Vacanti NM, ..., Børresen-Dale AL, Lehtiö J
Nat Commun 10 (1) 1600 [2019-04-08; online 2019-04-08]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Global Proteomics and Proteogenomics [Technology development] Integrated Microscopy Technologies Stockholm [Service]
PubMed DOI Crossref
A hybrid de novo genome assembly of the honeybee, Apis mellifera, with chromosome-length scaffolds.
Wallberg A, Bunikis I, Pettersson OV, ..., Robinson GE, Webster MT
BMC Genomics 20 (1) 275 [2019-04-08; online 2019-04-08]
Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
High-Quality Library Preparation for NGS-Based Immunoglobulin Germline Gene Inference and Repertoire Expression Analysis.
Vázquez Bernat N, Corcoran M, Hardt U, ..., Martin M, Karlsson Hedestam GB
Front Immunol 10 (-) 660 [2019-04-05; online 2019-04-05]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
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
Molecular Characterization and Comparative Genomics of Clinical Hybrid Shiga Toxin-Producing and Enterotoxigenic Escherichia coli (STEC/ETEC) Strains in Sweden.
Bai X, Zhang J, Ambikan A, ..., Xiong Y, Matussek A
Sci Rep 9 (1) 5619 [2019-04-04; online 2019-04-04]
Bioinformatics Compute and Storage [Service] Clinical Genomics Stockholm [Service]
PubMed DOI Crossref
Proteogenomics and Hi-C reveal transcriptional dysregulation in high hyperdiploid childhood acute lymphoblastic leukemia.
Yang M, Vesterlund M, Siavelis I, ..., Lehtiö J, Paulsson K
Nat Commun 10 (1) 1519 [2019-04-03; online 2019-04-03]
Bioinformatics Compute and Storage [Service] Clinical Genomics Lund [Service] Global Proteomics and Proteogenomics [Technology development]
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
B cell profiling in malaria reveals expansion and remodelling of CD11c+ B cell subsets.
Sundling C, Rönnberg C, Yman V, ..., Persson KE, Färnert A
JCI Insight 5 (-) - [2019-04-02; online 2019-04-02]
Bioinformatics Compute and Storage [Service] Cellular Immunomonitoring [Service]
PubMed DOI Crossref