Bioinformatics Support, Infrastructure and Training

Publications

Infrastructure Units

SciLifeLab Infrastructure Unit since 2021.

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

Started: 2021

Ended: Current

Year 2022

Weakened resilience of benthic microbial communities in the face of climate change

Seidel L, Ketzer M, Broman E, ..., Hylander S, Dopson M

ISME COMMUN. 2 (1) - [2022-12-00; online 2022-03-08]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Combined Transcriptomic and Protein Array Cytokine Profiling of Human Stem Cells from Dental Apical Papilla Modulated by Oral Bacteria

Zymovets V, Razghonova Y, Rakhimova O, ..., Landström M, Romani Vestman N

Int J Mol Sci 23 (9) 5098 [2022-05-03; online 2022-05-03]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

PubMed DOI Crossref

A starch- and sucrose-reduced dietary intervention in irritable bowel syndrome patients produced a shift in gut microbiota composition along with changes in phylum, genus, and amplicon sequence variant abundances, without affecting the micro-RNA levels.

Nilholm C, Manoharan L, Roth B, D'Amato M, Ohlsson B

United European Gastroenterol J - (-) - [2022-04-28; online 2022-04-28]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

PubMed DOI Crossref

Findzx: an automated pipeline for detecting and visualising sex chromosomes using whole-genome sequencing data.

Sigeman H, Sinclair B, Hansson B

BMC Genomics 23 (1) 328 [2022-04-27; online 2022-04-27]

Bioinformatics Long-term Support WABI [Service] Bioinformatics Support, Infrastructure and Training [Service]

PubMed DOI Crossref

App-based COVID-19 syndromic surveillance and prediction of hospital admissions in COVID Symptom Study Sweden.

Kennedy B, Fitipaldi H, Hammar U, ..., Franks PW, Fall T

Nat Commun 13 (1) 2110 [2022-04-21; online 2022-04-21]

Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

PubMed DOI Crossref

Evaluation of polarity switching for untargeted lipidomics using liquid chromatography coupled to high resolution mass spectrometry.

Carlsson H, Vaivade A, Emami Khoonsari P, Burman J, Kultima K

Journal of Chromatography B 1195 (-) 123200 [2022-04-15; online 2022-02-28]

Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Environmentally-induced DNA methylation is inherited across generations in an aquatic keystone species

Feiner N, Radersma R, Vasquez L, ..., Heijmans BT, Uller T

iScience - (-) 104303 [2022-04-00; online 2022-04-00]

Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

PubMed DOI Crossref

The genomic architecture of the passerine MHC region: High repeat content and contrasting evolutionary histories of single copy and tandemly duplicated MHC genes.

Westerdahl H, Mellinger S, Sigeman H, ..., Wolf JBW, Strandh M

Mol Ecol Resour - (-) - [2022-03-29; online 2022-03-29]

Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Long read [Collaborative] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

PubMed DOI Crossref

Clonotypic analysis of protective influenza M2e-specific lung resident Th17 memory cells reveals extensive functional diversity.

Omokanye A, Ong LC, Lebrero-Fernandez C, ..., Czarnewski P, Lycke N

Mucosal Immunol - (-) - [2022-03-08; online 2022-03-08]

Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

PubMed DOI Crossref

Clonal relations in the mouse brain revealed by single-cell and spatial transcriptomics.

Ratz M, von Berlin L, Larsson L, ..., Lundeberg J, Frisén J

Nat. Neurosci. 25 (3) 285-294 [2022-03-00; online 2022-02-24]

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

Regulatory networks and 5' partner usage of miRNA host gene fusions in breast cancer.

Hafstað V, Søkilde R, Häkkinen J, ..., Rovira C, Persson H

Int. J. Cancer - (-) - [2022-02-19; online 2022-02-19]

Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Transposon- and Genome Dynamics in the Fungal Genus Neurospora: Insights from Nearly Gapless Genome Assemblies

Nguyen D, Peona V, Unneberg P, ..., Jern P, Johannesson H

Fungal Genetics Reports 66 (1) - [2022-02-18; online 2022-02-18]

Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

PubMed DOI Crossref

Transcriptomic analysis reveals proinflammatory signatures associated with acute myeloid leukemia progression.

Stratmann S, Yones SA, Garbulowski M, ..., Komorowski J, Holmfeldt L

Blood Adv 6 (1) 152-164 [2022-01-11; online 2021-10-08]

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] National Genomics Infrastructure [Service]

PubMed DOI Crossref

Genomic Signatures of Sexual Selection on Pollen-Expressed Genes in Arabis alpina.

Gutiérrez-Valencia J, Fracassetti M, Horvath R, ..., Kolář F, Slotte T

Mol. Biol. Evol. 39 (1) - [2022-01-07; online 2021-12-09]

Bioinformatics Long-term Support WABI [Service] Bioinformatics Support, Infrastructure and Training [Service]

Year 2021

PubMed DOI Crossref

Whole-Exome Sequencing of HPV Positive Tonsillar and Base of Tongue Squamous Cell Carcinomas Reveals a Global Mutational Pattern along with Relapse-Specific Somatic Variants.

Ährlund-Richter A, Holzhauser S, Dalianis T, Näsman A, Mints M

Cancers (Basel) 14 (1) - [2021-12-24; online 2021-12-24]

Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]

Immune-Proteome Profiling in Classical Hodgkin Lymphoma Tumor Diagnostic Tissue

Gholiha AR, Hollander P, Löf L, ..., Kamali-Moghaddam M, Enblad G

Cancers (Basel) 14 (1) 9 [2021-12-21; online 2021-12-21]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

PubMed DOI Crossref

A Phase 2 Trial of the Effect of Antiandrogen Therapy on COVID-19 Outcome: No Evidence of Benefit, Supported by Epidemiology and In Vitro Data.

Welén K, Rosendal E, Gisslén M, ..., Överby AK, Josefsson A

Eur. Urol. - (-) - [2021-12-15; online 2021-12-15]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

PubMed DOI Crossref

Clinical and biological relevance of the transcriptomic-based prostate cancer metastasis subtypes MetA-C.

Thysell E, Köhn L, Semenas J, ..., Bergh A, Wikström P

Mol Oncol - (-) - [2021-12-10; online 2021-12-10]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

PubMed DOI Crossref

Identification and Functional Characterization of a Novel Susceptibility Locus for Small Vessel Vasculitis with MPO-ANCA.

Dahlqvist J, Ekman D, Sennblad B, ..., Eriksson P, Lindblad-Toh K

Rheumatology (Oxford) - (-) - [2021-12-09; online 2021-12-09]

Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Recommendations for connecting molecular sequence and biodiversity research infrastructures through ELIXIR

Waterhouse RM, Adam-Blondon AF, Agosti D, ..., Willassen NP, Lanfear J

F1000Res 10 (-) 1238 [2021-12-03; online 2021-12-03]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [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]

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

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

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

Leaf Apoplast of Field-Grown Potato Analyzed by Quantitative Proteomics and Activity-Based Protein Profiling.

Abreha KB, Alexandersson E, Resjö S, ..., Levander F, Andreasson E

Int J Mol Sci 22 (21) - [2021-11-06; online 2021-11-06]

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

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

Tonsillar Cancer with High CD8+ T-Cell Infiltration Features Increased Levels of Dendritic Cells and Transcriptional Regulation Associated with an Inflamed Tumor Microenvironment.

Jimenez DG, Sobti A, Askmyr D, ..., Greiff L, Lindstedt M

Cancers (Basel) 13 (21) - [2021-10-25; online 2021-10-25]

Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [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

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

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]

Population genomics of the critically endangered kākāpō

Dussex N, van der Valk T, Morales HE, ..., Robertson BC, Dalén L

Cell Genomics 1 (1) 100002 [2021-10-00; online 2021-10-00]

Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

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

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

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

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]

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]

Calcium and pH interaction limits bloom formation and expansion of a nuisance microalga

Gollnisch R, Alling T, Stockenreiter M, ..., Grabowska M, Rengefors K

Limnol Oceanogr 66 (9) 3523-3534 [2021-09-00; online 2021-07-30]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

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

Genome assemblies of three closely related leaf beetle species (Galerucella spp.).

Yang X, Slotte T, Dainat J, Hambäck PA

G3 (Bethesda) 11 (8) - [2021-08-07; online 2021-12-02]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

PubMed DOI Crossref

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]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

High-Resolution Proteomic Profiling Shows Sexual Dimorphism in Zebrafish Heart-Associated Proteins.

Niksirat H, Siino V, Steinbach C, Levander F

J. Proteome Res. 20 (8) 4075-4088 [2021-08-06; online 2021-06-29]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

PubMed DOI Crossref

Shifts in gene expression variability in the blood-stage of Plasmodium relictum.

Kalbskopf V, Ahrén D, Valkiūnas G, Palinauskas V, Hellgren O

Gene 792 (-) 145723 [2021-08-05; online 2021-05-18]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

PubMed DOI Crossref

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]

Affinity Proteomics Uppsala [Technology development] 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

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]

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) NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure

PubMed DOI Crossref

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]

PubMed DOI Crossref

The enigmatic RNase MRP of kinetoplastids.

Alm Rosenblad M, López MD, Samuelsson T

RNA Biol - (-) 1-9 [2021-07-25; online 2021-07-25]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

PubMed DOI Crossref

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]

PubMed DOI Crossref

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]

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

Monocytes in sarcoidosis are potent tumour necrosis factor producers and predict disease outcome.

Lepzien R, Liu S, Czarnewski P, ..., Grunewald J, Smed-Sörensen A

Eur. Respir. J. 58 (1) 2003468 [2021-07-00; online 2021-07-22]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

PubMed DOI Crossref

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]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Global Proteomics and Proteogenomics [Technology development]

PubMed DOI Crossref

Gene regulation of the avian malaria parasite Plasmodium relictum, during the different stages within the mosquito vector.

Sekar V, Rivero A, Pigeault R, ..., Ahren D, Hellgren O

Genomics 113 (4) 2327-2337 [2021-07-00; online 2021-05-21]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

PubMed DOI Crossref

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]

Bioinformatics Compute and Storage [Service] Bioinformatics Support, Infrastructure and Training [Collaborative]

PubMed DOI Crossref

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]

Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]

PubMed DOI Crossref

Methods to Identify and Study the Evolution of Pseudogenes Using a Phylogenetic Approach.

Dainat J, Pontarotti P

Methods Mol. Biol. 2324 (-) 21-34 [2021-06-25; online 2021-06-25]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

PubMed DOI Crossref

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]

Affinity Proteomics Uppsala [Service] 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]

PubMed DOI Crossref

Single-cell BCR and transcriptome analysis after influenza infection reveals spatiotemporal dynamics of antigen-specific B cells.

Mathew NR, Jayanthan JK, Smirnov IV, ..., Bemark M, Angeletti D

Cell Rep 35 (12) 109286 [2021-06-22; online 2021-06-24]

Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Systems Biology [Collaborative]

PubMed DOI Crossref

Profiling of Extracellular Small RNAs Highlights a Strong Bias towards Non-Vesicular Secretion.

Sork H, Conceicao M, Corso G, ..., El Andaloussi S, Mäger I

Cells 10 (6) 1543 [2021-06-18; online 2021-06-18]

Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

PubMed DOI Crossref

BUTTERFLY: addressing the pooled amplification paradox with unique molecular identifiers in single-cell RNA-seq.

Gustafsson J, Robinson J, Nielsen J, Pachter L

Genome Biol. 22 (1) 174 [2021-06-08; online 2021-06-08]

Bioinformatics Support, Infrastructure and Training [Collaborative] Systems Biology

PubMed DOI Crossref

Genomic and transcriptomic analysis of the thermophilic lignocellulose-degrading fungus Thielavia terrestris LPH172.

Tõlgo M, Hüttner S, Rugbjerg P, ..., Larsbrink J, Olsson L

Biotechnol Biofuels 14 (1) 131 [2021-06-03; online 2021-06-03]

Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]

PubMed DOI Crossref

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]

Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

PubMed DOI Crossref

Genomic Characterization of the Barnacle Balanus improvisus Reveals Extreme Nucleotide Diversity in Coding Regions.

Alm Rosenblad M, Abramova A, Lind U, ..., Nystedt B, Blomberg A

Mar Biotechnol (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

PubMed DOI Crossref

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]

Affinity Proteomics Uppsala [Technology development] Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

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

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Genetic Risk Score for Serum 25-Hydroxyvitamin D Concentration Helps to Guide Personalized Vitamin D Supplementation in Healthy Finnish Adults.

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New Insights into the Microbial Profiles of Infected Root Canals in Traumatized Teeth.

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Genome-Scale Mapping Reveals Complex Regulatory Activities of RpoN in Yersinia pseudotuberculosis.

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Evolution from adherent to suspension: systems biology of HEK293 cell line development.

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The influence of common polygenic risk and gene sets on social skills group training response in autism spectrum disorder.

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Reconstruction of the birth of a male sex chromosome present in Atlantic herring.

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Transcriptome analysis of EPO and GFP HEK293 Cell-lines Reveal Shifts in Energy and ER Capacity Support Improved Erythropoietin Production in HEK293F Cells

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Comparative analysis of genome-wide DNA methylation in Neurospora.

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High-Throughput Sequencing and Unsupervised Analysis of Formyltetrahydrofolate Synthetase (FTHFS) Gene Amplicons to Estimate Acetogenic Community Structure.

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Uncovering the hidden diversity of litter-decomposition mechanisms in mushroom-forming fungi.

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Prototypical pacemaker neurons interact with the resident microbiota.

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Genome assembly of the basket willow, Salix viminalis, reveals earliest stages of sex chromosome expansion.

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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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Single cell transcriptomics identifies stem cell-derived graft composition in a model of Parkinson's disease.

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Analysis of DNA methylation patterns in the tumor immune microenvironment of metastatic melanoma.

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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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Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

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Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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Robinson JL, Kocabaş P, Wang H, ..., Uhlén M, Nielsen J

Sci Signal 13 (624) - [2020-03-24; online 2020-03-24]

Bioinformatics Support, Infrastructure and Training [Technology development] Systems Biology [Technology development]

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Specific functions for Mediator complex subunits from different modules in the transcriptional response of Arabidopsis thaliana to abiotic stress.

Crawford T, Karamat F, Lehotai N, ..., Strand Å, Björklund S

Sci Rep 10 (1) 5073 [2020-03-19; online 2020-03-19]

Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]

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Proc. Natl. Acad. Sci. U.S.A. 117 (10) 5376-5385 [2020-03-10; online 2020-02-25]

Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

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Extensive dissemination and intraclonal maturation of HIV Env vaccine-induced B cell responses.

Phad GE, Pushparaj P, Tran K, ..., Wyatt RT, Karlsson Hedestam GB

J. Exp. Med. 217 (2) - [2020-02-03; online 2019-11-11]

Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

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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]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

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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.

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BMC Biol. 18 (1) 11 [2020-01-28; online 2020-01-28]

Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

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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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Transcriptomic profiling of skeletal muscle adaptations to exercise and inactivity.

Pillon NJ, Gabriel BM, Dollet L, ..., Krook A, Zierath JR

Nat Commun 11 (1) 470 [2020-01-24; online 2020-01-24]

Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]

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A spontaneous mitonuclear epistasis converging on Rieske Fe-S protein exacerbates complex III deficiency in mice.

Purhonen J, Grigorjev V, Ekiert R, ..., Fellman V, Kallijärvi J

Nat Commun 11 (1) 322 [2020-01-16; online 2020-01-16]

Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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DNA methylation changes in Down syndrome derived neural iPSCs uncover co-dysregulation of ZNF and HOX3 families of transcription factors.

Laan L, Klar J, Sobol M, ..., Schuster J, Dahl N

Clin Epigenetics 12 (1) 9 [2020-01-08; online 2020-01-08]

Bioinformatics Long-term Support WABI [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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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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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]

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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]

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Consequences of past climate change and recent human persecution on mitogenomic diversity in the arctic fox.

Larsson P, von Seth J, Hagen IJ, ..., Stanton DWG, Dalén L

Philos. Trans. R. Soc. Lond., B, Biol. Sci. 374 (1788) 20190212 [2019-12-23; online 2019-11-04]

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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Gene Expression Alterations during Development of Castration-Resistant Prostate Cancer Are Detected in Circulating Tumor Cells.

Josefsson A, Larsson K, Freyhult E, Damber J, Welén K

Cancers (Basel) 12 (1) - [2019-12-21; online 2019-12-21]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

PubMed DOI Crossref

Protein profiling and network enrichment analysis in individuals before and after the onset of rheumatoid arthritis.

Brink M, Lundquist A, Alexeyenko A, Lejon K, Rantapää-Dahlqvist S

Arthritis Res. Ther. 21 (1) 288 [2019-12-16; online 2019-12-16]

Affinity Proteomics Stockholm [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [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]

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iFISH is a publically available resource enabling versatile DNA FISH to study genome architecture

Gelali E, Girelli G, Matsumoto M, ..., Crosetto N, Bienko M

Nat Commun 10 (1) - [2019-12-00; online 2019-04-09]

Advanced FISH Technologies [Technology development] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]

PubMed DOI Crossref

Whole genome DNA sequencing provides an atlas of somatic mutagenesis in healthy human cells and identifies a tumor-prone cell type

Franco I, Helgadottir HT, Moggio A, ..., Supek F, Eriksson M

Genome Biol. 20 (1) - [2019-12-00; online 2019-12-18]

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Transmission dynamics study of tuberculosis isolates with whole genome sequencing in southern Sweden

Alaridah N, Hallbäck ET, Tångrot J, ..., Kaijser B, Godaly G

Sci Rep 9 (1) - [2019-12-00; online 2019-03-20]

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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Transcriptomes of Dravet syndrome iPSC derived GABAergic cells reveal dysregulated pathways for chromatin remodeling and neurodevelopment.

Schuster J, Laan L, Klar J, ..., Birnir B, Dahl N

Neurobiol. Dis. 132 (-) 104583 [2019-12-00; online 2019-08-21]

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Towards a standardized bioinformatics infrastructure for N- and O-glycomics

Rojas-Macias MA, Mariethoz J, Andersson P, ..., Lisacek F, Karlsson NG

Nat Commun 10 (1) - [2019-12-00; online 2019-07-22]

Bioinformatics Support and Infrastructure [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development] Glycoproteomics [Technology development]

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The genomic footprint of sexual conflict.

Sayadi A, Martinez Barrio A, Immonen E, ..., Nystedt B, Arnqvist G

Nat Ecol Evol 3 (12) 1725-1730 [2019-12-00; online 2019-11-18]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

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The bio.tools registry of software tools and data resources for the life sciences

Ison J, Ienasescu H, Chmura P, ..., Løngreen P, Brunak S

Genome Biol. 20 (1) 164 [2019-12-00; online 2019-08-12]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

PubMed DOI Crossref

Physiology, Metabolism, and Fossilization of Hot-Spring Filamentous Microbial Mats.

Dong Y, Sanford RA, Inskeep WP, ..., Fried GA, Fouke BW

Astrobiology 19 (12) 1442-1458 [2019-12-00; online 2019-04-30]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

PubMed DOI Crossref

Modelling of zero-inflation improves inference of metagenomic gene count data.

Jonsson V, Österlund T, Nerman O, Kristiansson E

Stat Methods Med Res 28 (12) 3712-3728 [2019-12-00; online 2018-11-25]

Bioinformatics Support, Infrastructure and Training [Technology development] Systems Biology [Technology development]

PubMed DOI Crossref

Improved power and precision with whole genome sequencing data in genome-wide association studies of inflammatory biomarkers

Höglund J, Rafati N, Rask-Andersen M, ..., Ek WE, Johansson Å

Sci Rep 9 (1) - [2019-12-00; online 2019-11-14]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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Conbase: a software for unsupervised discovery of clonal somatic mutations in single cells through read phasing

Hård J, Al Hakim E, Kindblom M, ..., Mold JE, Frisén J

Genome Biol. 20 (1) - [2019-12-00; online 2019-04-01]

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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ATAC-seq reveals alterations in open chromatin in pancreatic islets from subjects with type 2 diabetes

Bysani M, Agren R, Davegårdh C, ..., Bacos K, Ling C

Sci Rep 9 (1) - [2019-12-00; online 2019-05-23]

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]

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The Mastery Rubric for Bioinformatics: A tool to support design and evaluation of career-spanning education and training.

Tractenberg RE, Lindvall JM, Attwood TK, Via A

PLoS ONE 14 (11) e0225256 [2019-11-26; online 2019-11-26]

Bioinformatics Support and Infrastructure [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development]

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TcellSubC: An Atlas of the Subcellular Proteome of Human T Cells.

Joshi RN, Stadler C, Lehmann R, ..., Schmidt A, Vesterlund M

Front Immunol 10 (-) 2708 [2019-11-26; online 2019-11-26]

Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] Global Proteomics and Proteogenomics [Technology development] Spatial Proteomics [Collaborative]

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Optimizing cultivation of Cordyceps militaris for fast growth and cordycepin overproduction using rational design of synthetic media.

Raethong N, Wang H, Nielsen J, Vongsangnak W

Computational and Structural Biotechnology Journal 18 (-) 1-8 [2019-11-26; online 2019-11-26]

Bioinformatics Support, Infrastructure and Training [Collaborative] Systems Biology [Collaborative]

PubMed DOI Crossref

Lithium treatment reverses irradiation-induced changes in rodent neural progenitors and rescues cognition.

Zanni G, Goto S, Fragopoulou AF, ..., Hermanson O, Blomgren K

Mol. Psychiatry - (-) - [2019-11-14; online 2019-11-14]

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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Daytime melatonin levels in saliva are associated with inflammatory markers and anxiety disorders.

Sundberg I, Rasmusson AJ, Ramklint M, ..., Ekselius L, Cunningham JL

Psychoneuroendocrinology 112 (-) 104514 [2019-11-14; online 2019-11-14]

Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

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On-demand virtual research environments using microservices.

Capuccini M, Larsson A, Carone M, ..., Toor S, Spjuth O

PeerJ Comput Sci 5 (-) e232 [2019-11-11; online 2019-11-11]

Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

PubMed DOI Crossref

From cytogenetics to cytogenomics: whole-genome sequencing as a first-line test comprehensively captures the diverse spectrum of disease-causing genetic variation underlying intellectual disability.

Lindstrand A, Eisfeldt J, Pettersson M, ..., Lundin J, Nilsson D

Genome Med 11 (1) 68 [2019-11-07; online 2019-11-07]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Clinical Genomics Stockholm [Technology development] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

Leveraging European infrastructures to access 1 million human genomes by 2022.

Saunders G, Baudis M, Becker R, ..., Blomberg N, Scollen S

Nat. Rev. Genet. 20 (11) 693-701 [2019-11-00; online 2019-08-27]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

PubMed DOI Crossref

The architecture of the Plasmodiophora brassicae nuclear and mitochondrial genomes.

Stjelja S, Fogelqvist J, Tellgren-Roth C, Dixelius C

Sci Rep 9 (1) 15753 [2019-10-31; online 2019-10-31]

Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

PubMed DOI Crossref

Assembly and Analysis of the Genome Sequence of the Yeast Brettanomyces naardenensis CBS 7540.

Tiukova IA, Jiang H, Dainat J, ..., Gu Z, Passoth V

Microorganisms 7 (11) - [2019-10-26; online 2019-10-26]

Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]

PubMed DOI Crossref

Interoperable and scalable data analysis with microservices: applications in metabolomics.

Emami Khoonsari P, Moreno P, Bergmann S, ..., Kultima K, Spjuth O

Bioinformatics 35 (19) 3752-3760 [2019-10-01; online 2019-03-10]

Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

PubMed DOI Crossref

Industrial wastewater treatment plant enriches antibiotic resistance genes and alters the structure of microbial communities.

Bengtsson-Palme J, Milakovic M, Švecová H, ..., Grabic R, Udikovic-Kolic N

Water Res. 162 (-) 437-445 [2019-10-01; online 2019-07-04]

Bioinformatics Support, Infrastructure and Training [Collaborative] Systems Biology [Collaborative]

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Dissecting the Effects of Selection and Mutation on Genetic Diversity in Three Wood White (Leptidea) Butterfly Species.

Talla V, Soler L, Kawakami T, ..., Wiklund C, Backström N

Genome Biol Evol 11 (10) 2875-2886 [2019-10-01; online 2019-10-04]

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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Transcriptome and Proteome Profiling of Neural Induced Pluripotent Stem Cells from Individuals with Down Syndrome Disclose Dynamic Dysregulations of Key Pathways and Cellular Functions.

Sobol M, Klar J, Laan L, ..., Falk A, Dahl N

Mol Neurobiol 56 (10) 7113-7127 [2019-10-00; online 2019-04-13]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]

PubMed DOI Crossref

Exploring a Pool-seq-only approach for gaining population genomic insights in nonmodel species.

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]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

Clinical candidate and genistein analogue AXP107-11 has chemoenhancing functions in pancreatic adenocarcinoma through G protein-coupled estrogen receptor signaling.

Mesmar F, Dai B, Ibrahim A, ..., Fleming J, Williams C

Cancer Med - (-) - [2019-09-30; online 2019-09-30]

Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

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]

Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

PubMed DOI Crossref

Genome Sequencing of Pleurozium schreberi: The Assembled and Annotated Draft Genome of a Pleurocarpous Feather Moss.

Pederson ERA, Warshan D, Rasmussen U

G3 (Bethesda) 9 (9) 2791-2797 [2019-09-04; online 2019-09-04]

Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

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

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 M

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

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]

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

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

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

Comment on 'AIRE-deficient patients harbor unique high-affinity disease-ameliorating autoantibodies'.

Landegren N, Rosen LB, Freyhult E, ..., Anderson M, Kämpe O

Elife 8 (-) - [2019-06-27; online 2019-06-27]

Autoimmunity and Serology Profiling [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [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]

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

Microbiota data from low biomass milk samples is markedly affected by laboratory and reagent contamination.

Dahlberg J, Sun L, Persson Waller K, ..., Agenäs S, Dicksved J

PLoS ONE 14 (6) e0218257 [2019-06-13; online 2019-06-13]

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

Dysregulated autophagy in muscle precursor cells from humans with type 2 diabetes.

Henriksen TI, Wigge LV, Nielsen J, ..., Sandri M, Scheele C

Sci Rep 9 (1) 8169 [2019-06-03; online 2019-06-03]

Bioinformatics Support, Infrastructure and Training [Collaborative] Systems Biology [Collaborative]

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Ultrasensitive Immunoprofiling of Plasma Extracellular Vesicles Identifies Syndecan-1 as a Potential Tool for Minimally Invasive Diagnosis of Glioma.

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A comprehensive map coupling histone modifications with gene regulation in adult dopaminergic and serotonergic neurons

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Mutation, methylation, and gene expression profiles in dup(1q)-positive pediatric B-cell precursor acute lymphoblastic leukemia.

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Draft Genome Sequence for the Tree Pathogen Phytophthora plurivora.

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Genome Biol Evol 10 (9) 2432-2442 [2018-09-01; online 2018-09-01]

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Autosomal Recessive Osteogenesis Imperfecta Caused by a Novel Homozygous COL1A2 Mutation

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Calcif Tissue Int 103 (3) 353-358 [2018-09-00; online 2018-03-23]

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A fine-needle aspiration-based protein signature discriminates benign from malignant breast lesions

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Sequentially acting SOX proteins orchestrate astrocyte‐ and oligodendrocyte‐specific gene expression

Klum S, Zaouter C, Alekseenko Z, ..., Muhr J, Bergsland M

EMBO Rep. - (-) e46635 [2018-08-30; online 2018-08-30]

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Life history of Parnips and the evolutionary origin of gall wasps

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JHR 65 (-) 91-110 [2018-08-27; online 2018-08-27]

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Exploratory Profiling of Urine MicroRNAs in the dy Mouse Model of LAMA2-CMD: Relation to Disease Progression.2J/dy2J

Moreira Soares Oliveira B, Gawlik KI, Durbeej M, Holmberg J

PLoS Curr 10 (-) - [2018-08-27; online 2018-08-27]

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Global characterization of the Dicer-like protein DrnB roles in miRNA biogenesis in the social amoeba Dictyostelium discoideum.

Liao Z, Kjellin J, Hoeppner MP, Grabherr M, Söderbom F

RNA Biol 15 (7) 937-954 [2018-08-21; online 2018-08-21]

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Transcriptional Convergence of Oligodendrocyte Lineage Progenitors during Development.

Marques S, van Bruggen D, Vanichkina DP, ..., Taft RJ, Castelo-Branco G

Dev. Cell 46 (4) 504-517.e7 [2018-08-20; online 2018-08-02]

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Novel Autotrophic Organisms Contribute Significantly to the Internal Carbon Cycling Potential of a Boreal Lake

Peura S, Buck M, Aalto SL, ..., Nykänen H, Eiler A

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Reduction in White Blood Cell, Neutrophil and Red Blood Cell counts Related to Gender, HLA and Islet Autoantibodies in Swedish TEDDY Children at Increased Risk for Type 1 Diabetes

Salami F, Lee HS, Freyhult E, ..., Lernmark Å, Törn C

Diabetes - (-) db180355 [2018-08-13; online 2018-08-13]

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Stationary and portable sequencing-based approaches for tracing wastewater contamination in urban stormwater systems.

Hu YOO, Ndegwa N, Alneberg J, ..., Fagerberg J, Andersson AF

Sci Rep 8 (1) 11907 [2018-08-09; online 2018-08-09]

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Clonal relatedness in tumour pairs of breast cancer patients.

Biermann J, Parris TZ, Nemes S, ..., Karlsson P, Helou K

Breast Cancer Res. 20 (1) 96 [2018-08-09; online 2018-08-09]

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Plasma Protein Profiling Reveal Osteoprotegerin as a Marker of Prognostic Impact for Colorectal Cancer

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Transl Oncol 11 (4) 1034-1043 [2018-08-00; online 2018-08-00]

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Delineating closely related dinoflagellate lineages using phylotranscriptomics.

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Comprehensive RNA sequencing analysis in serum and muscle reveals novel small RNA signatures with biomarker potential for Duchenne Muscular Dystrophy

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Acute sleep loss results in tissue-specific alterations in genome-wide DNA methylation state and metabolic fuel utilization in humans

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Sci Adv 4 (8) eaar8590 [2018-08-00; online 2018-08-22]

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Model Communities Hint at Promiscuous Metabolic Linkages between Ubiquitous Free-Living Freshwater Bacteria.

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Current Opinion in Structural Biology 50 (-) 9-17 [2018-06-00; online 2018-06-00]

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Testis transcriptome alterations in zebrafish (Danio rerio) with reduced fertility due to developmental exposure to 17α-ethinyl estradiol

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SWI/SNF regulates half of its targets without the need of ATP-driven nucleosome remodeling by Brahma.

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BMC Genomics 19 (1) 367 [2018-05-18; online 2018-05-18]

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Transcriptomic analysis of the harvested endothelial cells in a swine model of mechanical thrombectomy.

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Neuroradiology - (-) - [2018-05-14; online 2018-05-14]

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Modulation of gene transcription and epigenetics of colon carcinoma cells by bacterial membrane vesicles.

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Sci Rep 8 (1) 7434 [2018-05-09; online 2018-05-09]

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Genome-wide multi-omics profiling of the 8p11-p12 amplicon in breast carcinoma.

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O6-methylguanine–induced transcriptional mutagenesis reduces p53 tumor-suppressor function

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Proc. Natl. Acad. Sci. U.S.A. 115 (18) 4731-4736 [2018-05-01; online 2018-04-17]

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Array profiling reveals contribution of Cthrc1 to growth of the denervated rat urinary bladder.

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Am. J. Physiol. Renal Physiol. 314 (5) F893-F905 [2018-05-01; online 2018-01-10]

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Mitochondrial Translation Efficiency Controls Cytoplasmic Protein Homeostasis

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Expression of scavenger receptor MARCO defines a targetable tumor-associated macrophage subset in non-small cell lung cancer.

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Arkani S, Cao J, Lundin J, ..., Matsson H, Nordenskjöld A

Hum Genome Var 5 (-) 18009 [2018-03-29; online 2018-03-29]

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Protein Expression in Tonsillar and Base of Tongue Cancer and in Relation to Human Papillomavirus (HPV) and Clinical Outcome.

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Int J Mol Sci 19 (4) 978 [2018-03-25; online 2018-03-25]

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Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow.

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Nat Commun 9 (1) 903 [2018-03-02; online 2018-03-02]

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Nubbin isoform antagonism governs Drosophila intestinal immune homeostasis.

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ISME J 12 (3) 802-812 [2018-03-00; online 2018-01-10]

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F1000Res 7 (-) 148 [2018-02-05; online 2018-02-05]

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The discovery of the virulence gene ToxA in the wheat and barley pathogen Bipolaris sorokiniana.

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Mol. Plant Pathol. 19 (2) 432-439 [2018-02-00; online 2017-03-12]

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Gene expression profiling across ontogenetic stages in the wood white (Leptidea sinapis) reveals pathways linked to butterfly diapause regulation.

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Mol. Ecol. 27 (4) 935-948 [2018-02-00; online 2018-02-26]

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Formation of mercury methylation hotspots as a consequence of forestry operations

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Science of The Total Environment 613-614 (-) 1069-1078 [2018-02-00; online 2018-02-00]

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Bacterial secretion of D-arginine controls environmental microbial biodiversity.

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ISME J 12 (2) 438-450 [2018-02-00; online 2017-10-13]

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Archaeal community changes in Lateglacial lake sediments: Evidence from ancient DNA

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Quaternary Science Reviews 181 (-) 19-29 [2018-02-00; online 2018-02-00]

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Sci Rep 8 (1) 1927 [2018-01-31; online 2018-01-31]

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Sci Rep 8 (1) 1878 [2018-01-30; online 2018-01-30]

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A protein interaction network centered on leucine-rich repeats and immunoglobulin-like domains 1 (LRIG1) regulates growth factor receptors

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MicroRNA expression profiles in non‑epithelial ovarian tumors.

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Int. J. Oncol. 52 (1) 55-66 [2018-01-00; online 2017-11-10]

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Phylogeny, species delimitation and revision of Pleioluma (Sapotaceae) in New Caledonia, a frequently gynodioecious genus

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Aust. Systematic Bot. 31 (2) 120 [2018-00-00; online 2018-00-00]

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Reading and editing the Pleurodeles waltl genome reveals novel features of tetrapod regeneration.

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Nat Commun 8 (1) 2286 [2017-12-22; online 2017-12-22]

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Journal of Experimental Biology - (-) - [2017-12-01; online 2017-11-27]

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Rho-kinase inhibitor Y-27632 and hypoxia synergistically enhance chondrocytic phenotype and modify S100 protein profiles in human chondrosarcoma cells

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Sci Rep 7 (1) - [2017-12-00; online 2017-06-16]

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RNA-sequence data normalization through in silico prediction of reference genes: the bacterial response to DNA damage as case study

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BioData Mining 10 (1) - [2017-12-00; online 2017-09-05]

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Mutational and putative neoantigen load predict clinical benefit of adoptive T cell therapy in melanoma

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Nat Commun 8 (1) - [2017-12-00; online 2017-11-23]

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Mitogenome evolution in the last surviving woolly mammoth population reveals neutral and functional consequences of small population size.

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Evolution Letters 1 (6) 292-303 [2017-12-00; online 2017-11-28]

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Combined genome and transcriptome sequencing to investigate the plant cell wall degrading enzyme system in the thermophilic fungus Malbranchea cinnamomea

Hüttner S, Nguyen TT, Granchi Z, ..., Thanh VN, Olsson L

Biotechnol Biofuels 10 (1) - [2017-12-00; online 2017-11-13]

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Genome-Based Sexing Provides Clues about Behavior and Social Structure in the Woolly Mammoth.

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Curr. Biol. 27 (22) 3505-3510.e3 [2017-11-20; online 2017-11-02]

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Dog ownership and the risk of cardiovascular disease and death - a nationwide cohort study.

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Sci Rep 7 (1) 15821 [2017-11-17; online 2017-11-17]

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Antibody Heavy Chain Variable Domains of Different Germline Gene Origins Diversify through Different Paths

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Front Immunol 8 (-) - [2017-11-13; online 2017-11-13]

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RNA-Seq de novo assembly and differential transcriptome analysis of the nematode Ascaridia galli in relation to in vivo exposure to flubendazole

Martis MM, Tarbiat B, Tydén E, Jansson DS, Höglund J

PLoS ONE 12 (11) e0185182 [2017-11-03; online 2017-11-03]

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SweGen: a whole-genome data resource of genetic variability in a cross-section of the Swedish population.

Ameur A, Dahlberg J, Olason P, ..., Magnusson PK, Gyllensten U

Eur. J. Hum. Genet. 25 (11) 1253-1260 [2017-11-00; online 2017-08-23]

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Proteomic Analysis of Phytophthora infestans Reveals the Importance of Cell Wall Proteins in Pathogenicity

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Mol Cell Proteomics 16 (11) 1958-1971 [2017-11-00; online 2017-09-21]

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Vitamin and Amino Acid Auxotrophy in Anaerobic Consortia Operating under Methanogenic Conditions

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mSystems 2 (5) e00038-17 [2017-10-31; online 2017-10-31]

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Effects of long-term low oxygen tension in human chondrosarcoma cells

Piltti J, Bygdell J, Qu C, Lammi MJ

J. Cell. Biochem. - (-) - [2017-10-18; online 2017-10-18]

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The Evolution of Dark Matter in the Mitogenome of Seed Beetles

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Genome Biol Evol 9 (10) 2697-2706 [2017-10-01; online 2017-09-27]

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The cagE gene sequence as a diagnostic marker to identify JP2 and non-JP2 highly leukotoxic Aggregatibacter actinomycetemcomitans serotype b strains.

Johansson A, Claesson R, Höglund Åberg C, Haubek D, Oscarsson J

J. Periodont. Res. 52 (5) 903-912 [2017-10-00; online 2017-04-10]

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Antibody Affinity Against 2009 A/H1N1 Influenza and Pandemrix Vaccine Nucleoproteins Differs Between Childhood Narcolepsy Patients and Controls.

Lind A, Freyhult E, Ramelius A, ..., Elding Larsson H, Lernmark Å

Viral Immunol. 30 (8) 590-600 [2017-10-00; online 2017-08-10]

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Alterations of c-di-GMP turnover proteins modulate semi-constitutive rdar biofilm formation in commensal and uropathogenic Escherichia coli.

Cimdins A, Simm R, Li F, ..., Brauner A, Römling U

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Anti-mycobacterial activity correlates with altered DNA methylation pattern in immune cells from BCG-vaccinated subjects.

Verma D, Parasa VR, Raffetseder J, ..., Netea M, Lerm M

Sci Rep 7 (1) 12305 [2017-09-26; online 2017-09-26]

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Genetic risk scores and family history as predictors of schizophrenia in Nordic registers.

Lu Y, Pouget JG, Andreassen OA, ..., Werge T, Sullivan PF

Psychol Med - (-) 1-9 [2017-09-25; online 2017-09-25]

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The regulation of hydroxysteroid 17β-dehydrogenase type 1 and 2 gene expression in breast cancer cell lines by estradiol, dihydrotestosterone, microRNAs, and genes related to breast cancer.

Hilborn E, Stål O, Alexeyenko A, Jansson A

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Copper chaperone ATOX1 regulates pluripotency factor OCT4 in preimplantation mouse embryos.

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Biochem. Biophys. Res. Commun. 491 (1) 147-153 [2017-09-09; online 2017-07-12]

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Fluorescent CRISPR Adaptation Reporter for rapid quantification of spacer acquisition.

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Sci Rep 7 (1) 10392 [2017-09-04; online 2017-09-04]

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The Huperzia selago Shoot Tip Transcriptome Sheds New Light on the Evolution of Leaves.

Evkaikina AI, Berke L, Romanova MA, ..., Pawlowski K, Voitsekhovskaja OV

Genome Biol Evol 9 (9) 2444-2460 [2017-09-01; online 2017-09-29]

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A practical guide to build de-novo assemblies for single tissues of non-model organisms: the example of a Neotropical frog

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PeerJ 5 (-) e3702 [2017-09-01; online 2017-09-01]

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Genome scale metabolic modeling of cancer.

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Cerium oxide nanoparticles inhibit differentiation of neural stem cells.

Gliga AR, Edoff K, Caputo F, ..., Ceccatelli S, Fadeel B

Sci Rep 7 (1) 9284 [2017-08-24; online 2017-08-24]

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SubCons: a new ensemble method for improved human subcellular localization predictions.

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Targeted sequencing of tonsillar and base of tongue cancer and human papillomavirus positive unknown primary of the head and neck reveals prognostic effects of mutated FGFR3

Bersani C, Sivars L, Haeggblom L, ..., Ramqvist T, Dalianis T

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Analysis of aquaporins from the euryhaline barnacle Balanus improvisus reveals differential expression in response to changes in salinity.

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Identifying Bird Remains Using Ancient DNA Barcoding.

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Defining the human copper proteome and analysis of its expression variation in cancers.

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Massive parallel sequencing questions the pathogenic role of missense variants in dilated cardiomyopathy

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Early onset of inflammation during ontogeny of bipolar disorder: the NLRP2 inflammasome gene distinctly differentiates between patients and healthy controls in the transition between iPS cell and neural stem cell stages

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Single-Cell Analysis Reveals a Close Relationship between Differentiating Dopamine and Subthalamic Nucleus Neuronal Lineages.

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Expression of Transient Receptor Potential Channels in the Purified Human Pancreatic β-Cells.

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A microarray whole-genome gene expression dataset in a rat model of inflammatory corneal angiogenesis.

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Deletion of FtsH11 protease has impact on chloroplast structure and function in Arabidopsis thaliana when grown under continuous light.

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Computational pan-genomics: status, promises and challenges.

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Advancing the global proteome survey platform by using an oriented single chain antibody fragment immobilization approach

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Short Chain Fatty Acids (SCFA) Reprogram Gene Expression in Human Malignant Epithelial and Lymphoid Cells.

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Peroxisome Proliferator-activated Receptor γ Coactivator-1 α Isoforms Selectively Regulate Multiple Splicing Events on Target Genes.

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Cloche is a bHLH-PAS transcription factor that drives haemato-vascular specification.

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Dysregulated signaling hubs of liver lipid metabolism reveal hepatocellular carcinoma pathogenesis.

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Science 353 (6294) 78-82 [2016-07-01; online 2016-07-02]

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Distinct transcription factor complexes act on a permissive chromatin landscape to establish regionalized gene expression in CNS stem cells.

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A draft fur seal genome provides insights into factors affecting SNP validation and how to mitigate them.

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PRECOG: a tool for automated extraction and visualization of fitness components in microbial growth phenomics.

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Glycosaminoglycan Profiling in Patients' Plasma and Urine Predicts the Occurrence of Metastatic Clear Cell Renal Cell Carcinoma.

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Metagenomic Analysis of the Indian Ocean Picocyanobacterial Community: Structure, Potential Function and Evolution.

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Detection of signal recognition particle (SRP) RNAs in the nuclear ribosomal internal transcribed spacer 1 (ITS1) of three lineages of ectomycorrhizal fungi (Agaricomycetes, Basidiomycota)

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The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing.

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Regulating retrotransposon activity through the use of alternative transcription start sites.

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The Bee Microbiome: Impact on Bee Health and Model for Evolution and Ecology of Host-Microbe Interactions.

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Identification and Characterization of IgdE, a Novel IgG-degrading Protease of Streptococcus suis with Unique Specificity for Porcine IgG.

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Metagenomic Analysis from the Interior of a Speleothem in Tjuv-Ante's Cave, Northern Sweden.

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In Situ Staining and Laser Capture Microdissection of Lymph Node Residing SIV Gag-Specific CD8+ T cells--A Tool to Interrogate a Functional Immune Response Ex Vivo.

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The role of transposable elements for gene expression in Capsella hybrids and allopolyploids

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The FAIR Guiding Principles for scientific data management and stewardship.

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Evolutionary history of host use, rather than plant phylogeny, determines gene expression in a generalist butterfly.

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Natural Selection and Recombination Rate Variation Shape Nucleotide Polymorphism Across the Genomes of Three Related Populus Species.

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Ectomycorrhizal fungi decompose soil organic matter using oxidative mechanisms adapted from saprotrophic ancestors.

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Altered DNA methylation of glycolytic and lipogenic genes in liver from obese and type 2 diabetic patients.

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A Multiplex Protein Panel Applied to Cerebrospinal Fluid Reveals Three New Biomarker Candidates in ALS but None in Neuropathic Pain Patients

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JOURNAL OF THE EUROPEAN MOSQUITO CONTROL ASSOCIATION 35 (-) 1-9 [2016-02-16; online 2016-02-16]

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Proteome-wide survey of the autoimmune target repertoire in autoimmune polyendocrine syndrome type 1.

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The Story of a Hitchhiker: Population Genetic Patterns in the Invasive Barnacle Balanus(Amphibalanus) improvisus Darwin 1854.

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Reconstructing ecosystem functions of the active microbial community of the Baltic Sea oxygen depleted sediments.

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Using Whole-Exome Sequencing to Identify Genetic Markers for Carboplatin and Gemcitabine-Induced Toxicities.

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Genome-wide identification of Wig-1 mRNA targets by RIP-Seq analysis.

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PGSB PlantsDB: updates to the database framework for comparative plant genome research.

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Structural genomic changes underlie alternative reproductive strategies in the ruff (Philomachus pugnax).

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Fat intake and breast milk fatty acid composition in farming and nonfarming women and allergy development in the offspring.

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Metabolic Profiling of Chicken Embryos Exposed to Perfluorooctanoic Acid (PFOA) and Agonists to Peroxisome Proliferator-Activated Receptors.

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The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome.

Hurst LD, Ghanbarian AT, Forrest AR, FANTOM consortium , Huminiecki L

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Captured metagenomics: large-scale targeting of genes based on 'sequence capture' reveals functional diversity in soils.

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Complete genome sequence of Staphylococcus aureus, strain ILRI_Eymole1/1, isolated from a Kenyan dromedary camel.

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RNA sequencing uncovers antisense RNAs and novel small RNAs in Streptococcus pyogenes.

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Quantitative proteogenomics of human pathogens using DIA-MS.

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Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers.

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Protein expansion is primarily due to indels in intrinsically disordered regions.

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Structural diversity of signal recognition particle RNAs in plastids.

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Improved production of membrane proteins in Escherichia coli by selective codon substitutions.

Nørholm MH, Toddo S, Virkki MT, ..., von Heijne G, Daley DO

FEBS Lett. 587 (15) 2352-2358 [2013-08-02; online 2013-06-19]

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Proteome of the nematode-trapping cells of the fungus Monacrosporium haptotylum.

Andersson KM, Meerupati T, Levander F, ..., Ahrén D, Tunlid A

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Response of Acidithiobacillus caldus toward suboptimal pH conditions.

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Extremophiles 17 (4) 689-696 [2013-07-00; online 2013-05-29]

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Lessons learned from implementing a national infrastructure in Sweden for storage and analysis of next-generation sequencing data.

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Vandetanib combined with a p38 MAPK inhibitor synergistically reduces glioblastoma cell survival.

Sooman L, Lennartsson J, Gullbo J, ..., Blomquist E, Ekman S

Med. Oncol. 30 (3) 638 [2013-06-20; online 2013-06-20]

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The impact of splicing on protein domain architecture.

Light S, Elofsson A

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The Norway spruce genome sequence and conifer genome evolution.

Nystedt B, Street NR, Wetterbom A, ..., Lundeberg J, Jansson S

Nature 497 (7451) 579-584 [2013-05-30; online 2013-05-22]

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Membrane protein shaving with thermolysin can be used to evaluate topology predictors.

Bendz M, Skwark M, Nilsson D, ..., Käll L, Elofsson A

Proteomics 13 (9) 1467-1480 [2013-05-00; online 2013-03-21]

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Long indels are disordered: a study of disorder and indels in homologous eukaryotic proteins.

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An adaptive alignment algorithm for quality-controlled label-free LC-MS.

Sandin M, Ali A, Hansson K, ..., Resjö S, Levander F

Mol. Cell Proteomics 12 (5) 1407-1420 [2013-05-00; online 2013-01-12]

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Hansen K, Perry BA, Dranginis AW, Pfister DH

Mol. Phylogenet. Evol. 67 (2) 311-335 [2013-05-00; online 2013-02-14]

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The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary.

Mayer G, Montecchi-Palazzi L, Ovelleiro D, ..., Eisenacher M, HUPO-PSI Group

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Origin and evolution of medium chain alcohol dehydrogenases.

Jörnvall H, Hedlund J, Bergman T, ..., Cederlund E, Persson B

Chem. Biol. Interact. 202 (1-3) 91-96 [2013-02-25; online 2012-12-04]

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Classification and nomenclature of the superfamily of short-chain dehydrogenases/reductases (SDRs).

Persson B, Kallberg Y

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Evolution of sperm structure and energetics in passerine birds.

Rowe M, Laskemoen T, Johnsen A, Lifjeld JT

Proc. Biol. Sci. 280 (1753) 20122616 [2013-02-22; online 2013-01-04]

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FANTOM: Functional and taxonomic analysis of metagenomes.

Sanli K, Karlsson FH, Nookaew I, Nielsen J

BMC Bioinformatics 14 (-) 38 [2013-02-01; online 2013-02-01]

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Adipose tissue resting energy expenditure and expression of genes involved in mitochondrial function are higher in women than in men.

Nookaew I, Svensson PA, Jacobson P, ..., Nielsen J, Carlsson LM

J. Clin. Endocrinol. Metab. 98 (2) E370-E378 [2013-02-00; online 2012-12-25]

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A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data.

Teschendorff AE, Marabita F, Lechner M, ..., Gomez-Cabrero D, Beck S

Bioinformatics 29 (2) 189-196 [2013-01-15; online 2012-11-24]

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Träger C, Rosenblad MA, Ziehe D, ..., Aronsson H, Schünemann D

Plant Cell 24 (12) 4819-4836 [2012-12-00; online 2012-12-28]

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Epitope-specificity of recombinant antibodies reveals promiscuous peptide-binding properties.

Olsson N, Wallin S, James P, Borrebaeck CA, Wingren C

Protein Sci. 21 (12) 1897-1910 [2012-12-00; online 2012-10-05]

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The plant short-chain dehydrogenase (SDR) superfamily: genome-wide inventory and diversification patterns.

Moummou H, Kallberg Y, Tonfack LB, Persson B, van der Rest B

BMC Plant Biol. 12 (-) 219 [2012-11-20; online 2012-11-20]

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A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae.

Nookaew I, Papini M, Pornputtapong N, ..., Uhlén M, Nielsen J

Nucleic Acids Res. 40 (20) 10084-10097 [2012-11-01; online 2012-09-12]

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Strategy for minimizing between-study variation of large-scale phenotypic experiments using multivariate analysis.

Pinto RC, Gerber L, Eliasson M, Sundberg B, Trygg J

Anal. Chem. 84 (20) 8675-8681 [2012-10-16; online 2012-09-18]

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Scheffersomyces stipitis: a comparative systems biology study with the Crabtree positive yeast Saccharomyces cerevisiae.

Papini M, Nookaew I, Uhlén M, Nielsen J

Microb. Cell Fact. 11 (-) 136 [2012-10-09; online 2012-10-09]

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Evolutionary conservation of the ribosomal biogenesis factor Rbm19/Mrd1: implications for function.

Kallberg Y, Segerstolpe Å, Lackmann F, Persson B, Wieslander L

PLoS ONE 7 (9) e43786 [2012-09-12; online 2012-09-12]

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Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences

Nilsson RH, Tedersoo L, Abarenkov K, ..., Larsson E, Kõljalg U

MycoKeys 4 (-) 37-63 [2012-09-05; online 2012-09-05]

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The evolution of filamin-a protein domain repeat perspective.

Light S, Sagit R, Ithychanda SS, Qin J, Elofsson A

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Proteomic screen reveals Fbw7 as a modulator of the NF-κB pathway.

Arabi A, Ullah K, Branca RM, ..., Lehtiö J, Sangfelt O

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Quantitative proteomics targeting classes of motif-containing peptides using immunoaffinity-based mass spectrometry.

Olsson N, James P, Borrebaeck CA, Wingren C

Mol. Cell Proteomics 11 (8) 342-354 [2012-08-00; online 2012-05-01]

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Polyploidy and the evolution of complex traits.

Huminiecki L, Conant GC

Int J Evol Biol 2012 (-) 292068 [2012-07-30; online 2012-07-30]

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Automated selected reaction monitoring software for accurate label-free protein quantification.

Teleman J, Karlsson C, Waldemarson S, ..., Malmström J, Levander F

J. Proteome Res. 11 (7) 3766-3773 [2012-07-06; online 2012-06-05]

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Lundin D, Severin I, Logue JB, ..., Andersson AF, Lindström ES

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Multimodel pathway enrichment methods for functional evaluation of expression regulation.

Kirik U, Cifani P, Albrekt AS, ..., Heyden A, Levander F

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Nørholm MH, Light S, Virkki MT, ..., von Heijne G, Daley DO

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A dimerized single-chain variable fragment system for the assessment of neutralizing activity of phage display-selected antibody fragments specific for cytomegalovirus.

Carlsson F, Trilling M, Perez F, Ohlin M

J. Immunol. Methods 376 (1-2) 69-78 [2012-02-28; online 2011-12-14]

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Characterization of the lipid droplet proteome of a clonal insulin-producing β-cell line (INS-1 832/13).

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