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] NGI Short read [Service] National Genomics Infrastructure [Service]

GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species

Kutschera VE, Kierczak M, van der Valk T, ..., Dalén L, Díez-del-Molino D

BMC Bioinformatics 23 (1) - [2022-12-00; online 2022-06-13]

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

PubMed DOI Crossref

Genomic analyses of the Linum distyly supergene reveal convergent evolution at the molecular level.

Gutiérrez-Valencia J, Fracassetti M, Berdan EL, ..., Arroyo J, Slotte T

Curr. Biol. - (-) - [2022-09-04; online 2022-09-04]

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

PubMed DOI Crossref

PRC2-mediated repression is essential to maintain identity and function of differentiated dopaminergic and serotonergic neurons.

Toskas K, Yaghmaeian-Salmani B, Skiteva O, ..., Perlmann T, Holmberg J

Sci Adv 8 (34) eabo1543 [2022-08-26; online 2022-08-26]

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

PubMed DOI Crossref

Single-cell multi-omics of human preimplantation embryos demonstrates susceptibility to glucocorticoids.

Zhao C, Biondic S, Vandal K, ..., Reik W, Petropoulos S

Genome Res. - (-) - [2022-08-10; online 2022-08-10]

Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Single cell [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

Nuclear-specific gene expression in heterokaryons of the filamentous ascomycete Neurospora tetrasperma.

Meunier C, Darolti I, Reimegård J, Mank JE, Johannesson H

Proc. Biol. Sci. 289 (1980) 20220971 [2022-08-10; online 2022-08-10]

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

PubMed DOI Crossref

Metatranscriptomics of Nasopharyngeal Microbiota and Host Distinguish between Pneumonia and Health.

Nannapaneni P, Sundh J, Prast-Nielsen S, ..., Naucler P, Henriques-Normark B

Am. J. Respir. Crit. Care Med. - (-) - [2022-08-10; online 2022-08-10]

Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] National Genomics Infrastructure [Service]

Ageing desexualizes the <i>Drosophila</i> brain transcriptome

Malacrinò A, Brengdahl MI, Kimber CM, ..., Mirabello C, Friberg U

Proc. R. Soc. B 289 (1980) - [2022-08-10; online 2022-08-10]

Bioinformatics Long-term Support WABI [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) 61 (8) 3461-3470 [2022-08-03; online 2021-12-11]

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

Characterization of hemocytes and hematopoietic cells of a freshwater crayfish based on single-cell transcriptome analysis

Söderhäll I, Fasterius E, Ekblom C, Söderhäll K

iScience 25 (8) 104850 [2022-08-00; online 2022-08-00]

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

PubMed DOI Crossref

Single-cell transcriptional pharmacodynamics of trifluridine in a tumor-immune model.

Selvin T, Fasterius E, Jarvius M, ..., Larsson R, Andersson CR

Sci Rep 12 (1) 11960 [2022-07-13; online 2022-07-13]

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

PubMed DOI Crossref

High-throughput muscle fiber typing from RNA sequencing data.

Oskolkov N, Santel M, Parikh HM, ..., Pääbo S, Hansson O

Skelet Muscle 12 (1) 16 [2022-07-02; online 2022-07-02]

Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

Genomic dynamics of brown trout populations released to a novel environment.

Kurland S, Rafati N, Ryman N, Laikre L

Ecol Evol 12 (7) e9050 [2022-07-00; online 2022-07-03]

Bioinformatics Long-term Support WABI [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] National Genomics Infrastructure [Service]

Evidence for further non-coding RNA genes in the fungal rDNA region

Rosenblad MA, Larsson E, Walker A, ..., Wurzbacher C, Nilsson RH

MycoKeys 90 (-) 203-213 [2022-06-30; online 2022-06-30]

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

PubMed DOI Crossref

Metatranscriptomics captures dynamic shifts in mycorrhizal coordination in boreal forests.

Law SR, Serrano AR, Daguerre Y, ..., Street NR, Hurry V

Proc. Natl. Acad. Sci. U.S.A. 119 (26) e2118852119 [2022-06-28; online 2022-06-21]

Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] National Genomics Infrastructure [Service]

Satellite DNA evolution in Corvoidea inferred from short and long reads

Peona V, Kutschera VE, Blom MPK, Irestedt M, Suh A

Mol Ecol - (-) - [2022-05-14; online 2022-05-14]

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

PubMed DOI Crossref

Contribution of rare whole-genome sequencing variants to plasma protein levels and the missing heritability.

Kierczak M, Rafati N, Höglund J, ..., Karlsson T, Johansson Å

Nat Commun 13 (1) 2532 [2022-05-09; online 2022-05-09]

Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] National Genomics Infrastructure [Service]

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 Short read [Service] NGI Single cell [Service] NGI Spatial omics [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

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]

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. 38 (12) 5275-5291 [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 Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] 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

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

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Epigenetic alterations in skin homing CD4+CLA+ T cells of atopic dermatitis patients.

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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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Pre-extinction Demographic Stability and Genomic Signatures of Adaptation in the Woolly Rhinoceros.

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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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Genome sequence of segmented filamentous bacteria present in the human intestine.

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Comparative analysis of genome-wide DNA methylation in Neurospora.

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A Shh/Gli-driven three-node timer motif controls temporal identity and fate of neural stem cells.

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

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

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

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

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Metagenomes from Coastal Marine Sediments Give Insights into the Ecological Role and Cellular Features of Loki- and Thorarchaeota.

Manoharan L, Kozlowski JA, Murdoch RW, ..., Sousa FL, Schleper C

MBio 10 (5) - [2019-09-10; online 2019-09-10]

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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]

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Lack of gene flow: Narrow and dispersed differentiation islands in a triplet of Leptidea butterfly species

Talla V, Johansson A, Dincă V, ..., Wiklund C, Backström N

Mol Ecol 28 (6) 3756-3770 [2019-08-08; online 2019-08-08]

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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]

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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]

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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]

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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]

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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]

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Identification of Salivary Microbiota and Its Association With Host Inflammatory Mediators in Periodontitis.

Lundmark A, Hu YOO, Huss M, ..., Andersson AF, Yucel-Lindberg T

Front. Cell. Infect. Microbiol. 9 (-) 216 [2019-06-21; online 2019-06-21]

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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]

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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]

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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]

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

Indira Chandran V, Welinder C, Månsson AS, ..., Sundgren PC, Belting M

Clin. Cancer Res. 25 (10) 3115-3127 [2019-05-15; online 2019-01-24]

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PubMed DOI Crossref

Software engineering for scientific big data analysis.

Grüning BA, Lampa S, Vaudel M, Blankenberg D

Gigascience 8 (5) - [2019-05-01; online 2019-05-24]

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

PubMed DOI Crossref

SciPipe: A workflow library for agile development of complex and dynamic bioinformatics pipelines.

Lampa S, Dahlö M, Alvarsson J, Spjuth O

Gigascience 8 (5) - [2019-05-01; online 2019-04-28]

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

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Chromosomal genome assembly of the ethanol production strain CBS 11270 indicates a highly dynamic genome structure in the yeast species Brettanomyces bruxellensis.

Tiukova IA, Pettersson ME, Hoeppner MP, ..., Söderberg J, Passoth V

PLoS ONE 14 (5) e0215077 [2019-05-01; online 2019-05-01]

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Pervasive hybridizations in the history of wheat relatives.

Glémin S, Scornavacca C, Dainat J, ..., David J, Ranwez V

Sci Adv 5 (5) eaav9188 [2019-05-00; online 2019-05-01]

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PubMed DOI Crossref

PKCζ facilitates lymphatic metastatic spread of prostate cancer cells in a mice xenograft model

Zang G, Mu Y, Gao L, Bergh A, Landström M

Oncogene 38 (22) 4215-4231 [2019-05-00; online 2019-01-31]

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

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Gene expression profile of extraocular muscles following resection strabismus surgery.

Rodríguez MA, Sandgren Hochhard K, Vicente A, Liu JX, Pedrosa Domellöf F

Exp. Eye Res. 182 (-) 182-193 [2019-05-00; online 2019-04-03]

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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Somatic mutation that affects transcription factor binding upstream of CD55 in the temporal cortex of a late-onset Alzheimer disease patient

Helgadottir HT, Lundin P, Wallén Arzt E, ..., Graff C, Eriksson M

Hum Mol Genet 28 (16) 2675-2685 [2019-04-24; online 2019-04-24]

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The complex barnacle perfume: identification of waterborne pheromone homologues in Balanus improvisus and their differential expression during settlement

Abramova A, Lind U, Blomberg A, Rosenblad MA

Biofouling 35 (4) 416-428 [2019-04-21; online 2019-05-30]

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Breast cancer quantitative proteome and proteogenomic landscape.

Johansson HJ, Socciarelli F, Vacanti NM, ..., Børresen-Dale AL, Lehtiö J

Nat Commun 10 (1) 1600 [2019-04-08; online 2019-04-08]

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High-Quality Library Preparation for NGS-Based Immunoglobulin Germline Gene Inference and Repertoire Expression Analysis.

Vázquez Bernat N, Corcoran M, Hardt U, ..., Martin M, Karlsson Hedestam GB

Front Immunol 10 (-) 660 [2019-04-05; online 2019-04-05]

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PubMed DOI Crossref

A geographically matched control population efficiently limits the number of candidate disease-causing variants in an unbiased whole-genome analysis

Rentoft M, Svensson D, Sjödin A, ..., Melin BS, Johansson E

PLoS ONE 14 (3) e0213350 [2019-03-27; online 2019-03-27]

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Helicase/SUMO-targeted ubiquitin ligase Uls1 interacts with the Holliday junction resolvase Yen1.

Bauer SL, Chen J, Åström SU

PLoS ONE 14 (3) e0214102 [2019-03-21; online 2019-03-21]

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

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An ABCA4 loss-of-function mutation causes a canine form of Stargardt disease

Mäkeläinen S, Gòdia M, Hellsand M, ..., Andersson G, Bergström TF

PLoS Genet. 15 (3) e1007873 [2019-03-19; online 2019-03-19]

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

Pax6 and KDM5C co-occupy a subset of developmentally critical genes including Notch signaling regulators in neural progenitors

Gaudenzi G, Dethlefsen O, Walfridsson J, Hermanson O

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PubMed DOI Crossref

The Interactome of Palmitoyl-Protein Thioesterase 1 (PPT1) Affects Neuronal Morphology and Function.

Sapir T, Segal M, Grigoryan G, ..., Segal M, Reiner O

Front Cell Neurosci 13 (-) 92 [2019-03-13; online 2019-03-13]

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PubMed DOI Crossref

Regulatory changes in pterin and carotenoid genes underlie balanced color polymorphisms in the wall lizard

Andrade P, Pinho C, Pérez i de Lanuza G, ..., Andersson L, Carneiro M

Proc Natl Acad Sci USA - (-) 201820320 [2019-02-28; online 2019-02-28]

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Rostania revised: testing generic delimitations in Collemataceae (Peltigerales, Lecanoromycetes).

Košuthová A, Westberg M, Tálora MAG, Wedin M

MycoKeys 47 (47) 17-33 [2019-02-20; online 2019-02-20]

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Prediction of response to anti-cancer drugs becomes robust via network integration of molecular data.

Franco M, Jeggari A, Peuget S, ..., Selivanova G, Alexeyenko A

Sci Rep 9 (1) 2379 [2019-02-20; online 2019-02-20]

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Single-cell RNA sequencing reveals midbrain dopamine neuron diversity emerging during mouse brain development.

Tiklová K, Björklund ÅK, Lahti L, ..., Parmar M, Perlmann T

Nat Commun 10 (1) 581 [2019-02-04; online 2019-02-04]

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PubMed DOI Crossref

Protein profiling of fine-needle aspirates reveals subtype-associated immune signatures and involvement of chemokines in breast cancer.

Franzén B, Alexeyenko A, Kamali-Moghaddam M, ..., Landegren U, Lewensohn R

Mol Oncol 13 (2) 376-391 [2019-02-00; online 2019-01-07]

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PubMed DOI Crossref

Plasma Profiles of Inflammatory Markers Associated With Active Tuberculosis in Antiretroviral Therapy-Naive Human Immunodeficiency Virus-Positive Individuals.

Olsson O, Björkman P, Jansson M, ..., Carlsson F, Skogmar S

Open Forum Infect Dis 6 (2) ofz015 [2019-02-00; online 2019-01-31]

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PubMed DOI Crossref

Transformation of mature mouse B cells into malignant plasma cells in vitro via introduction of defined genetic elements.

Högstrand K, Lindvall JM, Sundblad A, Grandien A

Eur. J. Immunol. - (-) - [2019-01-21; online 2019-01-21]

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The genetic diversity and evolution of diatom-diazotroph associations highlights traits favoring symbiont integration.

Caputo A, Nylander JAA, Foster RA

FEMS Microbiol. Lett. - (-) - [2019-01-09; online 2019-01-09]

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PubMed DOI Crossref

Introducing ribosomal tandem repeat barcoding for fungi.

Wurzbacher C, Larsson E, Bengtsson-Palme J, ..., Kagami M, Nilsson RH

Mol Ecol Resour 19 (1) 118-127 [2019-01-00; online 2018-10-24]

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Year 2018

Zebrafish larvae as a model system for systematic characterization of drugs and genes in dyslipidemia and atherosclerosis

Bandaru MK, Emmanouilidou A, Ranefall P, ..., Ingelsson E, den Hoed M

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PubMed DOI Crossref

Targeted Delivery of Stk25 Antisense Oligonucleotides to Hepatocytes Protects Mice Against Nonalcoholic Fatty Liver Disease.

Cansby E, Nuñez-Durán E, Magnusson E, ..., Aghajan M, Mahlapuu M

Cellular and Molecular Gastroenterology and Hepatology 7 (3) 597-618 [2018-12-19; online 2018-12-19]

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PhenoMeNal: Processing and analysis of Metabolomics data in the Cloud.

Peters K, Bradbury J, Bergmann S, ..., Zanetti G, Steinbeck C

Gigascience - (-) - [2018-12-07; online 2018-12-07]

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

PubMed DOI Crossref

Spatially and functionally distinct subclasses of breast cancer-associated fibroblasts revealed by single cell RNA sequencing.

Bartoschek M, Oskolkov N, Bocci M, ..., Björklund Å, Pietras K

Nat Commun 9 (1) 5150 [2018-12-04; online 2018-12-04]

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PubMed DOI Crossref

Transcriptional and Epigenetic Changes Influencing Skeletal Muscle Metabolism in Women With Polycystic Ovary Syndrome.

Nilsson E, Benrick A, Kokosar M, ..., Ling C, Stener-Victorin E

J. Clin. Endocrinol. Metab. 103 (12) 4465-4477 [2018-12-01; online 2018-08-17]

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PubMed DOI Crossref

Impact of forced fatty acid synthesis on metabolism and physiology of Saccharomyces cerevisiae.

Gossing M, Smialowska A, Nielsen J

FEMS Yeast Res. 18 (8) - [2018-12-01; online 2018-09-01]

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PubMed DOI Crossref

Somatic mutagenesis in satellite cells associates with human skeletal muscle aging

Franco I, Johansson A, Olsson K, ..., Fischer H, Eriksson M

Nat Commun 9 (1) - [2018-12-00; online 2018-02-23]

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RNA-sequencing reveals long-term effects of silver nanoparticles on human lung cells

Gliga AR, Di Bucchianico S, Lindvall J, Fadeel B, Karlsson HL

Sci Rep 8 (1) - [2018-12-00; online 2018-04-27]

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EMBLmyGFF3: a converter facilitating genome annotation submission to European Nucleotide Archive

Norling M, Jareborg N, Dainat J

BMC Res Notes 11 (1) - [2018-12-00; online 2018-08-13]

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PubMed DOI Crossref

A major locus controls local adaptation and adaptive life history variation in a perennial plant

Wang J, Ding J, Tan B, ..., Street NR, Ingvarsson PK

Genome Biol. 19 (1) - [2018-12-00; online 2018-06-04]

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PubMed DOI Crossref

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

Södersten E, Toskas K, Rraklli V, ..., Perlmann T, Holmberg J

Nat Commun 9 (1) - [2018-12-00; online 2018-03-26]

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Metatranscriptomes Reveal That All Three Domains of Life Are Active but Are Dominated by Bacteria in the Fennoscandian Crystalline Granitic Continental Deep Biosphere

Lopez-Fernandez M, Simone D, Wu X, ..., Bertilsson S, Dopson M

MBio 9 (6) - [2018-11-20; online 2018-11-20]

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Expression profiling and in situ screening of circular RNAs in human tissues.

Zaghlool A, Ameur A, Wu C, ..., Nilsson M, Feuk L

Sci Rep 8 (1) 16953 [2018-11-16; online 2018-11-16]

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Integrative Analysis of Three RNA Sequencing Methods Identifies Mutually Exclusive Exons of MADS-Box Isoforms During Early Bud Development in Picea abies

Akhter S, Kretzschmar WW, Nordal V, ..., Emanuelsson O, Sundström JF

Front Plant Sci 9 (-) - [2018-11-13; online 2018-11-13]

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PubMed DOI Crossref

Disease-specific oligodendrocyte lineage cells arise in multiple sclerosis

Falcão AM, van Bruggen D, Marques S, ..., Guerreiro-Cacais AO, Castelo-Branco G

Nat Med - (-) - [2018-11-12; online 2018-11-12]

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Preparation of plant tissue to enable Spatial Transcriptomics profiling using barcoded microarrays.

Giacomello S, Lundeberg J

Nat Protoc 13 (11) 2425-2446 [2018-11-00; online 2018-10-26]

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PubMed DOI Crossref

Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen

Lin YC, Wang J, Delhomme N, ..., Ingvarsson PK, Street NR

Proc Natl Acad Sci USA - (-) 201801437 [2018-10-29; online 2018-10-29]

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PubMed DOI Crossref

Transcriptomic and genomic profiling of early-stage ovarian carcinomas associated with histotype and overall survival.

Engqvist H, Parris TZ, Rönnerman EW, ..., Karlsson P, Helou K

Oncotarget 9 (80) 35162-35180 [2018-10-12; online 2018-10-12]

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PubMed DOI Crossref

De Novo Assembly of Two Swedish Genomes Reveals Missing Segments from the Human GRCh38 Reference and Improves Variant Calling of Population-Scale Sequencing Data.

Ameur A, Che H, Martin M, ..., Feuk L, Gyllensten U

Genes 9 (10) 486 [2018-10-09; online 2018-10-09]

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NormalyzerDE: Online tool for improved normalization of omics expression data and high-sensitivity differential expression analysis.

Willforss J, Chawade A, Levander F

J. Proteome Res. - (-) - [2018-10-02; online 2018-10-02]

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PubMed DOI Crossref

RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor.

Wang H, Marcišauskas S, Sánchez BJ, ..., Nielsen J, Kerkhoven EJ

PLoS Comput. Biol. 14 (10) e1006541 [2018-10-00; online 2018-10-18]

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PubMed DOI Crossref

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

Gunnarsson R, Dilorenzo S, Lundin-Ström KB, ..., Isaksson A, Johansson B

Leukemia 32 (10) 2117-2125 [2018-10-00; online 2018-03-12]

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PubMed DOI Crossref

Methanogens and Iron-Reducing Bacteria: the Overlooked Members of Mercury-Methylating Microbial Communities in Boreal Lakes

Bravo AG, Peura S, Buck M, ..., Björn E, Bertilsson S

Appl Environ Microbiol 84 (23) - [2018-09-21; online 2018-11-15]

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PubMed DOI Crossref

Draft Genome Sequence for the Tree Pathogen Phytophthora plurivora.

Vetukuri RR, Tripathy S, Malar C M, ..., Grenville-Briggs LJ, Whisson SC

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

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Autosomal Recessive Osteogenesis Imperfecta Caused by a Novel Homozygous COL1A2 Mutation

Costantini A, Tournis S, Kämpe A, ..., Doulgeraki A, Mäkitie O

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

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

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Fluorescent CRISPR Adaptation Reporter for rapid quantification of spacer acquisition.

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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

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Frequent low-level mutations of protein kinase D2 in angiolipoma

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Draft Genome Sequence of the Mycoparasitic Oomycete Pythium periplocum Strain CBS 532.74.

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RhoA knockout fibroblasts lose tumor-inhibitory capacity in vitro and promote tumor growth in vivo.

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BMC Genomics 18 (1) 177 [2017-02-16; online 2017-02-16]

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microRNAs with AAGUGC seed motif constitute an integral part of an oncogenic signaling network.

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

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International Journal of Cardiology 228 (-) 742-748 [2017-02-00; online 2017-02-00]

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Genomic analysis reveals major determinants of cis-regulatory variation in Capsella grandiflora.

Steige KA, Laenen B, Reimegård J, Scofield DG, Slotte T

Proc. Natl. Acad. Sci. U.S.A. 114 (5) 1087-1092 [2017-01-31; online 2017-01-17]

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Draft Genome Sequences of Semiconstitutive Red, Dry, and Rough Biofilm-Forming Commensal and Uropathogenic Escherichia coli Isolates.

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Genome Announc 5 (4) - [2017-01-26; online 2017-01-26]

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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

Vizlin-Hodzic D, Zhai Q, Illes S, ..., Ågren H, Funa K

Transl Psychiatry 7 (1) e1010 [2017-01-24; online 2017-01-24]

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NLK-mediated phosphorylation of HDAC1 negatively regulates Wnt signaling.

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Mol. Biol. Cell 28 (2) 346-355 [2017-01-15; online 2016-11-30]

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Identification of endoribonuclease specific cleavage positions reveals novel targets of RNase III inStreptococcus pyogenes

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

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Cell Stem Cell 20 (1) 29-40 [2017-01-05; online 2016-10-27]

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Rye B chromosomes encode a functional Argonaute-like protein with in vitro slicer activities similar to its A chromosome paralog.

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

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Pancreas 46 (1) 97-101 [2017-01-00; online 2016-07-29]

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Both maternal and offspring Elovl2 genotypes determine systemic DHA levels in perinatal mice.

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Production of individualized V gene databases reveals high levels of immunoglobulin genetic diversity.

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Validation and development of MTH1 inhibitors for treatment of cancer.

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Spatial subsidies in spider diets vary with shoreline structure: Complementary evidence from molecular diet analysis and stable isotopes.

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Identification of Shared and Unique Serum Lipid Profiles in Diabetes Mellitus and Myocardial Infarction.

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An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge.

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Genome Biol. 15 (3) R53 [2014-03-25; online 2014-03-25]

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Nylinder S, Lemey P, De Bruyn M, ..., Walsh N, Anderberg AA

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Dupont CL, Larsson J, Yooseph S, ..., Venter JC, Bergman B

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Browall S, Norman M, Tångrot J, ..., Normark S, Henriques-Normark B

J. Infect. Dis. 209 (3) 377-388 [2014-02-01; online 2013-09-07]

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Dating the diversification of the major lineages of Passeriformes (Aves).

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HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics.

Branca RM, Orre LM, Johansson HJ, ..., Käll L, Lehtiö J

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Automated quality control system for LC-SRM setups.

Teleman J, Waldemarson S, Malmström J, Levander F

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Linkage analysis in familial non-Lynch syndrome colorectal cancer families from Sweden.

Kontham V, von Holst S, Lindblom A

PLoS ONE 8 (12) e83936 [2013-12-11; online 2013-12-11]

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

Light S, Sagit R, Sachenkova O, Ekman D, Elofsson A

Mol. Biol. Evol. 30 (12) 2645-2653 [2013-12-00; online 2013-09-17]

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Early B-cell factor 1 regulates the expansion of B-cell progenitors in a dose-dependent manner.

Åhsberg J, Ungerbäck J, Strid T, ..., Qian H, Sigvardsson M

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Genomic mechanisms accounting for the adaptation to parasitism in nematode-trapping fungi.

Meerupati T, Andersson KM, Friman E, ..., Tunlid A, Ahrén D

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BMC Microbiol. 13 (-) 235 [2013-10-22; online 2013-10-22]

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BMC Med Genomics 6 (-) 41 [2013-10-11; online 2013-10-11]

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Lind U, Alm Rosenblad M, Wrange AL, ..., Havenhand J, Blomberg A

PLoS ONE 8 (10) e77069 [2013-10-09; online 2013-10-09]

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Rosenblad MA, Träger C, Schünemann D

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

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

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Mangold S, Rao Jonna V, Dopson M

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Lampa S, Dahlö M, Olason PI, Hagberg J, Spjuth O

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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

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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

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

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Evolution of sperm structure and energetics in passerine birds.

Rowe M, Laskemoen T, Johnsen A, Lifjeld JT

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FANTOM: Functional and taxonomic analysis of metagenomes.

Sanli K, Karlsson FH, Nookaew I, Nielsen J

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

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

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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

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Papini M, Nookaew I, Uhlén M, Nielsen J

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

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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

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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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