PLoS ONE

NGS method for parallel processing of high quality, damaged or fragmented input material using target enrichment.

Lyander A, Gellerbring A, Hägglund M, Elhami K, Wirta V

PLoS ONE 19 (5) e0304411 [2024-05-29; online 2024-05-29]

Clinical Genomics Stockholm [Technology development]

Species-specific dynamics may cause deviations from general biogeographical predictions - evidence from a population genomics study of a New Guinean endemic passerine bird family (Melampittidae).

Müller IA, Thörn F, Rajan S, ..., Jønsson KA, Irestedt M

PLoS ONE 19 (5) e0293715 [2024-05-23; online 2024-05-23]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Plastid phylogenomics and cytonuclear discordance in Rubioideae, Rubiaceae.

Thureborn O, Wikström N, Razafimandimbison SG, Rydin C

PLoS ONE 19 (5) e0302365 [2024-05-20; online 2024-05-20]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Complex genetic architecture of the chicken Growth1 QTL region.

Ou JH, Rönneburg T, Carlborg Ö, ..., Siegel PB, Rubin CJ

PLoS ONE 19 (5) e0295109 [2024-05-13; online 2024-05-13]

NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Whole genome case-control study of central nervous system toxicity due to antimicrobial drugs.

Ås J, Bertulyte I, Norgren N, ..., Wadelius M, Hallberg P

PLoS ONE 19 (2) e0299075 [2024-02-29; online 2024-02-29]

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

Gene co-expression network analysis reveal core responsive genes in Parascaris univalens tissues following ivermectin exposure.

Dube F, Delhomme N, Martin F, ..., Svärd S, Tydén E

PLoS ONE 19 (2) e0298039 [2024-02-15; online 2024-02-15]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Towards high-throughput parallel imaging and single-cell transcriptomics of microbial eukaryotic plankton.

Grujčić V, Saarenpää S, Sundh J, ..., Foster RA, Andersson AF

PLoS ONE 19 (1) e0296672 [2024-01-19; online 2024-01-19]

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

Development and validation of a quantitative Proximity Extension Assay instrument with 21 proteins associated with cardiovascular risk (CVD-21).

Siegbahn A, Eriksson N, Assarsson E, ..., Åberg M, Wallentin L

PLoS ONE 18 (11) e0293465 [2023-11-14; online 2023-11-14]

Affinity Proteomics Uppsala [Collaborative]

Transposable element insertions in 1000 Swedish individuals.

Bilgrav Saether K, Nilsson D, Thonberg H, ..., Eisfeldt J, Lindstrand A

PLoS ONE 18 (7) e0289346 [2023-07-28; online 2023-07-28]

Bioinformatics Support for Computational Resources [Service] Clinical Genomics Stockholm [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

FAVIS: Fast and versatile protocol for non-destructive metabarcoding of bulk insect samples.

Iwaszkiewicz-Eggebrecht E, Łukasik P, Buczek M, ..., Ronquist F, Miraldo A

PLoS ONE 18 (7) e0286272 [2023-07-19; online 2023-07-19]

Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Identification of potential biomarkers in active Lyme borreliosis.

Tjernberg I, Lager M, Furset Jensen G, ..., Brudin L, Henningsson AJ

PLoS ONE 18 (6) e0287586 [2023-06-26; online 2023-06-26]

Affinity Proteomics Uppsala [Service]

Adipokines and risk of rheumatoid arthritis: A two-sample multivariable Mendelian randomisation study.

Vasileiadis GK, Sayols S, Zhao SS, Fatima T, Maglio C

PLoS ONE 18 (6) e0286981 [2023-06-09; online 2023-06-09]

Clinical Genomics Gothenburg [Service]

Cohort profile: The Clinical and Multi-omic (CAMO) cohort, part of the Norwegian Women and Cancer (NOWAC) study.

Delgado AB, Tylden ES, Lukic M, ..., Lund E, Olsen KS

PLoS ONE 18 (2) e0281218 [2023-02-06; online 2023-02-06]

Divergent gene expression responses in two Baltic Sea heterotrophic model bacteria to dinoflagellate dissolved organic matter.

Osbeck CMG, Lundin D, Karlsson C, ..., Moran MA, Pinhassi J

PLoS ONE 17 (11) e0243406 [2022-11-17; online 2022-11-17]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Temporal patterns of inflammation-related proteins measured in the cerebrospinal fluid of patients with aneurysmal subarachnoid hemorrhage using multiplex Proximity Extension Assay technology.

Vlachogiannis P, Hillered L, Enblad P, Ronne-Engström E

PLoS ONE 17 (3) e0263460 [2022-03-24; online 2022-03-24]

Affinity Proteomics Uppsala [Service]

SARS-CoV-2 induces a durable and antigen specific humoral immunity after asymptomatic to mild COVID-19 infection.

Havervall S, Jernbom Falk A, Klingström J, ..., Nilsson P, Thålin C

PLoS ONE 17 (1) e0262169 [2022-01-12; online 2022-01-12]

Autoimmunity and Serology Profiling [Collaborative]

Changes in serum and urinary metabolomic profile after a dietary intervention in patients with irritable bowel syndrome.

Nybacka S, Simrén M, Störsrud S, ..., Winkvist A, Lindqvist HM

PLoS ONE 16 (10) e0257331 [2021-10-11; online 2021-10-11]

An evaluation of a FluoroSpot assay as a diagnostic tool to determine SARS-CoV-2 specific T cell responses.

Mangsbo SM, Havervall S, Laurén I, ..., Klingström J, Thålin C

PLoS ONE 16 (9) e0258041 [2021-09-30; online 2021-09-30]

Autoimmunity and Serology Profiling [Technology development]

The broad role of Nkx3.2 in the development of the zebrafish axial skeleton.

Waldmann L, Leyhr J, Zhang H, ..., Allalou A, Haitina T

PLoS ONE 16 (8) e0255953 [2021-08-19; online 2021-08-19]

BioImage Informatics [Collaborative] Genome Engineering Zebrafish [Service]

Single-cell RNAseq and longitudinal proteomic analysis of a novel semi-spontaneous urothelial cancer model reveals tumor cell heterogeneity and pretumoral urine protein alterations.

Kerzeli IK, Lord M, Doroszko M, ..., Segersten U, Mangsbo SM

PLoS ONE 16 (7) e0253178 [2021-07-07; online 2021-07-07]

Affinity Proteomics Uppsala [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Differences in the genome, methylome, and transcriptome do not differentiate isolates of Streptococcus equi subsp. equi from horses with acute clinical signs from isolates of inapparent carriers.

Morris ERA, Boyle AG, Riihimäki M, ..., Pringle J, Cohen ND

PLoS ONE 16 (6) e0252804 [2021-06-14; online 2021-06-14]

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

Sex-differences in circulating biomarkers during acute myocardial infarction: An analysis from the SWEDEHEART registry.

Eggers KM, Lindhagen L, Baron T, ..., Spaak J, Lindahl B

PLoS ONE 16 (4) e0249830 [2021-04-08; online 2021-04-08]

Affinity Proteomics Uppsala [Service]

Artificial intelligence for the classification of fractures around the knee in adults according to the 2018 AO/OTA classification system.

Lind A, Akbarian E, Olsson S, ..., Razavian AS, Gordon M

PLoS ONE 16 (4) e0248809 [2021-04-01; online 2021-04-01]

AIDA Data Hub [Service]

Transcriptional analysis of islets of Langerhans from organ donors of different ages.

Seiron P, Stenwall A, Hedin A, ..., Lundberg M, Skog O

PLoS ONE 16 (3) e0247888 [2021-03-12; online 2021-03-12]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Cell-free tumour DNA analysis detects copy number alterations in gastro-oesophageal cancer patients.

Wallander K, Eisfeldt J, Lindblad M, ..., Liedén A, Tham E

PLoS ONE 16 (2) e0245488 [2021-02-04; online 2021-02-04]

Bioinformatics Support for Computational Resources [Service] Clinical Genomics Stockholm [Service]

Umbilical cord blood metabolome differs in relation to delivery mode, birth order and sex, maternal diet and possibly future allergy development in rural children.

Ross AB, Barman M, Hartvigsson O, ..., Wold AE, Sandberg AS

PLoS ONE 16 (1) e0242978 [2021-01-25; online 2021-01-25]

Chalmers Mass Spectrometry Infrastructure [Service]

Genome-wide association study and pathway analysis identify NTRK2 as a novel candidate gene for litter size in sheep.

Esmaeili-Fard SM, Gholizadeh M, Hafezian SH, Abdollahi-Arpanahi R

PLoS ONE 16 (1) e0244408 [2021-01-22; online 2021-01-22]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

A shotgun metagenomic investigation of the microbiota of udder cleft dermatitis in comparison to healthy skin in dairy cows.

Ekman L, Bagge E, Nyman A, ..., Pringle M, Segerman B

PLoS ONE 15 (12) e0242880 [2020-12-02; online 2020-12-02]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Impacts of thermal fluctuations on heat tolerance and its metabolomic basis in Arabidopsis thaliana, Drosophila melanogaster, and Orchesella cincta.

Noer NK, Pagter M, Bahrndorff S, Malmendal A, Kristensen TN

PLoS ONE 15 (10) e0237201 [2020-10-29; online 2020-10-29]

DNA methylation in canine brains is related to domestication and dog-breed formation.

Sundman AS, Pértille F, Lehmann Coutinho L, ..., Guerrero-Bosagna C, Jensen P

PLoS ONE 15 (10) e0240787 [2020-10-29; online 2020-10-29]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Sources of variation in cell-type RNA-Seq profiles.

Gustafsson J, Held F, Robinson JL, ..., Jörnsten R, Nielsen J

PLoS ONE 15 (9) e0239495 [2020-09-21; online 2020-09-21]

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

A whole-genome sequenced control population in northern Sweden reveals subregional genetic differences.

Svensson D, Rentoft M, Dahlin AM, ..., Trygg J, Johansson E

PLoS ONE 15 (9) e0237721 [2020-09-11; online 2020-09-11]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Arachidonic acid promotes the binding of 5-lipoxygenase on nanodiscs containing 5-lipoxygenase activating protein in the absence of calcium-ions.

Kumar RB, Purhonen P, Hebert H, Jegerschöld C

PLoS ONE 15 (7) e0228607 [2020-07-09; online 2020-07-09]

Protein Science Facility (PSF) [Service]

Whole genome sequencing unveils genetic heterogeneity in optic nerve hypoplasia.

Dahl S, Pettersson M, Eisfeldt J, ..., Anderlid BM, Lindstrand A

PLoS ONE 15 (2) e0228622 [2020-02-10; online 2020-02-10]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Levels of caspase-3 and histidine-rich glycoprotein in the embryo secretome as biomarkers of good-quality day-2 embryos and high-quality blastocysts

Kaihola H, Yaldir FG, Bohlin T, ..., Hreinsson J, Åkerud H

PLoS ONE 14 (12) e0226419 [2019-12-19; online 2019-12-19]

Affinity Proteomics Uppsala [Service] PLA and Single Cell Proteomics [Service]

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]

Comparative distribution of extended-spectrum beta-lactamase-producing Escherichia coli from urine infections and environmental waters.

Fagerström A, Mölling P, Khan FA, ..., Jass J, Söderquist B

PLoS ONE 14 (11) e0224861 [2019-11-07; online 2019-11-07]

Clinical Genomics Örebro [Collaborative]

Phylogenetic microbiota profiling in fecal samples depends on combination of sequencing depth and choice of NGS analysis method.

Rajan SK, Lindqvist M, Brummer RJ, Schoultz I, Repsilber D

PLoS ONE 14 (9) e0222171 [2019-09-17; online 2019-09-17]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Differential gene expression in bovine endometrial epithelial cells after challenge with LPS; specific implications for genes involved in embryo maternal interactions.

Guo Y, van Schaik T, Jhamat N, ..., Andersson G, Humblot P

PLoS ONE 14 (9) e0222081 [2019-09-05; online 2019-09-05]

NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Global gene expression analysis in etiolated and de-etiolated seedlings in conifers.

Ranade SS, Delhomme N, García-Gil MR

PLoS ONE 14 (7) e0219272 [2019-07-05; online 2019-07-05]

Bioinformatics Support for Computational Resources [Service] Cryo-EM [Service] Integrated Microscopy Technologies Umeå [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Pharmacogenomics of statin-related myopathy: Meta-analysis of rare variants from whole-exome sequencing.

Floyd JS, Bloch KM, Brody JA, ..., Alfirevic A, PREDICTION-ADR Consortium and EUDRAGENE

PLoS ONE 14 (6) e0218115 [2019-06-26; online 2019-06-26]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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]

A urinary extracellular vesicle microRNA biomarker discovery pipeline; from automated extracellular vesicle enrichment by acoustic trapping to microRNA sequencing.

Ku A, Ravi N, Yang M, ..., Lilja H, Ceder Y

PLoS ONE 14 (5) e0217507 [2019-05-29; online 2019-05-29]

Clinical Genomics Lund [Service]

Plasma protein profiling reveals candidate biomarkers for multiple sclerosis treatment.

Bedri SK, Nilsson OB, Fink K, ..., Grönlund H, Glaser A

PLoS ONE 14 (5) e0217208 [2019-05-29; online 2019-05-29]

Affinity Proteomics Stockholm [Collaborative]

Metabolic profiling of zebrafish embryo development from blastula period to early larval stages.

Dhillon SS, Torell F, Donten M, ..., Trygg J, Lundstedt T

PLoS ONE 14 (5) e0213661 [2019-05-14; online 2019-05-14]

Sensory receptor repertoire in cyprid antennules of the barnacle Balanus improvisus.

Abramova A, Alm Rosenblad M, Blomberg A, Larsson TA

PLoS ONE 14 (5) e0216294 [2019-05-02; online 2019-05-02]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

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

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]

Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] 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] Systems Biology [Collaborative]

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 Support and Infrastructure [Service] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Service]

Longitudinal effects of aging on plasma proteins levels in older adults - associations with kidney function and hemoglobin levels.

Lind L, Sundström J, Larsson A, ..., Ärnlöv J, Ingelsson E

PLoS ONE 14 (2) e0212060 [2019-02-25; online 2019-02-25]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

Analysis of colony phase variation switch in Acinetobacter baumannii clinical isolates.

Ahmad I, Karah N, Nadeem A, Wai SN, Uhlin BE

PLoS ONE 14 (1) e0210082 [2019-01-04; online 2019-01-04]

Integrated Microscopy Technologies Umeå [Service]

A multigene typing system for human adenoviruses reveals a new genotype in a collection of Swedish clinical isolates.

Kaján GL, Lipiec A, Bartha D, Allard A, Arnberg N

PLoS ONE 13 (12) e0209038 [2018-12-14; online 2018-12-14]

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

Proteotyping bacteria: Characterization, differentiation and identification of pneumococcus and other species within the Mitis Group of the genus Streptococcus by tandem mass spectrometry proteomics.

Karlsson R, Gonzales-Siles L, Gomila M, ..., Kristiansson E, Moore ERB

PLoS ONE 13 (12) e0208804 [2018-12-10; online 2018-12-10]

Glycoproteomics and MS Proteomics [Service]

Structural and biochemical characterization of the Cutibacterium acnes exo-β-1,4-mannosidase that targets the N-glycan core of host glycoproteins

Reichenbach T, Kalyani D, Gandini R, ..., Aspeborg H, Divne C

PLoS ONE 13 (9) e0204703 [2018-09-27; online 2018-09-27]

Bioinformatics Support for Computational Resources [Service] Protein Science Facility (PSF) [Service]

BtsCI and BseGI display sequence preference in the nucleotides flanking the recognition sequence

Rosa J, Fernandez-Gonzalez E, Ducani C, Högberg B

PLoS ONE 13 (8) e0202057 [2018-08-17; online 2018-08-17]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Protein Science Facility (PSF) [Service]

SURGE complex of Plasmodium falciparum in the rhoptry-neck (SURFIN4.2-RON4-GLURP) contributes to merozoite invasion.

Quintana MDP, Ch'ng JH, Zandian A, ..., Chan S, Wahlgren M

PLoS ONE 13 (8) e0201669 [2018-08-09; online 2018-08-09]

Autoimmunity and Serology Profiling [Service] Bioinformatics Support for Computational Resources [Service]

Modeling the structural implications of an alternatively spliced Exoc3l2, a paralog of the tunneling nanotube-forming M-Sec

O’Callaghan P, Zarb Y, Noborn F, Kreuger J

PLoS ONE 13 (8) e0201557 [2018-08-07; online 2018-08-07]

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

Novel genetic associations for blood pressure identified via gene-alcohol interaction in up to 570K individuals across multiple ancestries.

Feitosa MF, Kraja AT, Chasman DI, ..., Province MA, Levy D

PLoS ONE 13 (6) e0198166 [2018-06-18; online 2018-06-18]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Discovery of SNPs for individual identification by reduced representation sequencing of moose (Alces alces).

Blåhed IM, Königsson H, Ericsson G, Spong G

PLoS ONE 13 (5) e0197364 [2018-05-30; online 2018-05-30]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Genome-wide association meta-analysis of circulating odd-numbered chain saturated fatty acids: Results from the CHARGE Consortium.

de Oliveira Otto MC, Lemaitre RN, Sun Q, ..., Siscovick DS, Mozaffarian D

PLoS ONE 13 (5) e0196951 [2018-05-08; online 2018-05-08]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Quantification of endogenous and exogenous protein expressions of Na,K-ATPase with super-resolution PALM/STORM imaging.

Bernhem K, Blom H, Brismar H

PLoS ONE 13 (4) e0195825 [2018-04-25; online 2018-04-25]

Bioinformatics Support for Computational Resources [Service] Integrated Microscopy Technologies Stockholm [Technology development]

Autophagic flux blockage by accumulation of weakly basic tenovins leads to elimination of B-Raf mutant tumour cells that survive vemurafenib

Ladds MJGW, Pastor-Fernández A, Popova G, ..., Bhatia R, Laín S

PLoS ONE 13 (4) e0195956 [2018-04-23; online 2018-04-23]

Drug Discovery and Development (DDD) [Service]

Data quality of whole genome bisulfite sequencing on Illumina platforms.

Raine A, Liljedahl U, Nordlund J

PLoS ONE 13 (4) e0195972 [2018-04-18; online 2018-04-18]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Technology development] National Genomics Infrastructure [Technology development]

AMYCNE: Confident copy number assessment using whole genome sequencing data.

Eisfeldt J, Nilsson D, Andersson-Assarsson JC, Lindstrand A

PLoS ONE 13 (3) e0189710 [2018-03-26; online 2018-03-26]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Recurrent, low-frequency coding variants contributing to colorectal cancer in the Swedish population.

Jiao X, Liu W, Mahdessian H, ..., Dunlop M, Lindblom A

PLoS ONE 13 (3) e0193547 [2018-03-16; online 2018-03-16]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

High-resolution detection of chromosomal rearrangements in leukemias through mate pair whole genome sequencing.

Tran AN, Taylan F, Zachariadis V, ..., Nilsson D, Barbany G

PLoS ONE 13 (3) e0193928 [2018-03-12; online 2018-03-12]

Bioinformatics Support for Computational Resources [Service] Clinical Genomics Stockholm [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Transcriptome analysis of embryonic domains in Norway spruce reveals potential regulators of suspensor cell death.

Reza SH, Delhomme N, Street NR, ..., Minina EA, Bozhkov PV

PLoS ONE 13 (3) e0192945 [2018-03-02; online 2018-03-02]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Mesenchymal stem cell-derived exosomes have altered microRNA profiles and induce osteogenic differentiation depending on the stage of differentiation.

Wang X, Omar O, Vazirisani F, Thomsen P, Ekström K

PLoS ONE 13 (2) e0193059 [2018-02-15; online 2018-02-15]

Integrated Microscopy Technologies Gothenburg [Service]

Advancing the immunoaffinity platform AFFIRM to targeted measurements of proteins in serum in the pg/ml range.

Säll A, Corbee D, Vikström S, ..., Persson H, Waldemarson S

PLoS ONE 13 (2) e0189116 [2018-02-13; online 2018-02-13]

Drug Discovery and Development (DDD) [Technology development]

A novel monoclonal antibody targeting carboxymethyllysine, an advanced glycation end product in atherosclerosis and pancreatic cancer.

Wendel U, Persson N, Risinger C, ..., Jansson B, Blixt O

PLoS ONE 13 (2) e0191872 [2018-02-08; online 2018-02-08]

Structural Proteomics [Service]

Angiopoietin-1 deficiency increases renal capillary rarefaction and tubulointerstitial fibrosis in mice

Loganathan K, Salem Said E, Winterrowd E, ..., Quaggin SE, Jeansson M

PLoS ONE 13 (1) e0189433 [2018-01-02; online 2018-01-02]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

A family-based genome-wide association study of chronic rhinosinusitis with nasal polyps implicates several genes in the disease pathogenesis

Bohman A, Juodakis J, Oscarsson M, ..., Bende M, Torinsson Naluai Å

PLoS ONE 12 (12) e0185244 [2017-12-18; online 2017-12-18]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

CELSR2 is a candidate susceptibility gene in idiopathic scoliosis

Einarsdottir E, Grauers A, Wang J, ..., Kere J, Gerdhem P

PLoS ONE 12 (12) e0189591 [2017-12-14; online 2017-12-14]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Comparative cell cycle transcriptomics reveals synchronization of developmental transcription factor networks in cancer cells

Boström J, Sramkova Z, Salašová A, ..., Altun M, Andäng M

PLoS ONE 12 (12) e0188772 [2017-12-11; online 2017-12-11]

Spatial Proteomics [Collaborative]

Genomic and phenotypic characteristics of Swedish C. jejuni water isolates.

Nilsson A, Johansson C, Skarp A, ..., Engstrand L, Rautelin H

PLoS ONE 12 (12) e0189222 [2017-12-07; online 2017-12-07]

Clinical Genomics Stockholm [Service]

A short feature vector for image matching: The Log-Polar Magnitude feature descriptor.

Matuszewski DJ, Hast A, Wählby C, Sintorn IM

PLoS ONE 12 (11) e0188496 [2017-11-30; online 2017-11-30]

BioImage Informatics [Technology development]

Integrative analysis of genome-wide gene copy number changes and gene expression in non-small cell lung cancer.

Jabs V, Edlund K, König H, ..., Hengstler JG, Micke P

PLoS ONE 12 (11) e0187246 [2017-11-07; online 2017-11-07]

Clinical Genomics Uppsala [Collaborative]

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]

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

Subphenotypes of inflammatory bowel disease are characterized by specific serum protein profiles.

Andersson E, Bergemalm D, Kruse R, ..., Repsilber D, Halfvarson J

PLoS ONE 12 (10) e0186142 [2017-10-05; online 2017-10-05]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

Effects of tumour necrosis factor α upon the metabolism of the endocannabinoid anandamide in prostate cancer cells.

Karlsson J, Gouveia-Figueira S, Alhouayek M, Fowler CJ

PLoS ONE 12 (9) e0185011 [2017-09-14; online 2017-09-14]

Nitrogen uptake and assimilation in proliferating embryogenic cultures of Norway spruce-Investigating the specific role of glutamine.

Carlsson J, Svennerstam H, Moritz T, Egertsdotter U, Ganeteg U

PLoS ONE 12 (8) e0181785 [2017-08-24; online 2017-08-24]

Genomic correlates of glatiramer acetate adverse cardiovascular effects lead to a novel locus mediating coronary risk

Brænne I, Zeng L, Willenborg C, ..., None , None

PLoS ONE 12 (8) e0182999 [2017-08-22; online 2017-08-22]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

High RBM3 expression is associated with an improved survival and oxaliplatin response in patients with metastatic colorectal cancer.

Siesing C, Sorbye H, Dragomir A, ..., Glimelius B, Eberhard J

PLoS ONE 12 (8) e0182512 [2017-08-11; online 2017-08-11]

Tissue Profiling [Collaborative]

Solution NMR structure of the TRIM21 B-box2 and identification of residues involved in its interaction with the RING domain

Wallenhammar A, Anandapadamanaban M, Lemak A, ..., Wallner B, Sunnerhagen M

PLoS ONE 12 (7) e0181551 [2017-07-28; online 2017-07-28]

Biophysical characterization of the calmodulin-like domain of Plasmodium falciparum calcium dependent protein kinase 3

Andresen C, Niklasson M, Cassman Eklöf S, Wallner B, Lundström P

PLoS ONE 12 (7) e0181721 [2017-07-26; online 2017-07-26]

Protein Science Facility (PSF) [Service] Swedish NMR Centre (SNC) [Service]

Transcriptional profiling of the rat nucleus accumbens after modest or high alcohol exposure.

Morud J, Ashouri A, Larsson E, Ericson M, Söderpalm B

PLoS ONE 12 (7) e0181084 [2017-07-17; online 2017-07-17]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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

Lind U, Järvå M, Alm Rosenblad M, ..., Hedfalk K, Blomberg A

PLoS ONE 12 (7) e0181192 [2017-07-17; online 2017-07-17]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Functional metabolomics as a tool to analyze Mediator function and structure in plants.

Davoine C, Abreu IN, Khajeh K, ..., Moritz T, Björklund S

PLoS ONE 12 (6) e0179640 [2017-06-22; online 2017-06-22]

Identification of novel small molecules that inhibit STAT3-dependent transcription and function.

Kolosenko I, Yu Y, Busker S, ..., Page BDG, Grander D

PLoS ONE 12 (6) e0178844 [2017-06-21; online 2017-06-21]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Effect of food intake on 92 biomarkers for cardiovascular disease.

Dencker M, Gårdinger Y, Björgell O, Hlebowicz J

PLoS ONE 12 (6) e0178656 [2017-06-06; online 2017-06-06]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

Correlation of histopathologic characteristics to protein expression and function in malignant melanoma.

Welinder C, Pawłowski K, Szasz AM, ..., Wieslander E, Marko-Varga G

PLoS ONE 12 (4) e0176167 [2017-04-26; online 2017-04-26]

Structural Proteomics [Service]

Improvement of identification methods for honeybee specific Lactic Acid Bacteria; future approaches.

Lamei S, Hu YO, Olofsson TC, ..., Forsgren E, Vásquez A

PLoS ONE 12 (3) e0174614 [2017-03-27; online 2017-03-27]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Structure determination of a major facilitator peptide transporter: Inward facing PepTSt from Streptococcus thermophilus crystallized in space group P3121.

Quistgaard EM, Martinez Molledo M, Löw C

PLoS ONE 12 (3) e0173126 [2017-03-06; online 2017-03-06]

Protein Science Facility (PSF) [Service]

Comparison of whole genome amplification techniques for human single cell exome sequencing.

Borgström E, Paterlini M, Mold JE, Frisen J, Lundeberg J

PLoS ONE 12 (2) e0171566 [2017-02-16; online 2017-02-16]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

A novel RNA sequencing data analysis method for cell line authentication.

Fasterius E, Raso C, Kennedy S, ..., Uhlén M, Al-Khalili Szigyarto C

PLoS ONE 12 (2) e0171435 [2017-02-13; online 2017-02-13]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Longitudinal analysis of hepatic transcriptome and serum metabolome demonstrates altered lipid metabolism following the onset of hyperglycemia in spontaneously diabetic biobreeding rats.

Regnell SE, Hessner MJ, Jia S, ..., La Torre D, Lernmark Å

PLoS ONE 12 (2) e0171372 [2017-02-13; online 2017-02-13]

Swedish Metabolomics Centre (SMC) [Collaborative]

A Combinatory Antibody-Antigen Microarray Assay for High-Content Screening of Single-Chain Fragment Variable Clones from Recombinant Libraries.

Persson N, Jansson B, Stuhr-Hansen N, ..., Danielsson L, Blixt O

PLoS ONE 11 (12) e0168761 [2016-12-21; online 2016-12-21]

Structural Proteomics [Service]

Identification of a Differentially Expressed TIR-NBS-LRR Gene in a Major QTL Associated to Leaf Rust Resistance in Salix.

Martin T, Rönnberg-Wästljung AC, Stenlid J, Samils B

PLoS ONE 11 (12) e0168776 [2016-12-21; online 2016-12-21]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Genetic Variants in CHIA and CHI3L1 Are Associated with the IgE Response to the Ascaris Resistance Marker ABA-1 and the Birch Pollen Allergen Bet v 1.

Acevedo N, Bornacelly A, Mercado D, ..., Scheynius A, Caraballo L

PLoS ONE 11 (12) e0167453 [2016-12-15; online 2016-12-15]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Collaborative] National Genomics Infrastructure [Service]

The In Vitro Stability of Circulating Tumour DNA.

Henao Diaz E, Yachnin J, Grönberg H, Lindberg J

PLoS ONE 11 (12) e0168153 [2016-12-13; online 2016-12-13]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Serum Autoantibody Profiling of Patients with Paraneoplastic and Non-Paraneoplastic Autoimmune Retinopathy.

Ten Berge JC, van Rosmalen J, Vermeer J, ..., Rothova A, Schreurs MW

PLoS ONE 11 (12) e0167909 [2016-12-08; online 2016-12-08]

Autoimmunity and Serology Profiling [Collaborative] Tissue Profiling [Collaborative]

Quantitative and Selective Analysis of Feline Growth Related Proteins Using Parallel Reaction Monitoring High Resolution Mass Spectrometry.

Sundberg M, Strage EM, Bergquist J, Holst BS, Ramström M

PLoS ONE 11 (12) e0167138 [2016-12-01; online 2016-12-01]

Mass Spectrometry-based Proteomics, Uppsala [Technology development]

Viral Metagenomic Analysis Displays the Co-Infection Situation in Healthy and PMWS Affected Pigs.

Blomström AL, Fossum C, Wallgren P, Berg M

PLoS ONE 11 (12) e0166863 [2016-12-01; online 2016-12-01]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Relation between Established Glioma Risk Variants and DNA Methylation in the Tumor.

Dahlin AM, Wibom C, Ghasimi S, ..., Andersson U, Melin B

PLoS ONE 11 (10) e0163067 [2016-10-25; online 2016-10-25]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Failure to Genotype: A Cautionary Note on an Elusive loxP Sequence.

Kreuger J, O'Callaghan P

PLoS ONE 11 (10) e0165012 [2016-10-21; online 2016-10-21]

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

Over Expression of NANOS3 and DAZL in Human Embryonic Stem Cells.

Panula S, Reda A, Stukenborg JB, ..., Reijo Pera RA, Hovatta O

PLoS ONE 11 (10) e0165268 [2016-10-21; online 2016-10-21]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

The Transcriptome of Rhabdomyosarcoma Cells Infected with Cytolytic and Non-Cytolytic Variants of Coxsackievirus B2 Ohio-1.

Sävneby A, Luthman J, Nordenskjöld F, Andersson B, Lindberg AM

PLoS ONE 11 (10) e0164548 [2016-10-19; online 2016-10-19]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Metabolite and Lipid Profiling of Biobank Plasma Samples Collected Prior to Onset of Rheumatoid Arthritis.

Surowiec I, Ärlestig L, Rantapää-Dahlqvist S, Trygg J

PLoS ONE 11 (10) e0164196 [2016-10-18; online 2016-10-18]

Discovery of Novel Viruses in Mosquitoes from the Zambezi Valley of Mozambique.

Cholleti H, Hayer J, Abilio AP, ..., Berg M, Blomström AL

PLoS ONE 11 (9) e0162751 [2016-09-28; online 2016-09-28]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Genetic Spectrum of Idiopathic Restrictive Cardiomyopathy Uncovered by Next-Generation Sequencing.

Kostareva A, Kiselev A, Gudkova A, ..., Sejersen T, Shlyakhto E

PLoS ONE 11 (9) e0163362 [2016-09-23; online 2016-09-23]

Clinical Genomics Stockholm [Service]

Linkage between Fitness of Yeast Cells and Adenylate Kinase Catalysis

Tükenmez H, Magnussen HM, Kovermann M, Byström A, Wolf-Watz M

PLoS ONE 11 (9) e0163115 [2016-09-19; online 2016-09-19]

Cinobufagin Modulates Human Innate Immune Responses and Triggers Antibacterial Activity.

Xie S, Spelmink L, Codemo M, ..., Henriques-Normark B, Olliver M

PLoS ONE 11 (8) e0160734 [2016-08-16; online 2016-08-16]

Mass Spectrometry-based Proteomics, Uppsala [Service]

MetLab: An In Silico Experimental Design, Simulation and Analysis Tool for Viral Metagenomics Studies.

Norling M, Karlsson-Lindsjö OE, Gourlé H, Bongcam-Rudloff E, Hayer J

PLoS ONE 11 (8) e0160334 [2016-08-01; online 2016-08-01]

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

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

Astakhova L, Ngara M, Babich O, ..., Ernberg I, Matskova L

PLoS ONE 11 (7) e0154102 [2016-07-21; online 2016-07-21]

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

Metabolic Profiling of Systemic Lupus Erythematosus and Comparison with Primary Sjögren's Syndrome and Systemic Sclerosis.

Bengtsson AA, Trygg J, Wuttge DM, ..., Rännar S, Lundstedt T

PLoS ONE 11 (7) e0159384 [2016-07-21; online 2016-07-21]

The De Novo Transcriptome and Its Functional Annotation in the Seed Beetle Callosobruchus maculatus.

Sayadi A, Immonen E, Bayram H, Arnqvist G

PLoS ONE 11 (7) e0158565 [2016-07-21; online 2016-07-21]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

DNA Content in Extracellular Vesicles Isolated from Porcine Coronary Venous Blood Directly after Myocardial Ischemic Preconditioning.

Svennerholm K, Rodsand P, Hellman U, ..., Ronquist G, Haney M

PLoS ONE 11 (7) e0159105 [2016-07-19; online 2016-07-19]

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

Gene-Expression Profiling Suggests Impaired Signaling via the Interferon Pathway in Cstb-/- Microglia.

Körber I, Katayama S, Einarsdottir E, ..., Lehesjoki AE, Joensuu T

PLoS ONE 11 (6) e0158195 [2016-06-29; online 2016-06-29]

Bioinformatics and Expression Analysis (BEA) [Service]

Targeting Serglycin Prevents Metastasis in Murine Mammary Carcinoma.

Roy A, Femel J, Huijbers EJ, ..., Olsson AK, Åbrink M

PLoS ONE 11 (5) e0156151 [2016-05-25; online 2016-05-25]

Array and Analysis Facility [Service]

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

Díez B, Nylander JA, Ininbergs K, ..., Rusch DB, Bergman B

PLoS ONE 11 (5) e0155757 [2016-05-19; online 2016-05-19]

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

Effects of Dispersal and Initial Diversity on the Composition and Functional Performance of Bacterial Communities.

Zha Y, Berga M, Comte J, Langenheder S

PLoS ONE 11 (5) e0155239 [2016-05-16; online 2016-05-16]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Asp-ase Activity of the Opossum Granzyme B Supports the Role of Granzyme B as Part of Anti-Viral Immunity Already during Early Mammalian Evolution.

Fu Z, Thorpe M, Akula S, Hellman L

PLoS ONE 11 (5) e0154886 [2016-05-06; online 2016-05-06]

Mass Spectrometry-based Proteomics, Uppsala [Service]

Elevated Levels of SOX10 in Serum from Vitiligo and Melanoma Patients, Analyzed by Proximity Ligation Assay

Blokzijl A, Chen LE, Gustafsdottir SM, ..., Kamali-Moghaddam M, Hedstrand H

PLoS ONE 11 (4) e0154214 [2016-04-25; online 2016-04-25]

Affinity Proteomics Uppsala [Collaborative] PLA and Single Cell Proteomics [Collaborative]

Using an Inbred Horse Breed in a High Density Genome-Wide Scan for Genetic Risk Factors of Insect Bite Hypersensitivity (IBH).

Velie BD, Shrestha M, Franҫois L, ..., Buys N, Lindgren G

PLoS ONE 11 (4) e0152966 [2016-04-12; online 2016-04-12]

Array and Analysis Facility [Service]

Tissue and Serum miRNA Profile in Locally Advanced Breast Cancer (LABC) in Response to Neo-Adjuvant Chemotherapy (NAC) Treatment.

Al-Khanbashi M, Caramuta S, Alajmi AM, ..., Lui WO, Al-Moundhri MS

PLoS ONE 11 (4) e0152032 [2016-04-11; online 2016-04-11]

Bioinformatics and Expression Analysis (BEA) [Service]

Modifications of the 7-Hydroxyl Group of the Transthyretin Ligand Luteolin Provide Mechanistic Insights into Its Binding Properties and High Plasma Specificity.

Nilsson L, Larsson A, Begum A, ..., Sauer-Eriksson AE, Olofsson A

PLoS ONE 11 (4) e0153112 [2016-04-06; online 2016-04-06]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

PopulationProfiler: A Tool for Population Analysis and Visualization of Image-Based Cell Screening Data.

Matuszewski DJ, Wählby C, Puigvert JC, Sintorn IM

PLoS ONE 11 (3) e0151554 [2016-03-17; online 2016-03-17]

BioImage Informatics [Service]

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.

Tjernlund A, Burgener A, Lindvall JM, ..., McElrath MJ, Corey L

PLoS ONE 11 (3) e0149907 [2016-03-17; online 2016-03-17]

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

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

Zepeda Mendoza ML, Lundberg J, Ivarsson M, ..., Sallstedt T, Dalen L

PLoS ONE 11 (3) e0151577 [2016-03-17; online 2016-03-17]

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

The Intestinal Eukaryotic Virome in Healthy and Diarrhoeic Neonatal Piglets.

Karlsson OE, Larsson J, Hayer J, Berg M, Jacobson M

PLoS ONE 11 (3) e0151481 [2016-03-16; online 2016-03-16]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Analysis of the Cerebrospinal Fluid Proteome in Alzheimer's Disease.

Khoonsari PE, Häggmark A, Lönnberg M, ..., Kultima K, Shevchenko G

PLoS ONE 11 (3) e0150672 [2016-03-07; online 2016-03-07]

Affinity Proteomics Stockholm [Collaborative]

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

Lind AL, Wu D, Freyhult E, ..., Landegren U, Kamali-Moghaddam M

PLoS ONE 11 (2) e0149821 [2016-02-25; online 2016-02-25]

Affinity Proteomics Uppsala [Technology development] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] PLA and Single Cell Proteomics [Technology development]

Bioelectric and Morphological Response of Liquid-Covered Human Airway Epithelial Calu-3 Cell Monolayer to Periodic Deposition of Colloidal 3-Mercaptopropionic-Acid Coated CdSe-CdS/ZnS Core-Multishell Quantum Dots.

Turdalieva A, Solandt J, Shambetova N, ..., Zelenina M, Fu Y

PLoS ONE 11 (2) e0149915 [2016-02-25; online 2016-02-25]

Integrated Microscopy Technologies Stockholm [Collaborative]

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

Wrange AL, Charrier G, Thonig A, ..., Jonsson PR, André C

PLoS ONE 11 (1) e0147082 [2016-01-28; online 2016-01-28]

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

Metabolites in Blood for Prediction of Bacteremic Sepsis in the Emergency Room.

Kauppi AM, Edin A, Ziegler I, ..., Strålin K, Johansson A

PLoS ONE 11 (1) e0147670 [2016-01-22; online 2016-01-22]

Backbone Assignment of the MALT1 Paracaspase by Solution NMR.

Unnerståle S, Nowakowski M, Baraznenok V, ..., Orekhov V, Agback T

PLoS ONE 11 (1) e0146496 [2016-01-20; online 2016-01-20]

Swedish NMR Centre (SNC) [Collaborative]

Genetic Determinants of Thrombin Generation and Their Relation to Venous Thrombosis: Results from the GAIT-2 Project.

Martin-Fernandez L, Ziyatdinov A, Carrasco M, ..., Souto JC, Soria JM

PLoS ONE 11 (1) e0146922 [2016-01-19; online 2016-01-19]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Serum Trimethylamine-N-Oxide Is Strongly Related to Renal Function and Predicts Outcome in Chronic Kidney Disease.

Missailidis C, Hällqvist J, Qureshi AR, ..., Stenvinkel P, Bergman P

PLoS ONE 11 (1) e0141738 [2016-01-11; online 2016-01-11]

Swedish Metabolomics Centre (SMC) [Collaborative]

Characterization and Expression of the Zebrafish qki Paralogs.

Radomska KJ, Sager J, Farnsworth B, ..., Jazin E, Emilsson LS

PLoS ONE 11 (1) e0146155 [2016-01-04; online 2016-01-04]

Genome Engineering Zebrafish [Service]

The Urinary Bladder Transcriptome and Proteome Defined by Transcriptomics and Antibody-Based Profiling.

Habuka M, Fagerberg L, Hallström BM, ..., Yamamoto T, Uhlen M

PLoS ONE 10 (12) e0145301 [2015-12-22; online 2015-12-22]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Tissue Profiling [Collaborative]

A Combination of Culture Conditions and Gene Expression Analysis Can Be Used to Investigate and Predict hES Cell Differentiation Potential towards Male Gonadal Cells.

Kjartansdóttir KR, Reda A, Panula S, ..., Hovatta O, Stukenborg JB

PLoS ONE 10 (12) e0144029 [2015-12-02; online 2015-12-02]

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

Mattsson A, Kärrman A, Pinto R, Brunström B

PLoS ONE 10 (12) e0143780 [2015-12-01; online 2015-12-01]

Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Genome-Wide Association Study Identifies That the ABO Blood Group System Influences Interleukin-10 Levels and the Risk of Clinical Events in Patients with Acute Coronary Syndrome.

Johansson Å, Alfredsson J, Eriksson N, Wallentin L, Siegbahn A

PLoS ONE 10 (11) e0142518 [2015-11-24; online 2015-11-24]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Combinations of Genetic Data Present in Bipolar Patients, but Absent in Control Persons.

Mellerup E, Andreassen OA, Bennike B, ..., Werge T, Moeller GL

PLoS ONE 10 (11) e0143432 [2015-11-20; online 2015-11-20]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Genetic Polymorphisms in Vitamin D Metabolism and Signaling Genes and Risk of Breast Cancer: A Nested Case-Control Study.

Clendenen TV, Ge W, Koenig KL, ..., Sund M, Zeleniuch-Jacquotte A

PLoS ONE 10 (10) e0140478 [2015-10-21; online 2015-10-21]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Growth of Chitinophaga pinensis on Plant Cell Wall Glycans and Characterisation of a Glycoside Hydrolase Family 27 β-l-Arabinopyranosidase Implicated in Arabinogalactan Utilisation.

McKee LS, Brumer H

PLoS ONE 10 (10) e0139932 [2015-10-08; online 2015-10-08]

Protein Science Facility (PSF) [Service]

Comparative Sigma Factor-mRNA Levels in Mycobacterium marinum under Stress Conditions and during Host Infection.

Pettersson BM, Das S, Behra PR, ..., Ennis DG, Kirsebom LA

PLoS ONE 10 (10) e0139823 [2015-10-07; online 2015-10-07]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Serendipitous Meta-Transcriptomics: The Fungal Community of Norway Spruce (Picea abies).

Delhomme N, Sundström G, Zamani N, ..., Grabherr MG, Street NR

PLoS ONE 10 (9) e0139080 [2015-09-28; online 2015-09-28]

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

Structure of the Glycosyltransferase Ktr4p from Saccharomyces cerevisiae.

Possner DD, Claesson M, Guy JE

PLoS ONE 10 (8) e0136239 [2015-08-21; online 2015-08-21]

Microstructural White Matter Properties Mediate the Association between APOE and Perceptual Speed in Very Old Persons without Dementia.

Laukka EJ, Lövdén M, Kalpouzos G, ..., Fratiglioni L, Bäckman L

PLoS ONE 10 (8) e0134766 [2015-08-07; online 2015-08-07]

Analysis of the Human Prostate-Specific Proteome Defined by Transcriptomics and Antibody-Based Profiling Identifies TMEM79 and ACOXL as Two Putative, Diagnostic Markers in Prostate Cancer.

O'Hurley G, Busch C, Fagerberg L, ..., Uhlén M, Pontén F

PLoS ONE 10 (8) e0133449 [2015-08-03; online 2015-08-03]

Affinity Proteomics Stockholm NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Spatial Proteomics Tissue Profiling [Technology development]

Bioinformatic Challenges in Clinical Diagnostic Application of Targeted Next Generation Sequencing: Experience from Pheochromocytoma.

Crona J, Ljungström V, Welin S, ..., Hellman P, Björklund P

PLoS ONE 10 (7) e0133210 [2015-07-31; online 2015-07-31]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Predisposition to Childhood Otitis Media and Genetic Polymorphisms within the Toll-Like Receptor 4 (TLR4) Locus.

Hafrén L, Einarsdottir E, Kentala E, ..., Kere J, Mattila PS

PLoS ONE 10 (7) e0132551 [2015-07-15; online 2015-07-15]

Differential Expression Analysis by RNA-Seq Reveals Perturbations in the Platelet mRNA Transcriptome Triggered by Pathogen Reduction Systems.

Osman A, Hitzler WE, Ameur A, Provost P

PLoS ONE 10 (7) e0133070 [2015-07-14; online 2015-07-14]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Structural Basis for the Specificity of Human NUDT16 and Its Regulation by Inosine Monophosphate

Trésaugues L, Lundbäck T, Welin M, ..., Gräslund S, Nordlund P

PLoS ONE 10 (6) e0131507 [2015-06-29; online 2015-06-29]

Chemical Biology Consortium Sweden (CBCS) [Collaborative] Protein Science Facility (PSF)

High BRAF Mutation Frequency and Marked Survival Differences in Subgroups According to KRAS/BRAF Mutation Status and Tumor Tissue Availability in a Prospective Population-Based Metastatic Colorectal Cancer Cohort.

Sorbye H, Dragomir A, Sundström M, ..., Qvortrup C, Glimelius B

PLoS ONE 10 (6) e0131046 [2015-06-29; online 2015-06-29]

Tissue Profiling [Collaborative]

Defining the Human Brain Proteome Using Transcriptomics and Antibody-Based Profiling with a Focus on the Cerebral Cortex.

Sjöstedt E, Fagerberg L, Hallström BM, ..., Uhlén M, Mulder J

PLoS ONE 10 (6) e0130028 [2015-06-15; online 2015-06-15]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Tissue Profiling [Collaborative]

Phylogeny, evolution and classification of gall wasps: the plot thickens.

Ronquist F, Nieves-Aldrey JL, Buffington ML, ..., Liljeblad J, Nylander JA

PLoS ONE 10 (5) e0123301 [2015-05-20; online 2015-05-20]

Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Circulating carnosine dipeptidase 1 associates with weight loss and poor prognosis in gastrointestinal cancer.

Arner P, Henjes F, Schwenk JM, ..., Nilsson P, Rydén M

PLoS ONE 10 (4) e0123566 [2015-04-21; online 2015-04-21]

Affinity Proteomics Stockholm

Methylation levels of SLC23A2 and NCOR2 genes correlate with spinal muscular atrophy severity.

Zheleznyakova GY, Nilsson EK, Kiselev AV, ..., Baranov VS, Schiöth HB

PLoS ONE 10 (3) e0121964 [2015-03-30; online 2015-03-30]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Modulation of genetic associations with serum urate levels by body-mass-index in humans.

Huffman JE, Albrecht E, Teumer A, ..., Köttgen A, Vitart V

PLoS ONE 10 (3) e0119752 [2015-03-26; online 2015-03-26]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Crystal structures of the kinase domain of the sulfate-activating complex in Mycobacterium tuberculosis.

Poyraz Ö, Brunner K, Lohkamp B, ..., Schnell R, Schneider G

PLoS ONE 10 (3) e0121494 [2015-03-25; online 2015-03-25]

Chemical Biology Consortium Sweden (CBCS) [Collaborative] Protein Science Facility (PSF)

Discovery of molecular markers to discriminate corneal endothelial cells in the human body.

Yoshihara M, Ohmiya H, Hara S, ..., Tsujikawa M, Nishida K

PLoS ONE 10 (3) e0117581 [2015-03-25; online 2015-03-25]

Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Low elastin content of carotid plaques is associated with increased risk of ipsilateral stroke.

Asciutto G, Dias NV, Edsfeldt A, ..., Nilsson J, Gonçalves I

PLoS ONE 10 (3) e0121086 [2015-03-24; online 2015-03-24]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

Complete genome sequence of Borrelia afzelii K78 and comparative genome analysis.

Schüler W, Bunikis I, Weber-Lehman J, ..., Bergström S, Lundberg U

PLoS ONE 10 (3) e0120548 [2015-03-23; online 2015-03-23]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Analysis of the role of interleukin 6 receptor haplotypes in the regulation of circulating levels of inflammatory biomarkers and risk of coronary heart disease.

Gigante B, Strawbridge RJ, Velasquez IM, ..., Humphries SE, de Faire U

PLoS ONE 10 (3) e0119980 [2015-03-17; online 2015-03-17]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Roux-en Y gastric bypass surgery induces genome-wide promoter-specific changes in DNA methylation in whole blood of obese patients.

Nilsson EK, Ernst B, Voisin S, ..., Schultes B, Schiöth HB

PLoS ONE 10 (2) e0115186 [2015-02-24; online 2015-02-24]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Microbial community composition and diversity via 16S rRNA gene amplicons: evaluating the illumina platform.

Sinclair L, Osman OA, Bertilsson S, Eiler A

PLoS ONE 10 (2) e0116955 [2015-02-03; online 2015-02-03]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Endonuclease specificity and sequence dependence of type IIS restriction enzymes.

Lundin S, Jemt A, Terje-Hegge F, ..., Lexow P, Lundeberg J

PLoS ONE 10 (1) e0117059 [2015-01-28; online 2015-01-28]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Inhibitory Activity of the Isoflavone Biochanin A on Intracellular Bacteria of Genus Chlamydia and Initial Development of a Buccal Formulation

Hanski L, Genina N, Uvell H, ..., Sandler N, Vuorela PM

PLoS ONE 9 (12) e115115 [2014-12-16; online 2014-12-16]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Acetate availability and utilization supports the growth of mutant sub-populations on aging bacterial colonies.

Bergman JM, Wrande M, Hughes D

PLoS ONE 9 (10) e109255 [2014-10-02; online 2014-10-02]

Mass Spectrometry-based Proteomics, Uppsala

Human cytomegalovirus tegument protein pp65 is detected in all intra- and extra-axial brain tumours independent of the tumour type or grade.

Libard S, Popova SN, Amini RM, ..., Ponten F, Alafuzoff I

PLoS ONE 9 (9) e108861 [2014-09-30; online 2014-09-30]

Plasmidome interchange between Clostridium botulinum, Clostridium novyi and Clostridium haemolyticum converts strains of independent lineages into distinctly different pathogens.

Skarin H, Segerman B

PLoS ONE 9 (9) e107777 [2014-09-25; online 2014-09-25]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Histidine-rich glycoprotein uptake and turnover is mediated by mononuclear phagocytes.

Tugues S, Roche F, Noguer O, ..., Tolmachev V, Claesson-Welsh L

PLoS ONE 9 (9) e107483 [2014-09-22; online 2014-09-22]

A universal approach to prepare reagents for DNA-assisted protein analysis.

Yan J, Gu GJ, Jost C, ..., Landegren U, Kamali-Moghaddam M

PLoS ONE 9 (9) e108061 [2014-09-18; online 2014-09-18]

Affinity Proteomics Uppsala [Technology development] Clinical Biomarkers PLA and Single Cell Proteomics [Technology development]

Characterization of stem-like cells in mucoepidermoid tracheal paediatric tumor.

Lim ML, Ooi BN, Jungebluth P, ..., Ahrlund-Richter L, Macchiarini P

PLoS ONE 9 (9) e107712 [2014-09-17; online 2014-09-17]

A multicentre hospital outbreak in Sweden caused by introduction of a vanB2 transposon into a stably maintained pRUM-plasmid in an Enterococcus faecium ST192 clone.

Sivertsen A, Billström H, Melefors Ö, ..., Sundsfjord A, Hegstad K

PLoS ONE 9 (8) e103274 [2014-08-25; online 2014-08-25]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Small RNA sequence analysis of adenovirus VA RNA-derived miRNAs reveals an unexpected serotype-specific difference in structure and abundance.

Kamel W, Segerman B, Punga T, Akusjärvi G

PLoS ONE 9 (8) e105746 [2014-08-21; online 2014-08-21]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Evaluation of exome sequencing to estimate tumor burden in plasma.

Klevebring D, Neiman M, Sundling S, ..., Grönberg H, Lindberg J

PLoS ONE 9 (8) e104417 [2014-08-18; online 2014-08-18]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Tandem RNA chimeras contribute to transcriptome diversity in human population and are associated with intronic genetic variants.

Greger L, Su J, Rung J, ..., Dermitzakis ET, Brazma A

PLoS ONE 9 (8) e104567 [2014-08-18; online 2014-08-18]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Genome analysis of Bacillus amyloliquefaciens Subsp. plantarum UCMB5113: a rhizobacterium that improves plant growth and stress management.

Niazi A, Manzoor S, Asari S, ..., Meijer J, Bongcam-Rudloff E

PLoS ONE 9 (8) e104651 [2014-08-13; online 2014-08-13]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Common genetic determinants of lung function, subclinical atherosclerosis and risk of coronary artery disease.

Sabater-Lleal M, Mälarstig A, Folkersen L, ..., Tobin MD, Hamsten A

PLoS ONE 9 (8) e104082 [2014-08-05; online 2014-08-05]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Differences in gene expression between mouse and human for dynamically regulated genes in early embryo.

Madissoon E, Töhönen V, Vesterlund L, ..., Hovatta O, Kere J

PLoS ONE 9 (8) e102949 [2014-08-04; online 2014-08-04]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Nuclease-assisted suppression of human DNA background in sepsis.

Song Y, Giske CG, Gille-Johnson P, ..., Lundeberg J, Gyarmati P

PLoS ONE 9 (7) e103610 [2014-07-30; online 2014-07-30]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

A Picea abies linkage map based on SNP markers identifies QTLs for four aspects of resistance to Heterobasidion parviporum infection.

Lind M, Källman T, Chen J, ..., Lascoux M, Stenlid J

PLoS ONE 9 (7) e101049 [2014-07-18; online 2014-07-18]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Single nucleotide polymorphisms with cis-regulatory effects on long non-coding transcripts in human primary monocytes.

Almlöf JC, Lundmark P, Lundmark A, ..., Ouwehand WH, Syvänen AC

PLoS ONE 9 (7) e102612 [2014-07-15; online 2014-07-15]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Structural and biochemical characterization of human PR70 in isolation and in complex with the scaffolding subunit of protein phosphatase 2A.

Dovega R, Tsutakawa S, Quistgaard EM, ..., Löw C, Nordlund P

PLoS ONE 9 (7) e101846 [2014-07-09; online 2014-07-09]

Transcriptome analysis reveals signature of adaptation to landscape fragmentation.

Somervuo P, Kvist J, Ikonen S, ..., Ahola V, Hanski I

PLoS ONE 9 (7) e101467 [2014-07-02; online 2014-07-02]

Karolinska High Throughput Center (KHTC)

Large-scale genome-wide association studies and meta-analyses of longitudinal change in adult lung function.

Tang W, Kowgier M, Loth DW, ..., Hall IP, Cassano PA

PLoS ONE 9 (7) e100776 [2014-07-01; online 2014-07-01]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Structure and inhibition of mouse leukotriene C4 synthase.

Niegowski D, Kleinschmidt T, Ahmad S, ..., Rinaldo-Matthis A, Haeggström JZ

PLoS ONE 9 (5) e96763 [2014-05-08; online 2014-05-08]

Chemical Biology Consortium Sweden (CBCS) [Service] Protein Science Facility (PSF)

Bead arrays for antibody and complement profiling reveal joint contribution of antibody isotypes to C3 deposition.

Ayoglu B, Szarka E, Huber K, ..., Nilsson P, Papp K

PLoS ONE 9 (5) e96403 [2014-05-05; online 2014-05-05]

Affinity Proteomics Stockholm [Collaborative] Autoimmunity and Serology Profiling [Technology development]

Seasonal pattern of lesion development in diseased Fraxinus excelsior infected by Hymenoscyphus pseudoalbidus.

Bengtsson SB, Barklund P, von Brömssen C, Stenlid J

PLoS ONE 9 (4) e76429 [2014-04-23; online 2014-04-23]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Systematic design of 18S rRNA gene primers for determining eukaryotic diversity in microbial consortia.

Hugerth LW, Muller EE, Hu YO, ..., Wilmes P, Andersson AF

PLoS ONE 9 (4) e95567 [2014-04-22; online 2014-04-22]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Autosomal recessive transmission of a rare KRT74 variant causes hair and nail ectodermal dysplasia: allelism with dominant woolly hair/hypotrichosis.

Raykova D, Klar J, Azhar A, ..., Baig SM, Dahl N

PLoS ONE 9 (4) e93607 [2014-04-08; online 2014-04-08]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

ZBED6 modulates the transcription of myogenic genes in mouse myoblast cells.

Jiang L, Wallerman O, Younis S, ..., Andersson G, Andersson L

PLoS ONE 9 (4) e94187 [2014-04-08; online 2014-04-08]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

NGI Uppsala (SNP&SEQ Technology Platform) NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Rask-Andersen M, Philippot G, Moschonis G, ..., Fredriksson R, Schiöth HB

PLoS ONE 9 (4) e93193 [2014-04-02; online 2014-04-02]

Genetic characterization of a novel Iflavirus associated with vomiting disease in the Chinese oak silkmoth Antheraea pernyi.

Geng P, Li W, Lin L, ..., An L, Terenius O

PLoS ONE 9 (3) e92107 [2014-03-17; online 2014-03-17]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Sequencing degraded RNA addressed by 3' tag counting.

Sigurgeirsson B, Emanuelsson O, Lundeberg J

PLoS ONE 9 (3) e91851 [2014-03-14; online 2014-03-14]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Functional tradeoffs underpin salinity-driven divergence in microbial community composition.

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

PLoS ONE 9 (2) e89549 [2014-02-27; online 2014-02-27]

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

Microevolution during an Anthrax outbreak leading to clonal heterogeneity and penicillin resistance.

Ågren J, Finn M, Bengtsson B, Segerman B

PLoS ONE 9 (2) e89112 [2014-02-13; online 2014-02-13]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Mycobacteria bypass mucosal NF-kB signalling to induce an epithelial anti-inflammatory IL-22 and IL-10 response.

Lutay N, Håkansson G, Alaridah N, ..., Westergren-Thorsson G, Godaly G

PLoS ONE 9 (1) e86466 [2014-01-28; online 2014-01-28]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

BDNF polymorphisms are linked to poorer working memory performance, reduced cerebellar and hippocampal volumes and differences in prefrontal cortex in a Swedish elderly population.

Brooks SJ, Nilsson EK, Jacobsson JA, ..., Lind L, Schiöth HB

PLoS ONE 9 (1) e82707 [2014-01-23; online 2014-01-23]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Integrative genetic characterization and phenotype correlations in pheochromocytoma and paraganglioma tumours.

Crona J, Nordling M, Maharjan R, ..., Hellman P, Björklund P

PLoS ONE 9 (1) e86756 [2014-01-22; online 2014-01-22]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Structural basis for binding of fluorinated glucose and galactose to Trametes multicolor pyranose 2-oxidase variants with improved galactose conversion.

Tan TC, Spadiut O, Gandini R, Haltrich D, Divne C

PLoS ONE 9 (1) e86736 [2014-01-21; online 2014-01-21]

Eight New Genomes and Synthetic Controls Increase the Accessibility of Rapid Melt-MAMA SNP Typing of Coxiella burnetii

Karlsson E, Macellaro A, Byström M, ..., Sjödin A, Myrtennäs K

PLoS ONE 9 (1) e85417 [2014-01-21; online 2014-01-21]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Host-specificity and dynamics in bacterial communities associated with Bloom-forming freshwater phytoplankton.

Bagatini IL, Eiler A, Bertilsson S, ..., Tessarolli LP, Vieira AAH

PLoS ONE 9 (1) e85950 [2014-01-20; online 2014-01-20]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Assessment of whole genome amplification for sequence capture and massively parallel sequencing.

Hasmats J, Gréen H, Orear C, ..., Käller M, Lundeberg J

PLoS ONE 9 (1) e84785 [2014-01-07; online 2014-01-07]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Association of STAT4 polymorphism with severe renal insufficiency in lupus nephritis.

Bolin K, Sandling JK, Zickert A, ..., Gunnarsson I, Nordmark G

PLoS ONE 8 (12) e84450 [2013-12-27; online 2013-12-27]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

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]

Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Utilizing twins as controls for non-twin case-materials in genome wide association studies.

Ganna A, Ortega-Alonso A, Havulinna A, ..., Hultman CM, Magnusson PKE

PLoS ONE 8 (12) e83101 [2013-12-10; online 2013-12-10]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Urinary prognostic biomarkers and classification of IgA nephropathy by high resolution mass spectrometry coupled with liquid chromatography.

Kalantari S, Rutishauser D, Samavat S, ..., Rezaei-Tavirani M, Zubarev RA

PLoS ONE 8 (12) e80830 [2013-12-05; online 2013-12-05]

Advanced Mass Spectrometry Proteomics

The resveratrol tetramer (-)-hopeaphenol inhibits type III secretion in the gram-negative pathogens Yersinia pseudotuberculosis and Pseudomonas aeruginosa.

Zetterström CE, Hasselgren J, Salin O, ..., Sundin C, Elofsson M

PLoS ONE 8 (12) e81969 [2013-12-04; online 2013-12-04]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Identification of candidate serum proteins for classifying well-differentiated small intestinal neuroendocrine tumors.

Darmanis S, Cui T, Drobin K, ..., Schwenk JM, Giandomenico V

PLoS ONE 8 (11) e81712 [2013-11-25; online 2013-11-25]

Affinity Proteomics Stockholm [Collaborative]

Rule-based models of the interplay between genetic and environmental factors in childhood allergy.

Bornelöv S, Sääf A, Melén E, ..., Pershagen G, Komorowski J

PLoS ONE 8 (11) e80080 [2013-11-19; online 2013-11-19]

De novo SNP discovery in the Scandinavian brown bear (Ursus arctos).

Norman AJ, Street NR, Spong G

PLoS ONE 8 (11) e81012 [2013-11-18; online 2013-11-18]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Nanobody mediated crystallization of an archeal mechanosensitive channel.

Löw C, Yau YH, Pardon E, ..., Steyaert J, Nordlund P

PLoS ONE 8 (10) e77984 [2013-10-21; online 2013-10-21]

Molecular characterization of the α-subunit of Na⁺/K⁺ ATPase from the euryhaline barnacle Balanus improvisus reveals multiple genes and differential expression of alternative splice variants.

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

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

Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

FHOD1, a formin upregulated in epithelial-mesenchymal transition, participates in cancer cell migration and invasion.

Gardberg M, Kaipio K, Lehtinen L, ..., Koivisto M, Carpén O

PLoS ONE 8 (9) e74923 [2013-09-26; online 2013-09-26]

Genetic variants of coagulation factor XI show association with ischemic stroke up to 70 years of age.

Hanson E, Nilsson S, Jood K, ..., Melander O, Jern C

PLoS ONE 8 (9) e75286 [2013-09-25; online 2013-09-25]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Spinal deformity in aged zebrafish is accompanied by degenerative changes to their vertebrae that resemble osteoarthritis.

Hayes AJ, Reynolds S, Nowell MA, ..., Caterson B, Hammond CL

PLoS ONE 8 (9) e75787 [2013-09-24; online 2013-09-24]

Genome Engineering Zebrafish

Equine multiple congenital ocular anomalies and silver coat colour result from the pleiotropic effects of mutant PMEL.

Andersson LS, Wilbe M, Viluma A, ..., Ewart S, Lindgren G

PLoS ONE 8 (9) e75639 [2013-09-23; online 2013-09-23]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

A metagenomics transect into the deepest point of the Baltic Sea reveals clear stratification of microbial functional capacities.

Thureborn P, Lundin D, Plathan J, ..., Sjöberg BM, Sjöling S

PLoS ONE 8 (9) e74983 [2013-09-23; online 2013-09-23]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Post-zygotic and inter-individual structural genetic variation in a presumptive enhancer element of the locus between the IL10Rβ and IFNAR1 genes.

Razzaghian HR, Forsberg LA, Prakash KR, ..., Absher D, Dumanski JP

PLoS ONE 8 (9) e67752 [2013-09-04; online 2013-09-04]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Comparison of the nodule vs. root transcriptome of the actinorhizal plant Datisca glomerata: actinorhizal nodules contain a specific class of defensins.

Demina IV, Persson T, Santos P, Plaszczyca M, Pawlowski K

PLoS ONE 8 (8) e72442 [2013-08-29; online 2013-08-29]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Svartström O, Mushtaq M, Pringle M, Segerman B

PLoS ONE 8 (8) e71281 [2013-08-19; online 2013-08-19]

The STK33-linked SNP rs4929949 is associated with obesity and BMI in two independent cohorts of Swedish and Greek children.

Rask-Andersen M, Moschonis G, Chrousos GP, ..., Fredriksson R, Schiöth HB

PLoS ONE 8 (8) e71353 [2013-08-15; online 2013-08-15]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Structural and biophysical characterization of the cytoplasmic domains of human BAP29 and BAP31.

Quistgaard EM, Löw C, Moberg P, ..., Maddi K, Nordlund P

PLoS ONE 8 (8) e71111 [2013-08-13; online 2013-08-13]

Advanced Mass Spectrometry Proteomics Protein Science Facility (PSF)

Temperament and character in the Child and Adolescent Twin Study in Sweden (CATSS): comparison to the general population, and genetic structure analysis.

Garcia D, Lundström S, Brändström S, ..., Nilsson T, Anckarsäter H

PLoS ONE 8 (8) e70475 [2013-08-05; online 2013-08-05]

Genetic variants in hormone-related genes and risk of breast cancer.

Clendenen T, Zeleniuch-Jacquotte A, Wirgin I, ..., Shore RE, Chen Y

PLoS ONE 8 (7) e69367 [2013-07-23; online 2013-07-23]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Prevalence, comorbidity and heritability of hoarding symptoms in adolescence: a population based twin study in 15-year olds.

Ivanov VZ, Mataix-Cols D, Serlachius E, ..., Långström N, Rück C

PLoS ONE 8 (7) e69140 [2013-07-10; online 2013-07-10]

Amyloid-β protofibrils: size, morphology and synaptotoxicity of an engineered mimic.

Dubnovitsky A, Sandberg A, Rahman MM, ..., Lendel C, Härd T

PLoS ONE 8 (7) e66101 [2013-07-02; online 2013-07-02]

Mass Spectrometry-based Proteomics, Uppsala

Unbiased approach for virus detection in skin lesions.

Bzhalava D, Johansson H, Ekström J, ..., Forslund O, Dillner J

PLoS ONE 8 (6) e65953 [2013-06-28; online 2013-06-28]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Continuous Aging of the Human DNA Methylome Throughout the Human Lifespan.

Johansson A, Enroth S, Gyllensten U

PLoS ONE 8 (6) e67378 [2013-06-27; online 2013-06-27]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Substrate Channel Flexibility in Pseudomonas aeruginosa MurB Accommodates Two Distinct Substrates.

Chen MW, Lohkamp B, Schnell R, Lescar J, Schneider G

PLoS ONE 8 (6) e66936 [2013-06-21; online 2013-06-21]

Behavioural and Brain Gene Expression Profiling in Pigs during Tail Biting Outbreaks - Evidence of a Tail Biting Resistant Phenotype.

Brunberg E, Jensen P, Isaksson A, Keeling LJ

PLoS ONE 8 (6) e66513 [2013-06-18; online 2013-06-18]

Array and Analysis Facility

Promoter DNA methylation pattern identifies prognostic subgroups in childhood T-cell acute lymphoblastic leukemia.

Borssén M, Palmqvist L, Karrman K, ..., Roos G, Degerman S

PLoS ONE 8 (6) e65373 [2013-06-06; online 2013-06-06]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

A texture based pattern recognition approach to distinguish melanoma from non-melanoma cells in histopathological tissue microarray sections.

Rexhepaj E, Agnarsdóttir M, Bergman J, ..., Lundberg E, Ponten F

PLoS ONE 8 (5) e62070 [2013-05-17; online 2013-05-17]

Spatial Proteomics Tissue Profiling

Adaptive mutations and replacements of virulence traits in the Escherichia coli O104:H4 outbreak population.

Guy L, Jernberg C, Arvén Norling J, ..., Engstrand L, Andersson SGE

PLoS ONE 8 (5) e63027 [2013-05-10; online 2013-05-10]

NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]

European H16N3 gull influenza virus attaches to the human respiratory tract and eye.

Lindskog C, Ellström P, Olsen B, ..., Kuiken T, Jourdain E

PLoS ONE 8 (4) e60757 [2013-04-08; online 2013-04-08]

The molecular genetic architecture of self-employment.

van der Loos MJHM, Rietveld CA, Eklund N, ..., Hofman A, Thurik AR

PLoS ONE 8 (4) e60542 [2013-04-04; online 2013-04-04]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Interaction between retinoid acid receptor-related orphan receptor alpha (RORA) and neuropeptide S receptor 1 (NPSR1) in asthma.

Acevedo N, Sääf A, Söderhäll C, ..., Kere J, Pulkkinen V

PLoS ONE 8 (4) e60111 [2013-04-02; online 2013-04-02]

β-thymosins and hemocyte homeostasis in a crustacean.

Saelee N, Noonin C, Nupan B, ..., Söderhäll K, Söderhäll I

PLoS ONE 8 (4) e60974 [2013-04-02; online 2013-04-02]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Genetic variants from lipid-related pathways and risk for incident myocardial infarction.

Song C, Pedersen NL, Reynolds CA, ..., Prince JA, Ingelsson E

PLoS ONE 8 (3) e60454 [2013-03-29; online 2013-03-29]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Transcriptome of the alternative ethanol production strain Dekkera bruxellensis CBS 11270 in sugar limited, low oxygen cultivation.

Tiukova IA, Petterson ME, Tellgren-Roth C, ..., Pettersson OV, Passoth V

PLoS ONE 8 (3) e58455 [2013-03-13; online 2013-03-13]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

TagGD: fast and accurate software for DNA Tag generation and demultiplexing.

Costea PI, Lundeberg J, Akan P

PLoS ONE 8 (3) e57521 [2013-03-04; online 2013-03-04]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Metagenomic detection of viral pathogens in Spanish honeybees: co-infection by Aphid Lethal Paralysis, Israel Acute Paralysis and Lake Sinai Viruses.

Granberg F, Vicente-Rubiano M, Rubio-Guerri C, ..., Belák S, Sánchez-Vizcaíno JM

PLoS ONE 8 (2) e57459 [2013-02-27; online 2013-02-27]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Imatinib ameliorates neuroinflammation in a rat model of multiple sclerosis by enhancing blood-brain barrier integrity and by modulating the peripheral immune response.

Adzemovic MV, Adzemovic MZ, Zeitelhofer M, ..., Olsson T, Nilsson I

PLoS ONE 8 (2) e56586 [2013-02-20; online 2013-02-20]

Coastal bacterioplankton community dynamics in response to a natural disturbance.

Yeo SK, Huggett MJ, Eiler A, Rappé MS

PLoS ONE 8 (2) e56207 [2013-02-07; online 2013-02-07]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

DNA methylation in the Neuropeptide S Receptor 1 (NPSR1) promoter in relation to asthma and environmental factors.

Reinius LE, Gref A, Sääf A, ..., Söderhäll C, Kere J

PLoS ONE 8 (1) e53877 [2013-01-23; online 2013-01-23]

Unveiling distribution patterns of freshwater phytoplankton by a next generation sequencing based approach.

Eiler A, Drakare S, Bertilsson S, ..., Znachor P, Lindström ES

PLoS ONE 8 (1) e53516 [2013-01-22; online 2013-01-22]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

A genome-wide association study identifies genomic regions for virulence in the non-model organism Heterobasidion annosum s.s.

Dalman K, Himmelstrand K, Olson Å, ..., Brandström-Durling M, Stenlid J

PLoS ONE 8 (1) e53525 [2013-01-16; online 2013-01-16]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Gene expression deregulation in postnatal skeletal muscle of TK2 deficient mice reveals a lower pool of proliferating myogenic progenitor cells.

Paredes JA, Zhou X, Höglund S, Karlsson A

PLoS ONE 8 (1) e53698 [2013-01-14; online 2013-01-14]

Powerful identification of cis-regulatory SNPs in human primary monocytes using allele-specific gene expression.

Almlöf JC, Lundmark P, Lundmark A, ..., Cambien F, Syvänen A

PLoS ONE 7 (12) e52260 [2012-12-26; online 2012-12-26]

NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]

Evidence for small RNAs homologous to effector-encoding genes and transposable elements in the oomycete Phytophthora infestans.

Vetukuri RR, Åsman AKM, Tellgren-Roth C, ..., Whisson SC, Dixelius C

PLoS ONE 7 (12) e51399 [2012-12-14; online 2012-12-14]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

EGFR gene variants are associated with specific somatic aberrations in glioma.

Wibom C, Ghasimi S, Van Loo P, ..., Rydén P, Melin B

PLoS ONE 7 (12) e47929 [2012-12-07; online 2012-12-07]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Automated analysis and reannotation of subcellular locations in confocal images from the Human Protein Atlas.

Li J, Newberg JY, Uhlén M, Lundberg E, Murphy RF

PLoS ONE 7 (11) e50514 [2012-11-30; online 2012-11-30]

Spatial Proteomics

Estimating microtubule distributions from 2D immunofluorescence microscopy images reveals differences among human cultured cell lines.

Li J, Shariff A, Wiking M, ..., Rohde GK, Murphy RF

PLoS ONE 7 (11) e50292 [2012-11-28; online 2012-11-28]

Spatial Proteomics

A 2nd generation linkage map of Heterobasidion annosum s.l. based on in silico anchoring of AFLP markers.

Lind M, van der Nest M, Olson Å, Brandström-Durling M, Stenlid J

PLoS ONE 7 (11) e48347 [2012-11-05; online 2012-11-05]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Library preparation and multiplex capture for massive parallel sequencing applications made efficient and easy.

Neiman M, Sundling S, Grönberg H, ..., Lindberg J, Klevebring D

PLoS ONE 7 (11) e48616 [2012-11-05; online 2012-11-05]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Human cord blood derived immature basophils show dual characteristics, expressing both basophil and eosinophil associated proteins.

Grundström J, Reimer JM, Magnusson SE, ..., Wernersson S, Hellman L

PLoS ONE 7 (10) e48308 [2012-10-31; online 2012-10-31]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Genome-wide and locus specific alterations in CDC73/HRPT2-mutated parathyroid tumors.

Sulaiman L, Haglund F, Hashemi J, ..., Larsson C, Juhlin CC

PLoS ONE 7 (9) e46325 [2012-09-28; online 2012-09-28]

Gene expression profiles in paired gingival biopsies from periodontitis-affected and healthy tissues revealed by massively parallel sequencing.

Davanian H, Stranneheim H, Båge T, ..., Lundeberg J, Yucel-Lindberg T

PLoS ONE 7 (9) e46440 [2012-09-28; online 2012-09-28]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Microscopic particles in two fractions of fresh cerebrospinal fluid in twins with schizophrenia or bipolar disorder and in healthy controls.

Johansson V, Nybom R, Wetterberg L, ..., Ekman CJ, Landén M

PLoS ONE 7 (9) e45994 [2012-09-25; online 2012-09-25]

Comprehensive exploration of the effects of miRNA SNPs on monocyte gene expression.

Greliche N, Zeller T, Wild PS, ..., Blankenberg S, Trégouët DA

PLoS ONE 7 (9) e45863 [2012-09-21; online 2012-09-21]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

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]

Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Platelet-derived growth factor over-expression in retinal progenitors results in abnormal retinal vessel formation.

Edqvist PH, Niklasson M, Vidal-Sanz M, Hallböök F, Forsberg-Nilsson K

PLoS ONE 7 (8) e42488 [2012-08-03; online 2012-08-03]

Differential DNA methylation in purified human blood cells: implications for cell lineage and studies on disease susceptibility.

Reinius LE, Acevedo N, Joerink M, ..., Scheynius A, Kere J

PLoS ONE 7 (7) e41361 [2012-07-25; online 2012-07-25]

Functional analysis of two PLA2G2A variants associated with secretory phospholipase A2-IIA levels.

Exeter HJ, Folkersen L, Palmen J, ..., Humphries SE, Talmud PJ

PLoS ONE 7 (7) e41139 [2012-07-17; online 2012-07-17]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Profiling cellular protein complexes by proximity ligation with dual tag microarray readout.

Hammond M, Nong RY, Ericsson O, Pardali K, Landegren U

PLoS ONE 7 (7) e40405 [2012-07-10; online 2012-07-10]

Affinity Proteomics Uppsala [Technology development] PLA and Single Cell Proteomics

GABA-A channel subunit expression in human glioma correlates with tumor histology and clinical outcome.

Smits A, Jin Z, Elsir T, ..., Aronica E, Birnir B

PLoS ONE 7 (5) e37041 [2012-05-17; online 2012-05-17]

Differential evolutionary wiring of the tyrosine kinase Btk.

Nawaz HM, Kylsten P, Hamada N, ..., Smith CI, Lindvall JM

PLoS ONE 7 (5) e35640 [2012-05-04; online 2012-05-04]

DNA methylation analysis of bone marrow cells at diagnosis of acute lymphoblastic leukemia and at remission.

Nordlund J, Milani L, Lundmark A, Lönnerholm G, Syvänen AC

PLoS ONE 7 (4) e34513 [2012-04-06; online 2012-04-06]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Inflammation-associated nitrotyrosination affects TCR recognition through reduced stability and alteration of the molecular surface of the MHC complex.

Madhurantakam C, Duru AD, Sandalova T, Webb JR, Achour A

PLoS ONE 7 (3) e32805 [2012-03-14; online 2012-03-14]

Antibiotic-induced change of bacterial communities associated with the copepod Nitocra spinipes.

Edlund A, Ek K, Breitholtz M, Gorokhova E

PLoS ONE 7 (3) e33107 [2012-03-12; online 2012-03-12]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Scalable in situ hybridization on tissue arrays for validation of novel cancer and tissue-specific biomarkers.

Kiflemariam S, Andersson S, Asplund A, Pontén F, Sjöblom T

PLoS ONE 7 (3) e32927 [2012-03-08; online 2012-03-08]

Combined chromatin and expression analysis reveals specific regulatory mechanisms within cytokine genes in the macrophage early immune response.

Iglesias MJ, Jesus Iglesias M, Reilly SJ, ..., Hamsten A, Odeberg J

PLoS ONE 7 (2) e32306 [2012-02-27; online 2012-02-27]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Tetrahydrodipicolinate N-succinyltransferase and dihydrodipicolinate synthase from Pseudomonas aeruginosa: structure analysis and gene deletion.

Schnell R, Oehlmann W, Sandalova T, ..., Singh M, Schneider G

PLoS ONE 7 (2) e31133 [2012-02-16; online 2012-02-16]

Genetic and environmental contributions to weight, height, and BMI from birth to 19 years of age: an international study of over 12,000 twin pairs.

Dubois L, Ohm Kyvik K, Girard M, ..., Lichtenstein P, Martin NG

PLoS ONE 7 (2) e30153 [2012-02-08; online 2012-02-08]

Combinations of histone modifications mark exon inclusion levels.

Enroth S, Bornelöv S, Wadelius C, Komorowski J

PLoS ONE 7 (1) e29911 [2012-01-05; online 2012-01-05]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

A genome-wide association search for type 2 diabetes genes in African Americans.

Palmer ND, McDonough CW, Hicks PJ, ..., Mooser V, Sladek R

PLoS ONE 7 (1) e29202 [2012-01-04; online 2012-01-04]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

siRNA silencing of proteasome maturation protein (POMP) activates the unfolded protein response and constitutes a model for KLICK genodermatosis.

Dahlqvist J, Törmä H, Badhai J, Dahl N

PLoS ONE 7 (1) e29471 [2012-01-03; online 2012-01-03]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Targeting acetylcholinesterase: identification of chemical leads by high throughput screening, structure determination and molecular modeling.

Berg L, Andersson CD, Artursson E, ..., Linusson A, Ekström F

PLoS ONE 6 (11) e26039 [2011-11-30; online 2011-11-30]

Chemical Biology Consortium Sweden (CBCS) [Service]

ProteinSeq: high-performance proteomic analyses by proximity ligation and next generation sequencing.

Darmanis S, Nong RY, Vänelid J, ..., Kamali-Moghaddam M, Landegren U

PLoS ONE 6 (9) e25583 [2011-09-29; online 2011-09-29]

Affinity Proteomics Uppsala [Technology development] PLA and Single Cell Proteomics

Combinations of SNPs related to signal transduction in bipolar disorder.

Koefoed P, Andreassen OA, Bennike B, ..., Werge T, Mellerup E

PLoS ONE 6 (8) e23812 [2011-08-29; online 2011-08-29]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

The genetic structure of the Swedish population.

Humphreys K, Grankvist A, Leu M, ..., Palmgren J, Magnusson PK

PLoS ONE 6 (8) e22547 [2011-08-04; online 2011-08-04]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Performance of ultra-deep pyrosequencing in analysis of HIV-1 pol gene variation.

Mild M, Hedskog C, Jernberg J, Albert J

PLoS ONE 6 (7) e22741 [2011-07-25; online 2011-07-25]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Structural alterations from multiple displacement amplification of a human genome revealed by mate-pair sequencing.

Jiao X, Rosenlund M, Hooper SD, ..., Mangion J, Sjöblom T

PLoS ONE 6 (7) e22250 [2011-07-22; online 2011-07-22]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

The use of genome-wide eQTL associations in lymphoblastoid cell lines to identify novel genetic pathways involved in complex traits.

Min JL, Taylor JM, Richards JB, ..., Spector TD, Zondervan KT

PLoS ONE 6 (7) e22070 [2011-07-15; online 2011-07-15]

Scalable transcriptome preparation for massive parallel sequencing.

Stranneheim H, Werne B, Sherwood E, Lundeberg J

PLoS ONE 6 (7) e21910 [2011-07-07; online 2011-07-07]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Specific syndecan-1 domains regulate mesenchymal tumor cell adhesion, motility and migration.

Zong F, Fthenou E, Mundt F, ..., Hjerpe A, Dobra K

PLoS ONE 6 (6) e14816 [2011-06-23; online 2011-06-23]

Translational database selection and multiplexed sequence capture for up front filtering of reliable breast cancer biomarker candidates.

Ståhl PL, Bjursell MK, Mahdessian H, ..., Jirström K, Lundeberg J

PLoS ONE 6 (6) e20794 [2011-06-15; online 2011-06-15]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Detailed analysis of variants in FTO in association with body composition in a cohort of 70-year-olds suggests a weakened effect among elderly.

Jacobsson JA, Almén MS, Benedict C, ..., Lind L, Schiöth HB

PLoS ONE 6 (5) e20158 [2011-05-27; online 2011-05-27]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Nitrogenase gene amplicons from global marine surface waters are dominated by genes of non-cyanobacteria.

Farnelid H, Andersson AF, Bertilsson S, ..., Hagström Å, Riemann L

PLoS ONE 6 (4) e19223 [2011-04-29; online 2011-04-29]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Large scale library generation for high throughput sequencing.

Borgström E, Lundin S, Lundeberg J

PLoS ONE 6 (4) e19119 [2011-04-27; online 2011-04-27]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Molecular characterization of acquired tolerance of tumor cells to picropodophyllin (PPP).

Hashemi J, Worrall C, Vasilcanu D, ..., Larsson O, Larsson C

PLoS ONE 6 (3) e14757 [2011-03-14; online 2011-03-14]

Decoding a substantial set of samples in parallel by massive sequencing.

Neiman M, Lundin S, Savolainen P, Ahmadian A

PLoS ONE 6 (3) e17785 [2011-03-09; online 2011-03-09]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Performance of microarray and liquid based capture methods for target enrichment for massively parallel sequencing and SNP discovery.

Kiialainen A, Karlberg O, Ahlford A, ..., Lindblad-Toh K, Syvänen AC

PLoS ONE 6 (2) e16486 [2011-02-09; online 2011-02-09]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Gene expression profiling and chromatin immunoprecipitation identify DBN1, SETMAR and HIG2 as direct targets of SOX11 in mantle cell lymphoma.

Wang X, Björklund S, Wasik AM, ..., Christensson B, Sander B

PLoS ONE 5 (11) e14085 [2010-11-22; online 2010-11-22]

Dynamics of HIV-1 quasispecies during antiviral treatment dissected using ultra-deep pyrosequencing.

Hedskog C, Mild M, Jernberg J, ..., Andersson B, Albert J

PLoS ONE 5 (7) e11345 [2010-07-07; online 2010-07-07]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Genetic risk factors in lupus nephritis and IgA nephropathy--no support of an overlap.

Vuong MT, Gunnarsson I, Lundberg S, ..., Jacobson SH, Padyukov L

PLoS ONE 5 (5) e10559 [2010-05-10; online 2010-05-10]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Increased throughput by parallelization of library preparation for massive sequencing.

Lundin S, Stranneheim H, Pettersson E, Klevebring D, Lundeberg J

PLoS ONE 5 (4) e10029 [2010-04-06; online 2010-04-06]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

In-depth transcriptome analysis reveals novel TARs and prevalent antisense transcription in human cell lines.

Klevebring D, Bjursell M, Emanuelsson O, Lundeberg J

PLoS ONE 5 (3) e9762 [2010-03-25; online 2010-03-25]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure