Publications 2013

318 publications

PubMed DOI Crossref
Association of STAT4 polymorphism with severe renal insufficiency in lupus nephritis.
Bolin K, Sandling JK, Zickert A, ..., Gunnarsson I, Nordmark G
pmc
PLoS ONE 8 (12) e84450 [2013-12-27; online 2013-12-27]
NGI Uppsala (SNP&SEQ Technology Platform)
PubMed DOI Crossref
Automated quality control system for LC-SRM setups.
Teleman J, Waldemarson S, Malmström J, Levander F
J Proteomics 95 (-) 77-83 [2013-12-16; online 2013-04-16]
Bioinformatics Support and Infrastructure
PubMed DOI Crossref
Profiling post-centrifugation delay of serum and plasma with antibody bead arrays.
Qundos U, Hong M, Tybring G, ..., Nilsson P, Schwenk JM
J Proteomics 95 (-) 46-54 [2013-12-16; online 2013-05-02]
Plasma Profiling [Collaborative]
PubMed DOI Crossref
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
pmc
PLoS ONE 8 (12) e83101 [2013-12-10; online 2013-12-10]
NGI Uppsala (SNP&SEQ Technology Platform)
PubMed DOI Crossref
Selectivity analysis of single binder assays used in plasma protein profiling.
Neiman M, Fredolini C, Johansson H, ..., Nilsson P, Schwenk JM
pmc
Proteomics 13 (23-24) 3406-3410 [2013-12-00; online 2013-10-24]
Plasma Profiling [Technology development]
PubMed DOI Crossref
Rule-based models of the interplay between genetic and environmental factors in childhood allergy.
Bornelöv S, Sääf A, Melén E, ..., Pershagen G, Komorowski J
pmc
PLoS ONE 8 (11) e80080 [2013-11-19; online 2013-11-19]
Mutation Analysis Facility (MAF)
PubMed DOI Crossref
Early B-cell factor 1 regulates the expansion of B-cell progenitors in a dose-dependent manner.
Åhsberg J, Ungerbäck J, Strid T, ..., Qian H, Sigvardsson M
pmc
J. Biol. Chem. 288 (46) 33449-33461 [2013-11-15; online 2013-10-01]
Bioinformatics Support and Infrastructure
PubMed DOI Crossref
Substrate specificity and oligomerization of human GMP synthetase.
Welin M, Lehtiö L, Johansson A, ..., Gräslund S, Nordlund P
PDB
J. Mol. Biol. 425 (22) 4323-4333 [2013-11-15; online 2013-07-03]
Protein Science Facility (PSF)
PubMed DOI Crossref
Association of genes in the NF-κB pathway with antibody-positive primary Sjögren's syndrome.
Nordmark G, Wang C, Vasaitis L, ..., Syvänen AC, UK Primary Sjögren’s Syndrome Registry
Scand. J. Immunol. 78 (5) 447-454 [2013-11-00; online 2013-08-16]
NGI Uppsala (SNP&SEQ Technology Platform)
PubMed DOI Crossref
Wobble decoding by the Escherichia coli selenocysteine insertion machinery.
Xu J, Croitoru V, Rutishauser D, Cheng Q, Arnér ES
pmc
Nucleic Acids Res. 41 (21) 9800-9811 [2013-11-00; online 2013-08-29]
Advanced Mass Spectrometry Proteomics
PubMed DOI Crossref
Genomic mechanisms accounting for the adaptation to parasitism in nematode-trapping fungi.
Meerupati T, Andersson KM, Friman E, ..., Tunlid A, Ahrén D
pmc
PLoS Genet. 9 (11) e1003909 [2013-11-00; online 2013-11-14]
Bioinformatics Support and Infrastructure
PubMed DOI Crossref
Discovery and refinement of loci associated with lipid levels.
Global Lipids Genetics Consortium N, Willer CJ, Schmidt EM, ..., Ingelsson E, Abecasis GR
pmc mid
Nat. Genet. 45 (11) 1274-1283 [2013-11-00; online 2013-10-08]
NGI Uppsala (SNP&SEQ Technology Platform) NGI Uppsala (Uppsala Genome Center)
PubMed DOI Crossref
Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories.
't Hoen PA, Friedländer MR, Almlöf J, ..., Dermitzakis ET, Lappalainen T
Nat. Biotechnol. 31 (11) 1015-1022 [2013-11-00; online 2013-09-17]
NGI Uppsala (SNP&SEQ Technology Platform)
PubMed DOI Crossref
In situ Protein Detection for Companion Diagnostics.
Gremel G, Grannas K, Sutton LA, Pontén F, Zieba A
pmc
Front Oncol 3 (-) 271 [2013-10-31; online 2013-10-31]
Tissue Profiling
PubMed DOI Crossref
Nanobody mediated crystallization of an archeal mechanosensitive channel.
Löw C, Yau YH, Pardon E, ..., Steyaert J, Nordlund P
pmc
PLoS ONE 8 (10) e77984 [2013-10-21; online 2013-10-21]
Protein Science Facility (PSF)
PubMed DOI Crossref
Eleven candidate susceptibility genes for common familial colorectal cancer.
Gylfe AE, Katainen R, Kondelin J, ..., Karhu A, Aaltonen LA
pmc
PLoS Genet. 9 (10) e1003876 [2013-10-17; online 2013-10-17]
Karolinska High Throughput Center (KHTC)
PubMed DOI Crossref
Heart research advances using database search engines, Human Protein Atlas and the Sydney Heart Bank.
Li A, Estigoy C, Raftery M, ..., Lal S, Dos Remedios CG
Heart Lung Circ 22 (10) 819-826 [2013-10-00; online 2013-07-17]
Tissue Profiling
PubMed DOI Crossref
Transcriptome and genome sequencing uncovers functional variation in humans.
Lappalainen T, Sammeth M, Friedländer MR, ..., Estivill X, Dermitzakis ET
pmc mid
Nature 501 (7468) 506-511 [2013-09-26; online 2013-09-17]
NGI Uppsala (SNP&SEQ Technology Platform)
PubMed DOI Crossref
Hydrogenosomes in the diplomonad Spironucleus salmonicida.
Jerlström-Hultqvist J, Einarsson E, Xu F, ..., Andersson JO, Svärd SG
pmc
Nat Commun 4 (-) 2493 [2013-09-18; online 2013-09-18]
Mass Spectrometry-based Proteomics, Uppsala
PubMed DOI Crossref
A tosyl-activated magnetic bead cellulose as solid support for sensitive protein detection.
Yan J, Horák D, Lenfeld J, Hammond M, Kamali-Moghaddam M
J. Biotechnol. 167 (3) 235-240 [2013-09-10; online 2013-07-03]
PLA Proteomics
PubMed DOI Crossref
Structural insights into substrate recognition in proton-dependent oligopeptide transporters.
Guettou F, Quistgaard EM, Trésaugues L, ..., Nordlund P, Löw C
pmc PDB
EMBO Rep. 14 (9) 804-810 [2013-09-00; online 2013-07-23]
Protein Science Facility (PSF)
PubMed DOI Crossref
Multilocus genetic risk scores for coronary heart disease prediction.
Ganna A, Magnusson PKE, Pedersen NL, ..., Hamsten A, Ingelsson E
Arterioscler. Thromb. Vasc. Biol. 33 (9) 2267-2272 [2013-09-00; online 2013-05-21]
NGI Uppsala (SNP&SEQ Technology Platform)
PubMed DOI Crossref
Identification of candidate oncogenes in human colorectal cancers with microsatellite instability.
Gylfe AE, Kondelin J, Turunen M, ..., Vahteristo P, Aaltonen LA
Gastroenterology 145 (3) 540-3.e22 [2013-09-00; online 2013-05-21]
Karolinska High Throughput Center (KHTC)
PubMed DOI Crossref
Genetic relationship between five psychiatric disorders estimated from genome-wide SNPs.
Cross-Disorder Group of the Psychiatric Genomics Consortium N, Lee SH, Ripke S, ..., Wray NR, International Inflammatory Bowel Disease Genetics Consortium (IIBDGC) N
pmc mid
Nat. Genet. 45 (9) 984-994 [2013-09-00; online 2013-08-13]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
PARP inhibitor with selectivity toward ADP-ribosyltransferase ARTD3/PARP3.
Lindgren AE, Karlberg T, Thorsell AG, ..., Elofsson M, Schüler H
PDB PDB PDB PDB
ACS Chem. Biol. 8 (8) 1698-1703 [2013-08-16; online 2013-06-08]
Protein Science Facility (PSF)
PubMed DOI Crossref
Improved production of membrane proteins in Escherichia coli by selective codon substitutions.
Nørholm MH, Toddo S, Virkki MT, ..., von Heijne G, Daley DO
FEBS Lett. 587 (15) 2352-2358 [2013-08-02; online 2013-06-19]
Bioinformatics Support and Infrastructure
PubMed DOI Crossref
Antibody-based profiling of cerebrospinal fluid within multiple sclerosis.
Häggmark A, Byström S, Ayoglu B, ..., Schwenk JM, Nilsson P
Proteomics 13 (15) 2256-2267 [2013-08-00; online 2013-05-23]
Plasma Profiling [Collaborative]
PubMed DOI Crossref
Expression of chondroitin/dermatan sulfate glycosyltransferases during early zebrafish development.
Filipek-Górniok B, Holmborn K, Haitina T, ..., Kreuger J, Ledin J
Dev. Dyn. 242 (8) 964-975 [2013-08-00; online 2013-05-25]
Genome Engineering Zebrafish
PubMed DOI Crossref
High-resolution structure of TBP with TAF1 reveals anchoring patterns in transcriptional regulation.
Anandapadamanaban M, Andresen C, Helander S, ..., Moche M, Sunnerhagen M
pmc mid PDB
Nat. Struct. Mol. Biol. 20 (8) 1008-1014 [2013-08-00; online 2013-07-16]
Protein Science Facility (PSF)
PubMed DOI Crossref
Tumour expression of bladder cancer-associated urinary proteins.
Lindén M, Segersten U, Runeson M, ..., Lind SB, Malmström PU
BJU Int. 112 (3) 407-415 [2013-08-00; online 2013-03-09]
Tissue Profiling
PubMed DOI Crossref
Proteome of the nematode-trapping cells of the fungus Monacrosporium haptotylum.
Andersson KM, Meerupati T, Levander F, ..., Ahrén D, Tunlid A
pmc
Appl. Environ. Microbiol. 79 (16) 4993-5004 [2013-08-00; online 2013-06-19]
Bioinformatics Support and Infrastructure
PubMed DOI Crossref
New viruses in veterinary medicine, detected by metagenomic approaches.
Belák S, Karlsson OE, Blomström AL, Berg M, Granberg F
Vet. Microbiol. 165 (1-2) 95-101 [2013-07-26; online 2013-02-23]
NGI Uppsala (Uppsala Genome Center)
PubMed DOI Crossref
NCR3/NKp30 contributes to pathogenesis in primary Sjogren's syndrome.
Rusakiewicz S, Nocturne G, Lazure T, ..., Zitvogel L, Mariette X
pmc mid
Sci Transl Med 5 (195) 195ra96 [2013-07-24; online 2013-07-26]
NGI Uppsala (SNP&SEQ Technology Platform)
PubMed DOI Crossref
Genetic variants in hormone-related genes and risk of breast cancer.
Clendenen T, Zeleniuch-Jacquotte A, Wirgin I, ..., Shore RE, Chen Y
pmc
PLoS ONE 8 (7) e69367 [2013-07-23; online 2013-07-23]
NGI Uppsala (SNP&SEQ Technology Platform)
PubMed DOI Crossref
Novel signatures of cancer-associated fibroblasts.
Bozóky B, Savchenko A, Csermely P, ..., Székely L, Klein G
Int. J. Cancer 133 (2) 286-293 [2013-07-15; online 2013-01-16]
Tissue Profiling
PubMed DOI Crossref
Amyloid-β protofibrils: size, morphology and synaptotoxicity of an engineered mimic.
Dubnovitsky A, Sandberg A, Rahman MM, ..., Lendel C, Härd T
pmc
PLoS ONE 8 (7) e66101 [2013-07-02; online 2013-07-02]
Mass Spectrometry-based Proteomics, Uppsala
PubMed DOI Crossref
Estrogen receptor β expression induces changes in the microRNA pool in human colon cancer cells.
Edvardsson K, Nguyen-Vu T, Kalasekar SM, ..., Gustafsson JÅ, Williams C
Carcinogenesis 34 (7) 1431-1441 [2013-07-00; online 2013-02-26]
Tissue Profiling
PubMed DOI Crossref
Unbiased approach for virus detection in skin lesions.
Bzhalava D, Johansson H, Ekström J, ..., Forslund O, Dillner J
pmc
PLoS ONE 8 (6) e65953 [2013-06-28; online 2013-06-28]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed DOI Crossref
The role of adiposity in cardiometabolic traits: a Mendelian randomization analysis.
Fall T, Hägg S, Mägi R, ..., Prokopenko I, European Network for Genetic and Genomic Epidemiology (ENGAGE) consortium N
pmc
PLoS Med. 10 (6) e1001474 [2013-06-25; online 2013-06-25]
NGI Uppsala (SNP&SEQ Technology Platform)
PubMed DOI Crossref
GWAS of 126,559 individuals identifies genetic variants associated with educational attainment.
Rietveld CA, Medland SE, Derringer J, ..., Cesarini D, Koellinger PD
pmc mid
Science 340 (6139) 1467-1471 [2013-06-21; online 2013-06-01]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
Molecular genetics and subjective well-being.
Rietveld CA, Cesarini D, Benjamin DJ, ..., Krueger RF, Bartels M
pmc
Proc. Natl. Acad. Sci. U.S.A. 110 (24) 9692-9697 [2013-06-11; online 2013-05-28]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed DOI Crossref
Parallel visualization of multiple protein complexes in individual cells in tumor tissue.
Leuchowius KJ, Clausson CM, Grannas K, ..., Landegren U, Söderberg O
pmc
Mol. Cell Proteomics 12 (6) 1563-1571 [2013-06-00; online 2013-02-26]
NGI Uppsala (Uppsala Genome Center) PLA Proteomics
PubMed DOI Crossref
Contribution of IKBKE and IFIH1 gene variants to SLE susceptibility.
Wang C, Ahlford A, Laxman N, ..., Rönnblom L, Syvänen AC
Genes Immun. 14 (4) 217-222 [2013-06-00; online 2013-03-29]
NGI Uppsala (SNP&SEQ Technology Platform)
PubMed DOI Crossref
Sortilin receptor 1 predicts longitudinal cognitive change.
Reynolds CA, Zavala C, Gatz M, ..., Prince JA, Pedersen NL
pmc mid
Neurobiol. Aging 34 (6) 1710.e11-1710.e18 [2013-06-00; online 2013-01-16]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
Gambogic acid is cytotoxic to cancer cells through inhibition of the ubiquitin-proteasome system.
Felth J, Lesiak-Mieczkowska K, D'Arcy P, ..., Fryknäs M, Rickardson L
Invest New Drugs 31 (3) 587-598 [2013-06-00; online 2012-11-28]
Array and Analysis Facility
PubMed DOI Crossref
No association of primary Sjögren's syndrome with Fcγ receptor gene variants.
Haldorsen K, Appel S, Le Hellard S, ..., Jonsson R, Bolstad AI
Genes Immun. 14 (4) 234-237 [2013-06-00; online 2013-04-05]
NGI Uppsala (SNP&SEQ Technology Platform)
PubMed DOI Crossref
Genome-wide association study of susceptibility loci for cervical cancer.
Chen D, Juko-Pecirep I, Hammer J, ..., Wilander E, Gyllensten U
J. Natl. Cancer Inst. 105 (9) 624-633 [2013-05-01; online 2013-03-14]
NGI Uppsala (SNP&SEQ Technology Platform)
PubMed DOI Crossref
An adaptive alignment algorithm for quality-controlled label-free LC-MS.
Sandin M, Ali A, Hansson K, ..., Resjö S, Levander F
pmc
Mol. Cell Proteomics 12 (5) 1407-1420 [2013-05-00; online 2013-01-12]
Bioinformatics Support and Infrastructure
DOI Crossref
Metagenomics sample preparation and sequencing.
Karlsson OE, Norling M, Bongcam-Rudloff E
EMBnet j. 19 (A) 55 [2013-04-08; online 2013-04-08]
NGI Uppsala (Uppsala Genome Center)
PubMed DOI Crossref
European H16N3 gull influenza virus attaches to the human respiratory tract and eye.
Lindskog C, Ellström P, Olsen B, ..., Kuiken T, Jourdain E
pmc
PLoS ONE 8 (4) e60757 [2013-04-08; online 2013-04-08]
Tissue Profiling
PubMed DOI Crossref
The molecular genetic architecture of self-employment.
van der Loos MJHM, Rietveld CA, Eklund N, ..., Hofman A, Thurik AR
pmc
PLoS ONE 8 (4) e60542 [2013-04-04; online 2013-04-04]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
β-thymosins and hemocyte homeostasis in a crustacean.
Saelee N, Noonin C, Nupan B, ..., Söderhäll K, Söderhäll I
pmc
PLoS ONE 8 (4) e60974 [2013-04-02; online 2013-04-02]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed DOI Crossref
Immunofluorescence and fluorescent-protein tagging show high correlation for protein localization in mammalian cells.
Stadler C, Rexhepaj E, Singan VR, ..., Simpson JC, Lundberg E
Nat. Methods 10 (4) 315-323 [2013-04-00; online 2013-02-26]
Cell Profiling
PubMed DOI Crossref
Genetic variants from lipid-related pathways and risk for incident myocardial infarction.
Song C, Pedersen NL, Reynolds CA, ..., Prince JA, Ingelsson E
pmc
PLoS ONE 8 (3) e60454 [2013-03-29; online 2013-03-29]
NGI Uppsala (SNP&SEQ Technology Platform)
PubMed DOI Crossref
Transcriptome profiling of Giardia intestinalis using strand-specific RNA-seq.
Franzén O, Jerlström-Hultqvist J, Einarsson E, ..., Andersson B, Svärd SG
pmc GEO
PLoS Comput. Biol. 9 (3) e1003000 [2013-03-28; online 2013-03-28]
NGI Uppsala (SNP&SEQ Technology Platform)
PubMed DOI Crossref
Integration of clinical data with a genome-scale metabolic model of the human adipocyte.
Mardinoglu A, Agren R, Kampf C, ..., Uhlen M, Nielsen J
pmc
Mol. Syst. Biol. 9 (-) 649 [2013-03-21; online 2013-03-21]
Tissue Profiling
PubMed DOI Crossref
The genomic signature of dog domestication reveals adaptation to a starch-rich diet.
Axelsson E, Ratnakumar A, Arendt M, ..., Hedhammar A, Lindblad-Toh K
Nature 495 (7441) 360-364 [2013-03-21; online 2013-01-29]
NGI Uppsala (Uppsala Genome Center)
PubMed DOI Crossref
Identification of genetic variants influencing the human plasma proteome.
Johansson Å, Enroth S, Palmblad M, ..., Bergquist J, Gyllensten U
pmc
Proc. Natl. Acad. Sci. U.S.A. 110 (12) 4673-4678 [2013-03-19; online 2013-03-15]
NGI Uppsala (SNP&SEQ Technology Platform)
PubMed DOI Crossref
The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary.
Mayer G, Montecchi-Palazzi L, Ovelleiro D, ..., Eisenacher M, HUPO-PSI Group
pmc
Database (Oxford) 2013 (-) bat009 [2013-03-12; online 2013-03-12]
Bioinformatics Support and Infrastructure
PubMed DOI Crossref
Recognition of mono-ADP-ribosylated ARTD10 substrates by ARTD8 macrodomains.
Forst AH, Karlberg T, Herzog N, ..., Schüler H, Lüscher B
PDB PDB PDB PDB PDB PDB PDB
Structure 21 (3) 462-475 [2013-03-05; online 2013-03-12]
Protein Science Facility (PSF)
PubMed DOI Crossref
Genetic effects on old-age cognitive functioning: a population-based study.
Laukka EJ, Lövdén M, Herlitz A, ..., Fratiglioni L, Bäckman L
Psychol Aging 28 (1) 262-274 [2013-03-00; online 2013-01-02]
Mutation Analysis Facility (MAF)
PubMed DOI Crossref
Origin and evolution of medium chain alcohol dehydrogenases.
Jörnvall H, Hedlund J, Bergman T, ..., Cederlund E, Persson B
Chem. Biol. Interact. 202 (1-3) 91-96 [2013-02-25; online 2012-12-04]
Bioinformatics Support and Infrastructure
PubMed DOI Crossref
Evolution of sperm structure and energetics in passerine birds.
Rowe M, Laskemoen T, Johnsen A, Lifjeld JT
pmc
Proc. Biol. Sci. 280 (1753) 20122616 [2013-02-22; online 2013-01-04]
Bioinformatics Support and Infrastructure
PubMed DOI Crossref
STC1 expression by cancer-associated fibroblasts drives metastasis of colorectal cancer.
Peña C, Céspedes MV, Lindh MB, ..., Augsten M, Ostman A
Cancer Res. 73 (4) 1287-1297 [2013-02-15; online 2012-12-18]
Tissue Profiling
PubMed DOI Crossref
The Swedish Twin Registry: establishment of a biobank and other recent developments.
Magnusson PKE, Almqvist C, Rahman I, ..., Pedersen NL, Lichtenstein P
Twin Res Hum Genet 16 (1) 317-329 [2013-02-00; online 2012-11-10]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
A gene-centric study of common carotid artery remodelling.
Harrison SC, Zabaneh D, Asselbergs FW, ..., Hamsten A, Humphries SE
pmc
Atherosclerosis 226 (2) 440-446 [2013-02-00; online 2012-12-19]
NGI Uppsala (SNP&SEQ Technology Platform)
PubMed DOI Crossref
Workshop on laboratory protocol standards for the Molecular Methods Database.
Klingström T, Soldatova L, Stevens R, ..., Landegren U, Bongcam-Rudloff E
N Biotechnol 30 (2) 109-113 [2013-01-25; online 2012-06-13]
PLA Proteomics
PubMed DOI Crossref
Protein tag-mediated conjugation of oligonucleotides to recombinant affinity binders for proximity ligation.
Gu GJ, Friedman M, Jost C, ..., Landegren U, Söderberg O
N Biotechnol 30 (2) 144-152 [2013-01-25; online 2012-06-06]
PLA Proteomics
PubMed DOI Crossref
Multiplex protein detection with DNA readout via mass spectrometry.
Flanigon J, Kamali-Moghaddam M, Burbulis I, ..., Landegren U, Cantor C
pmc mid
N Biotechnol 30 (2) 153-158 [2013-01-25; online 2012-12-04]
PLA Proteomics
PubMed DOI Crossref
DNA-binding specificities of human transcription factors.
Jolma A, Yan J, Whitington T, ..., Kivioja T, Taipale J
Cell 152 (1-2) 327-339 [2013-01-17; online 2013-01-22]
Karolinska High Throughput Center (KHTC)
DOI Crossref
The genetic structure of the Lithuanian wolf population
Baltrūnaitė L, Balčiauskas L, Åkesson M
Open Life Sci 8 (5) - [2013-01-01; online 2013-01-01]
NGI Uppsala (Uppsala Genome Center)
PubMed DOI Crossref
Large-scale association analysis identifies new risk loci for coronary artery disease.
CARDIoGRAMplusC4D Consortium N, Deloukas P, Kanoni S, ..., Schunkert H, Samani NJ
pmc mid
Nat. Genet. 45 (1) 25-33 [2013-01-00; online 2012-12-04]
NGI Uppsala (SNP&SEQ Technology Platform)