Publications 2013

320 publications

Automated quality control system for LC-SRM setups.
Teleman J, Waldemarson S, Malmström J, Levander F
pii: S1874-3919(13)00176-0
J Proteomics 95 (-) 77-83 [2013-12-16; online 2013-04-16]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training
Profiling post-centrifugation delay of serum and plasma with antibody bead arrays.
Qundos U, Hong M, Tybring G, ..., Nilsson P, Schwenk JM
pii: S1874-3919(13)00209-1
J Proteomics 95 (-) 46-54 [2013-12-16; online 2013-05-02]
Plasma Profiling [Collaborative]
The association between plasma homocysteine and coronary heart disease is modified by the MTHFR 677C>T polymorphism.
Mehlig K, Leander K, de Faire U, ..., Lissner L, Thelle D
pii: heartjnl-2013-304460
Heart 99 (23) 1761-1765 [2013-12-00; online 2013-09-10]
Mutation Analysis Facility (MAF)
Selectivity analysis of single binder assays used in plasma protein profiling.
Neiman M, Fredolini C, Johansson H, ..., Nilsson P, Schwenk JM
Proteomics 13 (23-24) 3406-3410 [2013-12-00; online 2013-10-24]
Plasma Profiling [Technology development]
Rule-based models of the interplay between genetic and environmental factors in childhood allergy.
Bornelöv S, Sääf A, Melén E, ..., Pershagen G, Komorowski J
pii: PONE-D-13-20229 pmc: PMC3833974
PLoS ONE 8 (11) e80080 [2013-11-19; online 2013-11-19]
Mutation Analysis Facility (MAF)
Substrate specificity and oligomerization of human GMP synthetase.
Welin M, Lehtiö L, Johansson A, ..., Gräslund S, Nordlund P
pii: S0022-2836(13)00427-0 PDB: 2VXO
J. Mol. Biol. 425 (22) 4323-4333 [2013-11-15; online 2013-07-03]
Protein Science Facility (PSF)
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) National Genomics Infrastructure
Wobble decoding by the Escherichia coli selenocysteine insertion machinery.
Xu J, Croitoru V, Rutishauser D, Cheng Q, Arnér ES
pii: gkt764 pmc: PMC3834832
Nucleic Acids Res. 41 (21) 9800-9811 [2013-11-00; online 2013-08-29]
Advanced Mass Spectrometry Proteomics
Antibodies biotinylated using a synthetic Z-domain from protein A provide stringent in situ protein detection.
Andersson S, Konrad A, Ashok N, ..., Hober S, Asplund A
pii: 0022155413502360 pmc: PMC3808578
J. Histochem. Cytochem. 61 (11) 773-784 [2013-11-00; online 2013-08-08]
Tissue Profiling
Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories.
't Hoen PA, Friedländer MR, Almlöf J, ..., Dermitzakis ET, Lappalainen T
pii: nbt.2702
Nat. Biotechnol. 31 (11) 1015-1022 [2013-11-00; online 2013-09-17]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
In situ Protein Detection for Companion Diagnostics.
Gremel G, Grannas K, Sutton LA, Pontén F, Zieba A
Front Oncol 3 (-) 271 [2013-10-31; online 2013-10-31]
Tissue Profiling
Proteins of novel lactic acid bacteria from Apis mellifera mellifera: an insight into the production of known extra-cellular proteins during microbial stress.
Butler È, Alsterfjord M, Olofsson TC, ..., Malmström J, Vásquez A
pii: 1471-2180-13-235 pmc: PMC4015849 GENBANK: KC776061 GENBANK: KC776062 GENBANK: KC776063 GENBANK: KC776064 GENBANK: KC776065 GENBANK: KC776066 GENBANK: KC776067 GENBANK: KC776068 GENBANK: KC776069 GENBANK: KC776070 GENBANK: KC776071 GENBANK: KC776073 GENBANK: KC776074 GENBANK: KC776075 GENBANK: KC776076 GENBANK: KC776077 GENBANK: KC776078 GENBANK: KC776079 GENBANK: KC776080 GENBANK: KC776081 GENBANK: KC776082 GENBANK: KC776083 GENBANK: KC776084 GENBANK: KC776085 GENBANK: KC776086 GENBANK: KC776087 GENBANK: KC776088 GENBANK: KC776089 GENBANK: KC776090 GENBANK: KC776091 GENBANK: KC776092 GENBANK: KC776093 GENBANK: KC776094 GENBANK: KC776095 GENBANK: KC776096 GENBANK: KC776097 GENBANK: KC776098 GENBANK: KC776099 GENBANK: KC776100 GENBANK: KC776101 GENBANK: KC776102 GENBANK: KC776103 GENBANK: KC776104 GENBANK: KC776105 GENBANK: KC776106 GENBANK: KC776107 GENBANK: KC776108 GENBANK: KC776109 GENBANK: KC776110 GENBANK: KC776111 GENBANK: KC789963 GENBANK: KC789964 GENBANK: KC789965 GENBANK: KC789966 GENBANK: KC789967 GENBANK: KC789968 GENBANK: KC789969 GENBANK: KC789970 GENBANK: KC789971 GENBANK: KC789972 GENBANK: KC789973 GENBANK: KC789974 GENBANK: KC789975 GENBANK: KC789976 GENBANK: KC789977 GENBANK: KC789978 GENBANK: KC789979 GENBANK: KC789980 GENBANK: KC789981 GENBANK: KC789982 GENBANK: KC789983 GENBANK: KC789984 GENBANK: KC789985 GENBANK: KC789986 GENBANK: KC789987 GENBANK: KC789988 GENBANK: KC789989 GENBANK: KC789990 GENBANK: KC789991 GENBANK: KC789992 GENBANK: KC789993 GENBANK: KC789994 GENBANK: KC789995 GENBANK: KC789996 GENBANK: KC789997 GENBANK: KC789998 GENBANK: KC789999 GENBANK: KC790000 GENBANK: KC790001 GENBANK: KC790002 GENBANK: KC790003 GENBANK: KC790004 GENBANK: KC790005 GENBANK: KC790006 GENBANK: KC790007 GENBANK: KC790008 GENBANK: KC790009 GENBANK: KC790010 GENBANK: KC790011 GENBANK: KC790012 GENBANK: KC790013 GENBANK: KC790014 GENBANK: KC790015 GENBANK: KC790016 GENBANK: KC790017 GENBANK: KC790018 GENBANK: KC801035
BMC Microbiol. 13 (-) 235 [2013-10-22; online 2013-10-22]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training
Nanobody mediated crystallization of an archeal mechanosensitive channel.
Löw C, Yau YH, Pardon E, ..., Steyaert J, Nordlund P
pii: PONE-D-13-33201 pmc: PMC3804602
PLoS ONE 8 (10) e77984 [2013-10-21; online 2013-10-21]
Protein Science Facility (PSF)
Eleven candidate susceptibility genes for common familial colorectal cancer.
Gylfe AE, Katainen R, Kondelin J, ..., Karhu A, Aaltonen LA
pii: PGENETICS-D-13-01401 pmc: PMC3798264
PLoS Genet. 9 (10) e1003876 [2013-10-17; online 2013-10-17]
Karolinska High Throughput Center (KHTC)
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
pii: S1443-9506(13)01036-6
Heart Lung Circ 22 (10) 819-826 [2013-10-00; online 2013-07-17]
Tissue Profiling
Transcriptome and genome sequencing uncovers functional variation in humans.
Lappalainen T, Sammeth M, Friedländer MR, ..., Estivill X, Dermitzakis ET
Nature 501 (7468) 506-511 [2013-09-26; online 2013-09-17]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
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
pii: PONE-D-13-15073 pmc: PMC3784416
PLoS ONE 8 (9) e74923 [2013-09-26; online 2013-09-26]
Tissue Profiling
Hydrogenosomes in the diplomonad Spironucleus salmonicida.
Jerlström-Hultqvist J, Einarsson E, Xu F, ..., Andersson JO, Svärd SG
pii: ncomms3493 pmc: PMC3778541
Nat Commun 4 (-) 2493 [2013-09-18; online 2013-09-18]
Mass Spectrometry-based Proteomics, Uppsala
Blood plasma IgG Fc glycans are significantly altered in Alzheimer's disease and progressive mild cognitive impairment.
Lundström SL, Yang H, Lyutvinskiy Y, ..., Soininen H, Zubarev RA
pii: D06G67816GG7R671
J. Alzheimers Dis. 38 (3) 567-579 [2013-09-14; online 2013-09-14]
Advanced Mass Spectrometry Proteomics
A tosyl-activated magnetic bead cellulose as solid support for sensitive protein detection.
Yan J, Horák D, Lenfeld J, Hammond M, Kamali-Moghaddam M
pii: S0168-1656(13)00266-6
J. Biotechnol. 167 (3) 235-240 [2013-09-10; online 2013-07-03]
PLA and Single Cell Proteomics
Progesterone receptor negativity is an independent risk factor for relapse in patients with early stage endometrioid endometrial adenocarcinoma.
Huvila J, Talve L, Carpén O, ..., Grénman S, Auranen A
pii: S0090-8258(13)00848-2
Gynecol. Oncol. 130 (3) 463-469 [2013-09-00; online 2013-06-20]
Tissue Profiling
Autoantibody profiling in multiple sclerosis using arrays of human protein fragments.
Ayoglu B, Häggmark A, Khademi M, ..., Schwenk JM, Nilsson P
pii: M112.026757 pmc: PMC3769337
Mol. Cell Proteomics 12 (9) 2657-2672 [2013-09-00; online 2013-06-05]
Autoimmunity Profiling [Technology development]
Structural insights into substrate recognition in proton-dependent oligopeptide transporters.
Guettou F, Quistgaard EM, Trésaugues L, ..., Nordlund P, Löw C
pii: embor2013107 pmc: PMC3790050 PDB: 4LEP
EMBO Rep. 14 (9) 804-810 [2013-09-00; online 2013-07-23]
Protein Science Facility (PSF)
Multilocus genetic risk scores for coronary heart disease prediction.
Ganna A, Magnusson PKE, Pedersen NL, ..., Hamsten A, Ingelsson E
pii: ATVBAHA.113.301218
Arterioscler. Thromb. Vasc. Biol. 33 (9) 2267-2272 [2013-09-00; online 2013-05-21]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
Identification of candidate oncogenes in human colorectal cancers with microsatellite instability.
Gylfe AE, Kondelin J, Turunen M, ..., Vahteristo P, Aaltonen LA
pii: S0016-5085(13)00747-6
Gastroenterology 145 (3) 540-3.e22 [2013-09-00; online 2013-05-21]
Karolinska High Throughput Center (KHTC)
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
Nat. Genet. 45 (9) 984-994 [2013-09-00; online 2013-08-13]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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]
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
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
New viruses in veterinary medicine, detected by metagenomic approaches.
Belák S, Karlsson OE, Blomström AL, Berg M, Granberg F
pii: S0378-1135(13)00074-6
Vet. Microbiol. 165 (1-2) 95-101 [2013-07-26; online 2013-02-23]
NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure
Retinoic acid receptor alpha is associated with tamoxifen resistance in breast cancer.
Johansson HJ, Sanchez BC, Mundt F, ..., Linderholm BK, Lehtiö J
pii: ncomms3175 pmc: PMC3759040
Nat Commun 4 (-) 2175 [2013-07-23; online 2013-07-23]
Drug Discovery and Development (DDD) [Collaborative]
Genetic variants in hormone-related genes and risk of breast cancer.
Clendenen T, Zeleniuch-Jacquotte A, Wirgin I, ..., Shore RE, Chen Y
pii: PONE-D-13-05381 pmc: PMC3720532
PLoS ONE 8 (7) e69367 [2013-07-23; online 2013-07-23]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
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
Amyloid-β protofibrils: size, morphology and synaptotoxicity of an engineered mimic.
Dubnovitsky A, Sandberg A, Rahman MM, ..., Lendel C, Härd T
pii: PONE-D-13-01978 pmc: PMC3699592
PLoS ONE 8 (7) e66101 [2013-07-02; online 2013-07-02]
Mass Spectrometry-based Proteomics, Uppsala
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
pii: bgt067
Carcinogenesis 34 (7) 1431-1441 [2013-07-00; online 2013-02-26]
Tissue Profiling
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
pii: PMEDICINE-D-12-03573 pmc: PMC3692470
PLoS Med. 10 (6) e1001474 [2013-06-25; online 2013-06-25]
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
pii: PONE-D-13-09972 pmc: PMC3689657
PLoS ONE 8 (6) e66936 [2013-06-21; online 2013-06-21]
Protein Science Facility (PSF)
Initial quantitative proteomic map of 28 mouse tissues using the SILAC mouse.
Geiger T, Velic A, Macek B, ..., Cox J, Mann M
pii: M112.024919 pmc: PMC3675825
Mol. Cell Proteomics 12 (6) 1709-1722 [2013-06-00; online 2013-02-26]
Cell Profiling Tissue Profiling
Contribution of IKBKE and IFIH1 gene variants to SLE susceptibility.
Wang C, Ahlford A, Laxman N, ..., Rönnblom L, Syvänen AC
pii: gene20139
Genes Immun. 14 (4) 217-222 [2013-06-00; online 2013-03-29]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
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
No association of primary Sjögren's syndrome with Fcγ receptor gene variants.
Haldorsen K, Appel S, Le Hellard S, ..., Jonsson R, Bolstad AI
pii: gene201312
Genes Immun. 14 (4) 234-237 [2013-06-00; online 2013-04-05]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
European H16N3 gull influenza virus attaches to the human respiratory tract and eye.
Lindskog C, Ellström P, Olsen B, ..., Kuiken T, Jourdain E
pii: PONE-D-12-38518 pmc: PMC3620227
PLoS ONE 8 (4) e60757 [2013-04-08; online 2013-04-08]
Tissue Profiling
The molecular genetic architecture of self-employment.
van der Loos MJHM, Rietveld CA, Eklund N, ..., Hofman A, Thurik AR
pii: PONE-D-12-39282 pmc: PMC3617140
PLoS ONE 8 (4) e60542 [2013-04-04; online 2013-04-04]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
Immunofluorescence and fluorescent-protein tagging show high correlation for protein localization in mammalian cells.
Stadler C, Rexhepaj E, Singan VR, ..., Simpson JC, Lundberg E
pii: nmeth.2377
Nat. Methods 10 (4) 315-323 [2013-04-00; online 2013-02-26]
Cell Profiling
Transcriptome profiling of Giardia intestinalis using strand-specific RNA-seq.
Franzén O, Jerlström-Hultqvist J, Einarsson E, ..., Andersson B, Svärd SG
pii: PCOMPBIOL-D-12-01572 pmc: PMC3610916 GEO: GSE36490
PLoS Comput. Biol. 9 (3) e1003000 [2013-03-28; online 2013-03-28]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
Offshoots of the ESF functional genomics programme.
Landegren U
pii: S1871-6784(12)00900-4
N Biotechnol 30 (3) 296-298 [2013-03-25; online 2013-01-09]
PLA and Single Cell Proteomics
Integration of clinical data with a genome-scale metabolic model of the human adipocyte.
Mardinoglu A, Agren R, Kampf C, ..., Uhlen M, Nielsen J
pii: msb20135 pmc: PMC3619940
Mol. Syst. Biol. 9 (-) 649 [2013-03-21; online 2013-03-21]
Tissue Profiling
The genomic signature of dog domestication reveals adaptation to a starch-rich diet.
Axelsson E, Ratnakumar A, Arendt M, ..., Hedhammar A, Lindblad-Toh K
pii: nature11837
Nature 495 (7441) 360-364 [2013-03-21; online 2013-01-29]
NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure
Genetic effects on old-age cognitive functioning: a population-based study.
Laukka EJ, Lövdén M, Herlitz A, ..., Fratiglioni L, Bäckman L
pii: 2012-34905-001
Psychol Aging 28 (1) 262-274 [2013-03-00; online 2013-01-02]
Mutation Analysis Facility (MAF)
Origin and evolution of medium chain alcohol dehydrogenases.
Jörnvall H, Hedlund J, Bergman T, ..., Cederlund E, Persson B
pii: S0009-2797(12)00252-9
Chem. Biol. Interact. 202 (1-3) 91-96 [2013-02-25; online 2012-12-04]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training
STC1 expression by cancer-associated fibroblasts drives metastasis of colorectal cancer.
Peña C, Céspedes MV, Lindh MB, ..., Augsten M, Ostman A
pii: 0008-5472.CAN-12-1875
Cancer Res. 73 (4) 1287-1297 [2013-02-15; online 2012-12-18]
Tissue Profiling
Early-phase GVHD gene expression profile in target versus non-target tissues: kidney, a possible target?
Sadeghi B, Al-Chaqmaqchi H, Al-Hashmi S, ..., Moshfegh A, Hassan M
pii: bmt2012120
Bone Marrow Transplant. 48 (2) 284-293 [2013-02-00; online 2012-07-25]
Bioinformatics and Expression Analysis (BEA)
A gene-centric study of common carotid artery remodelling.
Harrison SC, Zabaneh D, Asselbergs FW, ..., Hamsten A, Humphries SE
pii: S0021-9150(12)00797-6 pmc: PMC3573227
Atherosclerosis 226 (2) 440-446 [2013-02-00; online 2012-12-19]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
Workshop on laboratory protocol standards for the Molecular Methods Database.
Klingström T, Soldatova L, Stevens R, ..., Landegren U, Bongcam-Rudloff E
pii: S1871-6784(12)00121-5
N Biotechnol 30 (2) 109-113 [2013-01-25; online 2012-06-13]
PLA and Single Cell Proteomics
Protein tag-mediated conjugation of oligonucleotides to recombinant affinity binders for proximity ligation.
Gu GJ, Friedman M, Jost C, ..., Landegren U, Söderberg O
pii: S1871-6784(12)00107-0
N Biotechnol 30 (2) 144-152 [2013-01-25; online 2012-06-06]
PLA and Single Cell Proteomics
Multiplex protein detection with DNA readout via mass spectrometry.
Flanigon J, Kamali-Moghaddam M, Burbulis I, ..., Landegren U, Cantor C
pii: S1871-6784(12)00860-6 pmc: PMC3616745 mid: NIHMS425130
N Biotechnol 30 (2) 153-158 [2013-01-25; online 2012-12-04]
PLA and Single Cell Proteomics
Genomic insights into the atopic eczema-associated skin commensal yeast Malassezia sympodialis.
Gioti A, Nystedt B, Li W, ..., Heitman J, Scheynius A
MBio 4 (1) e00572-e00512 [2013-01-22; online 2013-01-22]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
DNA-binding specificities of human transcription factors.
Jolma A, Yan J, Whitington T, ..., Kivioja T, Taipale J
pii: S0092-8674(12)01496-1
Cell 152 (1-2) 327-339 [2013-01-17; online 2013-01-22]
Karolinska High Throughput Center (KHTC)