Publications 2011

163 publications

Mechanisms underlying the sparing of masticatory versus limb muscle function in an experimental critical illness model.
Aare S, Ochala J, Norman HS, ..., Hoffman EP, Larsson L
pii: physiolgenomics.00116.2011
Physiol. Genomics 43 (24) 1334-1350 [2011-12-16; online 2011-10-20]
Array and Analysis Facility
Muscle wasting and the temporal gene expression pattern in a novel rat intensive care unit model.
Llano-Diez M, Gustafson AM, Olsson C, Goransson H, Larsson L
pii: 1471-2164-12-602 pmc: PMC3266306
BMC Genomics 12 (-) 602 [2011-12-13; online 2011-12-13]
Array and Analysis Facility
Blood pressure loci identified with a gene-centric array.
Johnson T, Gaunt TR, Newhouse SJ, ..., Caulfield MJ, Munroe PB
pii: S0002-9297(11)00447-2 pmc: PMC3234370
Am. J. Hum. Genet. 89 (6) 688-700 [2011-12-09; online 2011-11-22]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
High nuclear RBM3 expression is associated with an improved prognosis in colorectal cancer.
Hjelm B, Brennan DJ, Zendehrokh N, ..., Jirström K, Uhlen M
Proteomics Clin Appl 5 (11-12) 624-635 [2011-12-00; online 2011-10-01]
Tissue Profiling
Counting absolute numbers of molecules using unique molecular identifiers.
Kivioja T, Vähärautio A, Karlsson K, ..., Linnarsson S, Taipale J
pii: nmeth.1778
Nat. Methods 9 (1) 72-74 [2011-11-20; online 2011-11-20]
Karolinska High Throughput Center (KHTC)
Variance decomposition of protein profiles from antibody arrays using a longitudinal twin model.
Kato BS, Nicholson G, Neiman M, ..., Spector TD, Schwenk JM
pii: 1477-5956-9-73 pmc: PMC3247853
Proteome Sci 9 (-) 73 [2011-11-17; online 2011-11-17]
Plasma Profiling [Collaborative]
Genome sequencing reveals a phage in Helicobacter pylori.
Lehours P, Vale FF, Bjursell MK, ..., Engstrand L, Andersson AF
MBio 2 (6) - [2011-11-15; online 2011-11-15]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
Inhibition of proteasome deubiquitinating activity as a new cancer therapy.
D'Arcy P, Brnjic S, Olofsson MH, ..., Larsson R, Linder S
pii: nm.2536 GEO: GSE24150
Nat. Med. 17 (12) 1636-1640 [2011-11-06; online 2011-11-06]
Array and Analysis Facility
Plasma profiling reveals human fibulin-1 as candidate marker for renal impairment.
Neiman M, Hedberg JJ, Dönnes PR, ..., Schwenk JM, Nilsson P
J. Proteome Res. 10 (11) 4925-4934 [2011-11-04; online 2011-09-29]
Plasma Profiling [Collaborative]
Hypothalamic mitochondrial dysfunction associated with anorexia in the anx/anx mouse.
Lindfors C, Nilsson IA, Garcia-Roves PM, ..., Schalling M, Johansen JE
pii: 1114863108 pmc: PMC3207677
Proc. Natl. Acad. Sci. U.S.A. 108 (44) 18108-18113 [2011-11-01; online 2011-10-26]
Fluorescence Tissue Profiling
Gene copy number aberrations are associated with survival in histologic subgroups of non-small cell lung cancer.
Micke P, Edlund K, Holmberg L, ..., Isaksson A, Botling J
pii: S1556-0864(15)32245-0
J Thorac Oncol 6 (11) 1833-1840 [2011-11-00; online 2011-10-21]
Array and Analysis Facility
Western blotting via proximity ligation for high performance protein analysis.
Liu Y, Gu J, Hagner-McWhirter Å, ..., Ivansson D, Landegren U
pii: O111.011031 pmc: PMC3226413
Mol. Cell Proteomics 10 (11) O111.011031 [2011-11-00; online 2011-08-05]
PLA and Single Cell Proteomics
Increasing the dynamic range of in situ PLA.
Clausson C, Allalou A, Weibrecht I, ..., Wählby C, Söderberg O
pii: nmeth.1743
Nat. Methods 8 (11) 892-893 [2011-10-28; online 2011-10-28]
BioImage Informatics [Collaborative] PLA and Single Cell Proteomics
Allele-specific copy number analysis of tumor samples with aneuploidy and tumor heterogeneity.
Rasmussen M, Sundström M, Göransson Kultima H, ..., Glimelius B, Isaksson A
pii: gb-2011-12-10-r108 pmc: PMC3333778
Genome Biol. 12 (10) R108 [2011-10-24; online 2011-10-24]
Array and Analysis Facility
MED12, the mediator complex subunit 12 gene, is mutated at high frequency in uterine leiomyomas.
Mäkinen N, Mehine M, Tolvanen J, ..., Vahteristo P, Aaltonen LA
pii: science.1208930 GEO: GSE30673
Science 334 (6053) 252-255 [2011-10-14; online 2011-08-27]
Karolinska High Throughput Center (KHTC)
Histone modifications influence mediator interactions with chromatin.
Zhu X, Zhang Y, Bjornsdottir G, ..., Gustafsson CM, Myers LC
pii: gkr551 pmc: PMC3201872
Nucleic Acids Res. 39 (19) 8342-8354 [2011-10-00; online 2011-07-12]
Bioinformatics and Expression Analysis (BEA)
The Lin28/let-7 axis regulates glucose metabolism.
Zhu H, Shyh-Chang N, Segrè AV, ..., Altshuler D, Daley GQ
pii: S0092-8674(11)01003-8 pmc: PMC3353524 mid: NIHMS322292
Cell 147 (1) 81-94 [2011-09-30; online 2011-10-04]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
ProteinSeq: high-performance proteomic analyses by proximity ligation and next generation sequencing.
Darmanis S, Nong RY, Vänelid J, ..., Kamali-Moghaddam M, Landegren U
pii: PONE-D-11-10457 pmc: PMC3183061
PLoS ONE 6 (9) e25583 [2011-09-29; online 2011-09-29]
PLA and Single Cell Proteomics
Large-scale protein profiling in human cell lines using antibody-based proteomics.
Fagerberg L, Strömberg S, El-Obeid A, ..., Ponten F, Asplund A
J. Proteome Res. 10 (9) 4066-4075 [2011-09-02; online 2011-07-06]
Tissue Profiling
Variants in STAT5B associate with serum TC and LDL-C levels.
Kornfeld JW, Isaacs A, Vitart V, ..., Pramstaller PP, Hicks AA
pii: jc.2011-0322
J. Clin. Endocrinol. Metab. 96 (9) E1496-E1501 [2011-09-00; online 2011-07-15]
NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure
Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis.
International Multiple Sclerosis Genetics Consortium , Wellcome Trust Case Control Consortium 2 , Sawcer S, ..., Donnelly P, Compston A
Nature 476 (7359) 214-219 [2011-08-10; online 2011-08-10]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
Functional and prognostic relevance of the homeobox protein MSX2 in malignant melanoma.
Gremel G, Ryan D, Rafferty M, ..., Ponten F, Gallagher WM
pii: bjc2011249 pmc: PMC3170959
Br. J. Cancer 105 (4) 565-574 [2011-08-09; online 2011-07-07]
Tissue Profiling
Mapping the subcellular protein distribution in three human cell lines.
Fagerberg L, Stadler C, Skogs M, ..., Uhlén M, Lundberg E
J. Proteome Res. 10 (8) 3766-3777 [2011-08-05; online 2011-06-17]
Cell Profiling
The genetic structure of the Swedish population.
Humphreys K, Grankvist A, Leu M, ..., Palmgren J, Magnusson PK
pii: PONE-D-11-01309 pmc: PMC3150368
PLoS ONE 6 (8) e22547 [2011-08-04; online 2011-08-04]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
Influence of the COMT genotype on working memory and brain activity changes during development.
Dumontheil I, Roggeman C, Ziermans T, ..., Kere J, Klingberg T
pii: S0006-3223(11)00202-2
Biol. Psychiatry 70 (3) 222-229 [2011-08-01; online 2011-04-26]
Mutation Analysis Facility (MAF)
Lack of association between two dopamine D2 receptor gene polymorphisms and schizophrenia.
Caprini S, Saetre P, Melle I, ..., Terenius L, Jönsson EG
pii: 00041444-201108000-00008
Psychiatr. Genet. 21 (4) 214-215 [2011-08-00; online 2011-06-30]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
Lack of association between genetic variations in the KALRN region and ischemic stroke.
Olsson S, Jood K, Melander O, ..., Lindgren A, Jern C
pii: S0009-9120(11)00376-6
Clin. Biochem. 44 (12) 1018-1020 [2011-08-00; online 2011-06-15]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
RBM3-regulated genes promote DNA integrity and affect clinical outcome in epithelial ovarian cancer.
Ehlén Å, Nodin B, Rexhepaj E, ..., Brennan DJ, Jirström K
Transl Oncol 4 (4) 212-221 [2011-08-00; online 2011-08-01]
Tissue Profiling
Potential association of muscarinic receptor 3 gene variants with primary Sjogren's syndrome.
Appel S, Le Hellard S, Bruland O, ..., Wahren-Herlenius M, Jonsson R
pii: ard.2010.138966
Ann. Rheum. Dis. 70 (7) 1327-1329 [2011-07-00; online 2011-04-01]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
SATB2 in combination with cytokeratin 20 identifies over 95% of all colorectal carcinomas.
Magnusson K, de Wit M, Brennan DJ, ..., Jirström K, Pontén F
pii: 00000478-201107000-00001
Am. J. Surg. Pathol. 35 (7) 937-948 [2011-07-00; online 2011-06-17]
Cell Profiling Tissue Profiling
Concomitant autoimmunity in myasthenia gravis--lack of association with IgA deficiency.
Ramanujam R, Piehl F, Pirskanen R, Gregersen PK, Hammarström L
pii: S0165-5728(11)00138-X pmc: PMC3230785 mid: NIHMS305414
J. Neuroimmunol. 236 (1-2) 118-122 [2011-07-00; online 2011-06-15]
Mutation Analysis Facility (MAF)
Prostasomal DNA characterization and transfer into human sperm.
Ronquist GK, Larsson A, Ronquist G, ..., Carlsson L, Stavreus-Evers A
Mol. Reprod. Dev. 78 (7) 467-476 [2011-07-00; online 2011-06-04]
Array and Analysis Facility
Specific syndecan-1 domains regulate mesenchymal tumor cell adhesion, motility and migration.
Zong F, Fthenou E, Mundt F, ..., Hjerpe A, Dobra K
pii: 10-PONE-RA-19265R1-CORRECTION pmc: PMC3121713
PLoS ONE 6 (6) e14816 [2011-06-23; online 2011-06-23]
Bioinformatics and Expression Analysis (BEA)
The fat mass and obesity gene is linked to reduced verbal fluency in overweight and obese elderly men.
Benedict C, Jacobsson JA, Rönnemaa E, ..., Kilander L, Schiöth HB
pii: S0197-4580(11)00019-4
Neurobiol. Aging 32 (6) 1159.e1-1159.e5 [2011-06-00; online 2011-04-05]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
Multiple recognition assay reveals prostasomes as promising plasma biomarkers for prostate cancer.
Tavoosidana G, Ronquist G, Darmanis S, ..., Landegren UD, Kamali-Moghaddam M
pii: 1019330108 pmc: PMC3102389
Proc. Natl. Acad. Sci. U.S.A. 108 (21) 8809-8814 [2011-05-24; online 2011-05-11]
Clinical Biomarkers PLA and Single Cell Proteomics
Growth differentiation factor 15: a prognostic marker for recurrence in colorectal cancer.
Wallin U, Glimelius B, Jirström K, ..., Påhlman L, Birgisson H
pii: bjc2011112 pmc: PMC3101900
Br. J. Cancer 104 (10) 1619-1627 [2011-05-10; online 2011-04-07]
Tissue Profiling
Novel asymmetrically localizing components of human centrosomes identified by complementary proteomics methods.
Jakobsen L, Vanselow K, Skogs M, ..., Hyman AA, Andersen JS
pii: emboj201163 pmc: PMC3102290
EMBO J. 30 (8) 1520-1535 [2011-04-20; online 2011-03-15]
Cell Profiling
Kynurenine 3-monooxygenase (KMO) polymorphisms in schizophrenia: an association study.
Holtze M, Saetre P, Erhardt S, ..., Jönsson EG, Schalling M
pii: S0920-9964(10)01575-6
Schizophr. Res. 127 (1-3) 270-272 [2011-04-00; online 2010-10-30]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
Utilizing twins concordance rates to infer the predisposition to myasthenia gravis.
Ramanujam R, Pirskanen R, Ramanujam S, Hammarström L
pii: 10.1375/twin.14.2.129
Twin Res Hum Genet 14 (2) 129-136 [2011-04-00; online 2011-03-24]
Mutation Analysis Facility (MAF)
CUBN is a gene locus for albuminuria.
Böger CA, Chen MH, Tin A, ..., Fox CS, Kao WH
pii: ASN.2010060598 pmc: PMC3060449
J. Am. Soc. Nephrol. 22 (3) 555-570 [2011-03-00; online 2011-03-01]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
Diagnostic biomarkers of prostate cancer.
Häggarth L, Hägglöf C, Jaraj SJ, ..., Ostman A, Egevad L
Scand. J. Urol. Nephrol. 45 (1) 60-67 [2011-02-00; online 2010-11-03]
Tissue Profiling
GAD1 is a biomarker for benign and malignant prostatic tissue.
Jaraj SJ, Augsten M, Häggarth L, ..., Ostman A, Egevad L
Scand. J. Urol. Nephrol. 45 (1) 39-45 [2011-02-00; online 2010-11-26]
Tissue Profiling
HRG inhibits tumor growth and metastasis by inducing macrophage polarization and vessel normalization through downregulation of PlGF.
Rolny C, Mazzone M, Tugues S, ..., Claesson-Welsh L, Carmeliet P
pii: S1535-6108(10)00474-5
Cancer Cell 19 (1) 31-44 [2011-01-18; online 2011-01-11]
Tissue Profiling
Vitamin D receptor genotypes, ultraviolet radiation exposure, and risk of non-Hodgkin lymphoma.
Smedby KE, Eloranta S, Duvefelt K, ..., Hjalgrim H, Chang ET
pii: kwq340
Am. J. Epidemiol. 173 (1) 48-54 [2011-01-01; online 2010-11-16]
Mutation Analysis Facility (MAF)
Mechanisms of blast induced brain injuries, experimental studies in rats.
Risling M, Plantman S, Angeria M, ..., Arborelius U, Davidsson J
pii: S1053-8119(10)00763-9
Neuroimage 54 Suppl 1 (-) S89-S97 [2011-01-00; online 2010-05-25]
Bioinformatics and Expression Analysis (BEA)
Meta-analysis of the association between variants in SORL1 and Alzheimer disease.
Reitz C, Cheng R, Rogaeva E, ..., Mayeux R, Genetic and Environmental Risk in Alzheimer Disease 1 Consortium
Arch. Neurol. 68 (1) 99-106 [2011-01-00; online 2011-01-12]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure