Publications 2010

Defining the transcriptome and proteome in three functionally different human cell lines.

Lundberg E, Fagerberg L, Klevebring D, ..., Mann M, Uhlen M

Mol. Syst. Biol. 6 (-) 450 [2010-12-21; online 2010-12-24]

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

Unbalanced translocation 9;16 in two children with dysmorphic features, and severe developmental delay: Evidence of cross-over within derivative chromosome 9 in patient #1.

Zambrano RM, Wohler E, Annerén G, ..., Cutting GR, Batista DA

Eur J Med Genet 54 (2) 189-193 [2010-12-07; online 2010-12-07]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Analysis of transcript and protein overlap in a human osteosarcoma cell line.

Klevebring D, Fagerberg L, Lundberg E, ..., Uhlén M, Lundeberg J

BMC Genomics 11 (-) 684 [2010-12-02; online 2010-12-02]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure Spatial Proteomics

Associations of gene sequence variation and serum levels of C-reactive protein and interleukin-6 with Alzheimer's disease and dementia.

Eriksson UK, Pedersen NL, Reynolds CA, ..., Dickman PW, Bennet AM

J. Alzheimers Dis. 23 (2) 361-369 [2010-12-01; online 2010-12-01]

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

Towards a knowledge-based Human Protein Atlas.

Uhlen M, Oksvold P, Fagerberg L, ..., Björling L, Ponten F

Nat. Biotechnol. 28 (12) 1248-1250 [2010-12-00; online 2010-12-09]

Thirty new loci for age at menarche identified by a meta-analysis of genome-wide association studies.

Elks CE, Perry JR, Sulem P, ..., Ong KK, Murray A

Nat. Genet. 42 (12) 1077-1085 [2010-12-00; online 2010-11-26]

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

The genetic architecture of domestication in the chicken: effects of pleiotropy and linkage.

Wright D, Rubin CJ, Martinez Barrio A, ..., Jensen P, Andersson L

Mol. Ecol. 19 (23) 5140-5156 [2010-12-00; online 2010-11-03]

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

SOX10 expression in superficial spreading and nodular malignant melanomas.

Agnarsdóttir M, Sooman L, Bolander A, ..., Uhlen M, Hedstrand H

Melanoma Res. 20 (6) 468-478 [2010-12-00; online 2010-10-05]

SNPs in genes coding for ROS metabolism and signalling in association with docetaxel clearance.

Edvardsen H, Brunsvig PF, Solvang H, ..., Aamdal S, Kristensen VN

Pharmacogenomics J. 10 (6) 513-523 [2010-12-00; online 2010-02-17]

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

Interactions of dietary whole-grain intake with fasting glucose- and insulin-related genetic loci in individuals of European descent: a meta-analysis of 14 cohort studies.

Nettleton JA, McKeown NM, Kanoni S, ..., Franks PW, Meigs JB

Diabetes Care 33 (12) 2684-2691 [2010-12-00; online 2010-08-10]

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

High frequency of p16(INK4A) promoter methylation in NRAS-mutated cutaneous melanoma.

Jonsson A, Tuominen R, Grafström E, Hansson J, Egyhazi S

J. Invest. Dermatol. 130 (12) 2809-2817 [2010-12-00; online 2010-08-13]

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

Distinct gene expression profiles in subsets of chronic lymphocytic leukemia expressing stereotyped IGHV4-34 B-cell receptors.

Marincevic M, Mansouri M, Kanduri M, ..., Stamatopoulos K, Rosenquist R

Haematologica 95 (12) 2072-2079 [2010-12-00; online 2010-08-31]

Array and Analysis Facility NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Common variants at 10 genomic loci influence hemoglobin A₁(C) levels via glycemic and nonglycemic pathways.

Soranzo N, Sanna S, Wheeler E, ..., Barroso I, Meigs JB

Diabetes 59 (12) 3229-3239 [2010-12-00; online 2010-09-21]

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

A pyrosequencing study in twins shows that gastrointestinal microbial profiles vary with inflammatory bowel disease phenotypes.

Willing BP, Dicksved J, Halfvarson J, ..., Jansson JK, Engstrand L

Gastroenterology 139 (6) 1844-1854.e1 [2010-12-00; online 2010-09-08]

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

A high-density scan of the Z chromosome in Ficedula flycatchers reveals candidate loci for diversifying selection.

Backström N, Lindell J, Zhang Y, ..., Saetre GP, Ellegren H

Evolution 64 (12) 3461-3475 [2010-12-00; online 2010-07-16]

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

Keller L, Xu W, Wang HX, ..., Fratiglioni L, Graff C

J. Alzheimers Dis. 23 (3) 461-469 [2010-11-26; online 2010-11-26]

SNP detection and prediction of variability between chicken lines using genome resequencing of DNA pools.

Marklund S, Carlborg O

BMC Genomics 11 (-) 665 [2010-11-25; online 2010-11-25]

NGI Uppsala (Uppsala Genome Center) 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]

Toward next generation plasma profiling via heat-induced epitope retrieval and array-based assays.

Schwenk JM, Igel U, Neiman M, ..., Nilsson P, Uhlen M

Mol. Cell Proteomics 9 (11) 2497-2507 [2010-11-00; online 2010-08-05]

Affinity Proteomics Stockholm [Technology development]

Meta-analysis identifies 13 new loci associated with waist-hip ratio and reveals sexual dimorphism in the genetic basis of fat distribution.

Heid IM, Jackson AU, Randall JC, ..., Mohlke KL, Lindgren CM

Nat. Genet. 42 (11) 949-960 [2010-11-00; online 2010-10-12]

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

Meiofauna reduces bacterial mineralization of naphthalene in marine sediment.

Näslund J, Nascimento FJ, Gunnarsson JS

ISME J 4 (11) 1421-1430 [2010-11-00; online 2010-05-14]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Creation of an antibody-based subcellular protein atlas.

Lundberg E, Uhlén M

Proteomics 10 (22) 3984-3996 [2010-11-00; online 2010-07-22]

Common variants in the ATP2B1 gene are associated with susceptibility to hypertension: the Japanese Millennium Genome Project.

Tabara Y, Kohara K, Kita Y, ..., Ueshima H, Miki T

Hypertension 56 (5) 973-980 [2010-11-00; online 2010-10-06]

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

Four novel Loci (19q13, 6q24, 12q24, and 5q14) influence the microcirculation in vivo.

Ikram MK, Sim X, Xueling S, ..., Vingerling JR, Wong TY

PLoS Genet. 6 (10) e1001184 [2010-10-28; online 2010-10-28]

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

Sensitive detection of Aβ protofibrils by proximity ligation--relevance for Alzheimer's disease.

Kamali-Moghaddam M, Pettersson FE, Wu D, ..., Lannfelt L, Landegren U

BMC Neurosci 11 (-) 124 [2010-10-05; online 2010-10-05]

PLA and Single Cell Proteomics

Association analysis of PALB2 and BRCA2 in bipolar disorder and schizophrenia in a scandinavian case-control sample.

Tesli M, Athanasiu L, Mattingsdal M, ..., Djurovic S, Andreassen OA

Am. J. Med. Genet. B Neuropsychiatr. Genet. 153B (7) 1276-1282 [2010-10-05; online 2010-09-28]

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

An exploratory model for G x E interaction on hippocampal volume in schizophrenia; obstetric complications and hypoxia-related genes.

Haukvik UK, Saetre P, McNeil T, ..., Jönsson EG, Agartz I

Prog. Neuropsychopharmacol. Biol. Psychiatry 34 (7) 1259-1265 [2010-10-01; online 2010-07-20]

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

Somatic mosaicism for chromosome X and Y aneuploidies in monozygotic twins heterozygous for sickle cell disease mutation.

Razzaghian HR, Shahi MH, Forsberg LA, ..., Westerman MP, Dumanski JP

Am. J. Med. Genet. A 152A (10) 2595-2598 [2010-10-00; online 2010-08-25]

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

DOI Crossref

Lycosid spiders and alternative food: Feeding behavior and implications for biological control

Kuusk AK, Ekbom B

Biological Control 55 (1) 20-26 [2010-10-00; online 2010-10-00]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Linkage to 20p13 including the ANGPT4 gene in families with mixed Alzheimer's disease and vascular dementia.

Sillén A, Brohede J, Lilius L, ..., Winblad B, Graff C

J. Hum. Genet. 55 (10) 649-655 [2010-10-00; online 2010-07-03]

Brain gene expression in relation to fearfulness in female red junglefowl (Gallus gallus).

Jöngren M, Westander J, Nätt D, Jensen P

Genes Brain Behav. 9 (7) 751-758 [2010-10-00; online 2010-07-06]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

A chromatin-remodeling protein is a component of fission yeast mediator.

Khorosjutina O, Wanrooij PH, Walfridsson J, ..., Ekwall K, Gustafsson CM

J. Biol. Chem. 285 (39) 29729-29737 [2010-09-24; online 2010-07-14]

A trans-acting locus regulates an anti-viral expression network and type 1 diabetes risk.

Heinig M, Petretto E, Wallace C, ..., Hubner N, Cook SA

Nature 467 (7314) 460-464 [2010-09-23; online 2010-09-10]

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

Pleiotropy in the presence of allelic heterogeneity: alternative genetic models for the influence of APOE on serum LDL, CSF amyloid-β42, and dementia.

Bennet AM, Reynolds CA, Gatz M, ..., Pedersen NL, Prince JA

J. Alzheimers Dis. 22 (1) 129-134 [2010-09-18; online 2010-09-18]

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

Trisomy and triploidy are sources of embryo mortality in the zebra finch.

Forstmeier W, Ellegren H

Proc. Biol. Sci. 277 (1694) 2655-2660 [2010-09-07; online 2010-05-07]

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

Small-molecule screening using a whole-cell viral replication reporter gene assay identifies 2-{[2-(benzoylamino)benzoyl]amino}-benzoic acid as a novel antiadenoviral compound.

Andersson EK, Strand M, Edlund K, ..., Mei Y, Wadell G

Antimicrob. Agents Chemother. 54 (9) 3871-3877 [2010-09-00; online 2010-06-30]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Profiling protein expression and interactions: proximity ligation as a tool for personalized medicine.

Blokzijl A, Friedman M, Pontén F, Landegren U

J. Intern. Med. 268 (3) 232-245 [2010-09-00; online 2010-08-11]

PLA and Single Cell Proteomics

Production of ectomycorrhizal mycelium peaks during canopy closure in Norway spruce forests.

Wallander H, Johansson U, Sterkenburg E, Brandström Durling M, Lindahl BD

New Phytol. 187 (4) 1124-1134 [2010-09-00; online 2010-06-22]

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

High-density screening reveals a different spectrum of genomic aberrations in chronic lymphocytic leukemia patients with 'stereotyped' IGHV3-21 and IGHV4-34 B-cell receptors.

Marincevic M, Cahill N, Gunnarsson R, ..., Stamatopoulos K, Rosenquist R

Haematologica 95 (9) 1519-1525 [2010-09-00; online 2010-04-28]

Association of IFIH1 and other autoimmunity risk alleles with selective IgA deficiency.

Ferreira RC, Pan-Hammarström Q, Graham RR, ..., Behrens TW, Hammarström L

Nat. Genet. 42 (9) 777-780 [2010-09-00; online 2010-08-10]

Expression of the RNA-binding protein RBM3 is associated with a favourable prognosis and cisplatin sensitivity in epithelial ovarian cancer.

Ehlén A, Brennan DJ, Nodin B, ..., Pontén F, Jirström K

J Transl Med 8 (-) 78 [2010-08-20; online 2010-08-20]

Familial cutaneous melanoma.

Hansson J

Adv. Exp. Med. Biol. 685 (-) 134-145 [2010-08-07; online 2010-08-07]

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

Biological, clinical and population relevance of 95 loci for blood lipids.

Teslovich TM, Musunuru K, Smith AV, ..., Boehnke M, Kathiresan S

Nature 466 (7307) 707-713 [2010-08-05; online 2010-08-06]

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

Topoisomerase I amplification in melanoma is associated with more advanced tumours and poor prognosis.

Ryan D, Rafferty M, Hegarty S, ..., Dervan PA, Gallagher WM

Pigment Cell Melanoma Res 23 (4) 542-553 [2010-08-00; online 2010-05-15]

The role of IL-1beta in reduced IL-7 production by stromal and epithelial cells: a model for impaired T-cell numbers in the gut during HIV-1 infection.

Thang PH, Ruffin N, Brodin D, ..., Vivar N, Chiodi F

J. Intern. Med. 268 (2) 181-193 [2010-08-00; online 2010-05-26]

Sex-linked barring in chickens is controlled by the CDKN2A /B tumour suppressor locus.

Hellström AR, Sundström E, Gunnarsson U, ..., Kerje S, Andersson L

Pigment Cell Melanoma Res 23 (4) 521-530 [2010-08-00; online 2010-03-29]

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

No evidence for Z-chromosome rearrangements between the pied flycatcher and the collared flycatcher as judged by gene-based comparative genetic maps.

Backström N, Palkopoulou E, Qvarnström A, Ellegren H

Mol. Ecol. 19 (16) 3394-3405 [2010-08-00; online 2010-07-31]

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

Niemann-Pick C1 modulates hepatic triglyceride metabolism and its genetic variation contributes to serum triglyceride levels.

Uronen RL, Lundmark P, Orho-Melander M, ..., Syvänen AC, Ikonen E

Arterioscler. Thromb. Vasc. Biol. 30 (8) 1614-1620 [2010-08-00; online 2010-05-22]

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

Genome-wide association study identifies a sequence variant within the DAB2IP gene conferring susceptibility to abdominal aortic aneurysm.

Gretarsdottir S, Baas AF, Thorleifsson G, ..., Thorsteinsdottir U, Stefansson K

Nat. Genet. 42 (8) 692-697 [2010-08-00; online 2010-07-14]

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

Association of genetic risk variants with expression of proximal genes identifies novel susceptibility genes for cardiovascular disease.

Folkersen L, van't Hooft F, Chernogubova E, ..., Eriksson P, BiKE and ASAP study groups

Circ Cardiovasc Genet 3 (4) 365-373 [2010-08-00; online 2010-06-22]

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

Identification of novel exons and transcribed regions by chimpanzee transcriptome sequencing.

Wetterbom A, Ameur A, Feuk L, Gyllensten U, Cavelier L

Genome Biol. 11 (7) R78 [2010-07-23; online 2010-07-23]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

A functional polymorphism in the HMGCR promoter affects transcriptional activity but not the risk for Alzheimer disease in Swedish populations.

Keller L, Murphy C, Wang HX, ..., Graff C, Meaney S

Brain Res. 1344 (-) 185-191 [2010-07-16; online 2010-05-11]

Induction patterns of new CYP1 genes in environmentally exposed rainbow trout.

Jönsson ME, Gao K, Olsson JA, Goldstone JV, Brandt I

Aquat. Toxicol. 98 (4) 311-321 [2010-07-15; online 2010-04-08]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Different SNP combinations in the GCH1 gene and use of labor analgesia.

Dabo F, Grönbladh A, Nyberg F, Sundström-Poromaa I, Akerud H

Mol Pain 6 (-) 41 [2010-07-15; online 2010-07-15]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Topoisomerase I regulates open chromatin and controls gene expression in vivo.

Durand-Dubief M, Persson J, Norman U, Hartsuiker E, Ekwall K

EMBO J. 29 (13) 2126-2134 [2010-07-07; online 2010-06-08]

Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo.

Wei GH, Badis G, Berger MF, ..., Bulyk ML, Taipale J

EMBO J. 29 (13) 2147-2160 [2010-07-07; online 2010-06-03]

Karolinska High Throughput Center (KHTC)

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

Classification of DNA sequences using Bloom filters.

Stranneheim H, Käller M, Allander T, ..., Arvestad L, Lundeberg J

Bioinformatics 26 (13) 1595-1600 [2010-07-01; online 2010-05-18]

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

Tissue factor pathway inhibitor-2 is induced by fluid shear stress in vascular smooth muscle cells and affects cell proliferation and survival.

Ekstrand J, Razuvaev A, Folkersen L, Roy J, Hedin U

J. Vasc. Surg. 52 (1) 167-175 [2010-07-00; online 2010-06-12]

Subcellular distribution and expression of prenylated Rab acceptor 1 domain family, member 2 (PRAF2) in malignant glioma: Influence on cell survival and migration.

Borsics T, Lundberg E, Geerts D, ..., Wester K, Bachmann AS

Cancer Sci. 101 (7) 1624-1631 [2010-07-00; online 2010-03-19]

Revolutionizing membrane protein overexpression in bacteria.

Schlegel S, Klepsch M, Gialama D, ..., Slotboom DJ, de Gier JW

Microb Biotechnol 3 (4) 403-411 [2010-07-00; online 2009-09-04]

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

Ontogenetic complexity of sexual dimorphism and sex-specific selection.

Mank JE, Nam K, Brunström B, Ellegren H

Mol. Biol. Evol. 27 (7) 1570-1578 [2010-07-00; online 2010-02-10]

Gene expression analysis in hypoplastic lungs in the nitrofen model of congenital diaphragmatic hernia.

Burgos CM, Uggla AR, Fagerström-Billai F, ..., Frenckner B, Nord M

J. Pediatr. Surg. 45 (7) 1445-1454 [2010-07-00; online 2010-07-20]

Characterization of the RNA content of chromatin.

Mondal T, Rasmussen M, Pandey GK, Isaksson A, Kanduri C

Genome Res. 20 (7) 899-907 [2010-07-00; online 2010-04-21]

Array and Analysis Facility NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Genetic evidence of multiple loci in dystocia--difficult labour.

Algovik M, Kivinen K, Peterson H, Westgren M, Kere J

BMC Med. Genet. 11 (-) 105 [2010-06-30; online 2010-06-30]

HIV-1 exposed uninfected men who have sex with men have increased levels of salivary CC-chemokines associated with sexual behavior.

Hasselrot K, Bratt G, Duvefelt K, ..., Sandström E, Broliden K

AIDS 24 (10) 1569-1575 [2010-06-19; online 2010-06-16]

Genome-wide mapping of estrogen receptor-beta-binding regions reveals extensive cross-talk with transcription factor activator protein-1.

Zhao C, Gao H, Liu Y, ..., Gustafsson JA, Dahlman-Wright K

Cancer Res. 70 (12) 5174-5183 [2010-06-15; online 2010-05-27]

Interstitial Deletions at 6q14.1-q15 Associated with Obesity, Developmental Delay and a Distinct Clinical Phenotype.

Wentzel C, Lynch SA, Stattin EL, ..., Annerén G, Thuresson AC

Mol Syndromol 1 (2) 75-81 [2010-06-09; online 2010-06-09]

Array and Analysis Facility NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Analysis of oestrogen regulation of alpha-, beta- and gamma-secretase gene and protein expression in cultured human neuronal and glial cells.

Nord LC, Sundqvist J, Andersson E, Fried G

Neurodegener Dis 7 (6) 349-364 [2010-06-04; online 2010-06-04]

Genetic diversity and differentiation among Lagopus lagopus populations in Scandinavia and Scotland: evolutionary significant units confirmed by SNP markers.

Quintela M, Berlin S, Wang B, Höglund J

Mol. Ecol. 19 (12) 2380-2393 [2010-06-01; online 2010-07-20]

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

Tissue tumor marker expression in smokers, including serum cotinine concentrations, in women with cervical intraepithelial neoplasia or normal squamous cervical epithelium.

Samir R, Asplund A, Tot T, Pekar G, Hellberg D

Am. J. Obstet. Gynecol. 202 (6) 579.e1-579.e7 [2010-06-00; online 2010-01-12]

Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities.

Jolma A, Kivioja T, Toivonen J, ..., Ukkonen E, Taipale J

Genome Res. 20 (6) 861-873 [2010-06-00; online 2010-04-10]

Karolinska High Throughput Center (KHTC) NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Improving Bayesian credibility intervals for classifier error rates using maximum entropy empirical priors.

Gustafsson MG, Wallman M, Wickenberg Bolin U, ..., Andersson CR, Isaksson A

Artif Intell Med 49 (2) 93-104 [2010-06-00; online 2010-03-30]

Genetics of HPA-axis, depression and suicidality.

Wasserman D, Wasserman J, Sokolowski M

Eur. Psychiatry 25 (5) 278-280 [2010-06-00; online 2010-05-07]

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

Genetic analysis of metabolic traits in an intercross between body weight-selected chicken lines.

Ek W, Strömstedt L, Wahlberg P, ..., Andersson L, Carlborg O

Physiol. Genomics 42 (1) 20-22 [2010-06-00; online 2010-03-25]

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

PubMed

Antibody-based proteomics for discovery and exploration of proteins expressed in pancreatic islets.

Lindskog C, Asplund A, Engkvist M, ..., Korsgren O, Ponten F

Discov Med 9 (49) 565-578 [2010-06-00; online 2010-07-01]

Alpha terpineol: a potential anticancer agent which acts through suppressing NF-kappaB signalling.

PubMed

Hassan SB, Gali-Muhtasib H, Göransson H, Larsson R

Anticancer Res. 30 (6) 1911-1919 [2010-06-00; online 2010-07-24]

A variant near the interleukin-6 gene is associated with fat mass in Caucasian men.

Andersson N, Strandberg L, Nilsson S, ..., Jansson JO, Osteoporotic Fractures in Men MrOS Research Group

Int J Obes (Lond) 34 (6) 1011-1019 [2010-06-00; online 2010-02-17]

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

Molecular make-up of the glomerular filtration barrier.

Patrakka J, Tryggvason K

Biochem. Biophys. Res. Commun. 396 (1) 164-169 [2010-05-21; online 2010-05-25]

Analysis of lipid pathway genes indicates association of sequence variation near SREBF1/TOM1L2/ATPAF2 with dementia risk.

Reynolds CA, Hong MG, Eriksson UK, ..., Pedersen NL, Prince JA

Hum. Mol. Genet. 19 (10) 2068-2078 [2010-05-15; online 2010-02-20]

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

Adipose tissue pathways involved in weight loss of cancer cachexia.

Dahlman I, Mejhert N, Linder K, ..., Rydén M, Arner P

Br. J. Cancer 102 (10) 1541-1548 [2010-05-11; online 2010-04-22]

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

Chd1 remodelers maintain open chromatin and regulate the epigenetics of differentiation.

Persson J, Ekwall K

Exp. Cell Res. 316 (8) 1316-1323 [2010-05-01; online 2010-03-10]

Variation in STAT4 is associated with systemic lupus erythematosus in a Finnish family cohort.

Hellquist A, Sandling JK, Zucchelli M, ..., Syvänen AC, Kere J

Ann. Rheum. Dis. 69 (5) 883-886 [2010-05-00; online 2009-09-01]

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

The impact of RNA standardization and heterogeneous gene expression on the results of cDNA array of human breast carcinoma.

Khoshnoud R, He Q, Sylván M, ..., Rutqvist L, Skog S

Int. J. Mol. Med. 25 (5) 735-741 [2010-05-00; online 2010-04-08]

Mapping of the fibroblast growth factors in human white adipose tissue.

Mejhert N, Galitzky J, Pettersson AT, ..., Arner P, Rydén M

J. Clin. Endocrinol. Metab. 95 (5) 2451-2457 [2010-05-00; online 2010-03-17]

Gene-specific and global methylation patterns predict outcome in patients with acute myeloid leukemia.

Deneberg S, Grövdal M, Karimi M, ..., Hellström-Lindberg E, Lehmann S

Leukemia 24 (5) 932-941 [2010-05-00; online 2010-03-20]

Detailed physiologic characterization reveals diverse mechanisms for novel genetic Loci regulating glucose and insulin metabolism in humans.

Ingelsson E, Langenberg C, Hivert MF, ..., Florez JC, MAGIC investigators

Diabetes 59 (5) 1266-1275 [2010-05-00; online 2010-02-27]

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

Abundance and expression of enantioselective rdpA and sdpA dioxygenase genes during degradation of the racemic herbicide (R,S)-2-(2,4-dichlorophenoxy)propionate in soil.

Paulin MM, Nicolaisen MH, Sørensen J

Appl. Environ. Microbiol. 76 (9) 2873-2883 [2010-05-00; online 2010-03-23]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

A STAT4 risk allele is associated with ischaemic cerebrovascular events and anti-phospholipid antibodies in systemic lupus erythematosus.

Svenungsson E, Gustafsson J, Leonard D, ..., Syvänen AC, Rönnblom L

Ann. Rheum. Dis. 69 (5) 834-840 [2010-05-00; online 2009-09-19]

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

A single fixation protocol for proteome-wide immunofluorescence localization studies.

Stadler C, Skogs M, Brismar H, Uhlén M, Lundberg E

J Proteomics 73 (6) 1067-1078 [2010-04-18; online 2009-11-10]

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

Tumour-specific HMG-CoAR is an independent predictor of recurrence free survival in epithelial ovarian cancer.

Brennan DJ, Brändstedt J, Rexhepaj E, ..., O'Herlihy C, Jirstrom K

BMC Cancer 10 (-) 125 [2010-04-01; online 2010-04-01]

The recombination landscape of the zebra finch Taeniopygia guttata genome.

Backström N, Forstmeier W, Schielzeth H, ..., Kempenaers B, Ellegren H

Genome Res. 20 (4) 485-495 [2010-04-00; online 2010-03-31]

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

Reaction mechanism of 5,8-linoleate diol synthase, 10R-dioxygenase, and 8,11-hydroperoxide isomerase of Aspergillus clavatus.

Jernerén F, Garscha U, Hoffmann I, Hamberg M, Oliw EH

Biochim. Biophys. Acta 1801 (4) 503-507 [2010-04-00; online 2010-01-05]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

PubMed

Increased serum progesterone and estradiol correlate to increased COX-2 tissue expression in cervical intraepithelial neoplasia.

Samir R, Tot T, Asplund A, Pekar G, Hellberg D

Anticancer Res. 30 (4) 1217-1222 [2010-04-00; online 2010-06-10]

ELMOD2, a candidate gene for idiopathic pulmonary fibrosis, regulates antiviral responses.

Pulkkinen V, Bruce S, Rintahaka J, ..., Matikainen S, Kere J

FASEB J. 24 (4) 1167-1177 [2010-04-00; online 2009-12-08]

Copy number variation, chromosome rearrangement, and their association with recombination during avian evolution.

Völker M, Backström N, Skinner BM, ..., Ellegren H, Griffin DK

Genome Res. 20 (4) 503-511 [2010-04-00; online 2010-03-31]

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

Novel associations of multiple genetic loci with plasma levels of factor VII, factor VIII, and von Willebrand factor: The CHARGE (Cohorts for Heart and Aging Research in Genome Epidemiology) Consortium.

Smith NL, Chen MH, Dehghan A, ..., Tang W, O'Donnell CJ

Circulation 121 (12) 1382-1392 [2010-03-30; online 2010-03-17]

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

Whole-genome resequencing reveals loci under selection during chicken domestication.

Rubin C, Zody MC, Eriksson J, ..., Lindblad-Toh K, Andersson L

Nature 464 (7288) 587-591 [2010-03-25; online 2010-03-12]

NGI Uppsala (Uppsala Genome Center) 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

Genome-wide characterisation of the Gcn5 histone acetyltransferase in budding yeast during stress adaptation reveals evolutionarily conserved and diverged roles.

Xue-Franzén Y, Johnsson A, Brodin D, ..., Bürglin TR, Wright AP

BMC Genomics 11 (-) 200 [2010-03-25; online 2010-03-25]

Short-term antibiotic treatment has differing long-term impacts on the human throat and gut microbiome.

Jakobsson HE, Jernberg C, Andersson AF, ..., Jansson JK, Engstrand L

PLoS ONE 5 (3) e9836 [2010-03-24; online 2010-03-24]

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

Sustained inflammation due to nuclear factor-kappa B activation in irradiated human arteries.

Halle M, Gabrielsen A, Paulsson-Berne G, ..., Farnebo F, Tornvall P

J. Am. Coll. Cardiol. 55 (12) 1227-1236 [2010-03-23; online 2010-03-20]

Investigation of gene dosage imbalances in patients with Noonan syndrome using multiplex ligation-dependent probe amplification analysis.

Nyström AM, Ekvall S, Thuresson AC, ..., Annerén G, Bondeson ML

Eur J Med Genet 53 (3) 117-121 [2010-03-17; online 2010-03-17]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Global and unbiased detection of splice junctions from RNA-seq data.

Ameur A, Wetterbom A, Feuk L, Gyllensten U

Genome Biol. 11 (3) R34 [2010-03-17; online 2010-03-17]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

The sexually antagonistic genes of Drosophila melanogaster.

Innocenti P, Morrow EH

PLoS Biol. 8 (3) e1000335 [2010-03-16; online 2010-03-16]

The tryptophan hydroxylase 1 (TPH1) gene, schizophrenia susceptibility, and suicidal behavior: a multi-centre case-control study and meta-analysis.

Saetre P, Lundmark P, Wang A, ..., Terenius L, Jönsson EG

Am. J. Med. Genet. B Neuropsychiatr. Genet. 153B (2) 387-396 [2010-03-05; online 2009-06-16]

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

Association between methylenetetrahydrofolate reductase (MTHFR) C677T polymorphism and age of onset in schizophrenia.

Vares M, Saetre P, Deng H, ..., Terenius L, Jönsson EG

Am. J. Med. Genet. B Neuropsychiatr. Genet. 153B (2) 610-618 [2010-03-05; online 2009-09-12]

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

The impact of tissue fixatives on morphology and antibody-based protein profiling in tissues and cells.

Paavilainen L, Edvinsson A, Asplund A, ..., Pontén F, Wester K

J. Histochem. Cytochem. 58 (3) 237-246 [2010-03-00; online 2009-11-11]

Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species.

Künstner A, Wolf JB, Backström N, ..., Warren WC, Ellegren H

Mol. Ecol. 19 Suppl 1 (-) 266-276 [2010-03-00; online 2010-04-02]

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

Appearance of Cxcl10-expressing cell clusters is common for traumatic brain injury and neurodegenerative disorders.

Israelsson C, Bengtsson H, Lobell A, ..., Hillered L, Ebendal T

Eur. J. Neurosci. 31 (5) 852-863 [2010-03-00; online 2010-04-09]

Molecular profiling using tissue microarrays as a tool to identify predictive biomarkers in laryngeal cancer treated with radiotherapy.

PubMed

Holgersson G, Ekman S, Reizenstein J, ..., Hellström K, Bergström S

Cancer Genomics Proteomics 7 (1) 1-7 [2010-02-26; online 2010-02-26]

Gene-specific FACS sorting method for target selection in high-throughput amplicon sequencing.

Sandberg J, Neiman M, Ahmadian A, Lundeberg J

BMC Genomics 11 (-) 140 [2010-02-26; online 2010-02-26]

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

High-density linkage mapping and evolution of paralogs and orthologs in Salix and Populus.

Berlin S, Lagercrantz U, von Arnold S, Ost T, Rönnberg-Wästljung AC

BMC Genomics 11 (-) 129 [2010-02-23; online 2010-02-23]

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

Coffee consumption and CYP1A2 genotype in relation to bone mineral density of the proximal femur in elderly men and women: a cohort study.

Hallström H, Melhus H, Glynn A, ..., Syvänen AC, Michaëlsson K

Nutr Metab (Lond) 7 (-) 12 [2010-02-22; online 2010-02-22]

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

DNA methylation for subtype classification and prediction of treatment outcome in patients with childhood acute lymphoblastic leukemia.

Milani L, Lundmark A, Kiialainen A, ..., Lönnerholm G, Syvänen AC

Blood 115 (6) 1214-1225 [2010-02-11; online 2009-11-25]

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

SUMOylation mediates the nuclear translocation and signaling of the IGF-1 receptor.

Sehat B, Tofigh A, Lin Y, ..., Lagergren J, Larsson O

Sci Signal 3 (108) ra10 [2010-02-09; online 2010-02-09]

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

Sequence variation in SORL1 and dementia risk in Swedes.

Reynolds CA, Hong MG, Eriksson UK, ..., Bennet AM, Prince JA

Neurogenetics 11 (1) 139-142 [2010-02-00; online 2009-08-05]

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

Sensitive plasma protein analysis by microparticle-based proximity ligation assays.

Darmanis S, Nong RY, Hammond M, ..., Landegren U, Kamali-Moghaddam M

Mol. Cell Proteomics 9 (2) 327-335 [2010-02-00; online 2009-12-04]

PLA and Single Cell Proteomics

Schizosaccharomyces pombe genome-wide nucleosome mapping reveals positioning mechanisms distinct from those of Saccharomyces cerevisiae.

Lantermann AB, Straub T, Strålfors A, ..., Ekwall K, Korber P

Nat. Struct. Mol. Biol. 17 (2) 251-257 [2010-02-00; online 2010-01-31]

New genetic loci implicated in fasting glucose homeostasis and their impact on type 2 diabetes risk.

Dupuis J, Langenberg C, Prokopenko I, ..., Florez JC, Barroso I

Nat. Genet. 42 (2) 105-116 [2010-02-00; online 2010-01-19]

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

Infection of mast cells with live streptococci causes a toll-like receptor 2- and cell-cell contact-dependent cytokine and chemokine response.

Rönnberg E, Guss B, Pejler G

Infect. Immun. 78 (2) 854-864 [2010-02-00; online 2009-11-26]

Global gene expression analysis of rodent motor neurons following spinal cord injury associates molecular mechanisms with development of postinjury spasticity.

Wienecke J, Westerdahl AC, Hultborn H, Kiehn O, Ryge J

J. Neurophysiol. 103 (2) 761-778 [2010-02-00; online 2009-11-27]

Genetic variation in GIPR influences the glucose and insulin responses to an oral glucose challenge.

Saxena R, Hivert MF, Langenberg C, ..., Wareham NJ, Watanabe RM

Nat. Genet. 42 (2) 142-148 [2010-02-00; online 2010-01-19]

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

Genetic variants and disease-associated factors contribute to enhanced interferon regulatory factor 5 expression in blood cells of patients with systemic lupus erythematosus.

Feng D, Stone RC, Eloranta ML, ..., Rönnblom L, Barnes BJ

Arthritis Rheum. 62 (2) 562-573 [2010-02-00; online 2010-01-30]

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

Connective tissue growth factor is expressed in malignant cells of Hodgkin lymphoma but not in other mature B-cell lymphomas.

Birgersdotter A, Baumforth KR, Wei W, ..., Porwit A, Ernberg I

Am. J. Clin. Pathol. 133 (2) 271-280 [2010-02-00; online 2010-01-23]

Comparative protein profiling of serum and plasma using an antibody suspension bead array approach.

Schwenk JM, Igel U, Kato BS, ..., Uhlén M, Nilsson P

Proteomics 10 (3) 532-540 [2010-02-00; online 2009-12-03]

Affinity Proteomics Stockholm [Technology development]

Coexisting NRAS and BRAF mutations in primary familial melanomas with specific CDKN2A germline alterations.

Jovanovic B, Egyhazi S, Eskandarpour M, ..., Hayward NK, Hansson J

J. Invest. Dermatol. 130 (2) 618-620 [2010-02-00; online 2009-09-18]

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

Genetic and biochemical studies of SNPs of the mitochondrial A beta-degrading protease, hPreP.

Pinho CM, Björk BF, Alikhani N, ..., Glaser E, Graff C

Neurosci. Lett. 469 (2) 204-208 [2010-01-22; online 2009-12-08]

Differential genome-wide array-based methylation profiles in prognostic subsets of chronic lymphocytic leukemia.

Kanduri M, Cahill N, Göransson H, ..., Isaksson A, Rosenquist R

Blood 115 (2) 296-305 [2010-01-14; online 2009-11-10]

Array and Analysis Facility NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Association study of PDE4B gene variants in Scandinavian schizophrenia and bipolar disorder multicenter case-control samples.

Kähler AK, Otnaess MK, Wirgenes KV, ..., Andreassen OA, Djurovic S

Am. J. Med. Genet. B Neuropsychiatr. Genet. 153B (1) 86-96 [2010-01-05; online 2009-04-08]

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

A computational screen for site selective A-to-I editing detects novel sites in neuron specific Hu proteins.

Ensterö M, Akerborg O, Lundin D, ..., Ohman M, Lagergren J

BMC Bioinformatics 11 (-) 6 [2010-01-04; online 2010-01-04]

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

The 2009 Nobel conference on the role of genetics in promoting suicide prevention and the mental health of the population.

Wasserman D, Terenius L, Wasserman J, Sokolowski M

Mol. Psychiatry 15 (1) 12-17 [2010-01-00; online 2009-12-24]

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

Large but not small copy-number alterations correlate to high-risk genomic aberrations and survival in chronic lymphocytic leukemia: a high-resolution genomic screening of newly diagnosed patients.

Gunnarsson R, Isaksson A, Mansouri M, ..., Juliusson G, Rosenquist R

Leukemia 24 (1) 211-215 [2010-01-00; online 2009-09-11]

Characterization of the cytotoxic properties of the benzimidazole fungicides, benomyl and carbendazim, in human tumour cell lines and primary cultures of patient tumour cells.

Laryea D, Gullbo J, Isaksson A, Larsson R, Nygren P

Anticancer Drugs 21 (1) 33-42 [2010-01-00; online 2009-09-30]