Publications 2011

Identification of immunogenic proteins in Treponema phagedenis-like strain V1 from digital dermatitis lesions by phage display.

Rosander A, Guss B, Frykberg L, ..., Näslund K, Pringle M

pii: S0378-1135(11)00333-6

Vet. Microbiol. 153 (3-4) 315-322 [2011-12-15; online 2011-07-19]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Polymorphisms in B3GAT1, SLC9A9 and MGAT5 are associated with variation within the human plasma N-glycome of 3533 European adults.

Huffman JE, Knezevic A, Vitart V, ..., Wright AF, Lauc G

pii: ddr414

Hum. Mol. Genet. 20 (24) 5000-5011 [2011-12-15; online 2011-09-13]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

The inner nuclear membrane proteins Man1 and Ima1 link to two different types of chromatin at the nuclear periphery in S. pombe.

Steglich B, Filion GJ, van Steensel B, Ekwall K

pii: 18825

Nucleus 3 (1) 77-87 [2011-12-14; online 2011-12-14]

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

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]

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

Common variants of the BRCA1 wild-type allele modify the risk of breast cancer in BRCA1 mutation carriers.

Cox DG, Simard J, Sinnett D, ..., Sinilnikova OM, Consortium of Investigators of Modifiers of BRCA1/2

pii: ddr388 pmc: PMC3733139

Hum. Mol. Genet. 20 (23) 4732-4747 [2011-12-01; online 2011-09-06]

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

Pathway-based analysis of genetic susceptibility to cervical cancer in situ: HLA-DPB1 affects risk in Swedish women.

Ivansson EL, Juko-Pecirep I, Erlich HA, Gyllensten UB

pii: gene201140

Genes Immun. 12 (8) 605-614 [2011-12-00; online 2011-07-01]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Salt-inducible kinase 1 influences Na(+),K(+)-ATPase activity in vascular smooth muscle cells and associates with variations in blood pressure.

Popov S, Silveira A, Wågsäter D, ..., Melander O, Bertorello AM

J. Hypertens. 29 (12) 2395-2403 [2011-12-00; online 2011-11-03]

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]

A complex genomic rearrangement involving the endothelin 3 locus causes dermal hyperpigmentation in the chicken.

Dorshorst B, Molin A, Rubin C, ..., Ashwell C, Andersson L

pii: PGENETICS-D-11-01394 pmc: PMC3245302

PLoS Genet. 7 (12) e1002412 [2011-12-00; online 2011-12-22]

NGI Uppsala (Uppsala Genome Center) 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

pii: PONE-D-11-11581 pmc: PMC3227566

PLoS ONE 6 (11) e26039 [2011-11-30; online 2011-11-30]

Chemical Biology Consortium Sweden (CBCS) [Service]

Next-generation sequencing technologies and applications for human genetic history and forensics.

Berglund EC, Kiialainen A, Syvänen AC

pii: 2041-2223-2-23 pmc: PMC3267688

Investig Genet 2 (-) 23 [2011-11-24; online 2011-11-24]

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

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)

Prognostic DNA methylation patterns in cytogenetically normal acute myeloid leukemia are predefined by stem cell chromatin marks.

Deneberg S, Guardiola P, Lennartsson A, ..., Döhner K, Lehmann S

pii: blood-2011-01-332353

Blood 118 (20) 5573-5582 [2011-11-17; online 2011-10-01]

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

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

Abdominal aortic aneurysm is associated with a variant in low-density lipoprotein receptor-related protein 1.

Bown MJ, Jones GT, Harrison SC, ..., Deloukas P, Samani NJ

pii: S0002-9297(11)00436-8 pmc: PMC3213391

Am. J. Hum. Genet. 89 (5) 619-627 [2011-11-11; online 2011-11-08]

NGI Uppsala (SNP&SEQ Technology Platform) 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]

Total RNA sequencing reveals nascent transcription and widespread co-transcriptional splicing in the human brain.

Ameur A, Zaghlool A, Halvardson J, ..., Cavelier L, Feuk L

pii: nsmb.2143

Nat. Struct. Mol. Biol. 18 (12) 1435-1440 [2011-11-06; online 2011-11-06]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

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]

SWI/SNF regulates the alternative processing of a specific subset of pre-mRNAs in Drosophila melanogaster.

Waldholm J, Wang Z, Brodin D, ..., Farrants AK, Visa N

pii: 1471-2199-12-46 pmc: PMC3221629

BMC Mol. Biol. 12 (-) 46 [2011-11-02; online 2011-11-02]

Abundant class of non-coding RNA regulates development in the social amoeba Dictyostelium discoideum.

Avesson L, Schumacher HT, Fechter P, ..., Hellman U, Söderbom F

pii: 17214

RNA Biol 8 (6) 1094-1104 [2011-11-01; online 2011-09-24]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

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

Targeted enrichment of genomic DNA regions for next-generation sequencing.

Mertes F, Elsharawy A, Sauer S, ..., Lehrach H, Brookes AJ

pii: elr033 pmc: PMC3245553

Brief Funct Genomics 10 (6) 374-386 [2011-11-00; online 2011-11-26]

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

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]

The Human Protein Atlas as a proteomic resource for biomarker discovery.

Pontén F, Schwenk JM, Asplund A, Edqvist PD

J. Intern. Med. 270 (5) 428-446 [2011-11-00; online 2011-07-15]

Plasma Profiling [Technology development] Tissue Profiling

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

Generation of monospecific antibodies based on affinity capture of polyclonal antibodies.

Hjelm B, Forsström B, Igel U, ..., Johansson C, Uhlén M

pmc: PMC3267947

Protein Sci. 20 (11) 1824-1835 [2011-11-00; online 2011-09-08]

Autoimmunity Profiling [Technology development] Cell Profiling Plasma Profiling [Technology development]

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]

Genome-wide association study identifies loci influencing concentrations of liver enzymes in plasma.

Chambers JC, Zhang W, Sehmi J, ..., Elliott P, Kooner JS

pii: ng.970 pmc: PMC3482372 mid: NIHMS411128

Nat. Genet. 43 (11) 1131-1138 [2011-10-16; online 2011-10-16]

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

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)

Deep resequencing of GWAS loci identifies independent rare variants associated with inflammatory bowel disease.

Rivas MA, Beaudoin M, Gardet A, ..., Xavier RJ, Daly MJ

pii: ng.952 pmc: PMC3378381 mid: NIHMS335188

Nat. Genet. 43 (11) 1066-1073 [2011-10-09; online 2011-10-09]

Pseudoceramines A-D, new antibacterial bromotyrosine alkaloids from the marine sponge Pseudoceratina sp.

Yin S, Davis RA, Shelper T, ..., Sundin C, Quinn RJ

Org. Biomol. Chem. 9 (19) 6755-6760 [2011-10-07; online 2011-08-19]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Adenosine kinase deficiency disrupts the methionine cycle and causes hypermethioninemia, encephalopathy, and abnormal liver function.

Bjursell MK, Blom HJ, Cayuela JA, ..., Lundeberg J, Wedell A

pii: S0002-9297(11)00394-6 pmc: PMC3188832

Am. J. Hum. Genet. 89 (4) 507-515 [2011-10-07; online 2011-10-04]

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

Genetic variation in complement component C3 shows association with ischaemic stroke.

Olsson S, Stokowska A, Holmegaard L, ..., Pekna M, Jern C

Eur. J. Neurol. 18 (10) 1272-1274 [2011-10-00; online 2011-03-19]

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

Evidence for involvement of Dicer-like, Argonaute and histone deacetylase proteins in gene silencing in Phytophthora infestans.

Vetukuri RR, Avrova AO, Grenville-Briggs LJ, ..., Whisson SC, Dixelius C

Mol. Plant Pathol. 12 (8) 772-785 [2011-10-00; online 2011-07-06]

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

DOI Crossref

Tracking Phytophthora infestans with SSR markers within and between seasons - a field study in Sweden

Widmark AK, Andersson B, Sandström M, Yuen JE

Plant Pathol 60 (5) 938-945 [2011-10-00; online 2011-03-16]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

No evidence for an association between genetic variation at the SERPINI1 locus and ischemic stroke.

Tjärnlund-Wolf A, Olsson S, Jood K, Blomstrand C, Jern C

J. Neurol. 258 (10) 1885-1887 [2011-10-00; online 2011-04-14]

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

Early transcriptional regulation by C-peptide in freshly isolated rat proximal tubular cells.

Lindahl E, Nordquist L, Müller P, ..., Palm F, Jörnvall H

Diabetes Metab. Res. Rev. 27 (7) 697-704 [2011-10-00; online 2011-05-28]

Genome-wide association identifies nine common variants associated with fasting proinsulin levels and provides new insights into the pathophysiology of type 2 diabetes.

Strawbridge RJ, Dupuis J, Prokopenko I, ..., Hamsten A, Florez JC

pii: db11-0415 pmc: PMC3178302

Diabetes 60 (10) 2624-2634 [2011-10-00; online 2011-08-30]

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

High-risk HPV infection and CIN grade correlates to the expression of c-myc, CD4+, FHIT, E-cadherin, Ki-67, and p16INK4a.

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

J Low Genit Tract Dis 15 (4) 280-286 [2011-10-00; online 2011-05-12]

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]

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

High RBM3 expression in prostate cancer independently predicts a reduced risk of biochemical recurrence and disease progression.

Jonsson L, Gaber A, Ulmert D, ..., Bjartell A, Jirström K

pii: 1746-1596-6-91 pmc: PMC3195697

Diagn Pathol 6 (-) 91 [2011-09-28; online 2011-09-28]

Genome-wide association study identifies six new loci influencing pulse pressure and mean arterial pressure.

Wain LV, Verwoert GC, O'Reilly PF, ..., Elliott P, van Duijn CM

pii: ng.922 pmc: PMC3445021 mid: NIHMS316759

Nat. Genet. 43 (10) 1005-1011 [2011-09-11; online 2011-09-11]

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

Engineering GST M2-2 for high activity with indene 1,2-oxide and indication of an H-site residue sustaining catalytic promiscuity.

Norrgård MA, Mannervik B

pii: S0022-2836(11)00804-7

J. Mol. Biol. 412 (1) 111-120 [2011-09-09; online 2011-08-09]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

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]

Transcriptional profiling of C. elegans DAF-19 uncovers a ciliary base-associated protein and a CDK/CCRK/LF2p-related kinase required for intraflagellar transport.

Phirke P, Efimenko E, Mohan S, ..., Leroux MR, Swoboda P

pii: S0012-1606(11)01088-8 pmc: PMC3888451 mid: NIHMS540805

Dev. Biol. 357 (1) 235-247 [2011-09-01; online 2011-07-12]

Genomic and clinical characteristics of six patients with partially overlapping interstitial deletions at 10p12p11.

Wentzel C, Rajcan-Separovic E, Ruivenkamp CA, ..., Giurgea I, Thuresson AC

pii: ejhg201171 pmc: PMC3179368

Eur. J. Hum. Genet. 19 (9) 959-964 [2011-09-00; online 2011-04-28]

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

Dystrobrevin-binding protein 1 gene (DTNBP1) variants associated with cerebrospinal fluid homovanillic acid and 5-hydroxyindoleacetic acid concentrations in healthy volunteers.

Andreou D, Saetre P, Kähler AK, ..., Terenius L, Jönsson EG

pii: S0924-977X(11)00004-6

Eur Neuropsychopharmacol 21 (9) 700-704 [2011-09-00; online 2011-02-08]

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

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

Structural features determining the intestinal epithelial permeability and efflux of novel HIV-1 protease inhibitors.

Lazorova L, Hubatsch I, Ekegren JK, ..., Larhed M, Artursson P

pmc: PMC3210832 pii: S0022-3549(15)31944-4

J Pharm Sci 100 (9) 3763-3772 [2011-09-00; online 2011-04-15]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Large-scale gene-centric analysis identifies novel variants for coronary artery disease.

IBC 50K CAD Consortium N

pmc: PMC3178591

PLoS Genet. 7 (9) e1002260 [2011-09-00; online 2011-09-22]

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

Total zinc intake may modify the glucose-raising effect of a zinc transporter (SLC30A8) variant: a 14-cohort meta-analysis.

Kanoni S, Nettleton JA, Hivert MF, ..., Franks PW, Dedoussis GV

pii: db11-0176 pmc: PMC3161318

Diabetes 60 (9) 2407-2416 [2011-09-00; online 2011-08-04]

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

Combinations of SNPs related to signal transduction in bipolar disorder.

Koefoed P, Andreassen OA, Bennike B, ..., Werge T, Mellerup E

pii: 10-PONE-RA-20023 pmc: PMC3163586

PLoS ONE 6 (8) e23812 [2011-08-29; online 2011-08-29]

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

Identification of Bacterial Target Proteins for the Salicylidene Acylhydrazide Class of Virulence-blocking Compounds

Wang D, Zetterström CE, Gabrielsen M, ..., Elofsson M, Roe AJ

J. Biol. Chem. 286 (34) 29922-29931 [2011-08-26; online 2011-07-01]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Changes in the acetogenic population in a mesophilic anaerobic digester in response to increasing ammonia concentration.

Westerholm M, Müller B, Arthurson V, Schnürer A

pii: JST.JSTAGE/jsme2/ME11123 GENBANK: HM365334 GENBANK: HM365335 GENBANK: HM365336 GENBANK: HM365337 GENBANK: HM365339 GENBANK: HM365340 GENBANK: HQ156223

Microbes Environ. 26 (4) 347-353 [2011-08-24; online 2011-08-24]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Identification of cis- and trans-acting genetic variants explaining up to half the variation in circulating vascular endothelial growth factor levels.

Debette S, Visvikis-Siest S, Chen MH, ..., Vasan RS, Seshadri S

pii: CIRCRESAHA.111.243790 pmc: PMC3193930 mid: NIHMS315529

Circ. Res. 109 (5) 554-563 [2011-08-19; online 2011-07-16]

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

Characterization of a 8q21.11 microdeletion syndrome associated with intellectual disability and a recognizable phenotype.

Palomares M, Delicado A, Mansilla E, ..., Hennekam RC, Lapunzina P

pii: S0002-9297(11)00266-7 pmc: PMC3155189

Am. J. Hum. Genet. 89 (2) 295-301 [2011-08-12; online 2011-08-02]

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

pii: nature10251 pmc: PMC3182531 mid: UKMS36028

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]

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

Complete genome sequence of Brachyspira intermedia reveals unique genomic features in Brachyspira species and phage-mediated horizontal gene transfer.

Håfström T, Jansson DS, Segerman B

pii: 1471-2164-12-395 pmc: PMC3163572

BMC Genomics 12 (-) 395 [2011-08-04; online 2011-08-04]

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

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]

Evaluation of Fanconi anaemia genes FANCA, FANCC and FANCL in cervical cancer susceptibility.

Juko-Pecirep I, Ivansson EL, Gyllensten UB

pii: S0090-8258(11)00276-9

Gynecol. Oncol. 122 (2) 377-381 [2011-08-00; online 2011-05-06]

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

Array-based genomic screening at diagnosis and during follow-up in chronic lymphocytic leukemia.

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

pii: haematol.2010.039768 pmc: PMC3148910

Haematologica 96 (8) 1161-1169 [2011-08-00; online 2011-05-07]

Array and Analysis Facility NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

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

Gene-environment interactions between CRHR1 variants and physical assault in suicide attempts.

Ben-Efraim YJ, Wasserman D, Wasserman J, Sokolowski M

Genes Brain Behav. 10 (6) 663-672 [2011-08-00; online 2011-05-25]

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

Hyphae-colonizing Burkholderia sp.--a new source of biological control agents against sheath blight disease (Rhizoctonia solani AG1-IA) in rice.

Cuong ND, Nicolaisen MH, Sørensen J, Olsson S

Microb. Ecol. 62 (2) 425-434 [2011-08-00; online 2011-03-03]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

The short non-coding transcriptome of the protozoan parasite Trypanosoma cruzi.

Franzén O, Arner E, Ferella M, ..., Andersson B, Daub CO

pii: PNTD-D-11-00417 pmc: PMC3166047

PLoS Negl Trop Dis 5 (8) e1283 [2011-08-00; online 2011-08-30]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Correlation between LRIG1 and LRIG2 expressions and expression of 11 tumor markers, with special reference to tumor suppressors, in CIN and normal cervical epithelium.

Lindström AK, Asplund A, Hellberg D

pii: S0090-8258(11)00350-7

Gynecol. Oncol. 122 (2) 372-376 [2011-08-00; online 2011-06-03]

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

Antimicrobial susceptibility of Brachyspira spp. isolated from commercial laying hens and free-living wild mallards (Anas platyrhynchos).

Jansson DS, Pringle M

Avian Pathol. 40 (4) 387-393 [2011-08-00; online 2011-08-05]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

PubMed

RBM3-regulated genes promote DNA integrity and affect clinical outcome in epithelial ovarian cancer.

Ehlén Å, Nodin B, Rexhepaj E, ..., Brennan DJ, Jirström K

pmc: PMC3140008

Transl Oncol 4 (4) 212-221 [2011-08-00; online 2011-08-01]

Performance of ultra-deep pyrosequencing in analysis of HIV-1 pol gene variation.

Mild M, Hedskog C, Jernberg J, Albert J

pii: PONE-D-11-01646 pmc: PMC3143174

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

pii: PONE-D-11-06066 pmc: PMC3142133

PLoS ONE 6 (7) e22250 [2011-07-22; online 2011-07-22]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Low RBM3 protein expression correlates with tumour progression and poor prognosis in malignant melanoma: an analysis of 215 cases from the Malmö Diet and Cancer Study.

Jonsson L, Bergman J, Nodin B, ..., Uhlén M, Jirström K

pii: 1479-5876-9-114 pmc: PMC3156749

J Transl Med 9 (-) 114 [2011-07-21; online 2011-07-21]

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

pii: PONE-D-10-04087 pmc: PMC3137612

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

pii: PONE-D-11-00159 pmc: PMC3131396

PLoS ONE 6 (7) e21910 [2011-07-07; online 2011-07-07]

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

Identification of noncoding transcripts from within CENP-A chromatin at fission yeast centromeres.

Choi ES, Strålfors A, Castillo AG, ..., Ekwall K, Allshire RC

pii: M111.228510 pmc: PMC3123123

J. Biol. Chem. 286 (26) 23600-23607 [2011-07-01; online 2011-05-03]

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

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

Species sorting and neutral processes are both important during the initial assembly of bacterial communities.

Langenheder S, Székely AJ

pii: ismej2010207 pmc: PMC3146284

ISME J 5 (7) 1086-1094 [2011-07-00; online 2011-01-29]

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

Genetic architecture of circulating lipid levels.

Demirkan A, Amin N, Isaacs A, ..., van Duijn CM, ENGAGE CONSORTIUM

pii: ejhg201121 pmc: PMC3137496

Eur. J. Hum. Genet. 19 (7) 813-819 [2011-07-00; online 2011-03-30]

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

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]

Replication and explorations of high-order epistasis using a large advanced intercross line pedigree.

Pettersson M, Besnier F, Siegel PB, Carlborg O

pii: PGENETICS-D-10-00335 pmc: PMC3140984

PLoS Genet. 7 (7) e1002180 [2011-07-00; online 2011-07-21]

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

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]

Genome wide association study identifies KCNMA1 contributing to human obesity.

Jiao H, Arner P, Hoffstedt J, ..., Clement K, Dahlman I

pii: 1755-8794-4-51 pmc: PMC3148553

BMC Med Genomics 4 (-) 51 [2011-06-28; online 2011-06-28]

Bioinformatics and Expression Analysis (BEA) Mutation Analysis Facility (MAF) NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Genetic variation near IRS1 associates with reduced adiposity and an impaired metabolic profile.

Kilpeläinen TO, Zillikens MC, Stančákova A, ..., Laakso M, Loos RJ

pii: ng.866 pmc: PMC3262230 mid: NIHMS329020

Nat. Genet. 43 (8) 753-760 [2011-06-26; online 2011-06-26]

NGI Uppsala (SNP&SEQ Technology Platform) 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

pii: 10-PONE-RA-19265R1-CORRECTION pmc: PMC3121713

PLoS ONE 6 (6) e14816 [2011-06-23; online 2011-06-23]

KIT pathway alterations in mucosal melanomas of the vulva and other sites.

Omholt K, Grafström E, Kanter-Lewensohn L, Hansson J, Ragnarsson-Olding BK

pii: 17/12/3933

Clin. Cancer Res. 17 (12) 3933-3942 [2011-06-15; online 2011-06-18]

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

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

pii: PONE-D-11-04237 pmc: PMC3115972

PLoS ONE 6 (6) e20794 [2011-06-15; online 2011-06-15]

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

(R,S)-dichlorprop herbicide in agricultural soil induces proliferation and expression of multiple dioxygenase-encoding genes in the indigenous microbial community.

Paulin MM, Nicolaisen MH, Sørensen J

GENBANK: HQ009355 GENBANK: HQ009356 GENBANK: HQ009357 GENBANK: HQ009358 GENBANK: HQ009359 GENBANK: HQ009360 GENBANK: HQ009361 GENBANK: HQ009362 GENBANK: HQ009363 GENBANK: HQ009364 GENBANK: HQ009365 GENBANK: HQ009366 GENBANK: HQ009367 GENBANK: HQ009368 GENBANK: HQ009369 GENBANK: HQ009370 GENBANK: HQ009371 GENBANK: HQ009372 GENBANK: HQ009373 GENBANK: HQ009374 GENBANK: HQ009375 GENBANK: HQ009376 GENBANK: HQ009377 GENBANK: HQ009378 GENBANK: HQ009379 GENBANK: HQ009380 GENBANK: HQ009381 GENBANK: HQ009382 GENBANK: HQ009383 GENBANK: HQ009384 GENBANK: HQ009385 GENBANK: HQ009386 GENBANK: HQ009387 GENBANK: HQ009388 GENBANK: HQ009389 GENBANK: HQ009390 GENBANK: HQ009391 GENBANK: HQ009392 GENBANK: HQ009393 GENBANK: HQ009394 GENBANK: HQ009395 GENBANK: HQ009396 GENBANK: HQ009397 GENBANK: HQ009398

Environ. Microbiol. 13 (6) 1513-1523 [2011-06-00; online 2011-03-23]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Genetic association and gene expression analysis identify FGFR1 as a new susceptibility gene for human obesity.

Jiao H, Arner P, Dickson SL, ..., Clement K, Dahlman I

pii: jc.2010-2639

J. Clin. Endocrinol. Metab. 96 (6) E962-E966 [2011-06-00; online 2011-03-25]

Bioinformatics and Expression Analysis (BEA) Mutation Analysis Facility (MAF) NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

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

Cytochrome P450 1A, 1B, and 1C mRNA induction patterns in three-spined stickleback exposed to a transient and a persistent inducer.

Gao K, Brandt I, Goldstone JV, Jönsson ME

pii: S1532-0456(11)00021-4 pmc: PMC3560405 mid: NIHMS278245

Comp. Biochem. Physiol. C Toxicol. Pharmacol. 154 (1) 42-55 [2011-06-00; online 2011-03-01]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Feather pecking behavior in laying hens: hypothalamic gene expression in birds performing and receiving pecks.

Brunberg E, Jensen P, Isaksson A, Keeling L

pii: 90/6/1145

Poult. Sci. 90 (6) 1145-1152 [2011-06-00; online 2011-05-21]

Co-occurring SHOC2 and PTPN11 mutations in a patient with severe/complex Noonan syndrome-like phenotype.

Ekvall S, Hagenäs L, Allanson J, Annerén G, Bondeson ML

Am. J. Med. Genet. A 155A (6) 1217-1224 [2011-06-00; online 2011-05-07]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Tepidanaerobacter acetatoxydans sp. nov., an anaerobic, syntrophic acetate-oxidizing bacterium isolated from two ammonium-enriched mesophilic methanogenic processes.

Westerholm M, Roos S, Schnürer A

pii: S0723-2020(11)00014-2 GENBANK: HQ290074 GENBANK: HQ290075 GENBANK: HQ290076 GENBANK: HQ290077

Syst. Appl. Microbiol. 34 (4) 260-266 [2011-06-00; online 2011-04-19]

NGI Uppsala (Uppsala Genome Center) 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

pii: PONE-D-11-00770 pmc: PMC3103532

PLoS ONE 6 (5) e20158 [2011-05-27; online 2011-05-27]

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

Sequence and generation of mature ribosomal RNA transcripts in Dictyostelium discoideum.

Boesler C, Kruse J, Söderbom F, Hammann C

pii: M110.208306 pmc: PMC3093845 GENBANK: FR733593 GENBANK: FR733594 GENBANK: FR733595 GENBANK: FR733596 GENBANK: FR733598 GENBANK: FR733599 GENBANK: FR733600

J. Biol. Chem. 286 (20) 17693-17703 [2011-05-20; online 2011-04-02]

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

A roadmap to generate renewable protein binders to the human proteome.

Colwill K, Renewable Protein Binder Working Group , Gräslund S

pii: nmeth.1607

Nat. Methods 8 (7) 551-558 [2011-05-15; online 2011-05-15]

Autoimmunity Profiling [Technology development] Plasma Profiling [Technology development]

Cardio-facio-cutaneous syndrome: does genotype predict phenotype?

Allanson JE, Annerén G, Aoki Y, ..., Verloes A, Zenker M

pmc: PMC3086095 mid: NIHMS282899

Am J Med Genet C Semin Med Genet 157C (2) 129-135 [2011-05-15; online 2011-04-16]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Experimental evidence supports a sex-specific selective sieve in mitochondrial genome evolution.

Innocenti P, Morrow EH, Dowling DK

pii: 332/6031/845 GEO: GSE24729

Science 332 (6031) 845-848 [2011-05-13; online 2011-05-14]

Cys-X scanning for expansion of active-site residues and modulation of catalytic functions in a glutathione transferase.

Norrgård MA, Hellman U, Mannervik B

pii: M111.230078 pmc: PMC3089530

J. Biol. Chem. 286 (19) 16871-16878 [2011-05-13; online 2011-04-02]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Methods for Analysis of Transcription Factor DNA-Binding Specificity In Vitro.

Jolma A, Taipale J

Subcell. Biochem. 52 (-) 155-173 [2011-05-11; online 2011-05-11]

Karolinska High Throughput Center (KHTC)

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]

Melanoma cells produce multiple laminin isoforms and strongly migrate on α5 laminin(s) via several integrin receptors.

Oikawa Y, Hansson J, Sasaki T, ..., Tryggvason K, Patarroyo M

pii: S0014-4827(10)00577-X

Exp. Cell Res. 317 (8) 1119-1133 [2011-05-01; online 2011-01-05]

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

Characterization of NPY Y2 receptor protein expression in the mouse brain. II. Coexistence with NPY, the Y1 receptor, and other neurotransmitter-related molecules.

Stanić D, Mulder J, Watanabe M, Hökfelt T

J. Comp. Neurol. 519 (7) 1219-1257 [2011-05-01; online 2011-04-01]

Fluorescence Tissue Profiling

Directional genetic selection by pulp mill effluent on multiple natural populations of three-spined stickleback (Gasterosteus aculeatus).

Lind EE, Grahn M

pmc: PMC3081435

Ecotoxicology 20 (3) 503-512 [2011-05-00; online 2011-04-02]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

The 12q14 microdeletion syndrome: six new cases confirming the role of HMGA2 in growth.

Lynch SA, Foulds N, Thuresson AC, ..., Ennis S, Sharkey F

pii: ejhg2010215 pmc: PMC3083609

Eur. J. Hum. Genet. 19 (5) 534-539 [2011-05-00; online 2011-01-27]

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

Parental criticism and externalizing behavior problems in adolescents: the role of environment and genotype-environment correlation.

Narusyte J, Neiderhiser JM, Andershed AK, ..., Ganiban J, Lichtenstein P

pii: 2011-01600-001 pmc: PMC3093313 mid: NIHMS289298

J Abnorm Psychol 120 (2) 365-376 [2011-05-00; online 2011-02-02]

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

pii: PONE-D-11-00451 pmc: PMC3084785

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

pii: PONE-D-10-05646 pmc: PMC3083417

PLoS ONE 6 (4) e19119 [2011-04-27; online 2011-04-27]

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

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

Structure and assembly-disassembly properties of wild-type transthyretin amyloid protofibrils observed with atomic force microscopy.

Pires RH, Saraiva MJ, Damas AM, Kellermayer MS

J. Mol. Recognit. 24 (3) 467-476 [2011-04-20; online 2011-04-20]

Mass Spectrometry-based Proteomics, Uppsala

Clostridium botulinum group III: a group with dual identity shaped by plasmids, phages and mobile elements.

Skarin H, Håfström T, Westerberg J, Segerman B

pii: 1471-2164-12-185 pmc: PMC3098183

BMC Genomics 12 (-) 185 [2011-04-12; online 2011-04-12]

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

Synthesis and application of a bromomethyl substituted scaffold to be used for efficient optimization of anti-virulence activity.

Chorell E, Bengtsson C, Sainte-Luce Banchelin T, ..., Hultgren SJ, Almqvist F

pii: S0223-5234(11)00045-6 pmc: PMC3694777 mid: NIHMS295032

Eur J Med Chem 46 (4) 1103-1116 [2011-04-00; online 2011-02-15]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

A candidate gene study of the type I interferon pathway implicates IKBKE and IL8 as risk loci for SLE.

Sandling JK, Garnier S, Sigurdsson S, ..., Rönnblom L, Syvänen AC

pii: ejhg2010197 pmc: PMC3060320

Eur. J. Hum. Genet. 19 (4) 479-484 [2011-04-00; online 2010-12-24]

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

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]

FATP4 missense and nonsense mutations cause similar features in Ichthyosis Prematurity Syndrome.

Sobol M, Dahl N, Klar J

pii: 1756-0500-4-90 pmc: PMC3072334

BMC Res Notes 4 (-) 90 [2011-03-30; online 2011-03-30]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Human oral, gut, and plaque microbiota in patients with atherosclerosis.

Koren O, Spor A, Felin J, ..., Ley RE, Bäckhed F

pii: 1011383107 pmc: PMC3063583

Proc. Natl. Acad. Sci. U.S.A. 108 Suppl 1 (-) 4592-4598 [2011-03-15; online 2010-10-13]

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

pmc: PMC3056661

PLoS ONE 6 (3) e14757 [2011-03-14; online 2011-03-14]

An assessment of CETP sequence variation in relation to cognitive decline and dementia risk.

PubMed

Reynolds CA, Gatz M, Pedersen NL, Prince JA

pmc: PMC3110386

Int J Mol Epidemiol Genet 2 (2) 122-129 [2011-03-10; online 2011-03-10]

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

Decoding a substantial set of samples in parallel by massive sequencing.

Neiman M, Lundin S, Savolainen P, Ahmadian A

pmc: PMC3052374

PLoS ONE 6 (3) e17785 [2011-03-09; online 2011-03-09]

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

A genome-wide association study in Europeans and South Asians identifies five new loci for coronary artery disease.

Coronary Artery Disease (C4D) Genetics Consortium

pii: ng.782

Nat. Genet. 43 (4) 339-344 [2011-03-06; online 2011-03-06]

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

Antibody suspension bead arrays.

Schwenk JM, Nilsson P

Methods Mol. Biol. 723 (-) 29-36 [2011-03-04; online 2011-03-04]

Plasma Profiling [Technology development]

Bioinformatic tools for using whole genome sequencing as a rapid high resolution diagnostic typing tool when tracing bioterror organisms in the food and feed chain.

Segerman B, De Medici D, Ehling Schulz M, ..., Van Rotterdam B, Knutsson R

pii: S0168-1605(10)00369-7

Int. J. Food Microbiol. 145 Suppl 1 (-) S167-S176 [2011-03-01; online 2010-09-10]

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

Association of EBF1, FAM167A(C8orf13)-BLK and TNFSF4 gene variants with primary Sjögren's syndrome.

Nordmark G, Kristjansdottir G, Theander E, ..., Jonsson R, Syvänen AC

pii: gene201044

Genes Immun. 12 (2) 100-109 [2011-03-00; online 2010-09-24]

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

Ultra-deep sequencing of mouse mitochondrial DNA: mutational patterns and their origins.

Ameur A, Stewart JB, Freyer C, ..., Larsson N, Gyllensten U

pmc: PMC3063763

PLoS Genet. 7 (3) e1002028 [2011-03-00; online 2011-03-24]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

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

A novel unstable duplication upstream of HAS2 predisposes to a breed-defining skin phenotype and a periodic fever syndrome in Chinese Shar-Pei dogs.

Olsson M, Meadows JRS, Truvé K, ..., Tintle L, Lindblad-Toh K

pmc: PMC3060080

PLoS Genet. 7 (3) e1001332 [2011-03-00; online 2011-03-17]

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

Genome-wide association analysis identifies variants associated with nonalcoholic fatty liver disease that have distinct effects on metabolic traits.

Speliotes EK, Yerges-Armstrong LM, Wu J, ..., Borecki IB, GOLD Consortium

pmc: PMC3053321

PLoS Genet. 7 (3) e1001324 [2011-03-00; online 2011-03-10]

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

Systematic antibody and antigen-based proteomic profiling with microarrays.

Ayoglu B, Häggmark A, Neiman M, ..., Schwenk JM, Nilsson P

Expert Rev. Mol. Diagn. 11 (2) 219-234 [2011-03-00; online 2011-03-17]

Autoimmunity Profiling [Technology development] Plasma Profiling [Technology development]

Expression of 5,8-LDS of Aspergillus fumigatus and its dioxygenase domain. A comparison with 7,8-LDS, 10-dioxygenase, and cyclooxygenase.

Hoffmann I, Jernerén F, Garscha U, Oliw EH

pii: S0003-9861(10)00495-9

Arch. Biochem. Biophys. 506 (2) 216-222 [2011-02-15; online 2010-12-07]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Identification of epigenetically regulated genes that predict patient outcome in neuroblastoma.

Carén H, Djos A, Nethander M, ..., Nilsson S, Martinsson T

pii: 1471-2407-11-66 pmc: PMC3045360

BMC Cancer 11 (-) 66 [2011-02-11; online 2011-02-11]

NGI Uppsala (SNP&SEQ Technology Platform) 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

pmc: PMC3036585

PLoS ONE 6 (2) e16486 [2011-02-09; online 2011-02-09]

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

Genetic association of sequence variants near AGER/NOTCH4 and dementia.

Bennet AM, Reynolds CA, Eriksson UK, ..., Pedersen NL, Prince JA

pii: JRM32751N8163TL3 pmc: PMC3477600 mid: NIHMS404211

J. Alzheimers Dis. 24 (3) 475-484 [2011-02-08; online 2011-02-08]

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]

The Swedish new variant of Chlamydia trachomatis.

Unemo M, Clarke IN

Curr. Opin. Infect. Dis. 24 (1) 62-69 [2011-02-00; online 2010-12-16]

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

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]

Sun-induced nonsynonymous p53 mutations are extensively accumulated and tolerated in normal appearing human skin.

Ståhl PL, Stranneheim H, Asplund A, ..., Pontén F, Lundeberg J

pii: S0022-202X(15)35132-0

J. Invest. Dermatol. 131 (2) 504-508 [2011-02-00; online 2010-10-15]

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

Common pathogenetic mechanism involving human chromosome 18 in familial and sporadic ileal carcinoid tumors.

Cunningham JL, Díaz de Ståhl T, Sjöblom T, ..., Dumanski JP, Janson ET

Genes Chromosomes Cancer 50 (2) 82-94 [2011-02-00; online 2010-11-26]

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

Reactive astrocytes and Wnt/β-catenin signaling link nigrostriatal injury to repair in 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine model of Parkinson's disease.

L'Episcopo F, Tirolo C, Testa N, ..., Pluchino S, Marchetti B

pii: S0969-9961(10)00366-9 pmc: PMC3558878 mid: EMS51159

Neurobiol. Dis. 41 (2) 508-527 [2011-02-00; online 2010-11-09]

High-resolution genomic screening in mantle cell lymphoma--specific changes correlate with genomic complexity, the proliferation signature and survival.

Halldórsdóttir AM, Sander B, Göransson H, ..., Rosenquist R, Ehrencrona H

Genes Chromosomes Cancer 50 (2) 113-121 [2011-02-00; online 2010-12-01]

Array and Analysis Facility NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Genetic variation on chromosome 9p21 shows association with the ischaemic stroke subtype large-vessel disease in a Swedish sample aged ≤ 70.

Olsson S, Jood K, Blomstrand C, Jern C

pii: ENE3096

Eur. J. Neurol. 18 (2) 365-367 [2011-02-00; online 2010-05-27]

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

Tumor-specific HMG-CoA reductase expression in primary premenopausal breast cancer predicts response to tamoxifen.

Brennan DJ, Laursen H, O'Connor DP, ..., Rydén L, Jirström K

pii: bcr2820 pmc: PMC3109580

Breast Cancer Res. 13 (1) R12 [2011-01-31; online 2011-01-31]

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]

Fine mapping and replication of QTL in outbred chicken advanced intercross lines.

Besnier F, Wahlberg P, Rönnegård L, ..., Siegel PB, Carlborg O

pii: 1297-9686-43-3 pmc: PMC3034666

Genet. Sel. Evol. 43 (1) 3 [2011-01-17; online 2011-01-17]

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

New CYP1 genes in the frog Xenopus (Silurana) tropicalis: induction patterns and effects of AHR agonists during development.

Jönsson ME, Berg C, Goldstone JV, Stegeman JJ

pii: S0041-008X(10)00395-9 pmc: PMC3014448 mid: NIHMS247860

Toxicol. Appl. Pharmacol. 250 (2) 170-183 [2011-01-15; online 2010-10-23]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

A systems biology model of the regulatory network in Populus leaves reveals interacting regulators and conserved regulation.

Street NR, Jansson S, Hvidsten TR

pii: 1471-2229-11-13 pmc: PMC3030533

BMC Plant Biol. 11 (-) 13 [2011-01-13; online 2011-01-13]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

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]

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]

Targeted resequencing of candidate genes using selector probes.

Johansson H, Isaksson M, Sörqvist EF, ..., Ericsson O, Nilsson M

pii: gkq1005 pmc: PMC3025563

Nucleic Acids Res. 39 (2) e8 [2011-01-00; online 2010-11-10]

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

Structure and etiology of co-occurring internalizing and externalizing disorders in adolescents.

Cosgrove VE, Rhee SH, Gelhorn HL, ..., Young SE, Hewitt JK

pmc: PMC3036783 mid: NIHMS243833

J Abnorm Child Psychol 39 (1) 109-123 [2011-01-00; online 2010-08-05]