Publications 2011

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

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

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

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

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

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

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

PubMed

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

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

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

Muscle wasting and the temporal gene expression pattern in a novel rat intensive care unit model.

Llano-Diez M, Gustafson AM, ..., Goransson H, Larsson L

BMC Genomics 12 (-) 602 [2011-12-13; online 2011-12-13]

Blood pressure loci identified with a gene-centric array.

Johnson T, Gaunt TR, ..., Caulfield MJ, Munroe PB

Am. J. Hum. Genet. 89 (6) 688-700 [2011-12-09; online 2011-11-22]

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

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

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

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

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

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

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, ..., Melander O, Bertorello AM

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

High nuclear RBM3 expression is associated with an improved prognosis in colorectal cancer.

Hjelm B, Brennan DJ, ..., 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 AM, ..., Ashwell C, Andersson L

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

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

Targeting acetylcholinesterase: identification of chemical leads by high throughput screening, structure determination and molecular modeling.

Berg L, Andersson CD, ..., Linusson A, Ekström F

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

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

Berglund EC, Kiialainen A, Syvänen AC

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

Counting absolute numbers of molecules using unique molecular identifiers.

Kivioja T, Vähärautio A, ..., Linnarsson S, Taipale J

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, ..., Döhner K, Lehmann S

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

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

Genome sequencing reveals a phage in Helicobacter pylori.

Lehours P, Vale FF, ..., Engstrand L, Andersson AF

MBio 2 (6) - [2011-11-15; online 2011-11-15]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

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

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

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

A lateral flow protein microarray for rapid and sensitive antibody assays.

Gantelius J, Bass T, ..., Nilsson P, Andersson-Svahn H

Int J Mol Sci 12 (11) 7748-7759 [2011-11-09; online 2011-11-09]

Protein and peptide arrays

Inhibition of proteasome deubiquitinating activity as a new cancer therapy.

D'Arcy P, Brnjic S, ..., Larsson R, Linder S

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, ..., Cavelier L, Feuk L

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

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

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

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

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, ..., Hellman U, Söderbom F

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

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

Hypothalamic mitochondrial dysfunction associated with anorexia in the anx/anx mouse.

Lindfors C, Nilsson IA, ..., Schalling M, Johansen JE

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, ..., Lehrach H, Brookes AJ

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

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

Gene copy number aberrations are associated with survival in histologic subgroups of non-small cell lung cancer.

Micke P, Edlund K, ..., Isaksson A, Botling J

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 PH

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

Western blotting via proximity ligation for high performance protein analysis.

Liu Y, Gu J, ..., Ivansson D, Landegren U

Mol. Cell Proteomics 10 (11) O111.011031 [2011-11-00; online 2011-08-05]

PLA Proteomics

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

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

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

Cell Profiling Protein and peptide arrays

Increasing the dynamic range of in situ PLA.

Clausson CM, Allalou A, ..., Wählby C, Söderberg O

Nat. Methods 8 (11) 892-893 [2011-10-28; online 2011-10-28]

PLA Proteomics

Allele-specific copy number analysis of tumor samples with aneuploidy and tumor heterogeneity.

Rasmussen M, Sundström M, ..., Glimelius B, Isaksson A

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, ..., Elliott P, Kooner JS

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

MED12, the mediator complex subunit 12 gene, is mutated at high frequency in uterine leiomyomas.

Mäkinen N, Mehine M, ..., Vahteristo P, Aaltonen LA

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, ..., Xavier RJ, Daly MJ

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, ..., Sundin C, Quinn RJ

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

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

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

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

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

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

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

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

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

Vetukuri RR, Avrova AO, ..., 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)

Fibroblast growth factor 10 haploinsufficiency causes chronic obstructive pulmonary disease.

Klar J, Blomstrand P, ..., Bergendal B, Dahl N

J. Med. Genet. 48 (10) 705-709 [2011-10-00; online 2011-07-12]

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

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]

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

Tjärnlund-Wolf A, Olsson S, ..., Blomstrand C, Jern C

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

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

Lindahl E, Nordquist L, ..., 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, ..., Hamsten A, Florez JC

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

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, ..., 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, ..., Gustafsson CM, Myers LC

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, ..., Altshuler D, Daley GQ

Cell 147 (1) 81-94 [2011-09-30; online 2011-10-04]

ProteinSeq: high-performance proteomic analyses by proximity ligation and next generation sequencing.

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

PLoS ONE 6 (9) e25583 [2011-09-29; online 2011-09-29]

PLA Proteomics

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

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

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

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

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

Large-scale protein profiling in human cell lines using antibody-based proteomics.

Fagerberg L, Strömberg S, ..., 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, ..., Leroux MR, Swoboda P

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, ..., Giurgea I, Thuresson AC

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

Array and Analysis Facility NGI Uppsala (Uppsala Genome Center)

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, ..., Terenius L, Jönsson EG

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

Variants in STAT5B associate with serum TC and LDL-C levels.

Kornfeld JW, Isaacs A, ..., Pramstaller PP, Hicks AA

J. Clin. Endocrinol. Metab. 96 (9) E1496-E1501 [2011-09-00; online 2011-07-15]

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

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

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

ADME of Therapeutics (UDOPP) Uppsala Drug Optimization and Pharmaceutical Profiling (UDOPP)

PubMed

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

IBC 50K CAD Consortium

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

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

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

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

Identification of bacterial target proteins for the salicylidene acylhydrazide class of virulence-blocking compounds.

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

J. Biol. Chem. 286 (34) 29922-29931 [2011-08-26; online 2011-07-05]

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

PubMed

Westerholm M, Müller B, Arthurson V, Schnürer A

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

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, ..., Vasan RS, Seshadri S

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

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

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

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

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 , ..., Donnelly P, Compston A

Nature 476 (7359) 214-219 [2011-08-10; online 2011-08-10]

Functional and prognostic relevance of the homeobox protein MSX2 in malignant melanoma.

Gremel G, Ryan D, ..., Ponten F, Gallagher WM

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, ..., 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

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

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

Influence of the COMT genotype on working memory and brain activity changes during development.

Dumontheil I, Roggeman C, ..., Kere J, Klingberg T

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

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

NGI Uppsala (SNP&SEQ Technology Platform) NGI Uppsala (Uppsala Genome Center)

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

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

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

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

Lack of association between two dopamine D2 receptor gene polymorphisms and schizophrenia.

Caprini S, Saetre P, ..., Terenius L, Jönsson EG

Psychiatr. Genet. 21 (4) 214-215 [2011-08-00; online 2011-06-30]

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]

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]

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

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

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)

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

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, ..., Lindgren A, Jern C

Clin. Biochem. 44 (12) 1018-1020 [2011-08-00; online 2011-06-15]

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]

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

PubMed

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

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

PLoS ONE 6 (7) e22741 [2011-07-25; online 2011-07-25]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

Structural alterations from multiple displacement amplification of a human genome revealed by mate-pair sequencing.

Jiao X, Rosenlund M, ..., Mangion J, Sjöblom T

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

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, ..., Uhlén M, Jirström K

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

FAAST: Flow-space Assisted Alignment Search Tool.

Lysholm F, Andersson B, Persson B

BMC Bioinformatics 12 (-) 293 [2011-07-19; online 2011-07-19]

The use of genome-wide eQTL associations in lymphoblastoid cell lines to identify novel genetic pathways involved in complex traits.

Min JL, Taylor JM, ..., Spector TD, Zondervan KT

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

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

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

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

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

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

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

Potential association of muscarinic receptor 3 gene variants with primary Sjogren's syndrome.

Appel S, Le Hellard S, ..., Wahren-Herlenius M, Jonsson R

Ann. Rheum. Dis. 70 (7) 1327-1329 [2011-07-00; online 2011-04-01]

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

Langenheder S, Székely AJ

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

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

SATB2 in combination with cytokeratin 20 identifies over 95% of all colorectal carcinomas.

Magnusson K, de Wit M, ..., Jirström K, Pontén F

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, ..., Gregersen PK, Hammarström L

J. Neuroimmunol. 236 (1-2) 118-122 [2011-07-00; online 2011-06-15]

Prostasomal DNA characterization and transfer into human sperm.

Ronquist GK, Larsson A, ..., 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, ..., Clement K, Dahlman I

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)

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

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

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

Specific syndecan-1 domains regulate mesenchymal tumor cell adhesion, motility and migration.

Zong F, Fthenou E, ..., Hjerpe A, Dobra K

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, ..., Hansson J, Ragnarsson-Olding BK

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

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

Translational database selection and multiplexed sequence capture for up front filtering of reliable breast cancer biomarker candidates.

Ståhl PL, Bjursell MK, ..., Jirström K, Lundeberg J

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

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

Mutations in Frizzled 6 cause isolated autosomal-recessive nail dysplasia.

Fröjmark AS, Schuster J, ..., Klar J, Dahl N

Am. J. Hum. Genet. 88 (6) 852-860 [2011-06-10; online 2011-06-15]

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

(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

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

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

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

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)

The fat mass and obesity gene is linked to reduced verbal fluency in overweight and obese elderly men.

Benedict C, Jacobsson JA, ..., Kilander L, Schiöth HB

Neurobiol. Aging 32 (6) 1159.e1-1159.e5 [2011-06-00; online 2011-04-05]

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

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

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

Brunberg E, Jensen P, Isaksson A, Keeling L

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, ..., Annerén G, Bondeson ML

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

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

Westerholm M, Roos S, Schnürer A

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

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, ..., Lind L, Schiöth HB

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

Multiple recognition assay reveals prostasomes as promising plasma biomarkers for prostate cancer.

Tavoosidana G, Ronquist G, ..., Landegren UD, Kamali-Moghaddam M

Proc. Natl. Acad. Sci. U.S.A. 108 (21) 8809-8814 [2011-05-24; online 2011-05-11]

Clinical Biomarkers PLA Proteomics

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

Boesler C, Kruse J, Söderbom F, Hammann C

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

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

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

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

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

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

Innocenti P, Morrow EH, Dowling DK

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

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

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, ..., Påhlman L, Birgisson H

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, ..., Tryggvason K, Patarroyo M

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

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

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

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

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

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

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

Array and Analysis Facility NGI Uppsala (Uppsala Genome Center)

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

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

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, ..., Hagström Å, Riemann L

PLoS ONE 6 (4) e19223 [2011-04-29; online 2011-04-29]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

Large scale library generation for high throughput sequencing.

Borgström E, Lundin S, Lundeberg J

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

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

Novel asymmetrically localizing components of human centrosomes identified by complementary proteomics methods.

Jakobsen L, Vanselow K, ..., Hyman AA, Andersen JS

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

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

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

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

Chorell E, Bengtsson C, ..., Hultgren SJ, Almqvist F

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

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

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

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

Kynurenine 3-monooxygenase (KMO) polymorphisms in schizophrenia: an association study.

Holtze M, Saetre P, ..., Jönsson EG, Schalling M

Schizophr. Res. 127 (1-3) 270-272 [2011-04-00; online 2010-10-30]

Utilizing twins concordance rates to infer the predisposition to myasthenia gravis.

Ramanujam R, Pirskanen R, Ramanujam S, Hammarström L

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

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

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

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

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

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)

Molecular characterization of acquired tolerance of tumor cells to picropodophyllin (PPP).

Hashemi J, Worrall C, ..., Larsson O, Larsson C

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

5'UTR variants of ribosomal protein S19 transcript determine translational efficiency: implications for Diamond-Blackfan anemia and tissue variability.

Badhai J, Schuster J, Gidlöf O, Dahl N

PLoS ONE 6 (3) e17672 [2011-03-11; online 2011-03-11]

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

PubMed

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

Reynolds CA, Gatz M, Pedersen NL, Prince JA

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

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

Neiman M, Lundin S, Savolainen P, Ahmadian A

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

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

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

Coronary Artery Disease (C4D) Genetics Consortium

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

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, ..., Van Rotterdam B, Knutsson R

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

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

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

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

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

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

Ameur A, Stewart JB, ..., Larsson NG, Gyllensten U

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

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

CUBN is a gene locus for albuminuria.

Böger CA, Chen MH, ..., Fox CS, Kao WH

J. Am. Soc. Nephrol. 22 (3) 555-570 [2011-03-00; online 2011-03-01]

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 JR, ..., Tintle L, Lindblad-Toh K

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

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (SNP&SEQ Technology Platform)

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

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

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

Systematic antibody and antigen-based proteomic profiling with microarrays.

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

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

Protein and peptide arrays

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

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

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

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

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

Performance of microarray and liquid based capture methods for target enrichment for massively parallel sequencing and SNP discovery.

Kiialainen A, Karlberg O, ..., Lindblad-Toh K, Syvänen AC

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

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

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

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

Diagnostic biomarkers of prostate cancer.

Häggarth L, Hägglöf C, ..., 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)

Genomic duplications mediate overexpression of lamin B1 in adult-onset autosomal dominant leukodystrophy (ADLD) with autonomic symptoms.

Schuster J, Sundblom J, ..., Melberg A, Dahl N

Neurogenetics 12 (1) 65-72 [2011-02-00; online 2011-01-13]

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

GAD1 is a biomarker for benign and malignant prostatic tissue.

Jaraj SJ, Augsten M, ..., 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, ..., Pontén F, Lundeberg J

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

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

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

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

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

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, ..., Pluchino S, Marchetti B

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, ..., 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)

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

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

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

Brennan DJ, Laursen H, ..., Rydén L, Jirström K

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, ..., Claesson-Welsh L, Carmeliet P

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, ..., Siegel PB, Carlborg O

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

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

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

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

Street NR, Jansson S, Hvidsten TR

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)

Vitamin D receptor genotypes, ultraviolet radiation exposure, and risk of non-Hodgkin lymphoma.

Smedby KE, Eloranta S, ..., Hjalgrim H, Chang ET

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, ..., Arborelius U, Davidsson J

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, ..., Ericsson O, Nilsson M

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

Array and Analysis Facility NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (Uppsala Genome Center)

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

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

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

Meta-analysis of the association between variants in SORL1 and Alzheimer disease.

Reitz C, Cheng R, ..., Mayeux R, Genetic and Environmental Risk in Alzheimer Disease 1 Consortium

Arch. Neurol. 68 (1) 99-106 [2011-01-00; online 2011-01-12]