Publications 2013

Glutamatergic GRIN2B and polyaminergic ODC1 genes in suicide attempts: associations and gene-environment interactions with childhood/adolescent physical assault.

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

Mol. Psychiatry 18 (9) 985-992 [2013-09-00; online 2012-08-02]

Global DNA hypermethylation is associated with high serum levels of persistent organic pollutants in an elderly population.

Lind L, Penell J, ..., Ingelsson E, Lind PM

Environ Int 59 (-) 456-461 [2013-09-00; online 2013-08-13]

Comparison of the nodule vs. root transcriptome of the actinorhizal plant Datisca glomerata: actinorhizal nodules contain a specific class of defensins.

Demina IV, Persson T, ..., Plaszczyca M, Pawlowski K

PLoS ONE 8 (8) e72442 [2013-08-29; online 2013-08-29]

NGI Stockholm (Genomics Applications) [] NGI Stockholm (Genomics Production) []

Genome-wide transcriptional analysis of Drosophila larvae infected by entomopathogenic nematodes shows involvement of complement, recognition and extracellular matrix proteins.

Arefin B, Kucerova L, ..., Zurovec M, Theopold U

J Innate Immun 6 (2) 192-204 [2013-08-27; online 2013-08-27]

NGI Stockholm (Genomics Applications) [] NGI Stockholm (Genomics Production) []

Structure-Guided Design of Novel Thiazolidine Inhibitors ofO-Acetyl Serine Sulfhydrylase from Mycobacterium tuberculosis

Poyraz Ö, Jeankumar VU, ..., Sriram D, Schneider G

J. Med. Chem. 56 (16) 6457-6466 [2013-08-22; online 2013-08-22]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

NGI Stockholm (Genomics Applications) [] NGI Stockholm (Genomics Production) []

Svartström O, Mushtaq M, Pringle M, Segerman B

PLoS ONE 8 (8) e71281 [2013-08-19; online 2013-08-19]

Automated serial extraction of DNA and RNA from biobanked tissue specimens.

Mathot L, Wallin M, Sjöblom T

BMC Biotechnol. 13 (-) 66 [2013-08-19; online 2013-08-19]

PARP inhibitor with selectivity toward ADP-ribosyltransferase ARTD3/PARP3.

Lindgren AE, Karlberg T, ..., Elofsson M, Schüler H

ACS Chem. Biol. 8 (8) 1698-1703 [2013-08-16; online 2013-06-08]

Transcription factor binding in human cells occurs in dense clusters formed around cohesin anchor sites.

Yan J, Enge M, ..., Taipale M, Taipale J

Cell 154 (4) 801-813 [2013-08-15; online 2013-08-21]

Bioinformatics and Expression Analysis (BEA) [] Karolinska High Throughput Center (KHTC) []

Investigation of six testicular germ cell tumor susceptibility genes suggests a parent-of-origin effect in SPRY4.

Karlsson R, Andreassen KE, ..., Grotmol T, Wiklund F

Hum. Mol. Genet. 22 (16) 3373-3380 [2013-08-15; online 2013-05-04]

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

The STK33-linked SNP rs4929949 is associated with obesity and BMI in two independent cohorts of Swedish and Greek children.

Rask-Andersen M, Moschonis G, ..., Fredriksson R, Schiöth HB

PLoS ONE 8 (8) e71353 [2013-08-15; online 2013-08-15]

Structural and biophysical characterization of the cytoplasmic domains of human BAP29 and BAP31.

Quistgaard EM, Löw C, ..., Maddi K, Nordlund P

PLoS ONE 8 (8) e71111 [2013-08-13; online 2013-08-13]

Advanced Mass Spectrometry Proteomics [] Protein Science Facility (PSF) []

Meta-analysis of gene-level associations for rare variants based on single-variant statistics.

Hu Y, Berndt SI, ..., Ingelsson E, Lin D

Am. J. Hum. Genet. 93 (2) 236-248 [2013-08-08; online 2013-07-31]

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

Temperament and character in the Child and Adolescent Twin Study in Sweden (CATSS): comparison to the general population, and genetic structure analysis.

Garcia D, Lundström S, ..., Nilsson T, Anckarsäter H

PLoS ONE 8 (8) e70475 [2013-08-05; online 2013-08-05]

An Integratedin VitroModel for Simultaneous Assessment of Drug Uptake, Metabolism, and Efflux

Neve EPA, Artursson P, Ingelman-Sundberg M, Karlgren M

Mol. Pharmaceutics 10 (8) 3152-3163 [2013-08-05; online 2013-08-05]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Improved production of membrane proteins in Escherichia coli by selective codon substitutions.

Nørholm MH, Toddo S, ..., von Heijne G, Daley DO

FEBS Lett. 587 (15) 2352-2358 [2013-08-02; online 2013-06-19]

Chronic airway-induced allergy in mice modifies gene expression in the brain toward insulin resistance and inflammatory responses.

Sarlus H, Wang X, ..., Schultzberg M, Oprica M

J Neuroinflammation 10 (-) 99 [2013-08-01; online 2013-08-01]

Identification of adenovirus-encoded small RNAs by deep RNA sequencing.

Zhao H, Chen M, Pettersson U

Virology 442 (2) 148-155 [2013-08-01; online 2013-05-11]

Antibody-based profiling of cerebrospinal fluid within multiple sclerosis.

Häggmark A, Byström S, ..., Schwenk JM, Nilsson P

Proteomics 13 (15) 2256-2267 [2013-08-00; online 2013-05-23]

Plasma Profiling [Collaborative]

Molecular identification and phylogenic analysis by sequencing the rDNA of copper-tolerant soft-rot Phialophora spp.

Karunasekera H, Daniel G

International Biodeterioration & Biodegradation 82 (-) 45-52 [2013-08-00; online 2013-08-00]

Genetic variation in the dimethylarginine dimethylaminohydrolase 1 gene (DDAH1) is related to asymmetric dimethylarginine (ADMA) levels, but not to endothelium-dependent vasodilation.

Lind L, Ingelsson E, ..., Axelsson T, Teerlink T

Vasc Med 18 (4) 192-199 [2013-08-00; online 2013-07-31]

Design of a Highly Selective and Potent Class of Non-planar Estrogen Receptor β Agonists

Sundén H, Ma JN, ..., Burstein ES, Olsson R

ChemMedChem 8 (8) 1283-1294 [2013-08-00; online 2013-06-19]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Expression of chondroitin/dermatan sulfate glycosyltransferases during early zebrafish development.

Filipek-Górniok B, Holmborn K, ..., Kreuger J, Ledin J

Dev. Dyn. 242 (8) 964-975 [2013-08-00; online 2013-05-25]

Genome Engineering Zebrafish []

Synergistic interactions between camptothecin and EGFR or RAC1 inhibitors and between imatinib and Notch signaling or RAC1 inhibitors in glioblastoma cell lines.

Sooman L, Ekman S, ..., Lennartsson J, Gullbo J

Cancer Chemother. Pharmacol. 72 (2) 329-340 [2013-08-00; online 2013-06-06]

High-resolution structure of TBP with TAF1 reveals anchoring patterns in transcriptional regulation.

Anandapadamanaban M, Andresen C, ..., Moche M, Sunnerhagen M

Nat. Struct. Mol. Biol. 20 (8) 1008-1014 [2013-08-00; online 2013-07-16]

A novel intellectual disability syndrome caused by GPI anchor deficiency due to homozygous mutations in PIGT.

Kvarnung M, Nilsson D, ..., Nordenskjöld M, Nordgren A

J. Med. Genet. 50 (8) 521-528 [2013-08-00; online 2013-05-03]

NGI Stockholm (Genomics Applications) [] NGI Stockholm (Genomics Production) []

Tumour expression of bladder cancer-associated urinary proteins.

Lindén M, Segersten U, ..., Lind SB, Malmström PU

BJU Int. 112 (3) 407-415 [2013-08-00; online 2013-03-09]

In silico instrumental response correction improves precision of label-free proteomics and accuracy of proteomics-based predictive models.

Lyutvinskiy Y, Yang H, Rutishauser D, Zubarev RA

Mol. Cell Proteomics 12 (8) 2324-2331 [2013-08-00; online 2013-04-17]

Advanced Mass Spectrometry Proteomics []

Proteome of the nematode-trapping cells of the fungus Monacrosporium haptotylum.

Andersson KM, Meerupati T, ..., Ahrén D, Tunlid A

Appl. Environ. Microbiol. 79 (16) 4993-5004 [2013-08-00; online 2013-06-19]

New viruses in veterinary medicine, detected by metagenomic approaches.

Belák S, Karlsson OE, ..., Berg M, Granberg F

Vet. Microbiol. 165 (1-2) 95-101 [2013-07-26; online 2013-02-23]

Gene × physical activity interactions in obesity: combined analysis of 111,421 individuals of European ancestry.

Ahmad S, Rukh G, ..., Orho-Melander M, Franks PW

PLoS Genet. 9 (7) e1003607 [2013-07-25; online 2013-07-25]

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

NCR3/NKp30 contributes to pathogenesis in primary Sjogren's syndrome.

Rusakiewicz S, Nocturne G, ..., Zitvogel L, Mariette X

Sci Transl Med 5 (195) 195ra96 [2013-07-24; online 2013-07-26]

Retinoic acid receptor alpha is associated with tamoxifen resistance in breast cancer.

Johansson HJ, Sanchez BC, ..., Linderholm BK, Lehtiö J

Nat Commun 4 (-) 2175 [2013-07-23; online 2013-07-23]

Drug Discovery and Development (DDD) [Collaborative]

Genetic variants in hormone-related genes and risk of breast cancer.

Clendenen T, Zeleniuch-Jacquotte A, ..., Shore RE, Chen Y

PLoS ONE 8 (7) e69367 [2013-07-23; online 2013-07-23]

SNP in TXNRD2 associated with radiation-induced fibrosis: a study of genetic variation in reactive oxygen species metabolism and signaling.

Edvardsen H, Landmark-Høyvik H, ..., Fosså SD, Kristensen VN

Int. J. Radiat. Oncol. Biol. Phys. 86 (4) 791-799 [2013-07-15; online 2013-04-20]

Novel signatures of cancer-associated fibroblasts.

Bozóky B, Savchenko A, ..., Székely L, Klein G

Int. J. Cancer 133 (2) 286-293 [2013-07-15; online 2013-01-16]

Prevalence, comorbidity and heritability of hoarding symptoms in adolescence: a population based twin study in 15-year olds.

Ivanov VZ, Mataix-Cols D, ..., Långström N, Rück C

PLoS ONE 8 (7) e69140 [2013-07-10; online 2013-07-10]

Amyloid-β protofibrils: size, morphology and synaptotoxicity of an engineered mimic.

Dubnovitsky A, Sandberg A, ..., Lendel C, Härd T

PLoS ONE 8 (7) e66101 [2013-07-02; online 2013-07-02]

Mass Spectrometry-based Proteomics, Uppsala []

Genome-wide association and longitudinal analyses reveal genetic loci linking pubertal height growth, pubertal timing and childhood adiposity.

Cousminer DL, Berry DJ, ..., Widén E, Early Growth Genetics (EGG) Consortium

Hum. Mol. Genet. 22 (13) 2735-2747 [2013-07-01; online 2013-02-27]

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

Active nitrogen-fixing heterotrophic bacteria at and below the chemocline of the central Baltic Sea.

Farnelid H, Bentzon-Tilia M, ..., Jürgens K, Riemann L

ISME J 7 (7) 1413-1423 [2013-07-00; online 2013-03-01]

NGI Stockholm (Genomics Applications) [] NGI Stockholm (Genomics Production) []

Family-based study of HTR2A in suicide attempts: observed gene, gene × environment and parent-of-origin associations.

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

Mol. Psychiatry 18 (7) 758-766 [2013-07-00; online 2012-07-04]

Republished: Non-heritable genetics of human disease: spotlight on post-zygotic genetic variation acquired during lifetime.

Forsberg LA, Absher D, Dumanski JP

Postgrad Med J 89 (1053) 417-426 [2013-07-00; online 2013-06-20]

Computational Prospecting for Drug–Transporter Interactions

Matsson P, Artursson P

Clin Pharmacol Ther 94 (1) 30-32 [2013-07-00; online 2013-04-02]

Chemical Biology Consortium Sweden (CBCS) [Technology development]

Massive functional mapping of a 5'-UTR by saturation mutagenesis, phenotypic sorting and deep sequencing.

Holmqvist E, Reimegård J, Wagner EG

Nucleic Acids Res. 41 (12) e122 [2013-07-00; online 2013-04-24]

Somatic mutations in H-RAS in sporadic pheochromocytoma and paraganglioma identified by exome sequencing.

Crona J, Delgado Verdugo A, ..., Hellman P, Björklund P

J. Clin. Endocrinol. Metab. 98 (7) E1266-E1271 [2013-07-00; online 2013-05-04]

Estrogen receptor β expression induces changes in the microRNA pool in human colon cancer cells.

Edvardsson K, Nguyen-Vu T, ..., Gustafsson JÅ, Williams C

Carcinogenesis 34 (7) 1431-1441 [2013-07-00; online 2013-02-26]

Implications of baseline polymorphisms for potential resistance to NS3 protease inhibitors in Hepatitis C virus genotypes 1a, 2b and 3a.

Palanisamy N, Danielsson A, ..., Duberg AS, Lennerstrand J

Antiviral Res. 99 (1) 12-17 [2013-07-00; online 2013-05-08]

Response of Acidithiobacillus caldus toward suboptimal pH conditions.

Mangold S, Rao Jonna V, Dopson M

Extremophiles 17 (4) 689-696 [2013-07-00; online 2013-05-29]

Family-based study of AVPR1B association and interaction with stressful life events on depression and anxiety in suicide attempts.

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

Neuropsychopharmacology 38 (8) 1504-1511 [2013-07-00; online 2013-02-21]

CDK-mediated activation of the SCF(FBXO) (28) ubiquitin ligase promotes MYC-driven transcription and tumourigenesis and predicts poor survival in breast cancer.

Cepeda D, Ng HF, ..., Larsson LG, Sangfelt O

EMBO Mol Med 5 (7) 1067-1086 [2013-07-00; online 2013-06-19]

Clinical depression, antidepressant use and risk of future cardiovascular disease.

Rahman I, Humphreys K, ..., Pedersen NL, Magnusson PK

Eur. J. Epidemiol. 28 (7) 589-595 [2013-07-00; online 2013-07-09]

NGI Stockholm (Genomics Applications) [] NGI Stockholm (Genomics Production) []

Cenani-Lenz syndrome restricted to limb and kidney anomalies associated with a novel LRP4 missense mutation.

Khan TN, Klar J, ..., Baig SM, Dahl N

Eur J Med Genet 56 (7) 371-374 [2013-07-00; online 2013-05-15]

NGI Stockholm (Genomics Applications) [] NGI Stockholm (Genomics Production) []

Enzymatic production of 'monoclonal stoichiometric' single-stranded DNA oligonucleotides.

Ducani C, Kaul C, ..., Shih WM, Högberg B

Nat. Methods 10 (7) 647-652 [2013-07-00; online 2013-06-04]

Unbiased approach for virus detection in skin lesions.

Bzhalava D, Johansson H, ..., Forslund O, Dillner J

PLoS ONE 8 (6) e65953 [2013-06-28; online 2013-06-28]

NGI Stockholm (Genomics Applications) [] NGI Stockholm (Genomics Production) []

Continuous Aging of the Human DNA Methylome Throughout the Human Lifespan.

Johansson A, Enroth S, Gyllensten U

PLoS ONE 8 (6) e67378 [2013-06-27; online 2013-06-27]

Constrained H-Phe-Phe-NH2 analogues with high affinity to the substance P 1-7 binding site and with improved metabolic stability and cell permeability.

Fransson R, Sköld C, ..., Hallberg M, Sandström A

J. Med. Chem. 56 (12) 4953-4965 [2013-06-27; online 2013-06-06]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

The crystal structure of the lumenal domain of Erv41p, a protein involved in transport between the endoplasmic reticulum and Golgi apparatus.

Biterova EI, Svärd M, Possner DD, Guy JE

J. Mol. Biol. 425 (12) 2208-2218 [2013-06-26; online 2013-03-26]

The role of adiposity in cardiometabolic traits: a Mendelian randomization analysis.

Fall T, Hägg S, ..., Prokopenko I, European Network for Genetic and Genomic Epidemiology (ENGAGE) consortium N

PLoS Med. 10 (6) e1001474 [2013-06-25; online 2013-06-25]

Lessons learned from implementing a national infrastructure in Sweden for storage and analysis of next-generation sequencing data.

Lampa S, Dahlö M, ..., Hagberg J, Spjuth O

Gigascience 2 (1) 9 [2013-06-25; online 2013-06-25]

Substrate Channel Flexibility in Pseudomonas aeruginosa MurB Accommodates Two Distinct Substrates.

Chen MW, Lohkamp B, ..., Lescar J, Schneider G

PLoS ONE 8 (6) e66936 [2013-06-21; online 2013-06-21]

GWAS of 126,559 individuals identifies genetic variants associated with educational attainment.

Rietveld CA, Medland SE, ..., Cesarini D, Koellinger PD

Science 340 (6139) 1467-1471 [2013-06-21; online 2013-06-01]

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

Vandetanib combined with a p38 MAPK inhibitor synergistically reduces glioblastoma cell survival.

Sooman L, Lennartsson J, ..., Blomquist E, Ekman S

Med. Oncol. 30 (3) 638 [2013-06-20; online 2013-06-20]

Bioinformatics Support and Infrastructure [] Tissue Profiling []

Behavioural and Brain Gene Expression Profiling in Pigs during Tail Biting Outbreaks - Evidence of a Tail Biting Resistant Phenotype.

Brunberg E, Jensen P, Isaksson A, Keeling LJ

PLoS ONE 8 (6) e66513 [2013-06-18; online 2013-06-18]

Stable isotope labeling methods in protein profiling.

Lengqvist J, Sandberg A

Methods Mol. Biol. 1023 (-) 21-51 [2013-06-15; online 2013-06-15]

Narrow-range peptide isoelectric focusing as peptide prefractionation method prior to tandem mass spectrometry analysis.

Pernemalm M

Methods Mol. Biol. 1023 (-) 3-11 [2013-06-15; online 2013-06-15]

Protein quantification by peptide quality control (PQPQ) of shotgun proteomics data.

Forshed J

Methods Mol. Biol. 1023 (-) 149-158 [2013-06-15; online 2013-06-15]

Comprehensive analysis of MHC ligands in clinical material by immunoaffinity-mass spectrometry.

Kasuga K

Methods Mol. Biol. 1023 (-) 203-218 [2013-06-15; online 2013-06-15]

Highly multiplexed antibody suspension bead arrays for plasma protein profiling.

Drobin K, Nilsson P, Schwenk JM

Methods Mol. Biol. 1023 (-) 137-145 [2013-06-15; online 2013-06-15]

Plasma Profiling [Technology development]

Molecular genetics and subjective well-being.

Rietveld CA, Cesarini D, ..., Krueger RF, Bartels M

Proc. Natl. Acad. Sci. U.S.A. 110 (24) 9692-9697 [2013-06-11; online 2013-05-28]

NGI Stockholm (Genomics Applications) [] NGI Stockholm (Genomics Production) []

The prognostic relevance of tumour-infiltrating plasma cells and immunoglobulin kappa C indicates an important role of the humoral immune response in non-small cell lung cancer.

Lohr M, Edlund K, ..., Rahnenführer J, Micke P

Cancer Lett. 333 (2) 222-228 [2013-06-10; online 2013-02-02]

Contribution of antibody-based protein profiling to the human Chromosome-centric Proteome Project (C-HPP).

Fagerberg L, Oksvold P, ..., von Feilitzen K, Uhlén M

J. Proteome Res. 12 (6) 2439-2448 [2013-06-07; online 2013-01-02]

Cell Profiling [] NGI Stockholm (Genomics Applications) [] NGI Stockholm (Genomics Production) [] Tissue Profiling []

Promoter DNA methylation pattern identifies prognostic subgroups in childhood T-cell acute lymphoblastic leukemia.

Borssén M, Palmqvist L, ..., Roos G, Degerman S

PLoS ONE 8 (6) e65373 [2013-06-06; online 2013-06-06]

Rapid Measurement of Intracellular Unbound Drug Concentrations

Mateus A, Matsson P, Artursson P

Mol. Pharmaceutics 10 (6) 2467-2478 [2013-06-03; online 2013-06-03]

Chemical Biology Consortium Sweden (CBCS) [Technology development]

Next-generation sequencing in the clinical genetic screening of patients with pheochromocytoma and paraganglioma.

Crona J, Verdugo AD, ..., Hellman P, Björklund P

Endocr Connect 2 (2) 104-111 [2013-06-01; online 2013-05-28]

Parallel visualization of multiple protein complexes in individual cells in tumor tissue.

Leuchowius KJ, Clausson CM, ..., Landegren U, Söderberg O

Mol. Cell Proteomics 12 (6) 1563-1571 [2013-06-00; online 2013-02-26]

NGI Uppsala (Uppsala Genome Center) [] PLA Proteomics []

Identification of heart rate-associated loci and their effects on cardiac conduction and rhythm disorders.

den Hoed M, Eijgelsheim M, ..., Samani NJ, Loos RJF

Nat. Genet. 45 (6) 621-631 [2013-06-00; online 2013-04-16]

Coronary heart disease in systemic lupus erythematosus is associated with interferon regulatory factor-8 gene variants.

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

Circ Cardiovasc Genet 6 (3) 255-263 [2013-06-00; online 2013-05-11]

A significant fraction of 21-nucleotide small RNA originates from phased degradation of resistance genes in several perennial species.

Källman T, Chen J, Gyllenstrand N, Lagercrantz U

Plant Physiol. 162 (2) 741-754 [2013-06-00; online 2013-04-13]

Initial quantitative proteomic map of 28 mouse tissues using the SILAC mouse.

Geiger T, Velic A, ..., Cox J, Mann M

Mol. Cell Proteomics 12 (6) 1709-1722 [2013-06-00; online 2013-02-26]

Cell Profiling [] Tissue Profiling []

The value of selected in vitro and in silico methods to predict acute oral toxicity in a regulatory context: results from the European Project ACuteTox.

Prieto P, Kinsner-Ovaskainen A, ..., Zurbano MJ, Kopp-Schneider A

Toxicol In Vitro 27 (4) 1357-1376 [2013-06-00; online 2012-08-28]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Solid-phase proximity ligation assays for individual or parallel protein analyses with readout via real-time PCR or sequencing.

Nong RY, Wu D, ..., Landegren U, Darmanis S

Nat Protoc 8 (6) 1234-1248 [2013-06-00; online 2013-05-30]

Contribution of IKBKE and IFIH1 gene variants to SLE susceptibility.

Wang C, Ahlford A, ..., Rönnblom L, Syvänen AC

Genes Immun. 14 (4) 217-222 [2013-06-00; online 2013-03-29]

Stepping-stone expansion and habitat loss explain a peculiar genetic structure and distribution of a forest insect.

Cassel-Lundhagen A, Ronnås C, ..., Wallén J, Larsson S

Mol. Ecol. 22 (12) 3362-3375 [2013-06-00; online 2013-05-31]

Sortilin receptor 1 predicts longitudinal cognitive change.

Reynolds CA, Zavala C, ..., Prince JA, Pedersen NL

Neurobiol. Aging 34 (6) 1710.e11-1710.e18 [2013-06-00; online 2013-01-16]

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

Gambogic acid is cytotoxic to cancer cells through inhibition of the ubiquitin-proteasome system.

Felth J, Lesiak-Mieczkowska K, ..., Fryknäs M, Rickardson L

Invest New Drugs 31 (3) 587-598 [2013-06-00; online 2012-11-28]

Exome sequencing in diagnostic evaluation of colorectal cancer predisposition in young patients.

Tanskanen T, Gylfe AE, ..., Vahteristo P, Aaltonen LA

Scand. J. Gastroenterol. 48 (6) 672-678 [2013-06-00; online 2013-04-03]

Karolinska High Throughput Center (KHTC) []

Circadian regulation of melanization and prokineticin homologues is conserved in the brain of freshwater crayfish and zebrafish.

Noonin C, Watthanasurorot A, Winberg S, Söderhäll I

Dev. Comp. Immunol. 40 (2) 218-226 [2013-06-00; online 2013-03-19]

Genome Engineering Zebrafish [] NGI Stockholm (Genomics Applications) [] NGI Stockholm (Genomics Production) []

Structural and dynamic insights into substrate binding and catalysis of human lipocalin prostaglandin D synthase.

Lim SM, Chen D, ..., Pervushin K, Nordlund P

J. Lipid Res. 54 (6) 1630-1643 [2013-06-00; online 2013-03-26]

Sex-stratified genome-wide association studies including 270,000 individuals show sexual dimorphism in genetic loci for anthropometric traits.

Randall JC, Winkler TW, ..., North KE, Heid IM

PLoS Genet. 9 (6) e1003500 [2013-06-00; online 2013-06-06]

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

Structural basis for substrate transport in the GLUT-homology family of monosaccharide transporters.

Quistgaard EM, Löw C, ..., Trésaugues L, Nordlund P

Nat. Struct. Mol. Biol. 20 (6) 766-768 [2013-06-00; online 2013-04-30]

The impact of splicing on protein domain architecture.

Light S, Elofsson A

Curr. Opin. Struct. Biol. 23 (3) 451-458 [2013-06-00; online 2013-04-09]

Prevalence of extended-spectrum beta-lactamase-producing Enterobacteriaceae in healthy Swedish preschool children.

Kaarme J, Molin Y, Olsen B, Melhus A

Acta Paediatr. 102 (6) 655-660 [2013-06-00; online 2013-02-20]

No association of primary Sjögren's syndrome with Fcγ receptor gene variants.

Haldorsen K, Appel S, ..., Jonsson R, Bolstad AI

Genes Immun. 14 (4) 234-237 [2013-06-00; online 2013-04-05]

The Norway spruce genome sequence and conifer genome evolution.

Nystedt B, Street NR, ..., Lundeberg J, Jansson S

Nature 497 (7451) 579-584 [2013-05-30; online 2013-05-24]

Bioinformatics Compute and Storage [] Bioinformatics Support and Infrastructure [] NGI Stockholm (Genomics Applications) [] NGI Stockholm (Genomics Production) []

Metagenomic de novo assembly of an aquatic representative of the verrucomicrobial class Spartobacteria.

Herlemann DP, Lundin D, ..., Aspeborg H, Andersson AF

MBio 4 (3) e00569-e00512 [2013-05-28; online 2013-05-28]

NGI Stockholm (Genomics Applications) [] NGI Stockholm (Genomics Production) []

Dynamic gradients of an intermediate filament-like cytoskeleton are recruited by a polarity landmark during apical growth.

Fuchino K, Bagchi S, ..., Flärdh K, Ausmees N

Proc. Natl. Acad. Sci. U.S.A. 110 (21) E1889-E1897 [2013-05-21; online 2013-05-04]

A texture based pattern recognition approach to distinguish melanoma from non-melanoma cells in histopathological tissue microarray sections.

Rexhepaj E, Agnarsdóttir M, ..., Lundberg E, Ponten F

PLoS ONE 8 (5) e62070 [2013-05-17; online 2013-05-17]

Cell Profiling [] Tissue Profiling []

Adaptive mutations and replacements of virulence traits in the Escherichia coli O104:H4 outbreak population.

Guy L, Jernberg C, ..., Engstrand L, Andersson SGE

PLoS ONE 8 (5) e63027 [2013-05-10; online 2013-05-10]

Age dependence of tumor genetics in unfavorable neuroblastoma: arrayCGH profiles of 34 consecutive cases, using a Swedish 25-year neuroblastoma cohort for validation.

Cetinkaya C, Martinsson T, ..., Díaz de Ståhl T, Hedborg F

BMC Cancer 13 (-) 231 [2013-05-09; online 2013-05-09]

NGI Stockholm (Genomics Applications) [] NGI Stockholm (Genomics Production) []

Active transcriptomic and proteomic reprogramming in the C. elegans nucleotide excision repair mutant xpa-1.

Arczewska KD, Tomazella GG, ..., Thiede B, Nilsen H

Nucleic Acids Res. 41 (10) 5368-5381 [2013-05-01; online 2013-04-13]

Genome-wide association study of susceptibility loci for cervical cancer.

Chen D, Juko-Pecirep I, ..., Wilander E, Gyllensten U

J. Natl. Cancer Inst. 105 (9) 624-633 [2013-05-01; online 2013-03-14]

The adenovirus VA RNA-derived miRNAs are not essential for lytic virus growth in tissue culture cells.

Kamel W, Segerman B, ..., Punga T, Akusjärvi G

Nucleic Acids Res. 41 (9) 4802-4812 [2013-05-00; online 2013-03-26]

NGI Stockholm (Genomics Applications) [] NGI Stockholm (Genomics Production) []

Identification of a functional apolipoprotein E promoter polymorphism regulating plasma apolipoprotein E concentration.

Mannila MN, Mahdessian H, ..., Hamsten A, van 't Hooft FM

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A genome-wide association study identifies genomic regions for virulence in the non-model organism Heterobasidion annosum s.s.

Dalman K, Himmelstrand K, ..., Brandström-Durling M, Stenlid J

PLoS ONE 8 (1) e53525 [2013-01-16; online 2013-01-16]

Meta-analysis investigating associations between healthy diet and fasting glucose and insulin levels and modification by loci associated with glucose homeostasis in data from 15 cohorts.

Nettleton JA, Hivert MF, ..., Meigs JB, Franks PW

Am. J. Epidemiol. 177 (2) 103-115 [2013-01-15; online 2012-12-21]

NGI Stockholm (Genomics Applications) [] NGI Stockholm (Genomics Production) []

A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data.

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Bioinformatics 29 (2) 189-196 [2013-01-15; online 2012-11-24]

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PLoS ONE 8 (1) e53698 [2013-01-14; online 2013-01-14]

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A chromosome-centric human proteome project (C-HPP) to characterize the sets of proteins encoded in chromosome 17.

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RNA deep sequencing as a tool for selection of cell lines for systematic subcellular localization of all human proteins.

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Biomarker discovery in non-small cell lung cancer: integrating gene expression profiling, meta-analysis, and tissue microarray validation.

Botling J, Edlund K, ..., Hengstler JG, Micke P

Clin. Cancer Res. 19 (1) 194-204 [2013-01-01; online 2012-10-04]

Array and Analysis Facility [] Tissue Profiling []

The genetic structure of the Lithuanian wolf population

Baltrūnaitė L, Balčiauskas L, Åkesson M

Open Life Sci 8 (5) - [2013-01-01; online 2013-01-01]

Proceedings of the 15th International Congress on Circumpolar Health

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Large-scale association analysis identifies new risk loci for coronary artery disease.

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Nat. Genet. 45 (1) 25-33 [2013-01-00; online 2012-12-04]

450K-array analysis of chronic lymphocytic leukemia cells reveals global DNA methylation to be relatively stable over time and similar in resting and proliferative compartments.

Cahill N, Bergh AC, ..., Rosén A, Rosenquist R

Leukemia 27 (1) 150-158 [2013-01-00; online 2012-08-28]

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Non-heritable genetics of human disease: spotlight on post-zygotic genetic variation acquired during lifetime.

Forsberg LA, Absher D, Dumanski JP

J. Med. Genet. 50 (1) 1-10 [2013-01-00; online 2012-11-23]

First Genome Sequence of a Syntrophic Acetate-Oxidizing Bacterium, Tepidanaerobacter acetatoxydans Strain Re1.

Manzoor S, Bongcam-Rudloff E, Schnürer A, Müller B

Genome Announc 1 (1) - [2013-01-00; online 2013-02-21]

Genome-wide profiling of target genes for the systemic lupus erythematosus-associated transcription factors IRF5 and STAT4.

Wang C, Sandling JK, ..., Eloranta ML, Syvänen AC

Ann. Rheum. Dis. 72 (1) 96-103 [2013-01-00; online 2012-06-26]

Nanoscale elucidation of Na,K-ATPase isoforms in dendritic spines

Liebmann T, Blom H, Aperia A, Brismar H

Optical Nanoscopy Opt Nanoscopy 2 (1) 6 [2013-00-00; online 2013-00-00]

Advanced Light Microscopy (ALM) [Technology development]