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, Luttropp K, ..., 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, Santos P, Plaszczyca M, Pawlowski K

pmc

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, Dobes P, ..., 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, Saxena S, ..., 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

pmc

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

pmc

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

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

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

PDB PDB PDB PDB

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, Whitington T, ..., Taipale M, Taipale J

GEO GEO

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, Kristiansen W, ..., 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, Chrousos GP, ..., Fredriksson R, Schiöth HB

pmc

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, Moberg P, ..., Maddi K, Nordlund P

pmc PDB PDB

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, Gustafsson S, ..., Ingelsson E, Lin D

pmc

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, Brändström S, ..., Nilsson T, Anckarsäter H

pmc

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, Virkki MT, ..., 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, Cedazo-Minguez A, Schultzberg M, Oprica M

pmc

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, Ayoglu B, ..., 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, Kumar J, ..., 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, Hansen LK, ..., 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, Haitina T, ..., 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, Andersson C, ..., 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, Helander S, ..., Moche M, Sunnerhagen M

pmc mid PDB

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, Lindstrand A, ..., 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, Runeson M, ..., 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

pmc

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, Levander F, ..., Ahrén D, Tunlid A

pmc

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, Blomström AL, 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, Varga TV, ..., Orho-Melander M, Franks PW

pmc

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, Lazure T, ..., Zitvogel L, Mariette X

pmc mid

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, Mundt F, ..., Linderholm BK, Lehtiö J

pmc

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, Wirgin I, ..., Shore RE, Chen Y

pmc

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, Reinertsen KV, ..., 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, Csermely P, ..., 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, Serlachius E, ..., Långström N, Rück C

pmc

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, Rahman MM, ..., Lendel C, Härd T

pmc

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, Timpson NJ, ..., Widén E, Early Growth Genetics (EGG) Consortium

pmc

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, Andersson AF, ..., Jürgens K, Riemann L

pmc

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

pmc

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

pmc

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, Maharjan R, ..., 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, Kalasekar SM, ..., 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, Kokkula C, ..., 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

pmc

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, Sharifi HR, ..., Larsson LG, Sangfelt O

pmc

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, Bennet AM, ..., 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, Ali Z, ..., 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, Moche M, Shih WM, Högberg B

pmc mid PDB

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, Ekström J, ..., Forslund O, Dillner J

pmc

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

pmc

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, Kratz JM, ..., 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

PDB

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, Mägi R, ..., Prokopenko I, European Network for Genetic and Genomic Epidemiology (ENGAGE) consortium N

pmc

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, Olason PI, Hagberg J, Spjuth O

pmc

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, Schnell R, Lescar J, Schneider G

pmc

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, Derringer J, ..., Cesarini D, Koellinger PD

pmc mid

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, Gullbo 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

pmc

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, Benjamin DJ, ..., Krueger RF, Bartels M

pmc

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, Botling J, ..., 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, Skogs M, ..., 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, Karrman K, ..., Roos G, Degerman S

pmc

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, Granberg D, ..., Hellman P, Björklund P

pmc

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, Grannas K, ..., Landegren U, Söderberg O

pmc

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

NGI Uppsala (Uppsala Genome Center) PLA and Single Cell Proteomics

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

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

pmc mid

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, Sandling JK, ..., 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

pmc GENBANK GENBANK GEO

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, Macek B, ..., Cox J, Mann M

pmc

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, Stanzel S, ..., 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, Yan J, ..., 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, Laxman N, ..., 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, Battisti A, Wallén J, Larsson S

GENBANK GENBANK

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

Sortilin receptor 1 predicts longitudinal cognitive change.

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

pmc mid

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, D'Arcy P, ..., 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, Katainen R, ..., 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, Teo H, ..., Pervushin K, Nordlund P

pmc

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, Kutalik Z, ..., North KE, Heid IM

pmc

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, Moberg P, Trésaugues L, Nordlund P

PDB PDB

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, Le Hellard 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, Wetterbom A, ..., 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, Labrenz M, ..., Aspeborg H, Andersson AF

pmc GENBANK GENBANK GENBANK GENBANK

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, Cantlay S, ..., Flärdh K, Ausmees N

pmc

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, Bergman J, ..., Lundberg E, Ponten F

pmc

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, Arvén Norling J, ..., Engstrand L, Andersson SGE

pmc

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, Sandgren J, ..., Díaz de Ståhl T, Hedborg F

pmc

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, Lindvall JM, ..., Thiede B, Nilsen H

pmc

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, Hammer J, ..., 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, Öberg D, Punga T, Akusjärvi G

pmc

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, Franco-Cereceda A, ..., Hamsten A, van 't Hooft FM

Arterioscler. Thromb. Vasc. Biol. 33 (5) 1063-1069 [2013-05-00; online 2013-02-23]

Genetic determinants of mortality. Can findings from genome-wide association studies explain variation in human mortality?

Ganna A, Rivadeneira F, Hofman A, ..., Ingelsson E, Tiemeier H

Hum. Genet. 132 (5) 553-561 [2013-05-00; online 2013-01-29]

Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture.

Berndt SI, Gustafsson S, Mägi R, ..., Loos RJF, Ingelsson E

pmc mid

Nat. Genet. 45 (5) 501-512 [2013-05-00; online 2013-04-09]

A phylogeny of the highly diverse cup-fungus family Pyronemataceae (Pezizomycetes, Ascomycota) clarifies relationships and evolution of selected life history traits.

Hansen K, Perry BA, Dranginis AW, Pfister DH

Mol. Phylogenet. Evol. 67 (2) 311-335 [2013-05-00; online 2013-02-14]

An adaptive alignment algorithm for quality-controlled label-free LC-MS.

Sandin M, Ali A, Hansson K, ..., Resjö S, Levander F

pmc

Mol. Cell Proteomics 12 (5) 1407-1420 [2013-05-00; online 2013-01-12]

Identification and expression of stressosomal proteins in Mycobacterium marinum under various growth and stress conditions.

Pettersson BMF, Nitharwal RG, Das S, ..., Bhattacharya A, Kirsebom LA

FEMS Microbiol. Lett. 342 (2) 98-105 [2013-05-00; online 2013-03-14]

Membrane protein shaving with thermolysin can be used to evaluate topology predictors.

Bendz M, Skwark M, Nilsson D, ..., Käll L, Elofsson A

Proteomics 13 (9) 1467-1480 [2013-05-00; online 2013-03-21]

Identification of acetate-oxidizing bacteria in a coastal marine surface sediment by RNA-stable isotope probing in anoxic slurries and intact cores.

Vandieken V, Thamdrup B

FEMS Microbiol. Ecol. 84 (2) 373-386 [2013-05-00; online 2013-01-08]

Genome-wide analysis in German shepherd dogs reveals association of a locus on CFA 27 with atopic dermatitis.

Tengvall K, Kierczak M, Bergvall K, ..., Hedhammar Å, Lindblad-Toh K

pmc

PLoS Genet. 9 (5) e1003475 [2013-05-00; online 2013-05-09]

The combined effects of single-nucleotide polymorphisms, tobacco products, and ethanol on normal resting blood mononuclear cells.

Cederblad L, Thunberg U, Engström M, ..., Rutqvist LE, Laytragoon-Lewin N

Nicotine Tob. Res. 15 (5) 890-895 [2013-05-00; online 2012-10-09]

Long indels are disordered: a study of disorder and indels in homologous eukaryotic proteins.

Light S, Sagit R, Ekman D, Elofsson A

Biochim. Biophys. Acta 1834 (5) 890-897 [2013-05-00; online 2013-01-22]

Variation in genes in the endothelin pathway and endothelium-dependent and endothelium-independent vasodilation in an elderly population.

Lind L, Syvänen AC, Axelsson T, ..., Hägg S, Larsson A

Acta Physiol (Oxf) 208 (1) 88-94 [2013-05-00; online 2013-01-23]

Comprehensive analysis of copy number variation in monozygotic twins discordant for bipolar disorder or schizophrenia.

Bloom RJ, Kähler AK, Collins AL, ..., Hultman C, Sullivan PF

pmc mid

Schizophr. Res. 146 (1-3) 289-290 [2013-05-00; online 2013-03-20]

Employment of complementary dissociation techniques for body fluid characterization and biomarker discovery.

Good DM, Rutishauser D

Methods Mol. Biol. 1002 (-) 223-232 [2013-04-30; online 2013-04-30]

Advanced Mass Spectrometry Proteomics

SoxB1-driven transcriptional network underlies neural-specific interpretation of morphogen signals.

Oosterveen T, Kurdija S, Ensterö M, ..., Muhr J, Ericson J

pmc

Proc. Natl. Acad. Sci. U.S.A. 110 (18) 7330-7335 [2013-04-30; online 2013-04-17]

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

Majority of differentially expressed genes are down-regulated during malignant transformation in a four-stage model.

Danielsson F, Skogs M, Huss M, ..., Uhlén M, Lundberg E

pmc

Proc. Natl. Acad. Sci. U.S.A. 110 (17) 6853-6858 [2013-04-23; online 2013-04-10]

Expression of fusion proteins of Aspergillus terreus reveals a novel allene oxide synthase.

Hoffmann I, Jernerén F, Oliw EH

pmc

J. Biol. Chem. 288 (16) 11459-11469 [2013-04-19; online 2013-03-13]

Renal sensory and sympathetic nerves reinnervate the kidney in a similar time-dependent fashion after renal denervation in rats.

Mulder J, Hökfelt T, Knuepfer MM, Kopp UC

pmc

Am. J. Physiol. Regul. Integr. Comp. Physiol. 304 (8) R675-R682 [2013-04-15; online 2013-02-15]

Fluorescence Tissue Profiling

Eating problems and overlap with ADHD and autism spectrum disorders in a nationwide twin study of 9- and 12-year-old children.

Råstam M, Täljemark J, Tajnia A, ..., Anckarsäter H, Kerekes N

pmc

ScientificWorldJournal 2013 (-) 315429 [2013-04-15; online 2013-04-15]

Ion Torrent sequencing and pipeline assembly of the first genome sequence of a mesophilic syntrophic acetate oxidizing bacterium (SAOB)

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

EMBnet j. 19 (A) 60 [2013-04-08; online 2013-04-08]

Metagenomics sample preparation and sequencing.

Karlsson OE, Norling M, Bongcam-Rudloff E

EMBnet j. 19 (A) 55 [2013-04-08; online 2013-04-08]

European H16N3 gull influenza virus attaches to the human respiratory tract and eye.

Lindskog C, Ellström P, Olsen B, ..., Kuiken T, Jourdain E

pmc

PLoS ONE 8 (4) e60757 [2013-04-08; online 2013-04-08]

Viral Metagenomics – New applications for the broad-range detection of viromes in veterinary and public health settings

Karlsson OE, Norling M, Granberg F, Belák S, Bongcam-Rudloff E

EMBnet j. 19 (A) 21 [2013-04-08; online 2013-04-08]

The molecular genetic architecture of self-employment.

van der Loos MJHM, Rietveld CA, Eklund N, ..., Hofman A, Thurik AR

pmc

PLoS ONE 8 (4) e60542 [2013-04-04; online 2013-04-04]

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

Systematic antibody generation and validation via tissue microarray technology leading to identification of a novel protein prognostic panel in breast cancer.

O Leary PC, Penny SA, Dolan RT, ..., Jirström K, Gallagher WM

pmc

BMC Cancer 13 (-) 175 [2013-04-02; online 2013-04-02]

Genetic determinants of dabigatran plasma levels and their relation to bleeding.

Paré G, Eriksson N, Lehr T, ..., Yusuf S, Wallentin L

ClinicalTrials.gov

Circulation 127 (13) 1404-1412 [2013-04-02; online 2013-03-08]

Interaction between retinoid acid receptor-related orphan receptor alpha (RORA) and neuropeptide S receptor 1 (NPSR1) in asthma.

Acevedo N, Sääf A, Söderhäll C, ..., Kere J, Pulkkinen V

pmc

PLoS ONE 8 (4) e60111 [2013-04-02; online 2013-04-02]

β-thymosins and hemocyte homeostasis in a crustacean.

Saelee N, Noonin C, Nupan B, ..., Söderhäll K, Söderhäll I

pmc

PLoS ONE 8 (4) e60974 [2013-04-02; online 2013-04-02]

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

RNA-binding protein QKI regulates Glial fibrillary acidic protein expression in human astrocytes.

Radomska KJ, Halvardson J, Reinius B, ..., Feuk L, Jazin E

Hum. Mol. Genet. 22 (7) 1373-1382 [2013-04-01; online 2013-01-17]

The transporter ABCB7 is a mediator of the phenotype of acquired refractory anemia with ring sideroblasts.

Nikpour M, Scharenberg C, Liu A, ..., Grandien A, Hellström-Lindberg E

pmc mid

Leukemia 27 (4) 889-896 [2013-04-00; online 2012-10-17]

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

Comparative genomics of Wolbachia and the bacterial species concept.

Ellegaard KM, Klasson L, Näslund K, Bourtzis K, Andersson SG

pmc

PLoS Genet. 9 (4) e1003381 [2013-04-00; online 2013-04-04]

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

Lack of dosage compensation accompanies the arrested stage of sex chromosome evolution in ostriches.

Adolfsson S, Ellegren H

pmc

Mol. Biol. Evol. 30 (4) 806-810 [2013-04-00; online 2013-01-19]

Degradation of Scots pine and beech wood exposed in four test fields used for testing of wood preservatives

Råberg U, Terziev N, Daniel G

International Biodeterioration & Biodegradation 79 (-) 20-27 [2013-04-00; online 2013-04-00]

Hereditary uveal melanoma: a report of a germline mutation in BAP1.

Höiom V, Edsgärd D, Helgadottir H, ..., Emanuelsson O, Hansson J

Genes Chromosomes Cancer 52 (4) 378-384 [2013-04-00; online 2013-01-24]

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

Identification of seven loci affecting mean telomere length and their association with disease.

Codd V, Nelson CP, Albrecht E, ..., van der Harst P, Samani NJ

pmc mid

Nat. Genet. 45 (4) 422-7, 427e1-2 [2013-04-00; online 2013-03-29]

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

Modelling the effects of dispersal mechanisms and hydrodynamic regimes upon the structure of microbial communities within fluvial biofilms.

Woodcock S, Besemer K, Battin TJ, Curtis TP, Sloan WT

Environ. Microbiol. 15 (4) 1216-1225 [2013-04-00; online 2012-12-18]

The mitochondrial and autosomal mutation landscapes of prostate cancer.

Lindberg J, Mills IG, Klevebring D, ..., Egevad L, Grönberg H

Eur. Urol. 63 (4) 702-708 [2013-04-00; online 2012-12-26]

Karolinska High Throughput Center (KHTC) NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

Immunofluorescence and fluorescent-protein tagging show high correlation for protein localization in mammalian cells.

Stadler C, Rexhepaj E, Singan VR, ..., Simpson JC, Lundberg E

Nat. Methods 10 (4) 315-323 [2013-04-00; online 2013-02-26]

Welander distal myopathy caused by an ancient founder mutation in TIA1 associated with perturbed splicing.

Klar J, Sobol M, Melberg A, ..., Casar-Borota O, Dahl N

Hum. Mutat. 34 (4) 572-577 [2013-04-00; online 2013-01-26]

Automated classification of immunostaining patterns in breast tissue from the human protein atlas.

Swamidoss IN, Kårsnäs A, Uhlmann V, ..., Wählby C, Strand R

pmc

J Pathol Inform 4 (Suppl) S14 [2013-03-30; online 2013-03-30]

BioImage Informatics [Technology development] Tissue Profiling

Genetic variants from lipid-related pathways and risk for incident myocardial infarction.

Song C, Pedersen NL, Reynolds CA, ..., Prince JA, Ingelsson E

pmc

PLoS ONE 8 (3) e60454 [2013-03-29; online 2013-03-29]

Transcriptome profiling of Giardia intestinalis using strand-specific RNA-seq.

Franzén O, Jerlström-Hultqvist J, Einarsson E, ..., Andersson B, Svärd SG

pmc GEO

PLoS Comput. Biol. 9 (3) e1003000 [2013-03-28; online 2013-03-28]

Optimizing Solubility and Permeability of a Biopharmaceutics Classification System (BCS) Class 4 Antibiotic Drug Using Lipophilic Fragments Disturbing the Crystal Lattice

Tehler U, Fagerberg JH, Svensson R, ..., Artursson P, Bergström CAS

J. Med. Chem. 56 (6) 2690-2694 [2013-03-28; online 2013-03-28]

Chemical Biology Consortium Sweden (CBCS) [Technology development]

Offshoots of the ESF functional genomics programme.

Landegren U

N Biotechnol 30 (3) 296-298 [2013-03-25; online 2013-01-09]

Patchwork: allele-specific copy number analysis of whole-genome sequenced tumor tissue.

Mayrhofer M, DiLorenzo S, Isaksson A

pmc

Genome Biol. 14 (3) R24 [2013-03-25; online 2013-03-25]

Genome Sequence of a Plant-Associated Bacterium, Bacillus amyloliquefaciens Strain UCMB5036.

Manzoor S, Niazi A, Bejai S, Meijer J, Bongcam-Rudloff E

pmc

Genome Announc 1 (2) e0011113 [2013-03-21; online 2013-03-21]

Integration of clinical data with a genome-scale metabolic model of the human adipocyte.

Mardinoglu A, Agren R, Kampf C, ..., Uhlen M, Nielsen J

pmc

Mol. Syst. Biol. 9 (-) 649 [2013-03-21; online 2013-03-21]

The genomic signature of dog domestication reveals adaptation to a starch-rich diet.

Axelsson E, Ratnakumar A, Arendt M, ..., Hedhammar A, Lindblad-Toh K

Nature 495 (7441) 360-364 [2013-03-21; online 2013-01-29]

Identification of genetic variants influencing the human plasma proteome.

Johansson Å, Enroth S, Palmblad M, ..., Bergquist J, Gyllensten U

pmc

Proc. Natl. Acad. Sci. U.S.A. 110 (12) 4673-4678 [2013-03-19; online 2013-03-15]

Identification and verification of microRNAs by high-throughput sequencing.

Hällman J, Avesson L, Reimegård J, Käller M, Söderbom F

Methods Mol. Biol. 983 (-) 125-138 [2013-03-16; online 2013-03-16]

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

DNA topoisomerase III localizes to centromeres and affects centromeric CENP-A levels in fission yeast.

Norman-Axelsson U, Durand-Dubief M, Prasad P, Ekwall K

pmc

PLoS Genet. 9 (3) e1003371 [2013-03-14; online 2013-03-14]

Transcriptome of the alternative ethanol production strain Dekkera bruxellensis CBS 11270 in sugar limited, low oxygen cultivation.

Tiukova IA, Petterson ME, Tellgren-Roth C, ..., Pettersson OV, Passoth V

pmc

PLoS ONE 8 (3) e58455 [2013-03-13; online 2013-03-13]

Gene rearrangements in hormone receptor negative breast cancers revealed by mate pair sequencing.

Jiao X, Hooper SD, Djureinovic T, ..., Botling J, Sjöblom T

pmc

BMC Genomics 14 (-) 165 [2013-03-12; online 2013-03-12]

The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary.

Mayer G, Montecchi-Palazzi L, Ovelleiro D, ..., Eisenacher M, HUPO-PSI Group

pmc

Database (Oxford) 2013 (-) bat009 [2013-03-12; online 2013-03-12]

Hierarchical molecular tagging to resolve long continuous sequences by massively parallel sequencing.

Lundin S, Gruselius J, Nystedt B, ..., Käller M, Lundeberg J

pmc

Sci Rep 3 (-) 1186 [2013-03-09; online 2013-03-09]

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

Recognition of mono-ADP-ribosylated ARTD10 substrates by ARTD8 macrodomains.

Forst AH, Karlberg T, Herzog N, ..., Schüler H, Lüscher B

PDB PDB PDB PDB PDB PDB PDB

Structure 21 (3) 462-475 [2013-03-05; online 2013-03-12]

TagGD: fast and accurate software for DNA Tag generation and demultiplexing.

Costea PI, Lundeberg J, Akan P

pmc

PLoS ONE 8 (3) e57521 [2013-03-04; online 2013-03-04]

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

Secretion of two novel enzymes, manganese 9S-lipoxygenase and epoxy alcohol synthase, by the rice pathogen Magnaporthe salvinii.

Wennman A, Oliw EH

pmc

J. Lipid Res. 54 (3) 762-775 [2013-03-00; online 2012-12-13]

A genome-wide assessment of variability in human serum metabolism.

Hong MG, Karlsson R, Magnusson PK, ..., Wiklund F, Prince JA

Hum. Mutat. 34 (3) 515-524 [2013-03-00; online 2013-01-03]

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

Genetic effects on old-age cognitive functioning: a population-based study.

Laukka EJ, Lövdén M, Herlitz A, ..., Fratiglioni L, Bäckman L

Psychol Aging 28 (1) 262-274 [2013-03-00; online 2013-01-02]

Genetic determinants of plasma β₂-glycoprotein I levels: a genome-wide association study in extended pedigrees from Spain.

Athanasiadis G, Sabater-Lleal M, Buil A, ..., Hamsten A, Soria JM

J. Thromb. Haemost. 11 (3) 521-528 [2013-03-00; online 2013-01-03]

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

Structure of LdtMt2, an L,D-transpeptidase from Mycobacterium tuberculosis.

Böth D, Steiner EM, Stadler D, ..., Schnell R, Schneider G

pmc PDB PDB

Acta Crystallogr. D Biol. Crystallogr. 69 (Pt 3) 432-441 [2013-03-00; online 2013-02-16]

Determination of the obesity-associated gene variants within the entire FTO gene by ultra-deep targeted sequencing in obese and lean children.

Sällman Almén M, Rask-Andersen M, Jacobsson JA, ..., Fredriksson R, Schiöth HB

pmc

Int J Obes (Lond) 37 (3) 424-431 [2013-03-00; online 2012-04-26]

A gene transfer agent and a dynamic repertoire of secretion systems hold the keys to the explosive radiation of the emerging pathogen Bartonella.

Guy L, Nystedt B, Toft C, ..., Eriksson AS, Andersson SG

pmc

PLoS Genet. 9 (3) e1003393 [2013-03-00; online 2013-03-28]

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

A modified Glenn shunt improves haemodynamics in acute right ventricular failure in an experimental model.

Vikholm P, Schiller P, Johansson J, Hellgren L

Eur J Cardiothorac Surg 43 (3) 612-618 [2013-03-00; online 2012-07-05]

The effect of substrate and operational parameters on the abundance of sulphate-reducing bacteria in industrial anaerobic biogas digesters.

Moestedt J, Nilsson Påledal S, Schnürer A

Bioresour. Technol. 132 (-) 327-332 [2013-03-00; online 2013-02-19]

Oral rehydration solution with glycerol to dairy calves: Effects on fluid balance, metabolism, and intestinal microbiota

Omazic AW, Tråvén M, Roos S, Mellgren E, Holtenius K

Acta Agriculturae Scandinavica, Section A - Animal Science 63 (1) 47-56 [2013-03-00; online 2013-03-00]

Astakine 2--the dark knight linking melatonin to circadian regulation in crustaceans.

Watthanasurorot A, Saelee N, Phongdara A, ..., Söderhäll K, Söderhäll I

pmc

PLoS Genet. 9 (3) e1003361 [2013-03-00; online 2013-03-21]

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

Brain gene expression differences are associated with abnormal tail biting behavior in pigs.

Brunberg E, Jensen P, Isaksson A, Keeling LJ

Genes Brain Behav. 12 (2) 275-281 [2013-03-00; online 2012-11-14]

Higher magnesium intake is associated with lower fasting glucose and insulin, with no evidence of interaction with select genetic loci, in a meta-analysis of 15 CHARGE Consortium Studies.

Hruby A, Ngwa JS, Renström F, ..., McKeown NM, Nettleton JA

pmc

J. Nutr. 143 (3) 345-353 [2013-03-00; online 2013-01-25]

Fine-mapping of restless legs locus 4 (RLS4) identifies a haplotype over the SPATS2L and KCTD18 genes.

Pichler I, Schwienbacher C, Zanon A, ..., Hicks AA, Pramstaller PP

J. Mol. Neurosci. 49 (3) 600-605 [2013-03-00; online 2012-10-12]

Metagenomic detection of viral pathogens in Spanish honeybees: co-infection by Aphid Lethal Paralysis, Israel Acute Paralysis and Lake Sinai Viruses.

Granberg F, Vicente-Rubiano M, Rubio-Guerri C, ..., Belák S, Sánchez-Vizcaíno JM

pmc

PLoS ONE 8 (2) e57459 [2013-02-27; online 2013-02-27]

Origin and evolution of medium chain alcohol dehydrogenases.

Jörnvall H, Hedlund J, Bergman T, ..., Cederlund E, Persson B

Chem. Biol. Interact. 202 (1-3) 91-96 [2013-02-25; online 2012-12-04]

Classification and nomenclature of the superfamily of short-chain dehydrogenases/reductases (SDRs).

Persson B, Kallberg Y

Chem. Biol. Interact. 202 (1-3) 111-115 [2013-02-25; online 2012-12-04]

Evolution of sperm structure and energetics in passerine birds.

Rowe M, Laskemoen T, Johnsen A, Lifjeld JT

pmc

Proc. Biol. Sci. 280 (1753) 20122616 [2013-02-22; online 2013-01-04]

Imatinib ameliorates neuroinflammation in a rat model of multiple sclerosis by enhancing blood-brain barrier integrity and by modulating the peripheral immune response.

Adzemovic MV, Adzemovic MZ, Zeitelhofer M, ..., Olsson T, Nilsson I

pmc

PLoS ONE 8 (2) e56586 [2013-02-20; online 2013-02-20]

The synthetic progestin levonorgestrel is a potent androgen in the three-spined stickleback (Gasterosteus aculeatus).

Svensson J, Fick J, Brandt I, Brunström B

Environ. Sci. Technol. 47 (4) 2043-2051 [2013-02-19; online 2013-02-01]

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

STC1 expression by cancer-associated fibroblasts drives metastasis of colorectal cancer.

Peña C, Céspedes MV, Lindh MB, ..., Augsten M, Ostman A

Cancer Res. 73 (4) 1287-1297 [2013-02-15; online 2012-12-18]

Coastal bacterioplankton community dynamics in response to a natural disturbance.

Yeo SK, Huggett MJ, Eiler A, Rappé MS

pmc

PLoS ONE 8 (2) e56207 [2013-02-07; online 2013-02-07]

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

Causal relationship between obesity and vitamin D status: bi-directional Mendelian randomization analysis of multiple cohorts.

Vimaleswaran KS, Berry DJ, Lu C, ..., Hingorani AD, Hyppönen E

pmc

PLoS Med. 10 (2) e1001383 [2013-02-05; online 2013-02-05]

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

FANTOM: Functional and taxonomic analysis of metagenomes.

Sanli K, Karlsson FH, Nookaew I, Nielsen J

pmc

BMC Bioinformatics 14 (-) 38 [2013-02-01; online 2013-02-01]

Olfactory receptor 51E1 protein as a potential novel tissue biomarker for small intestine neuroendocrine carcinomas.

Cui T, Tsolakis AV, Li S, ..., Öberg K, Giandomenico V

Eur. J. Endocrinol. 168 (2) 253-261 [2013-02-00; online 2012-11-28]

Epigenome-wide association data implicate DNA methylation as an intermediary of genetic risk in rheumatoid arthritis.

Liu Y, Aryee MJ, Padyukov L, ..., Ekström TJ, Feinberg AP

pmc mid GEO

Nat. Biotechnol. 31 (2) 142-147 [2013-02-00; online 2013-01-22]

Early cone setting in Picea abies acrocona is associated with increased transcriptional activity of a MADS box transcription factor.

Uddenberg D, Reimegård J, Clapham D, ..., Emanuelsson O, Sundström JF

pmc

Plant Physiol. 161 (2) 813-823 [2013-02-00; online 2012-12-12]

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

The Swedish Twin Registry: establishment of a biobank and other recent developments.

Magnusson PKE, Almqvist C, Rahman I, ..., Pedersen NL, Lichtenstein P

Twin Res Hum Genet 16 (1) 317-329 [2013-02-00; online 2012-11-10]

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

In vitro and in vivo activities of 2-aminopyrazines and 2-aminopyridines in experimental models of human African trypanosomiasis.

Vodnala SK, Lundbäck T, Sjöberg B, ..., Rottenberg ME, Hammarström LGJ

pmc

Antimicrob. Agents Chemother. 57 (2) 1012-1018 [2013-02-00; online 2012-12-21]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Sequence variation in mitochondrial ATP synthase subunit 6 & 8 and nuclear genes ITS1 and ITS2 in 17 cyprinid species

Demandt MH

J. Appl. Ichthyol. 29 (1) 278-280 [2013-02-00; online 2012-06-22]

Exome sequencing of prostate cancer supports the hypothesis of independent tumour origins.

Lindberg J, Klevebring D, Liu W, ..., Egevad L, Grönberg H

Eur. Urol. 63 (2) 347-353 [2013-02-00; online 2012-04-17]

Karolinska High Throughput Center (KHTC) NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

An MBL-like protein may interfere with the activation of the proPO-system, an important innate immune reaction in invertebrates.

Wu C, Charoensapsri W, Nakamura S, ..., Söderhäll I, Söderhäll K

Immunobiology 218 (2) 159-168 [2013-02-00; online 2012-03-31]

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

Adipose tissue resting energy expenditure and expression of genes involved in mitochondrial function are higher in women than in men.

Nookaew I, Svensson PA, Jacobson P, ..., Nielsen J, Carlsson LM

pmc

J. Clin. Endocrinol. Metab. 98 (2) E370-E378 [2013-02-00; online 2012-12-25]

Early-phase GVHD gene expression profile in target versus non-target tissues: kidney, a possible target?

Sadeghi B, Al-Chaqmaqchi H, Al-Hashmi S, ..., Moshfegh A, Hassan M

Bone Marrow Transplant. 48 (2) 284-293 [2013-02-00; online 2012-07-25]

The phylogeographic pattern of Francisella tularensis in Sweden indicates a Scandinavian origin of Eurosiberian tularaemia.

Karlsson E, Svensson K, Lindgren P, ..., Forsman M, Johansson A

Environ. Microbiol. 15 (2) 634-645 [2013-02-00; online 2012-12-21]

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

First insights into the syntrophic acetate-oxidizing bacteria--a genetic study.

Müller B, Sun L, Schnürer A

pmc GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK

Microbiologyopen 2 (1) 35-53 [2013-02-00; online 2012-12-15]

Population pharmacokinetic modeling and deconvolution of enantioselective absorption of eflornithine in the rat

Johansson CC, Gennemark P, Artursson P, ..., Ashton M, Jansson-Löfmark R

J Pharmacokinet Pharmacodyn 40 (1) 117-128 [2013-02-00; online 2013-01-10]

Chemical Biology Consortium Sweden (CBCS) [Service]

A gene-centric study of common carotid artery remodelling.

Harrison SC, Zabaneh D, Asselbergs FW, ..., Hamsten A, Humphries SE

pmc

Atherosclerosis 226 (2) 440-446 [2013-02-00; online 2012-12-19]

Genome-wide association analyses identify 18 new loci associated with serum urate concentrations.

Köttgen A, Albrecht E, Teumer A, ..., Bochud M, Gieger C

pmc mid

Nat. Genet. 45 (2) 145-154 [2013-02-00; online 2012-12-25]

Workshop on laboratory protocol standards for the Molecular Methods Database.

Klingström T, Soldatova L, Stevens R, ..., Landegren U, Bongcam-Rudloff E

N Biotechnol 30 (2) 109-113 [2013-01-25; online 2012-06-13]

Protein tag-mediated conjugation of oligonucleotides to recombinant affinity binders for proximity ligation.

Gu GJ, Friedman M, Jost C, ..., Landegren U, Söderberg O

N Biotechnol 30 (2) 144-152 [2013-01-25; online 2012-06-06]

Multiplex protein detection with DNA readout via mass spectrometry.

Flanigon J, Kamali-Moghaddam M, Burbulis I, ..., Landegren U, Cantor C

pmc mid

N Biotechnol 30 (2) 153-158 [2013-01-25; online 2012-12-04]

DNA methylation in the Neuropeptide S Receptor 1 (NPSR1) promoter in relation to asthma and environmental factors.

Reinius LE, Gref A, Sääf A, ..., Söderhäll C, Kere J

pmc

PLoS ONE 8 (1) e53877 [2013-01-23; online 2013-01-23]

Unveiling distribution patterns of freshwater phytoplankton by a next generation sequencing based approach.

Eiler A, Drakare S, Bertilsson S, ..., Znachor P, Lindström ES

pmc

PLoS ONE 8 (1) e53516 [2013-01-22; online 2013-01-22]

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

Genomic insights into the atopic eczema-associated skin commensal yeast Malassezia sympodialis.

Gioti A, Nystedt B, Li W, ..., Heitman J, Scheynius A

MBio 4 (1) e00572-e00512 [2013-01-22; online 2013-01-22]

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

DNA-binding specificities of human transcription factors.

Jolma A, Yan J, Whitington T, ..., Kivioja T, Taipale J

Cell 152 (1-2) 327-339 [2013-01-17; online 2013-01-22]

Karolinska High Throughput Center (KHTC)

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

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

pmc

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, Lemaitre RN, ..., Meigs JB, Franks PW

pmc

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.

Teschendorff AE, Marabita F, Lechner M, ..., Gomez-Cabrero D, Beck S

pmc

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

Gene expression deregulation in postnatal skeletal muscle of TK2 deficient mice reveals a lower pool of proliferating myogenic progenitor cells.

Paredes JA, Zhou X, Höglund S, Karlsson A

pmc

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

Exome RNA sequencing reveals rare and novel alternative transcripts.

Halvardson J, Zaghlool A, Feuk L

pmc

Nucleic Acids Res. 41 (1) e6 [2013-01-07; online 2012-09-04]

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

Liu S, Im H, Bairoch A, ..., Beavis RC, Hancock WS

pmc mid

J. Proteome Res. 12 (1) 45-57 [2013-01-04; online 2012-12-25]

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

Danielsson F, Wiking M, Mahdessian D, ..., Uhlén M, Lundberg E

J. Proteome Res. 12 (1) 299-307 [2013-01-04; online 2012-12-12]

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

Botling J, Edlund K, Lohr M, ..., 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

International Journal of Circumpolar Health 72 (1) 22447 [2013-01-00; online 2013-08-05]

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

CARDIoGRAMplusC4D Consortium N, Deloukas P, Kanoni S, ..., Schunkert H, Samani NJ

pmc mid

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, Kanduri M, ..., Rosén A, Rosenquist R

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

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

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

Forsberg LA, Absher D, Dumanski JP

pmc

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

pmc

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, Hagberg N, ..., 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]