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

pii: mp2012112

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

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

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

pii: S0160-4120(13)00152-9

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

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

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

pii: PONE-D-13-21713 pmc: PMC3756986

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

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

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

pii: 000353734

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

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

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) National Genomics Infrastructure

Svartström O, Mushtaq M, Pringle M, Segerman B

pii: PONE-D-13-11951 pmc: PMC3747143

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

pii: 1472-6750-13-66 pmc: PMC3751724

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

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

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

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

PDB: 4GV0 PDB: 4GV2 PDB: 4GV4 PDB: 4GV7

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

pii: S0092-8674(13)00942-2 GEO: GSE48448 GEO: GSE49402

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

pii: ddt188

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

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

pii: PONE-D-13-07092 pmc: PMC3744548

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

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

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

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

pii: PONE-D-13-14318 pmc: PMC3742741 PDB: 4JZL PDB: 4JZP

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

pii: S0002-9297(13)00280-2 pmc: PMC3738834

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

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

pii: PONE-D-13-13063 pmc: PMC3734246

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

pii: S0014-5793(13)00442-0

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

Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

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

pii: 1742-2094-10-99 pmc: PMC3750454

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

pii: S0042-6822(13)00200-6

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

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

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]

Translational 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]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

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

pii: 1358863X13496488

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

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

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

pii: nsmb.2611 pmc: PMC4972576 mid: CAMS4086 PDB: 4B0A

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

pii: jmedgenet-2013-101654

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

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

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

pii: O112.023804 pmc: PMC3734588

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

pii: AEM.01390-13 pmc: PMC3754708

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

Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

New viruses in veterinary medicine, detected by metagenomic approaches.

Belák S, Karlsson OE, Blomström AL, Berg M, Granberg F

pii: S0378-1135(13)00074-6

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

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

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

pii: PGENETICS-D-12-03208 pmc: PMC3723486

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

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

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

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

pii: 5/195/195ra96 pmc: PMC4237161 mid: NIHMS638202

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

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

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

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

pii: ncomms3175 pmc: PMC3759040

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

pii: PONE-D-13-05381 pmc: PMC3720532

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

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

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

pii: S0360-3016(13)00217-4

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

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

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

pii: PONE-D-13-13943 pmc: PMC3707873

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

pii: PONE-D-13-01978 pmc: PMC3699592

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

pii: ddt104 pmc: PMC3674797

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

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

pii: ismej201326 pmc: PMC3695292

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

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

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

pii: mp201286

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

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

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

Forsberg LA, Absher D, Dumanski JP

pii: postgradmedj-2012-101322rep pmc: PMC3711362

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

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

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

pii: gkt267 pmc: PMC3695526

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

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

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

pii: jc.2012-4257

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

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

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

pii: bgt067

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

pii: S0166-3542(13)00117-4

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

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

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]

Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

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

pii: npp201349 pmc: PMC3682145

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

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

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: PMC3721474

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) National Genomics Infrastructure

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

pii: S1769-7212(13)00091-8

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

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

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

Ducani C, Kaul C, Moche M, Shih WM, Högberg B

pii: nmeth.2503 pmc: PMC3843646 mid: NIHMS528250 PDB: 4B8D

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

pii: PONE-D-12-36687 pmc: PMC3696016

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

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

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

Johansson A, Enroth S, Gyllensten U

pii: PONE-D-13-02458 pmc: PMC3695075

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

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

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

pii: S0022-2836(13)00173-3 PDB: 3ZLC

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

pii: PMEDICINE-D-12-03573 pmc: PMC3692470

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

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

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

pii: 2047-217X-2-9 pmc: PMC3704847

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

Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

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

Chen MW, Lohkamp B, Schnell R, Lescar J, Schneider G

pii: PONE-D-13-09972 pmc: PMC3689657

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

pii: science.1235488 pmc: PMC3751588 mid: NIHMS495960

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

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [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 Bioinformatics Support, Infrastructure and Training 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

pii: PONE-D-12-16862 pmc: PMC3688911

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]

Translational Plasma Profiling [Technology development]

Molecular genetics and subjective well-being.

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

pii: 1222171110 pmc: PMC3683731

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) National Genomics Infrastructure

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

pii: S0304-3835(13)00080-3

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) National Genomics Infrastructure 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

pii: PONE-D-12-31749 pmc: PMC3675104

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

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

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

pii: EC130009 pmc: PMC3682230

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

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

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

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

pii: O112.023374 pmc: PMC3675814

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

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure 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

pii: ng.2610 pmc: PMC3696959 mid: NIHMS473857

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

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

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

pii: CIRCGENETICS.113.000044

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

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

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

pii: pp.113.214643 pmc: PMC3668067 GENBANK: ACN49932 GENBANK: TC161203 GEO: GSE28755

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

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

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

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

pii: M112.024919 pmc: PMC3675825

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

pii: S0887-2333(12)00217-2

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

pii: nprot.2013.070

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

pii: gene20139

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

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

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: JX243015 GENBANK: JX243021

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

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Sortilin receptor 1 predicts longitudinal cognitive change.

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

pii: S0197-4580(12)00621-5 pmc: PMC3839667 mid: NIHMS435934

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

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

pii: S0145-305X(13)00057-8

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) National Genomics Infrastructure

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

pii: jlr.M035410 pmc: PMC3646464

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

pii: PGENETICS-D-12-01098 pmc: PMC3674993

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

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

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

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

pii: nsmb.2569 PDB: 4JA3 PDB: 4JA4

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

pii: S0959-440X(13)00043-2

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

Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

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]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

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

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

pii: gene201312

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

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

The Norway spruce genome sequence and conifer genome evolution.

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

pii: nature12211

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

Bioinformatics Compute and Storage Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

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

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

pii: mBio.00569-12 pmc: PMC3663571 GENBANK: ADX05696 GENBANK: AF217460 GENBANK: AF217461 GENBANK: AF217462

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

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

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

pii: 1305358110 pmc: PMC3666699

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

pii: PONE-D-12-33946 pmc: PMC3656869

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

pii: PONE-D-13-05699 pmc: PMC3651199

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

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

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

pii: 1471-2407-13-231 pmc: PMC3664071

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

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

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

pii: gkt225 pmc: PMC3664812

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

pii: djt051

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

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

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

pii: gkt172 pmc: PMC3643585

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

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

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

pii: ATVBAHA.112.300353

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

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

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]

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

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

pii: ng.2606 pmc: PMC3973018 mid: NIHMS536922

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

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

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

pii: S1055-7903(13)00051-1

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

Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

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

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

pii: O112.021907 pmc: PMC3650348

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

Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

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]

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

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]

Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

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]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

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

pii: PGENETICS-D-12-01656 pmc: PMC3649999

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

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

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

pii: nts207

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

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

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

Light S, Sagit R, Ekman D, Elofsson A

pii: S1570-9639(13)00007-1

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

Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

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]

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

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

pii: S0920-9964(13)00113-8 pmc: PMC3650833 mid: NIHMS450150

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

pii: 1220010110 pmc: PMC3645538

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) National Genomics Infrastructure

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

pii: 1216436110 pmc: PMC3637701

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

pii: M113.458257 pmc: PMC3630850

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

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

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

pii: ajpregu.00599.2012 pmc: PMC3627950

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: PMC3654255

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]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Metagenomics sample preparation and sequencing.

Karlsson OE, Norling M, Bongcam-Rudloff E

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

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

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

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

pii: PONE-D-12-38518 pmc: PMC3620227

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]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

The molecular genetic architecture of self-employment.

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

pii: PONE-D-12-39282 pmc: PMC3617140

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

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

pii: 1471-2407-13-175 pmc: PMC3668187

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

pii: CIRCULATIONAHA.112.001233 ClinicalTrials.gov: NCT00262600

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

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

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

pii: PONE-D-12-35098 pmc: PMC3615072

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

pii: PONE-D-13-03793 pmc: PMC3614969

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

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

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

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

pii: dds553

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

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

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

pii: leu2012298 pmc: PMC3794445 mid: EMS53907

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

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

Comparative genomics of Wolbachia and the bacterial species concept.

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

pii: PGENETICS-D-12-02380 pmc: PMC3616963

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) National Genomics Infrastructure

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

Adolfsson S, Ellegren H

pii: mst009 pmc: PMC3603317

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

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

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]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

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) National Genomics Infrastructure

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

pii: ng.2528 pmc: PMC4006270 mid: NIHMS571267

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

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

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]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

The mitochondrial and autosomal mutation landscapes of prostate cancer.

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

pii: S0302-2838(12)01438-8

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) National Genomics Infrastructure

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

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

pii: nmeth.2377

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]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

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

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

pii: JPI-4-14 pmc: PMC3678740

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

pii: PONE-D-12-11381 pmc: PMC3612051

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

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

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

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

pii: PCOMPBIOL-D-12-01572 pmc: PMC3610916 GEO: GSE36490

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

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

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

pii: S1871-6784(12)00900-4

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

pii: gb-2013-14-3-r24 pmc: PMC4053982

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

pii: 1/2/e00111-13 pmc: PMC3622975

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

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

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

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

pii: msb20135 pmc: PMC3619940

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

pii: nature11837

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

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Identification of genetic variants influencing the human plasma proteome.

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

pii: 1217238110 pmc: PMC3606982

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

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

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) National Genomics Infrastructure

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

pii: PGENETICS-D-12-01254 pmc: PMC3597498

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

pii: PONE-D-12-35813 pmc: PMC3596373

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

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

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

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

pii: 1471-2164-14-165 pmc: PMC3600027

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

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary.

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

pii: bat009 pmc: PMC3594986

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

Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

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

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

pii: srep01186 pmc: PMC3592332

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

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

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

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

pii: S0969-2126(13)00019-1 PDB: 3Q6Z PDB: 3Q71 PDB: 3V2B PDB: 3VFQ PDB: 4ABK PDB: 4ABL PDB: 4D86

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

pii: PONE-D-12-34651 pmc: PMC3587622

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

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

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

Wennman A, Oliw EH

pii: jlr.M033787 pmc: PMC3617950

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

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

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) National Genomics Infrastructure

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

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

pii: 2012-34905-001

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) National Genomics Infrastructure

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

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

pii: S0907444912049268 pmc: PMC3605044 PDB: 4HU2 PDB: 4HUC

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

pii: ijo201257 pmc: PMC3595467

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

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

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

pii: PGENETICS-D-12-01962 pmc: PMC3610622

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

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

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

Vikholm P, Schiller P, Johansson J, Hellgren L

pii: ezs386

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

pii: S0960-8524(13)00066-7

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

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

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]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

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

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

pii: PGENETICS-D-12-01816 pmc: PMC3605217

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

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

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

pii: jn.112.172049 pmc: PMC3713023

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

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

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]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

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

pii: PONE-D-12-15653 pmc: PMC3583878

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

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

Origin and evolution of medium chain alcohol dehydrogenases.

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

pii: S0009-2797(12)00252-9

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

Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

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

Persson B, Kallberg Y

pii: S0009-2797(12)00253-0

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

Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Evolution of sperm structure and energetics in passerine birds.

Rowe M, Laskemoen T, Johnsen A, Lifjeld JT

pii: rspb.2012.2616 pmc: PMC3574354

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

Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

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

pii: PONE-D-12-27544 pmc: PMC3577871

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) National Genomics Infrastructure

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

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

pii: 0008-5472.CAN-12-1875

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

pii: PONE-D-12-27911 pmc: PMC3567041

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

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

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

pii: PMEDICINE-D-12-01552 pmc: PMC3564800

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

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

FANTOM: Functional and taxonomic analysis of metagenomes.

Sanli K, Karlsson FH, Nookaew I, Nielsen J

pii: 1471-2105-14-38 pmc: PMC3566963

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

Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

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

pii: EJE-12-0814

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

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

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

pii: nbt.2487 pmc: PMC3598632 mid: NIHMS430504 GEO: GSE42861

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

pii: pp.112.207746 pmc: PMC3561021

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

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

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

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

pii: S1832427412001041

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

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

pii: AAC.01870-12 pmc: PMC3553678

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]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

A versatile genome-scale PCR-based pipeline for high-definition DNA FISH.

Bienko M, Crosetto N, Teytelman L, ..., Itzkovitz S, van Oudenaarden A

pmc: PMC3735345 mid: NIHMS500266

Nat. Methods 10 (2) 122-124 [2013-02-00; online 2012-12-23]

Advanced FISH Technologies [Technology development]

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

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

pii: S0302-2838(12)00402-2

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) National Genomics Infrastructure

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

pii: S0171-2985(12)00056-3

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

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

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

pii: jc.2012-2764 pmc: PMC3633773

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

Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

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

pii: bmt2012120

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) National Genomics Infrastructure

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

Müller B, Sun L, Schnürer A

pmc: PMC3584212 GENBANK: JQ979072 GENBANK: JQ979073 GENBANK: JQ979074 GENBANK: JQ979075 GENBANK: JQ979076 GENBANK: JQ979077

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

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

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

pii: S0021-9150(12)00797-6 pmc: PMC3573227

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

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

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

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

pii: ng.2500 pmc: PMC3663712 mid: NIHMS458823

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

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

Workshop on laboratory protocol standards for the Molecular Methods Database.

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

pii: S1871-6784(12)00121-5

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

pii: S1871-6784(12)00107-0

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

pii: S1871-6784(12)00860-6 pmc: PMC3616745 mid: NIHMS425130

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

pii: PONE-D-12-14529 pmc: PMC3553086

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

pii: PONE-D-12-28577 pmc: PMC3551911

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

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

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

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

pii: mBio.00572-12 pmc: PMC3560662 GENBANK: HE999549 GENBANK: HE999550 GENBANK: HE999551 GENBANK: HE999552 GENBANK: HE999553 GENBANK: HE999554 GENBANK: HE999555 GENBANK: HE999556 GENBANK: HE999557 GENBANK: HE999558 GENBANK: HE999559 GENBANK: HE999560 GENBANK: HE999561 GENBANK: HE999562 GENBANK: HE999563 GENBANK: HE999564 GENBANK: HE999565 GENBANK: HE999566 GENBANK: HE999567 GENBANK: HE999568 GENBANK: HE999569 GENBANK: HE999570 GENBANK: HE999571 GENBANK: HE999572 GENBANK: HE999573 GENBANK: HE999574 GENBANK: HE999575 GENBANK: HE999576 GENBANK: HE999577 GENBANK: HE999578 GENBANK: HE999579 GENBANK: HE999580 GENBANK: HE999581 GENBANK: HE999582 GENBANK: HE999583 GENBANK: HE999584 GENBANK: HE999585 GENBANK: HE999586 GENBANK: HE999587 GENBANK: HE999588 GENBANK: HE999589 GENBANK: HE999590 GENBANK: HE999591 GENBANK: HE999592 GENBANK: HE999593 GENBANK: HE999594 GENBANK: HE999595 GENBANK: HE999596 GENBANK: HE999597 GENBANK: HE999598 GENBANK: HE999599 GENBANK: HE999600 GENBANK: HE999601 GENBANK: HE999602 GENBANK: HE999603 GENBANK: HE999604 GENBANK: HE999605 GENBANK: HE999606 GENBANK: HE999607 GENBANK: HE999608 GENBANK: HE999609 GENBANK: HE999610 GENBANK: HE999611 GENBANK: HE999612 GENBANK: HE999613 GENBANK: HF558646 GENBANK: JX964800 GENBANK: JX964801 GENBANK: JX964802 GENBANK: JX964840 GENBANK: JX964841 GENBANK: JX964842 GENBANK: JX964843 GENBANK: JX964844 GENBANK: JX964845 GENBANK: JX964846 GENBANK: JX964847 GENBANK: JX964848 GENBANK: JX964849 GENBANK: JX964850

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

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

DNA-binding specificities of human transcription factors.

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

pii: S0092-8674(12)01496-1

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

pii: PONE-D-12-26429 pmc: PMC3547014

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

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

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

pii: kws297 pmc: PMC3707424

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

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

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

pii: bts680 pmc: PMC3546795

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

Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

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

pii: PONE-D-12-23752 pmc: PMC3544874

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

pii: gks816 pmc: PMC3592422

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

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

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: PMC4142220 mid: NIHMS431316

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

pii: 1078-0432.CCR-12-1139

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]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Proceedings of the 15th International Congress on Circumpolar Health

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

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

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

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

pii: ng.2480 pmc: PMC3679547 mid: NIHMS468575

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

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

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

pii: leu2012245

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

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

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

Forsberg LA, Absher D, Dumanski JP

pii: jmedgenet-2012-101322 pmc: PMC3534255

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

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

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

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

pii: genomeA00213-12 pmc: PMC3587937

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

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

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

pii: annrheumdis-2012-201364

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

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

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]