Publications 2014

PubMed DOI Crossref

A novel cytosolic NADH:quinone oxidoreductase fromMethanothermobacter marburgensis

Ullmann E, Tan TC, Gundinger T, ..., Divne C, Spadiut O

PDB

Biosci. Rep. 34 (6) 893-904 [2014-12-23; online 2014-12-23]

Protein Science Facility (PSF) [Service]

PubMed DOI Crossref

Inhibitory Activity of the Isoflavone Biochanin A on Intracellular Bacteria of Genus Chlamydia and Initial Development of a Buccal Formulation

Hanski L, Genina N, Uvell H, ..., Sandler N, Vuorela PM

PLoS ONE 9 (12) e115115 [2014-12-16; online 2014-12-16]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

DOI Crossref

Exploration and Pharmacokinetic Profiling of Phenylalanine Based Carbamates as Novel Substance P 1–7 Analogues

Fransson R, Nordvall G, Bylund J, ..., Hallberg M, Sandström A

ACS Med Chem Lett 5 (12) 1272-1277 [2014-12-11; online 2014-12-11]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

PubMed DOI Crossref

Inhibition of tumor cell proliferation and motility by fibroblasts is both contact and soluble factor dependent.

Alkasalias T, Flaberg E, Kashuba V, ..., Klein G, Guven H

pii pmc GEO

Proc. Natl. Acad. Sci. U.S.A. 111 (48) 17188-17193 [2014-12-02; online 2014-11-19]

Bioinformatics Support and Infrastructure

PubMed DOI Crossref

Vinylated linear P2 pyrimidinyloxyphenylglycine based inhibitors of the HCV NS3/4A protease and corresponding macrocycles.

Lampa A, Alogheli H, Ehrenberg AE, ..., Karlén A, Sandström A

pii

Bioorg. Med. Chem. 22 (23) 6595-6615 [2014-12-01; online 2014-12-03]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

PubMed DOI Crossref

Both Lewis and secretor status mediate susceptibility to rotavirus infections in a rotavirus genotype-dependent manner.

Nordgren J, Sharma S, Bucardo F, ..., Larson G, Svensson L

pii pmc

Clin. Infect. Dis. 59 (11) 1567-1573 [2014-12-01; online 2014-08-07]

Mutation Analysis Facility (MAF)

PubMed DOI Crossref

An outbreak of respiratory tularemia caused by diverse clones of Francisella tularensis.

Johansson A, Lärkeryd A, Widerström M, ..., Forsman M, Larsson P

pii pmc

Clin. Infect. Dis. 59 (11) 1546-1553 [2014-12-01; online 2014-08-07]

NGI Uppsala (SNP&SEQ Technology Platform)

PubMed DOI Crossref

Inhibition of Insulin-Regulated Aminopeptidase (IRAP) by Arylsulfonamides.

Borhade SR, Rosenström U, Sävmarker J, ..., Larhed M, Hallberg M

pmc

ChemistryOpen 3 (6) 256-263 [2014-12-00; online 2014-11-21]

Chemical Biology Consortium Sweden (CBCS) [Collaborative] Drug Discovery and Development (DDD) [Collaborative]

PubMed DOI Crossref

Donor or recipient origin of posttransplant lymphoproliferative disorders following solid organ transplantation.

Kinch A, Cavelier L, Bengtsson M, ..., Sundström C, Pauksens K

Am. J. Transplant. 14 (12) 2838-2845 [2014-12-00; online 2014-10-14]

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

PubMed DOI Crossref

Peritoneal carcinomatosis from small intestinal neuroendocrine tumors: Clinical course and genetic profiling.

Norlén O, Edfeldt K, Akerstrom G, ..., Bjorklund P, Stalberg P

pii

Surgery 156 (6) 1512-21; discussion 1521-2 [2014-12-00; online 2014-11-11]

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

PubMed DOI Crossref

Intragenic duplication--a novel causative mechanism for SATB2-associated syndrome.

Liedén A, Kvarnung M, Nilssson D, Sahlin E, Lundberg ES

Am. J. Med. Genet. A 164A (12) 3083-3087 [2014-12-00; online 2014-09-25]

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

PubMed DOI Crossref

Efficient application of next-generation sequencing for the diagnosis of rare genetic syndromes.

Madrigal I, Alvarez-Mora MI, Karlberg O, ..., Syvänen AC, Milà M

pii

J. Clin. Pathol. 67 (12) 1099-1103 [2014-12-00; online 2014-10-02]

NGI Uppsala (SNP&SEQ Technology Platform)

PubMed DOI Crossref

Common genetic variants highlight the role of insulin resistance and body fat distribution in type 2 diabetes, independent of obesity.

Scott RA, Fall T, Pasko D, ..., Langenberg C, Wareham NJ

pmc mid

Diabetes 63 (12) 4378-4387 [2014-12-00; online 2014-06-19]

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

PubMed DOI Crossref

Insights into conifer giga-genomes.

De La Torre AR, Birol I, Bousquet J, ..., Zerbe P, Bohlmann J

pii pmc

Plant Physiol. 166 (4) 1724-1732 [2014-12-00; online 2014-10-29]

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

PubMed DOI Crossref

Studies of plant colonisation by closely related Bacillus amyloliquefaciens biocontrol agents using strain specific quantitative PCR assays.

Johansson AH, Bejai S, Niazi A, ..., Bongcam-Rudloff E, Meijer J

Antonie Van Leeuwenhoek 106 (6) 1247-1257 [2014-12-00; online 2014-10-09]

NGI Uppsala (SNP&SEQ Technology Platform)

PubMed DOI Crossref

Large-scale metabolomic profiling identifies novel biomarkers for incident coronary heart disease.

Ganna A, Salihovic S, Sundström J, ..., Fall T, Ingelsson E

pii pmc

PLoS Genet. 10 (12) e1004801 [2014-12-00; online 2014-12-11]

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

PubMed DOI Crossref

The lung-specific proteome defined by integration of transcriptomics and antibody-based profiling.

Lindskog C, Fagerberg L, Hallström B, ..., Pontén F, Micke P

pii

FASEB J. 28 (12) 5184-5196 [2014-12-00; online 2014-08-28]

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

PubMed DOI Crossref

Gene expression associated with intersterility in Heterobasidion

Van der Nest MA, Olson Å, Karlsson M, ..., Wingfield BD, Stenlid J

Fungal Genetics and Biology 73 (-) 104-119 [2014-12-00; online 2014-12-00]

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

PubMed DOI Crossref

Applying polygenic risk scores to postpartum depression.

Byrne EM, Carrillo-Roa T, Penninx BW, ..., Meltzer-Brody S, Wray NR

pmc mid

Arch Womens Ment Health 17 (6) 519-528 [2014-12-00; online 2014-07-19]

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

PubMed DOI Crossref

Serotonin receptor gene (5HT-2A) polymorphism is associated with provoked vestibulodynia and comorbid symptoms of pain.

Heddini U, Bohm-Starke N, Grönbladh A, ..., Nilsson KW, Johannesson U

pii

J Sex Med 11 (12) 3064-3071 [2014-12-00; online 2014-09-02]

NGI Uppsala (Uppsala Genome Center)

PubMed DOI Crossref

Evaluation of efficacy of a new MEK inhibitor, RO4987655, in human tumor xenografts by [(18)F] FDG-PET imaging combined with proteomic approaches.

Tegnebratt T, Ruge E, Bader S, ..., Tessier J, Stone-Elander S

pmc

EJNMMI Res 4 (1) 34 [2014-12-00; online 2014-09-09]

Fluorescence Tissue Profiling

PubMed DOI Crossref

High opsin diversity in a non-visual infaunal brittle star.

Delroisse J, Ullrich-Lüter E, Ortega-Martinez O, ..., Mallefet J, Flammang P

pii pmc

BMC Genomics 15 (-) 1035 [2014-11-28; online 2014-11-28]

Bioinformatics Support and Infrastructure [Service]

PubMed DOI Crossref

Complete Genome Sequence of Francisella endociliophora Strain FSC1006, Isolated from a Laboratory Culture of the Marine Ciliate Euplotes raikovi.

Sjödin A, Ohrman C, Bäckman S, ..., Stenberg P, Thelaus J

pii pmc

Genome Announc 2 (6) - [2014-11-26; online 2014-11-26]

Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Service]

PubMed DOI Crossref

1p36 deletion is a marker for tumour dissemination in microsatellite stable stage II-III colon cancer.

Mayrhofer M, Kultima HG, Birgisson H, ..., Glimelius B, Isaksson A

pii pmc

BMC Cancer 14 (-) 872 [2014-11-24; online 2014-11-24]

Array and Analysis Facility

DOI Crossref

Microwave Heated Flow Synthesis of Spiro-oxindole Dihydroquinazolinone Based IRAP Inhibitors

Engen K, Sävmarker J, Rosenström U, ..., Jenmalm-Jensen A, Larhed M

Org. Process Res. Dev. 18 (11) 1582-1588 [2014-11-21; online 2014-11-21]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

PubMed DOI Crossref

The Eph tyrosine kinase receptors EphB2 and EphA2 are novel proteolytic substrates of tissue factor/coagulation factor VIIa.

Eriksson O, Ramström M, Hörnaeus K, ..., Mokhtari D, Siegbahn A

pii pmc

J. Biol. Chem. 289 (47) 32379-32391 [2014-11-21; online 2014-10-05]

PLA and Single Cell Proteomics

PubMed DOI Crossref

Growth differentiation factor 15, a marker of oxidative stress and inflammation, for risk assessment in patients with atrial fibrillation: insights from the Apixaban for Reduction in Stroke and Other Thromboembolic Events in Atrial Fibrillation (ARISTOTLE) trial.

Wallentin L, Hijazi Z, Andersson U, ..., Siegbahn A, ARISTOTLE Investigators

pii ClinicalTrials.gov

Circulation 130 (21) 1847-1858 [2014-11-18; online 2014-10-09]

Clinical Biomarkers

PubMed DOI Crossref

Metagenomic approaches to disclose disease-associated pathogens: detection of viral pathogens in honeybees.

Granberg F, Karlsson OE, Belák S

Methods Mol. Biol. 1247 (-) 491-511 [2014-11-17; online 2014-11-17]

NGI Uppsala (Uppsala Genome Center)

PubMed DOI Crossref

Leachability and desorption of PCBs from soil and their dependency on pH and dissolved organic matter.

Badea SL, Mustafa M, Lundstedt S, Tysklind M

pii

Sci. Total Environ. 499 (-) 220-227 [2014-11-15; online 2014-09-07]

Bioinformatics Support and Infrastructure

PubMed DOI Crossref

Pathway analysis of cervical cancer genome-wide association study highlights the MHC region and pathways involved in response to infection.

Chen D, Enroth S, Ivansson E, Gyllensten U

pii

Hum. Mol. Genet. 23 (22) 6047-6060 [2014-11-15; online 2014-06-18]

NGI Uppsala (SNP&SEQ Technology Platform)

PubMed DOI Crossref

Defining the human adipose tissue proteome to reveal metabolic alterations in obesity.

Mardinoglu A, Kampf C, Asplund A, ..., Uhlen M, Nielsen J

J. Proteome Res. 13 (11) 5106-5119 [2014-11-07; online 2014-09-16]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) Tissue Profiling

PubMed DOI Crossref

Genomic identification and characterization of the pseudoautosomal region in highly differentiated avian sex chromosomes

Smeds L, Kawakami T, Burri R, ..., Uebbing S, Ellegren H

Nat Commun 5 (-) 5448 [2014-11-07; online 2014-11-07]

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

PubMed DOI Crossref

Affinity proteomic profiling of plasma, cerebrospinal fluid, and brain tissue within multiple sclerosis.

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

J. Proteome Res. 13 (11) 4607-4619 [2014-11-07; online 2014-09-19]

Fluorescence Tissue Profiling Plasma Profiling [Collaborative]

PubMed DOI Crossref

Analysis of autoantibody profiles in osteoarthritis using comprehensive protein array concepts.

Henjes F, Lourido L, Ruiz-Romero C, ..., Nilsson P, Fuentes M

J. Proteome Res. 13 (11) 5218-5229 [2014-11-07; online 2014-10-09]

Autoimmunity Profiling [Collaborative]

PubMed DOI Crossref

Aberrantly activated claudin 6 and 18.2 as potential therapy targets in non-small-cell lung cancer.

Micke P, Mattsson JS, Edlund K, ..., Sahin U, Türeci O

Int. J. Cancer 135 (9) 2206-2214 [2014-11-01; online 2014-04-09]

Tissue Profiling

PubMed DOI Crossref

Multimodal fluorescence microscopy of prion strain specific PrP deposits stained by thiophene-based amyloid ligands.

Magnusson K, Simon R, Sjölander D, ..., Hammarström P, Nilsson KP

pmc

Prion 8 (4) 319-329 [2014-11-01; online 2014-11-01]

Bioinformatics Support and Infrastructure

PubMed DOI Crossref

Fat mass and obesity-associated gene (FTO) is linked to higher plasma levels of the hunger hormone ghrelin and lower serum levels of the satiety hormone leptin in older adults.

Benedict C, Axelsson T, Söderberg S, ..., Lind L, Schiöth HB

pii

Diabetes 63 (11) 3955-3959 [2014-11-00; online 2014-06-06]

NGI Uppsala (SNP&SEQ Technology Platform)

PubMed DOI Crossref

Evolution reveals a glutathione-dependent mechanism of 3-hydroxypropionic acid tolerance.

Kildegaard KR, Hallström BM, Blicher TH, ..., Nielsen J, Borodina I

pii

Metab. Eng. 26 (-) 57-66 [2014-11-00; online 2014-09-30]

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

PubMed DOI Crossref

Antibody validation of immunohistochemistry for biomarker discovery: recommendations of a consortium of academic and pharmaceutical based histopathology researchers.

Howat WJ, Lewis A, Jones P, ..., Womack C, Warford A

pii pmc

Methods 70 (1) 34-38 [2014-11-00; online 2014-02-15]

Tissue Profiling

PubMed DOI Crossref

Bcl-2 maintains the mitochondrial membrane potential, but fails to affect production of reactive oxygen species and endoplasmic reticulum stress, in sodium palmitate-induced β-cell death.

Wang X, Welsh N

pmc

Ups. J. Med. Sci. 119 (4) 306-315 [2014-11-00; online 2014-10-01]

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

PubMed DOI Crossref

Binning metagenomic contigs by coverage and composition.

Alneberg J, Bjarnason BS, de Bruijn I, ..., Andersson AF, Quince C

pii

Nat. Methods 11 (11) 1144-1146 [2014-11-00; online 2014-09-15]

Bioinformatics Support and Infrastructure

PubMed DOI Crossref

Estimation of linkage disequilibrium and interspecific gene flow in Ficedula flycatchers by a newly developed 50k single-nucleotide polymorphism array.

Kawakami T, Backström N, Burri R, ..., Qvarnström A, Ellegren H

pmc dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP dbSNP

Mol Ecol Resour 14 (6) 1248-1260 [2014-11-00; online 2014-05-03]

NGI Uppsala (SNP&SEQ Technology Platform)

PubMed DOI Crossref

Human isolates of Listeria monocytogenes in Sweden during half a century (1958-2010).

Lopez-Valladares G, Tham W, Parihar VS, ..., Henriques-Normark B, Danielsson-Tham ML

pii

Epidemiol. Infect. 142 (11) 2251-2260 [2014-11-00; online 2014-02-01]

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

PubMed DOI Crossref

Defining the human gallbladder proteome by transcriptomics and affinity proteomics.

Kampf C, Mardinoglu A, Fagerberg L, ..., Pontén F, Uhlen M

Proteomics 14 (21-22) 2498-2507 [2014-11-00; online 2014-09-02]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) Tissue Profiling

PubMed DOI Crossref

Defining the role of common variation in the genomic and biological architecture of adult human height.

Wood AR, Esko T, Yang J, ..., Hirschhorn JN, Frayling TM

pii pmc mid

Nat. Genet. 46 (11) 1173-1186 [2014-11-00; online 2014-10-06]

NGI Uppsala (SNP&SEQ Technology Platform)

PubMed DOI Crossref

Integration of genome-wide of Stat3 binding and epigenetic modification mapping with transcriptome reveals novel Stat3 target genes in glioma cells.

Kruczyk M, Przanowski P, Dabrowski M, ..., Kaminska B, Komorowski J

pii

Biochim. Biophys. Acta 1839 (11) 1341-1350 [2014-11-00; online 2014-08-12]

NGI Uppsala (Uppsala Genome Center)

PubMed DOI Crossref

Parallel barcoding of antibodies for DNA-assisted proteomics.

Dezfouli M, Vickovic S, Iglesias MJ, Schwenk JM, Ahmadian A

Proteomics 14 (21-22) 2432-2436 [2014-11-00; online 2014-09-30]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) Plasma Profiling [Technology development]

PubMed DOI Crossref

Cesarean delivery and hematopoietic stem cell epigenetics in the newborn infant: implications for future health?

Almgren M, Schlinzig T, Gomez-Cabrero D, ..., Norman M, Ekström TJ

pii

Am. J. Obstet. Gynecol. 211 (5) 502.e1-502.e8 [2014-11-00; online 2014-07-06]

Bioinformatics and Expression Analysis (BEA)

PubMed DOI Crossref

Abolished InsP3R2 function inhibits sweat secretion in both humans and mice.

Klar J, Hisatsune C, Baig SM, ..., Mikoshiba K, Dahl N

pii pmc

J. Clin. Invest. 124 (11) 4773-4780 [2014-11-00; online 2014-10-21]

NGI Uppsala (Uppsala Genome Center)

PubMed DOI Crossref

Replicability and robustness of genome-wide-association studies for behavioral traits.

Rietveld CA, Conley D, Eriksson N, ..., Koellinger PD, Social Science Genetics Association Consortium

pii pmc mid

Psychol Sci 25 (11) 1975-1986 [2014-11-00; online 2014-10-06]

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

PubMed DOI Crossref

Melanoma patient-derived xenografts accurately model the disease and develop fast enough to guide treatment decisions.

Einarsdottir BO, Bagge RO, Bhadury J, ..., Ny L, Nilsson JA

pii pmc

Oncotarget 5 (20) 9609-9618 [2014-10-30; online 2014-09-18]

Bioinformatics Support and Infrastructure

DOI Crossref

Photocatalysis induces bioactivity of an organic polymer based material

Cai Y, Strømme M, Zhang P, Engqvist H, Welch K

RSC Adv. 4 (101) 57715-57723 [2014-10-28; online 2014-10-28]

BioMaterial Interactions (BioMat)

PubMed DOI Crossref

Populus tremula (European aspen) shows no evidence of sexual dimorphism.

Robinson KM, Delhomme N, Mähler N, ..., Jansson S, Street NR

pii pmc

BMC Plant Biol. 14 (-) 276 [2014-10-16; online 2014-10-16]

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

PubMed DOI Crossref

Allelic expression mapping across cellular lineages to establish impact of non-coding SNPs.

Adoue V, Schiavi A, Light N, ..., Syvänen A, Pastinen T

pmc GEO GEO GEO

Mol. Syst. Biol. 10 (-) 754 [2014-10-16; online 2014-10-16]

NGI Uppsala (SNP&SEQ Technology Platform)

PubMed DOI Crossref

Identification of 33 candidate oncogenes by screening for base-specific mutations.

Tuupanen S, Hänninen UA, Kondelin J, ..., Pitkänen E, Aaltonen LA

pii pmc

Br. J. Cancer 111 (8) 1657-1662 [2014-10-14; online 2014-08-15]

Karolinska High Throughput Center (KHTC)

PubMed DOI Crossref

Human genetic evidence for involvement of CD137 in atherosclerosis.

Söderström LÅ, Gertow K, Folkersen L, ..., Hansson GK, Olofsson PS

pii pmc

Mol. Med. 20 (-) 456-465 [2014-10-14; online 2014-07-18]

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

PubMed DOI Crossref

Gene and protein expression and cellular localisation of cytochrome P450 enzymes of the 1A, 2A, 2C, 2D and 2E subfamilies in equine intestine and liver.

Tydén E, Tjälve H, Larsson P

pii pmc

Acta Vet. Scand. 56 (-) 69 [2014-10-08; online 2014-10-08]

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

PubMed DOI Crossref

CanvasDB: a local database infrastructure for analysis of targeted- and whole genome re-sequencing projects.

Ameur A, Bunikis I, Enroth S, Gyllensten U

pii pmc

Database (Oxford) 2014 (-) - [2014-10-03; online 2014-10-03]

NGI Uppsala (Uppsala Genome Center)

PubMed DOI Crossref

Biofuels. Altered sterol composition renders yeast thermotolerant.

Caspeta L, Chen Y, Ghiaci P, ..., Petranovic D, Nielsen J

pii

Science 346 (6205) 75-78 [2014-10-03; online 2014-10-02]

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

PubMed DOI Crossref

Acetate availability and utilization supports the growth of mutant sub-populations on aging bacterial colonies.

Bergman JM, Wrande M, Hughes D

pii pmc

PLoS ONE 9 (10) e109255 [2014-10-02; online 2014-10-02]

Mass Spectrometry-based Proteomics, Uppsala

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Perry JR, Day F, Elks CE, ..., Murabito JM, Ong KK

pmc mid

Nature 514 (7520) 92-97 [2014-10-02; online 2014-07-23]

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

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Lindholm ME, Huss M, Solnestam BW, ..., Lundeberg J, Sundberg CJ

The FASEB Journal 28 (10) 4571-4581 [2014-10-01; online 2014-07-11]

Bioinformatics Long-term Support WABI [Collaborative]

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Medium from γ-irradiated Escherichia coli bacteria stimulates a unique immune response in Drosophila cells.

Lindberg BG, Oldenvi S, Steiner H

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Bioinformatics and Expression Analysis (BEA)

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In situ sequencing identifies TMPRSS2-ERG fusion transcripts, somatic point mutations and gene expression levels in prostate cancers.

Kiflemariam S, Mignardi M, Ali MA, ..., Nilsson M, Sjöblom T

J. Pathol. 234 (2) 253-261 [2014-10-00; online 2014-06-17]

Tissue Profiling

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Signals that regulate the oncogenic fate of neural stem cells and progenitors.

Swartling FJ, Bolin S, Phillips JJ, Persson AI

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Exp. Neurol. 260 (-) 56-68 [2014-10-00; online 2013-02-05]

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

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Glickman JF, Lundbäck T, Napper AD, ..., Zaman GJR, Osada H

ASSAY and Drug Development Technologies 12 (8) 443-451 [2014-10-00; online 2014-10-00]

Chemical Biology Consortium Sweden (CBCS) [Technology development]

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A worldwide survey of genome sequence variation provides insight into the evolutionary history of the honeybee Apis mellifera.

Wallberg A, Han F, Wellhagen G, ..., Pirk CW, Webster MT

pii BioProject

Nat. Genet. 46 (10) 1081-1088 [2014-10-00; online 2014-08-26]

NGI Uppsala (Uppsala Genome Center)

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The DMRT3 'Gait keeper' mutation affects performance of Nordic and Standardbred trotters.

Jäderkvist K, Andersson LS, Johansson AM, ..., Andersson L, Lindgren G

pii

J. Anim. Sci. 92 (10) 4279-4286 [2014-10-00; online 2014-08-03]

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

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NPSR1 polymorphisms influence recurrent abdominal pain in children: a population-based study.

Henström M, Zucchelli M, Söderhäll C, ..., Olén O, D'Amato M

Neurogastroenterol. Motil. 26 (10) 1417-1425 [2014-10-00; online 2014-08-06]

Mutation Analysis Facility (MAF)

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Design of a general-purpose European compound screening library for EU-OPENSCREEN.

Horvath D, Lisurek M, Rupp B, ..., Quintana J, Frank R

ChemMedChem 9 (10) 2309-2326 [2014-10-00; online 2014-07-22]

Chemical Biology Consortium Sweden (CBCS) [Technology development]

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Evidence for autosomal recessive inheritance in SPG3A caused by homozygosity for a novel ATL1 missense mutation.

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

pii pmc

Eur. J. Hum. Genet. 22 (10) 1180-1184 [2014-10-00; online 2014-01-30]

NGI Uppsala (Uppsala Genome Center)

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Uneven distribution of human papillomavirus 16 in cervical carcinoma in situ and squamous cell carcinoma in older females: A retrospective database study.

Andersson S, Mints M, Gyllensten U, ..., Lambe M, Wilander E

pii pmc

Oncol Lett 8 (4) 1528-1532 [2014-10-00; online 2014-09-10]

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

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Epoxy alcohol synthase of the rice blast fungus represents a novel subfamily of dioxygenase-cytochrome P450 fusion enzymes.

Hoffmann I, Jernerén F, Oliw EH

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J. Lipid Res. 55 (10) 2113-2123 [2014-10-00; online 2014-08-15]

NGI Uppsala (Uppsala Genome Center)

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HemR is an OmpR/PhoB-like response regulator from Leptospira, which simultaneously effects transcriptional activation and repression of key haem metabolism genes.

Morero NR, Botti H, Nitta KR, ..., Picardeau M, Buschiazzo A

Mol. Microbiol. 94 (2) 340-352 [2014-10-00; online 2014-08-26]

Karolinska High Throughput Center (KHTC)

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Analyses of historical and current populations of black grouse in Central Europe reveal strong effects of genetic drift and loss of genetic diversity

Segelbacher G, Strand TM, Quintela M, ..., Koelewijn HP, Höglund J

Conserv Genet 15 (5) 1183-1195 [2014-10-00; online 2014-04-27]

NGI Uppsala (SNP&SEQ Technology Platform)

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Human cytomegalovirus tegument protein pp65 is detected in all intra- and extra-axial brain tumours independent of the tumour type or grade.

Libard S, Popova SN, Amini RM, ..., Ponten F, Alafuzoff I

pii pmc

PLoS ONE 9 (9) e108861 [2014-09-30; online 2014-09-30]

Tissue Profiling

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The Chironomus tentans genome sequence and the organization of the Balbiani ring genes.

Kutsenko A, Svensson T, Nystedt B, ..., Visa N, Wieslander L

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BMC Genomics 15 (-) 819 [2014-09-27; online 2014-09-27]

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

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Plasmidome interchange between Clostridium botulinum, Clostridium novyi and Clostridium haemolyticum converts strains of independent lineages into distinctly different pathogens.

Skarin H, Segerman B

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PLoS ONE 9 (9) e107777 [2014-09-25; online 2014-09-25]

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

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Glial origin of mesenchymal stem cells in a tooth model system.

Kaukua N, Shahidi MK, Konstantinidou C, ..., Fried K, Adameyko I

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Nature 513 (7519) 551-554 [2014-09-25; online 2014-08-01]

Advanced Light Microscopy (ALM) [Collaborative]

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Oncoprotein stabilization in brain tumors.

Hede SM, Savov V, Weishaupt H, Sangfelt O, Swartling FJ

pii

Oncogene 33 (39) 4709-4721 [2014-09-25; online 2013-10-30]

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

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Common genetic variants associated with cognitive performance identified using the proxy-phenotype method.

Rietveld CA, Esko T, Davies G, ..., Cesarini D, Koellinger PD

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Proc. Natl. Acad. Sci. U.S.A. 111 (38) 13790-13794 [2014-09-23; online 2014-09-08]

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

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Evidence that breast cancer risk at the 2q35 locus is mediated through IGFBP5 regulation.

Ghoussaini M, Edwards SL, Michailidou K, ..., Dunning AM, Australian Ovarian Cancer Management Group

pii pmc mid

Nat Commun 4 (-) 4999 [2014-09-23; online 2014-09-23]

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

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Histidine-rich glycoprotein uptake and turnover is mediated by mononuclear phagocytes.

Tugues S, Roche F, Noguer O, ..., Tolmachev V, Claesson-Welsh L

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PLoS ONE 9 (9) e107483 [2014-09-22; online 2014-09-22]

Tissue Profiling

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Distinguishing between driver and passenger mutations in individual cancer genomes by network enrichment analysis.

Merid SK, Goranskaya D, Alexeyenko A

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BMC Bioinformatics 15 (-) 308 [2014-09-19; online 2014-09-19]

Bioinformatics Support and Infrastructure

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A Universal Approach to Prepare Reagents for DNA-Assisted Protein Analysis

Yan J, Gu GJ, Jost C, ..., Landegren U, Kamali-Moghaddam M

PLoS ONE 9 (9) e108061 [2014-09-18; online 2014-09-18]

Clinical Biomarkers PLA and Single Cell Proteomics [Technology development]

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Characterization of stem-like cells in mucoepidermoid tracheal paediatric tumor.

Lim ML, Ooi BN, Jungebluth P, ..., Ahrlund-Richter L, Macchiarini P

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PLoS ONE 9 (9) e107712 [2014-09-17; online 2014-09-17]

Bioinformatics and Expression Analysis (BEA)

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Structural and functional characterization of ochratoxinase, a novel mycotoxin-degrading enzyme.

Dobritzsch D, Wang H, Schneider G, Yu S

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Biochem. J. 462 (3) 441-452 [2014-09-15; online 2014-06-21]

Protein Science Facility (PSF)

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The DEK oncoprotein binds to highly and ubiquitously expressed genes with a dual role in their transcriptional regulation.

Sandén C, Järvstråt L, Lennartsson A, ..., Nilsson B, Gullberg U

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Mol. Cancer 13 (-) 215 [2014-09-12; online 2014-09-12]

Bioinformatics and Expression Analysis (BEA) NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

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Genome-wide analysis reveals DNA methylation markers that vary with both age and obesity.

Almén MS, Nilsson EK, Jacobsson JA, ..., Fredriksson R, Schiöth HB

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Gene 548 (1) 61-67 [2014-09-10; online 2014-07-11]

NGI Uppsala (SNP&SEQ Technology Platform)

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The prognostic value and therapeutic target role of stathmin-1 in urinary bladder cancer.

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

pii pmc

Br. J. Cancer 111 (6) 1180-1187 [2014-09-09; online 2014-07-29]

Tissue Profiling [Collaborative]

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The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera.

Ahola V, Lehtonen R, Somervuo P, ..., Frilander MJ, Hanski I

pii pmc mid GENBANK

Nat Commun 5 (-) 4737 [2014-09-05; online 2014-09-05]

Karolinska High Throughput Center (KHTC)

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Neu-Laxova syndrome is a heterogeneous metabolic disorder caused by defects in enzymes of the L-serine biosynthesis pathway.

Acuna-Hidalgo R, Schanze D, Kariminejad A, ..., Hoischen A, Zenker M

pii pmc

Am. J. Hum. Genet. 95 (3) 285-293 [2014-09-04; online 2014-08-26]

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

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Predictive urinary biomarkers for steroid-resistant and steroid-sensitive focal segmental glomerulosclerosis using high resolution mass spectrometry and multivariate statistical analysis.

Kalantari S, Nafar M, Rutishauser D, ..., Yang H, Zubarev RA

pii pmc

BMC Nephrol 15 (-) 141 [2014-09-02; online 2014-09-02]

Advanced Mass Spectrometry Proteomics

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An integrative analysis of the tumorigenic role of TAZ in human non-small cell lung cancer.

Noguchi S, Saito A, Horie M, ..., Micke P, Nagase T

pii

Clin. Cancer Res. 20 (17) 4660-4672 [2014-09-01; online 2014-06-22]

Tissue Profiling

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Metagenomics reveals that detoxification systems are underrepresented in marine bacterial communities.

Bengtsson-Palme J, Alm Rosenblad M, Molin M, Blomberg A

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BMC Genomics 15 (-) 749 [2014-09-01; online 2014-09-01]

Bioinformatics Support and Infrastructure

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Interactive effects of KIBRA and CLSTN2 polymorphisms on episodic memory in old-age unipolar depression.

Pantzar A, Laukka EJ, Atti AR, ..., Fratiglioni L, Bäckman L

pii

Neuropsychologia 62 (-) 137-142 [2014-09-00; online 2014-08-01]

Mutation Analysis Facility (MAF)

DOI Crossref

Cu(OAc)2 promoted Chan–Evans–Lam C–N cross coupling reactions on the N- and N′-nitrogen atoms of sulfonimidamides with aryl boronic acids

Nandi GC, Kota SR, Govender T, Kruger HG, Arvidsson PI

Tetrahedron 70 (35) 5428-5433 [2014-09-00; online 2014-09-00]

Drug Discovery and Development (DDD) [Technology development]

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Picocyanobacteria containing a novel pigment gene cluster dominate the brackish water Baltic Sea.

Larsson J, Celepli N, Ininbergs K, ..., Bergman B, Ekman M

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ISME J 8 (9) 1892-1903 [2014-09-00; online 2014-03-14]

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

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Abstract of the 35th Scandinavian Congress of Rheumatology, Stockholm, Sweden, September 20th – 23rd, 2014

Scandinavian Journal of Rheumatology 43 (sup127) 1-97 [2014-09-00; online 2014-09-03]

Clinical Proteomics Mass spectrometry

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Recurrent GATA1 mutations in Diamond-Blackfan anaemia.

Klar J, Khalfallah A, Arzoo PS, Gazda HT, Dahl N

Br. J. Haematol. 166 (6) 949-951 [2014-09-00; online 2014-04-29]

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

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Sexual structures and recombination of the wheat rust fungus Puccinia striiformis on Berberis vulgaris.

Rodriguez-Algaba J, Walter S, Sørensen CK, Hovmøller MS, Justesen AF

pii

Fungal Genet. Biol. 70 (-) 77-85 [2014-09-00; online 2014-07-22]

NGI Uppsala (Uppsala Genome Center)

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Do the same genes underlie parallel phenotypic divergence in different Littorina saxatilis populations?

Westram AM, Galindo J, Alm Rosenblad M, ..., Panova M, Butlin RK

pmc Dryad

Mol. Ecol. 23 (18) 4603-4616 [2014-09-00; online 2014-08-13]

Bioinformatics Support and Infrastructure NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

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Hypomethylated pollen bypasses the interploidy hybridization barrier in Arabidopsis.

Schatlowski N, Wolff P, Santos-González J, ..., Tamaru H, Köhler C

pii pmc

Plant Cell 26 (9) 3556-3568 [2014-09-00; online 2014-09-12]

NGI Uppsala (SNP&SEQ Technology Platform)

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Identification of three novel FGF16 mutations in X-linked recessive fusion of the fourth and fifth metacarpals and possible correlation with heart disease.

Laurell T, Nilsson D, Hofmeister W, ..., Grigelioniene G, Nordgren A

pmc

Mol Genet Genomic Med 2 (5) 402-411 [2014-09-00; online 2014-05-14]

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

PubMed DOI Crossref

Genome of the avirulent human-infective trypanosome--Trypanosoma rangeli.

Stoco PH, Wagner G, Talavera-Lopez C, ..., de Vasconcelos AT, Grisard EC

pii pmc

PLoS Negl Trop Dis 8 (9) e3176 [2014-09-00; online 2014-09-18]

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

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Productivity and salinity structuring of the microplankton revealed by comparative freshwater metagenomics.

Eiler A, Zaremba-Niedzwiedzka K, Martínez-García M, ..., Andersson SG, Bertilsson S

pmc

Environ. Microbiol. 16 (9) 2682-2698 [2014-09-00; online 2013-10-15]

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

PubMed DOI Crossref

Splicing in the human brain.

Zaghlool A, Ameur A, Cavelier L, Feuk L

pii

Int. Rev. Neurobiol. 116 (-) 95-125 [2014-08-31; online 2014-08-31]

NGI Uppsala (Uppsala Genome Center)

PubMed DOI Crossref

Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication.

Carneiro M, Rubin CJ, Di Palma F, ..., Lindblad-Toh K, Andersson L

pii BioProject BioProject BioProject GENBANK

Science 345 (6200) 1074-1079 [2014-08-29; online 2014-08-30]

Bioinformatics Compute and Storage NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

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Deep amplicon sequencing of preselected isolates of Parascaris equorum in β-tubulin codons associated with benzimidazole resistance in other nematodes.

Tydén E, Dahlberg J, Karlberg O, Höglund J

pii pmc

Parasit Vectors 7 (-) 410 [2014-08-29; online 2014-08-29]

NGI Uppsala (SNP&SEQ Technology Platform)

PubMed DOI Crossref

Structural basis for regulation of the human acetyl-CoA thioesterase 12 and interactions with the steroidogenic acute regulatory protein-related lipid transfer (START) domain.

Swarbrick CM, Roman N, Cowieson N, ..., Lehtiö L, Forwood JK

pii pmc PDB PDB PDB PDB PDB PDB PDB PDB

J. Biol. Chem. 289 (35) 24263-24274 [2014-08-29; online 2014-07-09]

Protein Science Facility (PSF)

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The Arthonialean challenge: Restructuring Arthoniaceae

Frisch A, Thor G, Ertz D, Grube M

Taxon 63 (4) 727-744 [2014-08-28; online 2014-08-28]

NGI Uppsala (Uppsala Genome Center)

PubMed DOI Crossref

A multicentre hospital outbreak in Sweden caused by introduction of a vanB2 transposon into a stably maintained pRUM-plasmid in an Enterococcus faecium ST192 clone.

Sivertsen A, Billström H, Melefors Ö, ..., Sundsfjord A, Hegstad K

pii pmc

PLoS ONE 9 (8) e103274 [2014-08-25; online 2014-08-25]

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

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Missing genes, multiple ORFs, and C-to-U type RNA editing in Acrasis kona (Heterolobosea, Excavata) mitochondrial DNA.

Fu CJ, Sheikh S, Miao W, Andersson SG, Baldauf SL

pii pmc GENBANK

Genome Biol Evol 6 (9) 2240-2257 [2014-08-21; online 2014-08-21]

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

PubMed DOI Crossref

Small RNA sequence analysis of adenovirus VA RNA-derived miRNAs reveals an unexpected serotype-specific difference in structure and abundance.

Kamel W, Segerman B, Punga T, Akusjärvi G

pii pmc

PLoS ONE 9 (8) e105746 [2014-08-21; online 2014-08-21]

NGI Uppsala (Uppsala Genome Center)

PubMed DOI Crossref

Winter bloom of a rare betaproteobacterium in the Arctic Ocean.

Alonso-Sáez L, Zeder M, Harding T, ..., Bertilsson S, Pedrós-Alió C

pmc

Front Microbiol 5 (-) 425 [2014-08-20; online 2014-08-20]

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

PubMed DOI Crossref

Meta-analysis in more than 17,900 cases of ischemic stroke reveals a novel association at 12q24.12.

Kilarski LL, Achterberg S, Devan WJ, ..., Bevan S, GARNET Collaborative Research Group WTCCC2ASGCtMCatISGC

pii pmc

Neurology 83 (8) 678-685 [2014-08-19; online 2014-07-16]

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

PubMed DOI Crossref

Evaluation of exome sequencing to estimate tumor burden in plasma.

Klevebring D, Neiman M, Sundling S, ..., Grönberg H, Lindberg J

pii pmc

PLoS ONE 9 (8) e104417 [2014-08-18; online 2014-08-18]

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

PubMed DOI Crossref

Species and gene divergence in Littorina snails detected by array comparative genomic hybridization.

Panova M, Johansson T, Canbäck B, ..., Tunlid A, André C

pii pmc GEO

BMC Genomics 15 (-) 687 [2014-08-18; online 2014-08-18]

Bioinformatics Support and Infrastructure NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

PubMed DOI Crossref

Tandem RNA chimeras contribute to transcriptome diversity in human population and are associated with intronic genetic variants.

Greger L, Su J, Rung J, ..., Dermitzakis ET, Brazma A

pii pmc

PLoS ONE 9 (8) e104567 [2014-08-18; online 2014-08-18]

NGI Uppsala (SNP&SEQ Technology Platform)

PubMed DOI Crossref

BESST--efficient scaffolding of large fragmented assemblies.

Sahlin K, Vezzi F, Nystedt B, Lundeberg J, Arvestad L

pii pmc

BMC Bioinformatics 15 (-) 281 [2014-08-15; online 2014-08-15]

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

PubMed DOI Crossref

Genome analysis of Bacillus amyloliquefaciens Subsp. plantarum UCMB5113: a rhizobacterium that improves plant growth and stress management.

Niazi A, Manzoor S, Asari S, ..., Meijer J, Bongcam-Rudloff E

pii pmc GENBANK

PLoS ONE 9 (8) e104651 [2014-08-13; online 2014-08-13]

NGI Uppsala (SNP&SEQ Technology Platform)

PubMed DOI Crossref

The cellular thermal shift assay for evaluating drug target interactions in cells

Jafari R, Almqvist H, Axelsson H, ..., Nordlund P, Molina DM

Nat Protoc 9 (9) 2100-2122 [2014-08-07; online 2014-08-07]

Chemical Biology Consortium Sweden (CBCS) [Technology development]

PubMed DOI Crossref

Common genetic determinants of lung function, subclinical atherosclerosis and risk of coronary artery disease.

Sabater-Lleal M, Mälarstig A, Folkersen L, ..., Tobin MD, Hamsten A

pii pmc

PLoS ONE 9 (8) e104082 [2014-08-05; online 2014-08-05]

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

PubMed DOI Crossref

Differences in gene expression between mouse and human for dynamically regulated genes in early embryo.

Madissoon E, Töhönen V, Vesterlund L, ..., Hovatta O, Kere J

pii pmc

PLoS ONE 9 (8) e102949 [2014-08-04; online 2014-08-04]

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

PubMed DOI Crossref

Exome sequencing reveals frequent inactivating mutations in ARID1A, ARID1B, ARID2 and ARID4A in microsatellite unstable colorectal cancer.

Cajuso T, Hänninen UA, Kondelin J, ..., Kilpivaara O, Vahteristo P

Int. J. Cancer 135 (3) 611-623 [2014-08-01; online 2014-01-03]

Karolinska High Throughput Center (KHTC)

PubMed DOI Crossref

IgA measurements in over 12 000 Swedish twins reveal sex differential heritability and regulatory locus near CD30L.

Viktorin A, Frankowiack M, Padyukov L, ..., Hammarström L, Magnusson PK

pii pmc

Hum. Mol. Genet. 23 (15) 4177-4184 [2014-08-01; online 2014-03-27]

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

PubMed DOI Crossref

Analysis of candidate genes for lineage-specific expression changes in humans and primates.

Lindskog C, Kuhlwilm M, Davierwala A, ..., Pääbo S, Pontén F

J. Proteome Res. 13 (8) 3596-3606 [2014-08-01; online 2014-06-10]

Tissue Profiling

PubMed DOI Crossref

The human carotid body releases acetylcholine, ATP and cytokines during hypoxia.

Kåhlin J, Mkrtchian S, Ebberyd A, ..., Fagerlund MJ, Eriksson LI

pii

Exp. Physiol. 99 (8) 1089-1098 [2014-08-00; online 2014-06-03]

Bioinformatics and Expression Analysis (BEA)

PubMed DOI Crossref

Differential methylation in CN-AML preferentially targets non-CGI regions and is dictated by DNMT3A mutational status and associated with predominant hypomethylation of HOX genes.

Qu Y, Lennartsson A, Gaidzik VI, ..., Döhner K, Lehmann S

pii pmc

Epigenetics 9 (8) 1108-1119 [2014-08-00; online 2014-05-29]

Bioinformatics and Expression Analysis (BEA) NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

PubMed DOI Crossref

Mechanisms of mRNA export.

Björk P, Wieslander L

pii

Semin. Cell Dev. Biol. 32 (-) 47-54 [2014-08-00; online 2014-05-13]

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

PubMed DOI Crossref

A high-density linkage map enables a second-generation collared flycatcher genome assembly and reveals the patterns of avian recombination rate variation and chromosomal evolution.

Kawakami T, Smeds L, Backström N, ..., Olason P, Ellegren H

pmc GENBANK

Mol. Ecol. 23 (16) 4035-4058 [2014-08-00; online 2014-05-28]

NGI Uppsala (SNP&SEQ Technology Platform)

PubMed DOI Crossref

Fusions involving protein kinase C and membrane-associated proteins in benign fibrous histiocytoma.

Płaszczyca A, Nilsson J, Magnusson L, ..., Nord KH, Mertens F

pii

Int. J. Biochem. Cell Biol. 53 (-) 475-481 [2014-08-00; online 2014-04-12]

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

PubMed DOI Crossref

High risk of tobacco-related cancers in CDKN2A mutation-positive melanoma families.

Helgadottir H, Höiom V, Jönsson G, ..., Olsson H, Hansson J

pii pmc

J. Med. Genet. 51 (8) 545-552 [2014-08-00; online 2014-06-18]

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

PubMed DOI Crossref

Genetic variation in the CYP1A1 gene is related to circulating PCB118 levels in a population-based sample.

Lind L, Penell J, Syvänen AC, ..., van Bavel B, Lind PM

pii

Environ. Res. 133 (-) 135-140 [2014-08-00; online 2014-06-14]

NGI Uppsala (SNP&SEQ Technology Platform)

PubMed DOI Crossref

Plasma profiling reveals three proteins associated to amyotrophic lateral sclerosis.

Häggmark A, Mikus M, Mohsenchian A, ..., Kuźma-Kozakiewicz M, Nilsson P

pmc

Ann Clin Transl Neurol 1 (8) 544-553 [2014-08-00; online 2014-07-14]

Plasma Profiling [Collaborative]

PubMed DOI Crossref

Cluster of infections caused by methicillin-resistant Staphylococcus pseudintermedius in humans in a tertiary hospital.

Starlander G, Börjesson S, Grönlund-Andersson U, Tellgren-Roth C, Melhus A

pii pmc

J. Clin. Microbiol. 52 (8) 3118-3120 [2014-08-00; online 2014-05-30]

NGI Uppsala (Uppsala Genome Center)

PubMed DOI Crossref

Systematic investigation of contribution of genetic variation in the HLA-DP region to cervical cancer susceptibility.

Chen D, Gyllensten U

pii

Carcinogenesis 35 (8) 1765-1769 [2014-08-00; online 2014-04-17]

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

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Distinct roles of Candida albicans-specific genes in host-pathogen interactions.

Wilson D, Mayer FL, Miramón P, ..., Jacobsen ID, Hube B

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Nat. Struct. Mol. Biol. 21 (8) 728-731 [2014-08-00; online 2014-07-30]

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Nat. Genet. 46 (8) 826-836 [2014-08-00; online 2014-06-24]

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Appl. Environ. Microbiol. 80 (16) 5116-5123 [2014-08-00; online 2014-06-15]

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Bruzelius M, Strawbridge RJ, Trégouët D, ..., Odeberg J, Hamsten A

pii

Thromb. Res. 134 (2) 426-432 [2014-08-00; online 2014-04-22]

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Song Y, Giske CG, Gille-Johnson P, ..., Lundeberg J, Gyarmati P

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PLoS ONE 9 (7) e103610 [2014-07-30; online 2014-07-30]

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Polymorphisms in genes implicated in dopamine, serotonin and noradrenalin metabolism suggest association with cerebrospinal fluid monoamine metabolite concentrations in psychosis.

Andreou D, Söderman E, Axelsson T, ..., Agartz I, Jönsson EG

pii pmc

Behav Brain Funct 10 (-) 26 [2014-07-29; online 2014-07-29]

NGI Uppsala (SNP&SEQ Technology Platform)

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Analysis of stranded information using an automated procedure for strand specific RNA sequencing.

Sigurgeirsson B, Emanuelsson O, Lundeberg J

pii pmc

BMC Genomics 15 (-) 631 [2014-07-28; online 2014-07-28]

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

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Larsson M, Caraballo R, Ericsson M, ..., Nilsson SK, Olivecrona G

pii

Biochem. Biophys. Res. Commun. 450 (2) 1063-1069 [2014-07-25; online 2014-07-02]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

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Biological insights from 108 schizophrenia-associated genetic loci.

Schizophrenia Working Group of the Psychiatric Genomics Consortium

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Nature 511 (7510) 421-427 [2014-07-24; online 2014-07-22]

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A Picea abies linkage map based on SNP markers identifies QTLs for four aspects of resistance to Heterobasidion parviporum infection.

Lind M, Källman T, Chen J, ..., Lascoux M, Stenlid J

pii pmc

PLoS ONE 9 (7) e101049 [2014-07-18; online 2014-07-18]

NGI Uppsala (SNP&SEQ Technology Platform)

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Single nucleotide polymorphisms with cis-regulatory effects on long non-coding transcripts in human primary monocytes.

Almlöf JC, Lundmark P, Lundmark A, ..., Ouwehand WH, Syvänen AC

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PLoS ONE 9 (7) e102612 [2014-07-15; online 2014-07-15]

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Zhao C, Qiao Y, Jonsson P, ..., Williams C, Dahlman-Wright K

pii

Cancer Res. 74 (14) 3983-3994 [2014-07-15; online 2014-05-17]

Bioinformatics and Expression Analysis (BEA)

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Comparative structural analysis of the putative mono-ADP-ribosyltransferases of the ARTD/PARP family.

Pinto AF, Schüler H

Curr. Top. Microbiol. Immunol. 384 (-) 153-166 [2014-07-13; online 2014-07-13]

Protein Science Facility (PSF)

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Peroxiredoxin-1 protects estrogen receptor α from oxidative stress-induced suppression and is a protein biomarker of favorable prognosis in breast cancer.

O'Leary PC, Terrile M, Bajor M, ..., Zagozdzon R, Gallagher WM

pii pmc

Breast Cancer Res. 16 (4) R79 [2014-07-10; online 2014-07-10]

Tissue Profiling

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Structural and biochemical characterization of human PR70 in isolation and in complex with the scaffolding subunit of protein phosphatase 2A.

Dovega R, Tsutakawa S, Quistgaard EM, ..., Löw C, Nordlund P

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PLoS ONE 9 (7) e101846 [2014-07-09; online 2014-07-09]

Protein Science Facility (PSF)

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The archaeal legacy of eukaryotes: a phylogenomic perspective.

Guy L, Saw JH, Ettema TJ

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Cold Spring Harb Perspect Biol 6 (10) a016022 [2014-07-03; online 2014-07-03]

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

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Transcriptome analysis reveals signature of adaptation to landscape fragmentation.

Somervuo P, Kvist J, Ikonen S, ..., Ahola V, Hanski I

pii pmc GEO

PLoS ONE 9 (7) e101467 [2014-07-02; online 2014-07-02]

Karolinska High Throughput Center (KHTC)

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Large-scale genome-wide association studies and meta-analyses of longitudinal change in adult lung function.

Tang W, Kowgier M, Loth DW, ..., Hall IP, Cassano PA

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PLoS ONE 9 (7) e100776 [2014-07-01; online 2014-07-01]

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

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The human liver-specific proteome defined by transcriptomics and antibody-based profiling.

Kampf C, Mardinoglu A, Fagerberg L, ..., Nielsen J, Uhlen M

pii

FASEB J. 28 (7) 2901-2914 [2014-07-00; online 2014-03-22]

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

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Management intensity at field and landscape levels affects the structure of generalist predator communities.

Rusch A, Birkhofer K, Bommarco R, Smith HG, Ekbom B

Oecologia 175 (3) 971-983 [2014-07-00; online 2014-05-09]

NGI Uppsala (Uppsala Genome Center)

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Harmonization of Neuroticism and Extraversion phenotypes across inventories and cohorts in the Genetics of Personality Consortium: an application of Item Response Theory.

van den Berg SM, de Moor MH, McGue M, ..., Martin NG, Boomsma DI

pmc

Behav. Genet. 44 (4) 295-313 [2014-07-00; online 2014-05-15]

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

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Novel approach identifies SNPs in SLC2A10 and KCNK9 with evidence for parent-of-origin effect on body mass index.

Hoggart CJ, Venturini G, Mangino M, ..., Loos RJ, Kutalik Z

pii pmc

PLoS Genet. 10 (7) e1004508 [2014-07-00; online 2014-07-31]

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l-Proline organocatalyzed Michael synthesis of monobactam and carbapenem β-lactam cores

Khanyase S, Naicker T, Maguire GEM, ..., Arvidsson PI, Govender T

Tetrahedron: Asymmetry 25 (13-14) 969-973 [2014-07-00; online 2014-07-00]

Drug Discovery and Development (DDD) [Collaborative]

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Genetic variants in CDC42 and NXPH1 as susceptibility factors for constipation and diarrhoea predominant irritable bowel syndrome.

Wouters MM, Lambrechts D, Knapp M, ..., D'Amato M, Boeckxstaens G

pii

Gut 63 (7) 1103-1111 [2014-07-00; online 2013-09-18]

Mutation Analysis Facility (MAF)

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Screening for inhibition of Vibrio cholerae VipA-VipB interaction identifies small-molecule compounds active against type VI secretion.

Sun K, Bröms J, Lavander M, ..., Elofsson M, Sjöstedt A

pii pmc GENBANK GENBANK

Antimicrob. Agents Chemother. 58 (7) 4123-4130 [2014-07-00; online 2014-05-07]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

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'Geoarchaeote NAG1' is a deeply rooting lineage of the archaeal order Thermoproteales rather than a new phylum.

Guy L, Spang A, Saw JH, Ettema TJ

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ISME J 8 (7) 1353-1357 [2014-07-00; online 2014-02-14]

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

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Structural basis for PTPA interaction with the invariant C-terminal tail of PP2A.

Löw C, Quistgaard EM, Kovermann M, ..., Balbach J, Nordlund P

pii PDB

Biol. Chem. 395 (7-8) 881-889 [2014-07-00; online 2014-07-09]

Protein Science Facility (PSF)

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Autosomal dominant brachyolmia in a large Swedish family: phenotypic spectrum and natural course.

Grigelioniene G, Geiberger S, Horemuzova E, ..., Nordgren A, Mäkitie O

OMIM

Am. J. Med. Genet. A 164A (7) 1635-1641 [2014-07-00; online 2014-03-29]

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

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Genome-wide association analysis identifies six new loci associated with forced vital capacity.

Loth DW, Soler Artigas M, Gharib SA, ..., Tobin MD, London SJ

pii pmc mid GEO

Nat. Genet. 46 (7) 669-677 [2014-07-00; online 2014-06-15]

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

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Polymorphism of the cystatin C gene in patients with acute coronary syndromes: Results from the PLATelet inhibition and patient Outcomes study.

Akerblom A, Eriksson N, Wallentin L, ..., James SK, PLATO Investigators

pii

Am. Heart J. 168 (1) 96-102.e2 [2014-07-00; online 2014-04-04]

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

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Genome wide association identifies common variants at the SERPINA6/SERPINA1 locus influencing plasma cortisol and corticosteroid binding globulin.

Bolton JL, Hayward C, Direk N, ..., Walker BR, CORtisol NETwork (CORNET) Consortium

pii pmc

PLoS Genet. 10 (7) e1004474 [2014-07-00; online 2014-07-10]

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

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Characterization of an experimental vaccine for bovine respiratory syncytial virus.

Hägglund S, Hu K, Blodörn K, ..., Valarcher JF, Eléouët JF

pii pmc

Clin. Vaccine Immunol. 21 (7) 997-1004 [2014-07-00; online 2014-05-16]

Mass Spectrometry-based Proteomics, Uppsala

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Affinity proteomics within rare diseases: a BIO-NMD study for blood biomarkers of muscular dystrophies.

Ayoglu B, Chaouch A, Lochmüller H, ..., Nilsson P, Al-Khalili Szigyarto C

pii pmc

EMBO Mol Med 6 (7) 918-936 [2014-07-00; online 2014-06-13]

Plasma Profiling [Collaborative]

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CXCR4 Antagonists

Castaldo C, Benicchi T, Otrocka M, ..., Varrone M, Porcari V

J Biomol Screen 19 (6) 859-869 [2014-07-00; online 2014-07-00]

Chemical Biology Consortium Sweden (CBCS) [Service]

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MiR-146a negatively regulates TLR2-induced inflammatory responses in keratinocytes.

Meisgen F, Xu Landén N, Wang A, ..., Breton L, Pivarcsi A

pii

J. Invest. Dermatol. 134 (7) 1931-1940 [2014-07-00; online 2014-03-29]

Bioinformatics and Expression Analysis (BEA)

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Haplotypes of the inducible nitric oxide synthase gene are strongly associated with exhaled nitric oxide levels in adults: a population-based study.

Dahgam S, Modig L, Torinsson Naluai Å, Olin AC, Nyberg F

pii

J. Med. Genet. 51 (7) 449-454 [2014-07-00; online 2014-04-15]

Mutation Analysis Facility (MAF)

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A universal genomic coordinate translator for comparative genomics.

Zamani N, Sundström G, Meadows JR, ..., Haas BJ, Grabherr MG

pii pmc

BMC Bioinformatics 15 (-) 227 [2014-06-30; online 2014-06-30]

Bioinformatics Support and Infrastructure

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Large tilts in transmembrane helices can be induced during tertiary structure formation.

Virkki M, Boekel C, Illergård K, ..., von Heijne G, Nilsson I

pii

J. Mol. Biol. 426 (13) 2529-2538 [2014-06-26; online 2014-05-06]

Bioinformatics Support and Infrastructure

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Exome sequencing circumvents missing clinical data and identifies a BSCL2 mutation in congenital lipodystrophy.

Schuster J, Khan TN, Tariq M, ..., Baig SM, Klar J

pii pmc

BMC Med. Genet. 15 (-) 71 [2014-06-24; online 2014-06-24]

NGI Uppsala (Uppsala Genome Center)

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Short-term variation in sperm competition causes sperm-mediated epigenetic effects on early offspring performance in the zebrafish.

Zajitschek S, Hotzy C, Zajitschek F, Immler S

pii pmc

Proc. Biol. Sci. 281 (1785) 20140422 [2014-06-22; online 2014-05-03]

Genome Engineering Zebrafish

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The genomic landscape underlying phenotypic integrity in the face of gene flow in crows

Poelstra JW, Vijay N, Bossu CM, ..., Grabherr MG, Wolf JBW

Science 344 (6190) 1410-1414 [2014-06-20; online 2014-06-19]

Bioinformatics Long-term Support WABI [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

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Myelodysplastic syndromes are propagated by rare and distinct human cancer stem cells in vivo.

Woll PS, Kjällquist U, Chowdhury O, ..., Linnarsson S, Jacobsen SE

pii GEO SRA

Cancer Cell 25 (6) 794-808 [2014-06-16; online 2014-05-20]

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

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Complete genome sequence of a plant associated bacterium Bacillus amyloliquefaciens subsp. plantarum UCMB5033.

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

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Stand Genomic Sci 9 (3) 718-725 [2014-06-15; online 2014-02-15]

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Tyrosine phosphorylation profiling via in situ proximity ligation assay.

Elfineh L, Classon C, Asplund A, ..., Kamali-Moghaddam M, Lind SB

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BMC Cancer 14 (-) 435 [2014-06-13; online 2014-06-13]

PLA and Single Cell Proteomics

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Patterns of sequencing coverage bias revealed by ultra-deep sequencing of vertebrate mitochondria.

Ekblom R, Smeds L, Ellegren H

pii pmc

BMC Genomics 15 (-) 467 [2014-06-12; online 2014-06-12]

NGI Uppsala (SNP&SEQ Technology Platform)

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Mapping-by-sequencing accelerates forward genetics in barley.

Mascher M, Jost M, Kuon JE, ..., Graner A, Stein N

pii pmc

Genome Biol. 15 (6) R78 [2014-06-10; online 2014-06-10]

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

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Efficient de novo assembly of large and complex genomes by massively parallel sequencing of Fosmid pools.

Alexeyenko A, Nystedt B, Vezzi F, ..., Wu CC, Lundeberg J

pii pmc

BMC Genomics 15 (-) 439 [2014-06-06; online 2014-06-06]

Bioinformatics Support and Infrastructure NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

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Normalyzer: a tool for rapid evaluation of normalization methods for omics data sets.

Chawade A, Alexandersson E, Levander F

pmc

J. Proteome Res. 13 (6) 3114-3120 [2014-06-06; online 2014-04-29]

Bioinformatics Support and Infrastructure

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Scanning inverse fluorescence correlation spectroscopy.

Bergstrand J, Rönnlund D, Widengren J, Wennmalm S

pii

Opt Express 22 (11) 13073-13090 [2014-06-02; online 2014-06-13]

Fluorescence Correlation Spectroscopy [Technology development]

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Crystal structure of human CRMP-4: correction of intensities for lattice-translocation disorder

Ponnusamy R, Lebedev AA, Pahlow S, Lohkamp B

PDB PDB PDB

Acta Crystallogr. D Biol. Crystallogr. 70 (6) 1680-1694 [2014-06-01; online 2014-05-30]

Protein Science Facility (PSF) [Service]

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Impact of type 2 diabetes susceptibility variants on quantitative glycemic traits reveals mechanistic heterogeneity.

Dimas AS, Lagou V, Barker A, ..., Prokopenko I, MAGIC Investigators

pii pmc

Diabetes 63 (6) 2158-2171 [2014-06-00; online 2013-12-04]

NGI Uppsala (SNP&SEQ Technology Platform)

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Simultaneous uptake of lignocellulose-based monosaccharides by Escherichia coli.

Jarmander J, Hallström BM, Larsson G

Biotechnol. Bioeng. 111 (6) 1108-1115 [2014-06-00; online 2014-01-03]

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

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Genetic associations to germinal centre formation in primary Sjogren's syndrome.

Reksten TR, Johnsen SJ, Jonsson MV, ..., Jonsson R, Nordmark G

pii

Ann. Rheum. Dis. 73 (6) 1253-1258 [2014-06-00; online 2013-04-23]

NGI Uppsala (SNP&SEQ Technology Platform)

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Decreased decorin expression in the tumor microenvironment.

Bozoky B, Savchenko A, Guven H, ..., Klein G, Szekely L

pmc

Cancer Med 3 (3) 485-491 [2014-06-00; online 2014-03-19]

Tissue Profiling

PubMed DOI Crossref

Numerical compression schemes for proteomics mass spectrometry data.

Teleman J, Dowsey AW, Gonzalez-Galarza FF, ..., Deutsch EW, Levander F

pii pmc

Mol. Cell Proteomics 13 (6) 1537-1542 [2014-06-00; online 2014-03-29]

Bioinformatics Support and Infrastructure

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Identification of a large protein network involved in epigenetic transmission in replicating DNA of embryonic stem cells.

Aranda S, Rutishauser D, Ernfors P

pii pmc

Nucleic Acids Res. 42 (11) 6972-6986 [2014-06-00; online 2014-05-24]

Advanced Mass Spectrometry Proteomics

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Immunoproteomics using polyclonal antibodies and stable isotope-labeled affinity-purified recombinant proteins.

Edfors F, Boström T, Forsström B, ..., Mann M, Uhlen M

pii pmc

Mol. Cell Proteomics 13 (6) 1611-1624 [2014-06-00; online 2014-04-12]

Cell Profiling

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Nucleosome regulatory dynamics in response to TGFβ.

Enroth S, Andersson R, Bysani M, ..., Komorowski J, Wadelius C

pii pmc

Nucleic Acids Res. 42 (11) 6921-6934 [2014-06-00; online 2014-04-29]

NGI Uppsala (Uppsala Genome Center)

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SpliceVista, a tool for splice variant identification and visualization in shotgun proteomics data.

Zhu Y, Hultin-Rosenberg L, Forshed J, ..., Orre LM, Lehtiö J

pii pmc

Mol. Cell Proteomics 13 (6) 1552-1562 [2014-06-00; online 2014-04-03]

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

PubMed DOI Crossref

The age and genomic integrity of neurons after cortical stroke in humans.

Huttner HB, Bergmann O, Salehpour M, ..., Lundeberg J, Frisén J

pii GEO SRA

Nat. Neurosci. 17 (6) 801-803 [2014-06-00; online 2014-04-22]

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

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Genetic factors may play a prominent role in the development of coronary heart disease dependent on important environmental factors.

Song C, Chang Z, Magnusson PK, Ingelsson E, Pedersen NL

pmc

J. Intern. Med. 275 (6) 631-639 [2014-06-00; online 2013-12-18]

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

PubMed DOI Crossref

Proteome-wide epitope mapping of antibodies using ultra-dense peptide arrays.

Forsström B, Axnäs BB, Stengele K, ..., Rockberg J, Uhlen M

pii pmc

Mol. Cell Proteomics 13 (6) 1585-1597 [2014-06-00; online 2014-04-08]

Autoimmunity Profiling [Technology development]

PubMed DOI Crossref

Recurrent EWSR1-CREB3L1 gene fusions in sclerosing epithelioid fibrosarcoma.

Arbajian E, Puls F, Magnusson L, ..., Kindblom LG, Mertens F

Am. J. Surg. Pathol. 38 (6) 801-808 [2014-06-00; online 2014-01-21]

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

PubMed DOI Crossref

The human testis-specific proteome defined by transcriptomics and antibody-based profiling.

Djureinovic D, Fagerberg L, Hallström B, ..., Uhlén M, Pontén F

pii

Mol. Hum. Reprod. 20 (6) 476-488 [2014-06-00; online 2014-03-07]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) Tissue Profiling

PubMed DOI Crossref

Diversity and abundance of aromatic catabolic genes in lake sediments in response to temperature change.

Osman OA, Gudasz C, Bertilsson S

GENBANK GENBANK GENBANK GENBANK

FEMS Microbiol. Ecol. 88 (3) 468-481 [2014-06-00; online 2014-03-07]

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

PubMed DOI Crossref

Old but not (so) degenerated--slow evolution of largely homomorphic sex chromosomes in ratites.

Yazdi HP, Ellegren H

pii

Mol. Biol. Evol. 31 (6) 1444-1453 [2014-06-00; online 2014-03-13]

NGI Uppsala (SNP&SEQ Technology Platform)

PubMed DOI Crossref

Recurrent activating mutation in PRKACA in cortisol-producing adrenal tumors.

Goh G, Scholl UI, Healy JM, ..., Carling T, Lifton RP

pii pmc mid GEO

Nat. Genet. 46 (6) 613-617 [2014-06-00; online 2014-04-22]

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

PubMed DOI Crossref

microRNA-34b/c on chromosome 11q23 is aberrantly methylated in chronic lymphocytic leukemia.

Deneberg S, Kanduri M, Ali D, ..., Lennartsson A, Lehmann S

pii pmc

Epigenetics 9 (6) 910-917 [2014-06-00; online 2014-04-02]

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

PubMed DOI Crossref

Mosaic loss of chromosome Y in peripheral blood is associated with shorter survival and higher risk of cancer.

Forsberg LA, Rasi C, Malmqvist N, ..., Lind L, Dumanski JP

pii

Nat. Genet. 46 (6) 624-628 [2014-06-00; online 2014-04-30]

NGI Uppsala (SNP&SEQ Technology Platform)

PubMed DOI Crossref

The HLA locus contains novel foetal susceptibility alleles for congenital heart block with significant paternal influence.

Meisgen S, Östberg T, Salomonsson S, ..., Kockum I, Wahren-Herlenius M

J. Intern. Med. 275 (6) 640-651 [2014-06-00; online 2013-12-21]

NGI Uppsala (SNP&SEQ Technology Platform)

PubMed DOI Crossref

p53 protein expression independently predicts outcome in patients with lower-risk myelodysplastic syndromes with del(5q).

Saft L, Karimi M, Ghaderi M, ..., MacBeth KJ, Hellström-Lindberg E

pii pmc ClinicalTrials.gov

Haematologica 99 (6) 1041-1049 [2014-06-00; online 2014-04-01]

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

PubMed DOI Crossref

The benefits of staying active in old age: physical activity counteracts the negative influence of PICALM, BIN1, and CLU risk alleles on episodic memory functioning.

Ferencz B, Laukka EJ, Welmer AK, ..., Lövdén M, Bäckman L

pii

Psychol Aging 29 (2) 440-449 [2014-06-00; online 2014-03-26]

Mutation Analysis Facility (MAF)

PubMed DOI Crossref

Immunomodulatory activity of commonly used drugs on Fc-receptor-mediated human natural killer cell activation.

Theorell J, Gustavsson A, Tesi B, ..., Lundbäck T, Bryceson YT

Cancer Immunol. Immunother. 63 (6) 627-641 [2014-06-00; online 2014-03-30]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

PubMed DOI Crossref

Garbage in, garbage out: a critical evaluation of strategies used for validation of immunohistochemical biomarkers.

O'Hurley G, Sjöstedt E, Rahman A, ..., Gallagher WM, Lindskog C

pii

Mol Oncol 8 (4) 783-798 [2014-06-00; online 2014-04-15]

Tissue Profiling

DOI Crossref

Hepatic Uptake of Atorvastatin: Influence of Variability in Transporter Expression on Uptake Clearance and Drug-Drug Interactions

Vildhede A, Karlgren M, Svedberg EK, ..., Noren A, Artursson P

Drug Metab. Dispos. 42 (7) 1210-1218 [2014-05-30; online 2014-05-05]

Chemical Biology Consortium Sweden (CBCS) [Service]

PubMed DOI Crossref

Identification of candidate risk gene variations by whole-genome sequence analysis of four rat strains commonly used in inflammation research.

Bäckdahl L, Ekman D, Jagodic M, Olsson T, Holmdahl R

pii pmc SRA

BMC Genomics 15 (-) 391 [2014-05-21; online 2014-05-21]

NGI Uppsala (Uppsala Genome Center)

PubMed DOI Crossref

Genetic architecture of main effect QTL for heading date in European winter wheat.

Zanke C, Ling J, Plieske J, ..., Ganal MW, Röder MS

pmc

Front Plant Sci 5 (-) 217 [2014-05-20; online 2014-05-20]

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

PubMed DOI Crossref

Genomic diversity and admixture differs for Stone-Age Scandinavian foragers and farmers.

Skoglund P, Malmström H, Omrak A, ..., Götherström A, Jakobsson M

pii

Science 344 (6185) 747-750 [2014-05-16; online 2014-04-26]

NGI Uppsala (SNP&SEQ Technology Platform)

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

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Environ Health 13 (1) 34 [2014-05-08; online 2014-05-08]

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Niegowski D, Kleinschmidt T, Ahmad S, ..., Rinaldo-Matthis A, Haeggström JZ

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Garcia D, Stråge A, Lundström S, ..., Kerekes N, Anckarsäter H

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Trésaugues L, Silvander C, Flodin S, ..., Berglund H, Nordlund P

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Ayoglu B, Szarka E, Huber K, ..., Nilsson P, Papp K

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Hammond M, Wik L, Deslys JP, ..., Landegren U, Kamali-Moghaddam M

Prion 8 (3) 261-265 [2014-05-04; online 2014-11-00]

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Perry JR, Hsu YH, Chasman DI, ..., Karasik D, Murray A

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Hum. Mol. Genet. 23 (9) 2490-2497 [2014-05-01; online 2013-12-19]

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Besingi W, Johansson A

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Hum. Mol. Genet. 23 (9) 2290-2297 [2014-05-01; online 2013-12-18]

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Xu D, Lin F, Jiang Y, ..., Holm M, Deng XW

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Plant Cell 26 (5) 1981-1991 [2014-05-00; online 2014-05-16]

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Wahlestedt M, Ameur A, Moraghebi R, ..., Woods NB, Bryder D

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Hatemi PK, Medland SE, Klemmensen R, ..., Eaves LJ, Martin NG

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Anvari E, Fred RG, Welsh N

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Winkler TW, Day FR, Croteau-Chonka DC, ..., Loos RJ, Genetic Investigation of Anthropometric Traits (GIANT) Consortium

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Nord KH, Lilljebjörn H, Vezzi F, ..., Hogendoorn PC, Szuhai K

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Tumour Biol. 35 (5) 4479-4488 [2014-05-00; online 2014-02-11]

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Marwaha S, Uvell H, Salin O, ..., Elofsson M, Gylfe A

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Antimicrob. Agents Chemother. 58 (5) 2968-2971 [2014-05-00; online 2014-02-26]

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Zhao H, Chen M, Pettersson U

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Zhao W, Andersson SG

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Johnsson M, Rubin CJ, Höglund A, ..., Jensen P, Wright D

Mol. Ecol. 23 (9) 2275-2286 [2014-05-00; online 2014-03-25]

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Saleiban A, Faxälv L, Claesson K, Jönsson JI, Osman A

Pigment Cell Melanoma Res 27 (3) 431-441 [2014-05-00; online 2014-01-11]

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International Wood Products Journal 5 (2) 83-91 [2014-05-00; online 2013-12-19]

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Blokzijl A, Nong R, Darmanis S, ..., Landegren U, Kamali-Moghaddam M

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Tillander V, Bjørndal B, Burri L, ..., Berge RK, Alexson SE

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Rönnerblad M, Andersson R, Olofsson T, ..., Lennartsson A, FANTOM consortium

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Kunze G, Gaillardin C, Czernicka M, ..., Scholz U, Neuvéglise C

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Biotechnol Biofuels 7 (-) 66 [2014-04-24; online 2014-04-24]

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Bengtsson SB, Barklund P, von Brömssen C, Stenlid J

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PLoS ONE 9 (4) e76429 [2014-04-23; online 2014-04-23]

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PeerJ 2 (-) e359 [2014-04-22; online 2014-04-22]

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Elucidating the interactions between the human gut microbiota and its host through metabolic modeling.

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Erysipelothrix rhusiopathiae contamination in the poultry house environment during erysipelas outbreaks in organic laying hen flocks.

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Avian Pathol. 43 (3) 231-237 [2014-04-22; online 2014-03-26]

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Hauling T, Krautz R, Markus R, ..., Kucerova L, Theopold U

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Biol Open 3 (4) 250-260 [2014-04-15; online 2014-03-25]

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Carcinogenesis 35 (4) 784-794 [2014-04-00; online 2013-12-03]

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J. Pathol. 232 (5) 534-540 [2014-04-00; online 2014-01-01]

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NGI Uppsala (SNP&SEQ Technology Platform)

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Bachmann J, Burté F, Pramana S, ..., Fernandez-Reyes D, Nilsson P

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Plasma Profiling [Collaborative]

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Org. Biomol. Chem. 12 (12) 1942-1956 [2014-03-28; online 2014-02-18]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

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Ran C, Graae L, Magnusson PK, ..., Olson L, Belin AC

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BMC Med. Genet. 15 (-) 38 [2014-03-28; online 2014-03-28]

NGI Uppsala (SNP&SEQ Technology Platform)

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Over B, McCarren P, Artursson P, ..., Duvall JR, Kihlberg J

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J. Med. Chem. 57 (6) 2746-2754 [2014-03-27; online 2014-02-15]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

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Golassa L, Enweji N, Erko B, Aseffa A, Swedberg G

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Malar. J. 13 (-) 120 [2014-03-27; online 2014-03-27]

NGI Uppsala (Uppsala Genome Center)

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Liscio P, Carotti A, Asciutti S, ..., Pellicciari R, Camaioni E

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J. Med. Chem. 57 (6) 2807-2812 [2014-03-27; online 2014-02-18]

Protein Science Facility (PSF)

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BMC Neurosci 15 (-) 45 [2014-03-26; online 2014-03-26]

Advanced Light Microscopy (ALM) [Technology development]

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The novel diagnostic biomarkers for focal segmental glomerulosclerosis.

Nafar M, Kalantari S, Samavat S, ..., Rutishuser D, Zubarev RA

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Int J Nephrol 2014 (-) 574261 [2014-03-26; online 2014-03-26]

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