Publications 2014

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346 publications

PubMed DOI Crossref
Sensitive detection of aggregated prion protein via proximity ligation.
Hammond M, Wik L, ..., Landegren U, Kamali-Moghaddam M
Prion 8 (3) 261-265 [2014-12-09; online 2014-12-09]
Clinical Biomarkers PLA Proteomics
PubMed DOI Crossref
Inhibition of tumor cell proliferation and motility by fibroblasts is both contact and soluble factor dependent.
Alkasalias T, Flaberg E, ..., Klein G, Guven H
Proc. Natl. Acad. Sci. U.S.A. 111 (48) 17188-17193 [2014-12-02; online 2014-11-19]
Bioinformatics Short-term Support and Infrastructure (BILS)
PubMed DOI Crossref
Vinylated linear P2 pyrimidinyloxyphenylglycine based inhibitors of the HCV NS3/4A protease and corresponding macrocycles.
Lampa A, Alogheli H, ..., Karlén A, Sandström A
Bioorg. Med. Chem. 22 (23) 6595-6615 [2014-12-01; online 2014-12-03]
ADME of Therapeutics (UDOPP) Uppsala Drug Optimization and Pharmaceutical Profiling (UDOPP)
PubMed DOI Crossref
Both Lewis and secretor status mediate susceptibility to rotavirus infections in a rotavirus genotype-dependent manner.
Nordgren J, Sharma S, ..., Larson G, Svensson L
Clin. Infect. Dis. 59 (11) 1567-1573 [2014-12-01; online 2014-08-07]
Mutation Analysis Facility (MAF)
PubMed DOI Crossref
TGFβ receptor 1: an immune susceptibility gene in HPV-associated cancer.
Levovitz C, Chen D, ..., Boffetta P, Sikora AG
Cancer Res. 74 (23) 6833-6844 [2014-12-01; online 2014-10-03]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed DOI Crossref
An outbreak of respiratory tularemia caused by diverse clones of Francisella tularensis.
Johansson A, Lärkeryd A, ..., Forsman M, Larsson P
Clin. Infect. Dis. 59 (11) 1546-1553 [2014-12-01; online 2014-08-07]
NGI Uppsala (SNP&SEQ Technology Platform)
PubMed DOI Crossref
Donor or recipient origin of posttransplant lymphoproliferative disorders following solid organ transplantation.
Kinch A, Cavelier L, ..., 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
Intragenic duplication--a novel causative mechanism for SATB2-associated syndrome.
Liedén A, Kvarnung M, ..., 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, ..., Syvänen AC, Milà M
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, ..., Langenberg C, Wareham NJ
Diabetes 63 (12) 4378-4387 [2014-12-00; online 2014-06-21]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed DOI Crossref
Insights into conifer giga-genomes.
De La Torre AR, Birol I, ..., Zerbe P, Bohlmann J
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, ..., 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
MICA polymorphism: biology and importance in cancer.
Chen D, Gyllensten U
Carcinogenesis 35 (12) 2633-2642 [2014-12-00; online 2014-10-22]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed DOI Crossref
The lung-specific proteome defined by integration of transcriptomics and antibody-based profiling.
Lindskog C, Fagerberg L, ..., Pontén F, Micke P
FASEB J. 28 (12) 5184-5196 [2014-12-00; online 2014-08-30]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) Tissue Profiling
PubMed DOI Crossref
Serotonin receptor gene (5HT-2A) polymorphism is associated with provoked vestibulodynia and comorbid symptoms of pain.
Heddini U, Bohm-Starke N, ..., Nilsson KW, Johannesson U
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, ..., Tessier J, Stone-Elander S
EJNMMI Res 4 (1) 34 [2014-12-00; online 2014-09-09]
Fluorescence Tissue Profiling
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, ..., Stenberg P, Thelaus J
Genome Announc 2 (6) - [2014-11-26; online 2014-11-26]
Bioinformatics Compute and Storage (UPPNEX) NGI Uppsala (Uppsala Genome Center)
PubMed DOI Crossref
1p36 deletion is a marker for tumour dissemination in microsatellite stable stage II-III colon cancer.
Mayrhofer M, Kultima HG, ..., Glimelius B, Isaksson A
BMC Cancer 14 (-) 872 [2014-11-24; online 2014-11-24]
Array and Analysis Facility
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, ..., Mokhtari D, Siegbahn A
J. Biol. Chem. 289 (47) 32379-32391 [2014-11-21; online 2014-10-05]
PLA 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, ..., Siegbahn A, ARISTOTLE Investigators
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
Sci. Total Environ. 499 (-) 220-227 [2014-11-15; online 2014-09-07]
Bioinformatics Short-term Support and Infrastructure (BILS)
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
Hum. Mol. Genet. 23 (22) 6047-6060 [2014-11-15; online 2014-06-18]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (SNP&SEQ Technology Platform) NGI Uppsala (Uppsala Genome Center)
PubMed DOI Crossref
Defining the human adipose tissue proteome to reveal metabolic alterations in obesity.
Mardinoglu A, Kampf C, ..., 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
Affinity proteomic profiling of plasma, cerebrospinal fluid, and brain tissue within multiple sclerosis.
Byström S, Ayoglu B, ..., Nilsson P, Schwenk JM
J. Proteome Res. 13 (11) 4607-4619 [2014-11-07; online 2014-09-19]
Fluorescence Tissue Profiling
PubMed DOI Crossref
Aberrantly activated claudin 6 and 18.2 as potential therapy targets in non-small-cell lung cancer.
Micke P, Mattsson JS, ..., 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, ..., Hammarström P, Nilsson KP
Prion 8 (4) 319-329 [2014-11-01; online 2014-11-01]
Bioinformatics Short-term Support and Infrastructure (BILS)
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, ..., Lind L, Schiöth HB
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, ..., Nielsen J, Borodina I
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, ..., Womack C, Warford A
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
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, ..., Andersson AF, Quince C
Nat. Methods 11 (11) 1144-1146 [2014-11-00; online 2014-09-15]
Bioinformatics Short-term Support and Infrastructure (BILS)
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, ..., Qvarnström A, Ellegren H
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, ..., Henriques-Normark B, Danielsson-Tham ML
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, ..., 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, ..., Hirschhorn JN, Frayling TM
Nat. Genet. 46 (11) 1173-1186 [2014-11-00; online 2014-10-06]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) 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, ..., Kaminska B, Komorowski J
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, ..., 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)
PubMed DOI Crossref
Cesarean delivery and hematopoietic stem cell epigenetics in the newborn infant: implications for future health?
Almgren M, Schlinzig T, ..., Norman M, Ekström TJ
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, ..., Mikoshiba K, Dahl N
J. Clin. Invest. 124 (11) 4773-4780 [2014-11-00; online 2014-10-21]
NGI Uppsala (Uppsala Genome Center)
PubMed DOI Crossref
Melanoma patient-derived xenografts accurately model the disease and develop fast enough to guide treatment decisions.
Einarsdottir BO, Bagge RO, ..., Ny L, Nilsson JA
Oncotarget 5 (20) 9609-9618 [2014-10-30; online 2014-09-18]
Bioinformatics Short-term Support and Infrastructure (BILS)
DOI Crossref
Photocatalysis induces bioactivity of an organic polymer based material
Cai Y, Strømme M, ..., 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, ..., Jansson S, Street NR
BMC Plant Biol. 14 (-) 276 [2014-10-16; online 2014-10-16]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed
Allelic expression mapping across cellular lineages to establish impact of non-coding SNPs.
Adoue V, Schiavi A, ..., Syvänen AC, Pastinen T
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, ..., Pitkänen E, Aaltonen LA
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, ..., Hansson GK, Olofsson PS
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
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
Database (Oxford) 2014 (-) - [2014-10-03; online 2014-10-03]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (Uppsala Genome Center)
PubMed DOI Crossref
Biofuels. Altered sterol composition renders yeast thermotolerant.
Caspeta L, Chen Y, ..., Petranovic D, Nielsen J
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
PLoS ONE 9 (10) e109255 [2014-10-02; online 2014-10-02]
Mass Spectrometry-based Proteomics, Uppsala
PubMed DOI Crossref
Medium from γ-irradiated Escherichia coli bacteria stimulates a unique immune response in Drosophila cells.
Lindberg BG, Oldenvi S, Steiner H
Dev. Comp. Immunol. 46 (2) 392-400 [2014-10-00; online 2014-06-04]
Bioinformatics and Expression Analysis (BEA)
PubMed DOI Crossref
In situ sequencing identifies TMPRSS2-ERG fusion transcripts, somatic point mutations and gene expression levels in prostate cancers.
Kiflemariam S, Mignardi M, ..., Nilsson M, Sjöblom T
J. Pathol. 234 (2) 253-261 [2014-10-00; online 2014-06-17]
Tissue Profiling
PubMed DOI Crossref
Signals that regulate the oncogenic fate of neural stem cells and progenitors.
Swartling FJ, Bolin S, Phillips JJ, Persson AI
Exp. Neurol. 260 (-) 56-68 [2014-10-00; online 2013-02-05]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed DOI Crossref
A worldwide survey of genome sequence variation provides insight into the evolutionary history of the honeybee Apis mellifera.
Wallberg A, Han F, ..., Pirk CW, Webster MT
Nat. Genet. 46 (10) 1081-1088 [2014-10-00; online 2014-08-26]
NGI Uppsala (Uppsala Genome Center)
PubMed DOI Crossref
The DMRT3 'Gait keeper' mutation affects performance of Nordic and Standardbred trotters.
Jäderkvist K, Andersson LS, ..., Andersson L, Lindgren G
J. Anim. Sci. 92 (10) 4279-4286 [2014-10-00; online 2014-08-03]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed DOI Crossref
NPSR1 polymorphisms influence recurrent abdominal pain in children: a population-based study.
Henström M, Zucchelli M, ..., Olén O, D'Amato M
Neurogastroenterol. Motil. 26 (10) 1417-1425 [2014-10-00; online 2014-08-06]
Mutation Analysis Facility (MAF)
PubMed DOI Crossref
Design of a general-purpose European compound screening library for EU-OPENSCREEN.
Horvath D, Lisurek M, ..., Quintana J, Frank R
ChemMedChem 9 (10) 2309-2326 [2014-10-00; online 2014-07-22]
Laboratories for Chemical Biology Umeå (LCBU)
PubMed DOI Crossref
Evidence for autosomal recessive inheritance in SPG3A caused by homozygosity for a novel ATL1 missense mutation.
Khan TN, Klar J, ..., Baig SM, Dahl N
Eur. J. Hum. Genet. 22 (10) 1180-1184 [2014-10-00; online 2014-01-30]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (Uppsala Genome Center)
PubMed DOI Crossref
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, ..., Lambe M, Wilander E
Oncol Lett 8 (4) 1528-1532 [2014-10-00; online 2014-09-10]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed DOI Crossref
Epoxy alcohol synthase of the rice blast fungus represents a novel subfamily of dioxygenase-cytochrome P450 fusion enzymes.
Hoffmann I, Jernerén F, Oliw EH
J. Lipid Res. 55 (10) 2113-2123 [2014-10-00; online 2014-08-15]
NGI Uppsala (Uppsala Genome Center)
PubMed DOI Crossref
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, ..., Picardeau M, Buschiazzo A
Mol. Microbiol. 94 (2) 340-352 [2014-10-00; online 2014-08-26]
Karolinska High Throughput Center (KHTC)
DOI Crossref
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, ..., Koelewijn HP, Höglund J
Conserv Genet 15 (5) 1183-1195 [2014-10-00; online 2014-04-27]
NGI Uppsala (SNP&SEQ Technology Platform)
PubMed DOI Crossref
The human skeletal muscle transcriptome: sex differences, alternative splicing, and tissue homogeneity assessed with RNA sequencing.
Lindholm ME, Huss M, ..., Lundeberg J, Sundberg CJ
FASEB J. 28 (10) 4571-4581 [2014-10-00; online 2014-07-13]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed DOI Crossref
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, ..., Ponten F, Alafuzoff I
PLoS ONE 9 (9) e108861 [2014-09-30; online 2014-09-30]
Tissue Profiling
PubMed DOI Crossref
The Chironomus tentans genome sequence and the organization of the Balbiani ring genes.
Kutsenko A, Svensson T, ..., Visa N, Wieslander L
BMC Genomics 15 (-) 819 [2014-09-27; online 2014-09-27]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed DOI Crossref
Plasmidome interchange between Clostridium botulinum, Clostridium novyi and Clostridium haemolyticum converts strains of independent lineages into distinctly different pathogens.
Skarin H, Segerman B
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)
PubMed DOI Crossref
Glial origin of mesenchymal stem cells in a tooth model system.
Kaukua N, Shahidi MK, ..., Fried K, Adameyko I
Nature 513 (7519) 551-554 [2014-09-25; online 2014-08-01]
Advanced Light Microscopy
PubMed DOI Crossref
Oncoprotein stabilization in brain tumors.
Hede SM, Savov V, ..., Sangfelt O, Swartling FJ
Oncogene 33 (39) 4709-4721 [2014-09-25; online 2013-10-30]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed DOI Crossref
Evidence that breast cancer risk at the 2q35 locus is mediated through IGFBP5 regulation.
Ghoussaini M, Edwards SL, ..., Dunning AM, Australian Ovarian Cancer Management Group
Nat Commun 4 (-) 4999 [2014-09-23; online 2014-09-23]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed DOI Crossref
Histidine-rich glycoprotein uptake and turnover is mediated by mononuclear phagocytes.
Tugues S, Roche F, ..., Tolmachev V, Claesson-Welsh L
PLoS ONE 9 (9) e107483 [2014-09-22; online 2014-09-22]
Tissue Profiling
PubMed DOI Crossref
Distinguishing between driver and passenger mutations in individual cancer genomes by network enrichment analysis.
Merid SK, Goranskaya D, Alexeyenko A
BMC Bioinformatics 15 (-) 308 [2014-09-19; online 2014-09-19]
Bioinformatics Short-term Support and Infrastructure (BILS)
PubMed DOI Crossref
A universal approach to prepare reagents for DNA-assisted protein analysis.
Yan J, Gu GJ, ..., Landegren U, Kamali-Moghaddam M
PLoS ONE 9 (9) e108061 [2014-09-18; online 2014-09-18]
Clinical Biomarkers PLA Proteomics
PubMed DOI Crossref
Characterization of stem-like cells in mucoepidermoid tracheal paediatric tumor.
Lim ML, Ooi BN, ..., Ahrlund-Richter L, Macchiarini P
PLoS ONE 9 (9) e107712 [2014-09-17; online 2014-09-17]
Bioinformatics and Expression Analysis (BEA)
PubMed DOI Crossref
Structural and functional characterization of ochratoxinase, a novel mycotoxin-degrading enzyme.
Dobritzsch D, Wang H, Schneider G, Yu S
Biochem. J. 462 (3) 441-452 [2014-09-15; online 2014-06-21]
Protein Science Facility
PubMed DOI Crossref
The DEK oncoprotein binds to highly and ubiquitously expressed genes with a dual role in their transcriptional regulation.
Sandén C, Järvstråt L, ..., Nilsson B, Gullberg U
Mol. Cancer 13 (-) 215 [2014-09-12; online 2014-09-12]
Bioinformatics and Expression Analysis (BEA) NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed DOI Crossref
Genome-wide analysis reveals DNA methylation markers that vary with both age and obesity.
Almén MS, Nilsson EK, ..., Fredriksson R, Schiöth HB
Gene 548 (1) 61-67 [2014-09-10; online 2014-07-11]
NGI Uppsala (SNP&SEQ Technology Platform)
PubMed DOI Crossref
The prognostic value and therapeutic target role of stathmin-1 in urinary bladder cancer.
Hemdan T, Lindén M, ..., Malmström PU, Segersten U
Br. J. Cancer 111 (6) 1180-1187 [2014-09-09; online 2014-07-30]
Tissue Profiling
PubMed DOI Crossref
The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera.
Ahola V, Lehtonen R, ..., Frilander MJ, Hanski I
Nat Commun 5 (-) 4737 [2014-09-05; online 2014-09-05]
Karolinska High Throughput Center (KHTC)
PubMed DOI Crossref
Neu-Laxova syndrome is a heterogeneous metabolic disorder caused by defects in enzymes of the L-serine biosynthesis pathway.
Acuna-Hidalgo R, Schanze D, ..., Hoischen A, Zenker M
Am. J. Hum. Genet. 95 (3) 285-293 [2014-09-04; online 2014-08-26]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed DOI Crossref
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, ..., Yang H, Zubarev RA
BMC Nephrol 15 (-) 141 [2014-09-02; online 2014-09-02]
Advanced Mass Spectrometry Proteomics
PubMed DOI Crossref
An integrative analysis of the tumorigenic role of TAZ in human non-small cell lung cancer.
Noguchi S, Saito A, ..., Micke P, Nagase T
Clin. Cancer Res. 20 (17) 4660-4672 [2014-09-01; online 2014-06-22]
Tissue Profiling
PubMed DOI Crossref
Metagenomics reveals that detoxification systems are underrepresented in marine bacterial communities.
Bengtsson-Palme J, Alm Rosenblad M, Molin M, Blomberg A
BMC Genomics 15 (-) 749 [2014-09-01; online 2014-09-01]
Bioinformatics Short-term Support and Infrastructure (BILS)
PubMed DOI Crossref
Interactive effects of KIBRA and CLSTN2 polymorphisms on episodic memory in old-age unipolar depression.
Pantzar A, Laukka EJ, ..., Fratiglioni L, Bäckman L
Neuropsychologia 62 (-) 137-142 [2014-09-00; online 2014-08-01]
Mutation Analysis Facility (MAF)
PubMed DOI Crossref
Picocyanobacteria containing a novel pigment gene cluster dominate the brackish water Baltic Sea.
Larsson J, Celepli N, ..., Bergman B, Ekman M
ISME J 8 (9) 1892-1903 [2014-09-00; online 2014-03-14]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
DOI Crossref
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
PubMed DOI Crossref
Recurrent GATA1 mutations in Diamond-Blackfan anaemia.
Klar J, Khalfallah A, ..., 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, ..., Hovmøller MS, Justesen AF
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, ..., Panova M, Butlin RK
Mol. Ecol. 23 (18) 4603-4616 [2014-09-00; online 2014-08-13]
Bioinformatics Short-term Support and Infrastructure (BILS) 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, ..., Tamaru H, Köhler C
Plant Cell 26 (9) 3556-3568 [2014-09-00; online 2014-09-12]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) 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, ..., Grigelioniene G, Nordgren A
Mol Genet Genomic Med 2 (5) 402-411 [2014-09-00; online 2014-05-14]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
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Genome of the avirulent human-infective trypanosome--Trypanosoma rangeli.
Stoco PH, Wagner G, ..., de Vasconcelos AT, Grisard EC
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, ..., Andersson SG, Bertilsson S
Environ. Microbiol. 16 (9) 2682-2698 [2014-09-00; online 2013-10-15]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
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Systematic validation of hypothesis-driven candidate genes for cervical cancer in a genome-wide association study.
Johanneson B, Chen D, ..., Cui T, Gyllensten U
Carcinogenesis 35 (9) 2084-2088 [2014-09-00; online 2014-06-01]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (SNP&SEQ Technology Platform) NGI Uppsala (Uppsala Genome Center)
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Splicing in the human brain.
Zaghlool A, Ameur A, Cavelier L, Feuk L
Int. Rev. Neurobiol. 116 (-) 95-125 [2014-08-31; online 2014-08-31]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (Uppsala Genome Center)
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Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication.
Carneiro M, Rubin CJ, ..., Lindblad-Toh K, Andersson L
Science 345 (6200) 1074-1079 [2014-08-29; online 2014-08-30]
Bioinformatics Compute and Storage (UPPNEX) 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
Parasit Vectors 7 (-) 410 [2014-08-29; online 2014-08-29]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (SNP&SEQ Technology Platform)
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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, ..., Lehtiö L, Forwood JK
J. Biol. Chem. 289 (35) 24263-24274 [2014-08-29; online 2014-07-09]
Protein Science Facility
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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)
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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, ..., Sundsfjord A, Hegstad K
PLoS ONE 9 (8) e103274 [2014-08-25; online 2014-08-25]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
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Strong effects of genetic and lifestyle factors on biomarker variation and use of personalized cutoffs.
Enroth S, Johansson A, Enroth SB, Gyllensten U
Nat Commun 5 (-) 4684 [2014-08-22; online 2014-08-22]
Clinical Biomarkers NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (SNP&SEQ Technology Platform) NGI Uppsala (Uppsala Genome Center)
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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, ..., Andersson SG, Baldauf SL
Genome Biol Evol 6 (9) 2240-2257 [2014-08-21; online 2014-08-21]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
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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
PLoS ONE 9 (8) e105746 [2014-08-21; online 2014-08-21]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (Uppsala Genome Center)
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Winter bloom of a rare betaproteobacterium in the Arctic Ocean.
Alonso-Sáez L, Zeder M, ..., Bertilsson S, Pedrós-Alió C
Front Microbiol 5 (-) 425 [2014-08-20; online 2014-08-20]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
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Meta-analysis in more than 17,900 cases of ischemic stroke reveals a novel association at 12q24.12.
Kilarski LL, Achterberg S, ..., Bevan S, GARNET Collaborative Research Group, Wellcome Trust Case Control Consortium 2, Australian Stroke Genetic Collaborative, the METASTROKE Consortium, and the International Stroke Genetics Consortium
Neurology 83 (8) 678-685 [2014-08-19; online 2014-07-18]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
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Evaluation of exome sequencing to estimate tumor burden in plasma.
Klevebring D, Neiman M, ..., Grönberg H, Lindberg J
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)
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Species and gene divergence in Littorina snails detected by array comparative genomic hybridization.
Panova M, Johansson T, ..., Tunlid A, André C
BMC Genomics 15 (-) 687 [2014-08-18; online 2014-08-18]
Bioinformatics Short-term Support and Infrastructure (BILS) NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
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Tandem RNA chimeras contribute to transcriptome diversity in human population and are associated with intronic genetic variants.
Greger L, Su J, ..., Dermitzakis ET, Brazma A
PLoS ONE 9 (8) e104567 [2014-08-18; online 2014-08-18]
NGI Uppsala (SNP&SEQ Technology Platform)
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BESST--efficient scaffolding of large fragmented assemblies.
Sahlin K, Vezzi F, ..., Lundeberg J, Arvestad L
BMC Bioinformatics 15 (-) 281 [2014-08-15; online 2014-08-15]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
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Genome analysis of Bacillus amyloliquefaciens Subsp. plantarum UCMB5113: a rhizobacterium that improves plant growth and stress management.
Niazi A, Manzoor S, ..., Meijer J, Bongcam-Rudloff E
PLoS ONE 9 (8) e104651 [2014-08-13; online 2014-08-13]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (SNP&SEQ Technology Platform)
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Common genetic determinants of lung function, subclinical atherosclerosis and risk of coronary artery disease.
Sabater-Lleal M, Mälarstig A, ..., Tobin MD, Hamsten A
PLoS ONE 9 (8) e104082 [2014-08-05; online 2014-08-05]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
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Differences in gene expression between mouse and human for dynamically regulated genes in early embryo.
Madissoon E, Töhönen V, ..., Hovatta O, Kere J
PLoS ONE 9 (8) e102949 [2014-08-04; online 2014-08-04]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
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Exome sequencing reveals frequent inactivating mutations in ARID1A, ARID1B, ARID2 and ARID4A in microsatellite unstable colorectal cancer.
Cajuso T, Hänninen UA, ..., Kilpivaara O, Vahteristo P
Int. J. Cancer 135 (3) 611-623 [2014-08-01; online 2014-01-03]
Karolinska High Throughput Center (KHTC)
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Analysis of candidate genes for lineage-specific expression changes in humans and primates.
Lindskog C, Kuhlwilm M, ..., Pääbo S, Pontén F
J. Proteome Res. 13 (8) 3596-3606 [2014-08-01; online 2014-06-10]
Tissue Profiling
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The human carotid body releases acetylcholine, ATP and cytokines during hypoxia.
Kåhlin J, Mkrtchian S, ..., Fagerlund MJ, Eriksson LI
Exp. Physiol. 99 (8) 1089-1098 [2014-08-00; online 2014-06-03]
Bioinformatics and Expression Analysis (BEA)
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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, ..., Döhner K, Lehmann S
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)
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Mechanisms of mRNA export.
Björk P, Wieslander L
Semin. Cell Dev. Biol. 32 (-) 47-54 [2014-08-00; online 2014-05-13]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
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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, ..., Olason P, Ellegren H
Mol. Ecol. 23 (16) 4035-4058 [2014-08-00; online 2014-05-28]
NGI Uppsala (SNP&SEQ Technology Platform)
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Fusions involving protein kinase C and membrane-associated proteins in benign fibrous histiocytoma.
Płaszczyca A, Nilsson J, ..., Nord KH, Mertens F
Int. J. Biochem. Cell Biol. 53 (-) 475-481 [2014-08-00; online 2014-04-12]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
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High risk of tobacco-related cancers in CDKN2A mutation-positive melanoma families.
Helgadottir H, Höiom V, ..., Olsson H, Hansson J
J. Med. Genet. 51 (8) 545-552 [2014-08-00; online 2014-06-18]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
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Genetic variation in the CYP1A1 gene is related to circulating PCB118 levels in a population-based sample.
Lind L, Penell J, ..., van Bavel B, Lind PM
Environ. Res. 133 (-) 135-140 [2014-08-00; online 2014-06-14]
NGI Uppsala (SNP&SEQ Technology Platform)
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Plasma profiling reveals three proteins associated to amyotrophic lateral sclerosis.
Häggmark A, Mikus M, ..., Kuźma-Kozakiewicz M, Nilsson P
Ann Clin Transl Neurol 1 (8) 544-553 [2014-08-00; online 2014-07-14]
Protein and peptide arrays
PubMed DOI Crossref
Cluster of infections caused by methicillin-resistant Staphylococcus pseudintermedius in humans in a tertiary hospital.
Starlander G, Börjesson S, ..., Tellgren-Roth C, Melhus A
J. Clin. Microbiol. 52 (8) 3118-3120 [2014-08-00; online 2014-05-30]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (Uppsala Genome Center)
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Systematic investigation of contribution of genetic variation in the HLA-DP region to cervical cancer susceptibility.
Chen D, Gyllensten U
Carcinogenesis 35 (8) 1765-1769 [2014-08-00; online 2014-04-20]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (Uppsala Genome Center)
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Distinct roles of Candida albicans-specific genes in host-pathogen interactions.
Wilson D, Mayer FL, ..., Jacobsen ID, Hube B
Eukaryotic Cell 13 (8) 977-989 [2014-08-00; online 2014-03-13]
NGI Uppsala (Uppsala Genome Center)
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Multifactorial analysis of changes in body mass index across the adult life course: a study with 65 years of follow-up.
Dahl AK, Reynolds CA, ..., Magnusson PK, Pedersen NL
Int J Obes (Lond) 38 (8) 1133-1141 [2014-08-00; online 2013-11-07]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
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Selectivity mechanism of a bacterial homolog of the human drug-peptide transporters PepT1 and PepT2.
Guettou F, Quistgaard EM, ..., Löw C, Nordlund P
Nat. Struct. Mol. Biol. 21 (8) 728-731 [2014-08-00; online 2014-07-30]
Protein Science Facility
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Genetic association study of QT interval highlights role for calcium signaling pathways in myocardial repolarization.
Arking DE, Pulit SL, ..., de Bakker PI, Newton-Cheh C
Nat. Genet. 46 (8) 826-836 [2014-08-00; online 2014-06-24]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (SNP&SEQ Technology Platform)
PubMed DOI Crossref
DegePrime, a program for degenerate primer design for broad-taxonomic-range PCR in microbial ecology studies.
Hugerth LW, Wefer HA, ..., Engstrand L, Andersson AF
Appl. Environ. Microbiol. 80 (16) 5116-5123 [2014-08-00; online 2014-06-15]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
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Influence of coronary artery disease-associated genetic variants on risk of venous thromboembolism.
Bruzelius M, Strawbridge RJ, ..., Odeberg J, Hamsten A
Thromb. Res. 134 (2) 426-432 [2014-08-00; online 2014-04-22]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (SNP&SEQ Technology Platform)
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Nuclease-assisted suppression of human DNA background in sepsis.
Song Y, Giske CG, ..., Lundeberg J, Gyarmati P
PLoS ONE 9 (7) e103610 [2014-07-30; online 2014-07-30]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
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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, ..., Agartz I, Jönsson EG
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
BMC Genomics 15 (-) 631 [2014-07-28; online 2014-07-28]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed DOI Crossref
Identification of a small molecule that stabilizes lipoprotein lipase in vitro and lowers triglycerides in vivo.
Larsson M, Caraballo R, ..., Nilsson SK, Olivecrona G
Biochem. Biophys. Res. Commun. 450 (2) 1063-1069 [2014-07-25; online 2014-07-02]
Laboratories for Chemical Biology Umeå (LCBU)
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Biological insights from 108 schizophrenia-associated genetic loci.
Schizophrenia Working Group of the Psychiatric Genomics Consortium
Nature 511 (7510) 421-427 [2014-07-24; online 2014-07-22]
NGI Uppsala (SNP&SEQ Technology Platform)
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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, ..., Lascoux M, Stenlid J
PLoS ONE 9 (7) e101049 [2014-07-18; online 2014-07-18]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (SNP&SEQ Technology Platform)
PubMed DOI Crossref
Single nucleotide polymorphisms with cis-regulatory effects on long non-coding transcripts in human primary monocytes.
Almlöf JC, Lundmark P, ..., Ouwehand WH, Syvänen AC
PLoS ONE 9 (7) e102612 [2014-07-15; online 2014-07-15]
NGI Uppsala (SNP&SEQ Technology Platform)
PubMed DOI Crossref
Genome-wide profiling of AP-1-regulated transcription provides insights into the invasiveness of triple-negative breast cancer.
Zhao C, Qiao Y, ..., Williams C, Dahlman-Wright K
Cancer Res. 74 (14) 3983-3994 [2014-07-15; online 2014-05-17]
Bioinformatics and Expression Analysis (BEA)
PubMed DOI Crossref
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
PubMed DOI Crossref
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, ..., Zagozdzon R, Gallagher WM
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, ..., Löw C, Nordlund P
PLoS ONE 9 (7) e101846 [2014-07-09; online 2014-07-09]
Protein Science Facility
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The archaeal legacy of eukaryotes: a phylogenomic perspective.
Guy L, Saw JH, Ettema TJ
Cold Spring Harb Perspect Biol 6 (10) a016022 [2014-07-03; online 2014-07-03]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed DOI Crossref
Transcriptome analysis reveals signature of adaptation to landscape fragmentation.
Somervuo P, Kvist J, ..., Ahola V, Hanski I
PLoS ONE 9 (7) e101467 [2014-07-02; online 2014-07-02]
Karolinska High Throughput Center (KHTC)
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The human liver-specific proteome defined by transcriptomics and antibody-based profiling.
Kampf C, Mardinoglu A, ..., Nielsen J, Uhlen M
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
PubMed DOI Crossref
Management intensity at field and landscape levels affects the structure of generalist predator communities.
Rusch A, Birkhofer K, ..., 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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Hepatic uptake of atorvastatin: influence of variability in transporter expression on uptake clearance and drug-drug interactions.
Vildhede A, Karlgren M, ..., Norén A, Artursson P
Drug Metab. Dispos. 42 (7) 1210-1218 [2014-07-00; online 2014-05-07]
ADME of Therapeutics (UDOPP) Uppsala Drug Optimization and Pharmaceutical Profiling (UDOPP)
PubMed DOI Crossref
Genetic variants in CDC42 and NXPH1 as susceptibility factors for constipation and diarrhoea predominant irritable bowel syndrome.
Wouters MM, Lambrechts D, ..., D'Amato M, Boeckxstaens G
Gut 63 (7) 1103-1111 [2014-07-00; online 2013-09-18]
Mutation Analysis Facility (MAF)
PubMed DOI Crossref
Screening for inhibition of Vibrio cholerae VipA-VipB interaction identifies small-molecule compounds active against type VI secretion.
Sun K, Bröms J, ..., Elofsson M, Sjöstedt A
Antimicrob. Agents Chemother. 58 (7) 4123-4130 [2014-07-00; online 2014-05-07]
Laboratories for Chemical Biology Umeå (LCBU)
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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
ISME J 8 (7) 1353-1357 [2014-07-00; online 2014-02-14]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed DOI Crossref
Structural basis for PTPA interaction with the invariant C-terminal tail of PP2A.
Löw C, Quistgaard EM, ..., Balbach J, Nordlund P
Biol. Chem. 395 (7-8) 881-889 [2014-07-00; online 2014-07-09]
Protein Science Facility
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Autosomal dominant brachyolmia in a large Swedish family: phenotypic spectrum and natural course.
Grigelioniene G, Geiberger S, ..., Nordgren A, Mäkitie O
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, ..., Tobin MD, London SJ
Nat. Genet. 46 (7) 669-677 [2014-07-00; online 2014-06-16]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
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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, ..., James SK, PLATO Investigators
Am. Heart J. 168 (1) 96-102.e2 [2014-07-00; online 2014-06-24]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
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Characterization of an experimental vaccine for bovine respiratory syncytial virus.
Hägglund S, Hu K, ..., Valarcher JF, Eléouët JF
Clin. Vaccine Immunol. 21 (7) 997-1004 [2014-07-00; online 2014-05-16]
Mass Spectrometry-based Proteomics, Uppsala
PubMed DOI Crossref
Affinity proteomics within rare diseases: a BIO-NMD study for blood biomarkers of muscular dystrophies.
Ayoglu B, Chaouch A, ..., Nilsson P, Al-Khalili Szigyarto C
EMBO Mol Med 6 (7) 918-936 [2014-07-00; online 2014-06-13]
Protein and peptide arrays
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MiR-146a negatively regulates TLR2-induced inflammatory responses in keratinocytes.
Meisgen F, Xu Landén N, ..., Breton L, Pivarcsi A
J. Invest. Dermatol. 134 (7) 1931-1940 [2014-07-00; online 2014-03-29]
Bioinformatics and Expression Analysis (BEA)
PubMed DOI Crossref
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, ..., Olin AC, Nyberg F
J. Med. Genet. 51 (7) 449-454 [2014-07-00; online 2014-04-15]
Mutation Analysis Facility (MAF)
PubMed DOI Crossref
A universal genomic coordinate translator for comparative genomics.
Zamani N, Sundström G, ..., Haas BJ, Grabherr MG
BMC Bioinformatics 15 (-) 227 [2014-06-30; online 2014-06-30]
Bioinformatics Short-term Support and Infrastructure (BILS)
PubMed DOI Crossref
Large tilts in transmembrane helices can be induced during tertiary structure formation.
Virkki M, Boekel C, ..., von Heijne G, Nilsson I
J. Mol. Biol. 426 (13) 2529-2538 [2014-06-26; online 2014-05-06]
Bioinformatics Short-term Support and Infrastructure (BILS)
PubMed DOI Crossref
Exome sequencing circumvents missing clinical data and identifies a BSCL2 mutation in congenital lipodystrophy.
Schuster J, Khan TN, ..., Baig SM, Klar J
BMC Med. Genet. 15 (-) 71 [2014-06-24; online 2014-06-24]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (Uppsala Genome Center)
PubMed DOI Crossref
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
Proc. Biol. Sci. 281 (1785) 20140422 [2014-06-22; online 2014-05-03]
Zebrafish
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The genomic landscape underlying phenotypic integrity in the face of gene flow in crows.
Poelstra JW, Vijay N, ..., Grabherr MG, Wolf JB
Science 344 (6190) 1410-1414 [2014-06-20; online 2014-06-21]
Bioinformatics Compute and Storage (UPPNEX) Bioinformatics Short-term Support and Infrastructure (BILS) NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (SNP&SEQ Technology Platform)
PubMed DOI Crossref
Myelodysplastic syndromes are propagated by rare and distinct human cancer stem cells in vivo.
Woll PS, Kjällquist U, ..., Linnarsson S, Jacobsen SE
Cancer Cell 25 (6) 794-808 [2014-06-16; online 2014-05-20]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed DOI Crossref
Complete genome sequence of a plant associated bacterium Bacillus amyloliquefaciens subsp. plantarum UCMB5033.
Niazi A, Manzoor S, ..., Meijer J, Bongcam-Rudloff E
Stand Genomic Sci 9 (3) 718-725 [2014-06-15; online 2014-02-15]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (SNP&SEQ Technology Platform) NGI Uppsala (Uppsala Genome Center)
PubMed DOI Crossref
Tyrosine phosphorylation profiling via in situ proximity ligation assay.
Elfineh L, Classon C, ..., Kamali-Moghaddam M, Lind SB
BMC Cancer 14 (-) 435 [2014-06-13; online 2014-06-13]
PLA Proteomics
PubMed DOI Crossref
Patterns of sequencing coverage bias revealed by ultra-deep sequencing of vertebrate mitochondria.
Ekblom R, Smeds L, Ellegren H
BMC Genomics 15 (-) 467 [2014-06-12; online 2014-06-12]
NGI Uppsala (SNP&SEQ Technology Platform)
PubMed DOI Crossref
Mapping-by-sequencing accelerates forward genetics in barley.
Mascher M, Jost M, ..., Graner A, Stein N
Genome Biol. 15 (6) R78 [2014-06-10; online 2014-06-10]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed DOI Crossref
Efficient de novo assembly of large and complex genomes by massively parallel sequencing of Fosmid pools.
Alexeyenko A, Nystedt B, ..., Wu CC, Lundeberg J
BMC Genomics 15 (-) 439 [2014-06-06; online 2014-06-06]
Bioinformatics Short-term Support and Infrastructure (BILS) NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed DOI Crossref
Normalyzer: a tool for rapid evaluation of normalization methods for omics data sets.
Chawade A, Alexandersson E, Levander F
J. Proteome Res. 13 (6) 3114-3120 [2014-06-06; online 2014-04-29]
Bioinformatics Short-term Support and Infrastructure (BILS)
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Scanning inverse fluorescence correlation spectroscopy.
Bergstrand J, Rönnlund D, Widengren J, Wennmalm S
Opt Express 22 (11) 13073-13090 [2014-06-02; online 2014-06-13]
Fluorescence Correlation Spectroscopy
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Impact of type 2 diabetes susceptibility variants on quantitative glycemic traits reveals mechanistic heterogeneity.
Dimas AS, Lagou V, ..., Prokopenko I, MAGIC Investigators
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 R, Nordmark G
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, ..., Klein G, Szekely L
Cancer Med 3 (3) 485-491 [2014-06-00; online 2014-03-19]
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Numerical compression schemes for proteomics mass spectrometry data.
Teleman J, Dowsey AW, ..., Deutsch EW, Levander F
Mol. Cell Proteomics 13 (6) 1537-1542 [2014-06-00; online 2014-03-29]
Bioinformatics Short-term Support and Infrastructure (BILS)
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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
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, ..., Mann M, Uhlen M
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, ..., Komorowski J, Wadelius C
Nucleic Acids Res. 42 (11) 6921-6934 [2014-06-00; online 2014-04-29]
NGI Uppsala (Uppsala Genome Center)
PubMed DOI Crossref
SpliceVista, a tool for splice variant identification and visualization in shotgun proteomics data.
Zhu Y, Hultin-Rosenberg L, ..., Orre LM, Lehtiö J
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, ..., Lundeberg J, Frisén J
Nat. Neurosci. 17 (6) 801-803 [2014-06-00; online 2014-04-22]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed DOI Crossref
Genetic factors may play a prominent role in the development of coronary heart disease dependent on important environmental factors.
Song C, Chang Z, ..., Ingelsson E, Pedersen NL
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, ..., Rockberg J, Uhlen M
Mol. Cell Proteomics 13 (6) 1585-1597 [2014-06-00; online 2014-04-08]
Protein and peptide arrays
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Recurrent EWSR1-CREB3L1 gene fusions in sclerosing epithelioid fibrosarcoma.
Arbajian E, Puls F, ..., 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, ..., Uhlén M, Pontén F
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
FEMS Microbiol. Ecol. 88 (3) 468-481 [2014-06-00; online 2014-03-07]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
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Old but not (so) degenerated--slow evolution of largely homomorphic sex chromosomes in ratites.
Yazdi HP, Ellegren H
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, ..., Carling T, Lifton RP
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, ..., Lennartsson A, Lehmann S
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, ..., Lind L, Dumanski JP
Nat. Genet. 46 (6) 624-628 [2014-06-00; online 2014-04-30]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) 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, ..., 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, ..., MacBeth KJ, Hellström-Lindberg E
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, ..., Lövdén M, Bäckman L
Psychol Aging 29 (2) 440-449 [2014-06-00; online 2014-03-26]
Mutation Analysis Facility (MAF)
PubMed DOI Crossref
Garbage in, garbage out: a critical evaluation of strategies used for validation of immunohistochemical biomarkers.
O'Hurley G, Sjöstedt E, ..., Gallagher WM, Lindskog C
Mol Oncol 8 (4) 783-798 [2014-06-00; online 2014-04-15]
Tissue Profiling
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Identification of candidate risk gene variations by whole-genome sequence analysis of four rat strains commonly used in inflammation research.
Bäckdahl L, Ekman D, ..., Olsson T, Holmdahl R
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, ..., Ganal MW, Röder MS
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, ..., Götherström A, Jakobsson M
Science 344 (6185) 747-750 [2014-05-16; online 2014-04-26]
NGI Uppsala (SNP&SEQ Technology Platform)
PubMed DOI Crossref
Genetic variation in the CYP2B6 gene is related to circulating 2,2',4,4'-tetrabromodiphenyl ether (BDE-47) concentrations: an observational population-based study.
Penell J, Lind L, ..., Ingelsson E, Lind PM
Environ Health 13 (1) 34 [2014-05-08; online 2014-05-08]
NGI Uppsala (SNP&SEQ Technology Platform)
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Structure and inhibition of mouse leukotriene C4 synthase.
Niegowski D, Kleinschmidt T, ..., Rinaldo-Matthis A, Haeggström JZ
PLoS ONE 9 (5) e96763 [2014-05-08; online 2014-05-08]
Laboratories for Chemical Biology at Karolinska Institutet (LCBKI) Protein Science Facility
PubMed DOI Crossref
Responsibility and cooperativeness are constrained, not determined.
Garcia D, Stråge A, ..., Kerekes N, Anckarsäter H
Front Psychol 5 (-) 308 [2014-05-07; online 2014-05-07]
Mutation Analysis Facility (MAF)
PubMed DOI Crossref
Structural basis for phosphoinositide substrate recognition, catalysis, and membrane interactions in human inositol polyphosphate 5-phosphatases.
Trésaugues L, Silvander C, ..., Berglund H, Nordlund P
Structure 22 (5) 744-755 [2014-05-06; online 2014-04-08]
Protein Science Facility
PubMed DOI Crossref
Bead arrays for antibody and complement profiling reveal joint contribution of antibody isotypes to C3 deposition.
Ayoglu B, Szarka E, ..., Nilsson P, Papp K
PLoS ONE 9 (5) e96403 [2014-05-05; online 2014-05-05]
Protein and peptide arrays
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Smoke-related DNA methylation changes in the etiology of human disease.
Besingi W, Johansson A
Hum. Mol. Genet. 23 (9) 2290-2297 [2014-05-01; online 2013-12-18]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (SNP&SEQ Technology Platform)
PubMed DOI Crossref
The RING-Finger E3 Ubiquitin Ligase COP1 SUPPRESSOR1 Negatively Regulates COP1 Abundance in Maintaining COP1 Homeostasis in Dark-Grown Arabidopsis Seedlings.
Xu D, Lin F, ..., Holm M, Deng XW
Plant Cell 26 (5) 1981-1991 [2014-05-00; online 2014-05-16]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (Uppsala Genome Center)
PubMed DOI Crossref
The role of SATB2 as a diagnostic marker for tumors of colorectal origin: Results of a pathology-based clinical prospective study.
Dragomir A, de Wit M, ..., Uhlen M, Pontén F
Am. J. Clin. Pathol. 141 (5) 630-638 [2014-05-00; online 2014-04-10]
Tissue Profiling
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Somatic cells with a heavy mitochondrial DNA mutational load render induced pluripotent stem cells with distinct differentiation defects.
Wahlestedt M, Ameur A, ..., Woods NB, Bryder D
Stem Cells 32 (5) 1173-1182 [2014-05-00; online 2014-01-22]
NGI Uppsala (Uppsala Genome Center)
PubMed DOI Crossref
Genetic influences on political ideologies: twin analyses of 19 measures of political ideologies from five democracies and genome-wide findings from three populations.
Hatemi PK, Medland SE, ..., Eaves LJ, Martin NG
Behav. Genet. 44 (3) 282-294 [2014-05-00; online 2014-02-27]
NGI Uppsala (SNP&SEQ Technology Platform)
PubMed DOI Crossref
The H1-receptor antagonist cetirizine protects partially against cytokine- and hydrogen peroxide-induced β-TC6 cell death in vitro.
Anvari E, Fred RG, Welsh N
Pancreas 43 (4) 624-629 [2014-05-00; online 2014-04-11]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed DOI Crossref
GRM1 is upregulated through gene fusion and promoter swapping in chondromyxoid fibroma.
Nord KH, Lilljebjörn H, ..., Hogendoorn PC, Szuhai K
Nat. Genet. 46 (5) 474-477 [2014-05-00; online 2014-03-25]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed DOI Crossref
PTPN6 expression is epigenetically regulated and influences survival and response to chemotherapy in high-grade gliomas.
Sooman L, Ekman S, ..., Gullbo J, Lennartsson J
Tumour Biol. 35 (5) 4479-4488 [2014-05-00; online 2014-02-11]
Tissue Profiling
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N-acylated derivatives of sulfamethoxazole and sulfafurazole inhibit intracellular growth of Chlamydia trachomatis.
Marwaha S, Uvell H, ..., Elofsson M, Gylfe A
Antimicrob. Agents Chemother. 58 (5) 2968-2971 [2014-05-00; online 2014-02-26]
Laboratories for Chemical Biology Umeå (LCBU)
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A new look at adenovirus splicing.
Zhao H, Chen M, Pettersson U
Virology 456-457 (-) 329-341 [2014-05-00; online 2014-04-25]
NGI Uppsala (SNP&SEQ Technology Platform)
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Single cell genomics of deep ocean bacteria.
Zhao W, Andersson SG
Trends Microbiol. 22 (5) 233-234 [2014-05-00; online 2014-04-02]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed DOI Crossref
The role of pleiotropy and linkage in genes affecting a sexual ornament and bone allocation in the chicken.
Johnsson M, Rubin CJ, ..., Jensen P, Wright D
Mol. Ecol. 23 (9) 2275-2286 [2014-05-00; online 2014-03-25]
NGI Uppsala (SNP&SEQ Technology Platform)
PubMed DOI Crossref
miR-20b regulates expression of proteinase-activated receptor-1 (PAR-1) thrombin receptor in melanoma cells.
Saleiban A, Faxälv L, ..., Jönsson JI, Osman A
Pigment Cell Melanoma Res 27 (3) 431-441 [2014-05-00; online 2014-01-11]
Bioinformatics Short-term Support and Infrastructure (BILS)
DOI Crossref
Impact of soil transfer between test fields on fungal diversity and wood durability
Råberg U, Terziev N, Daniel G
International Wood Products Journal 5 (2) 83-91 [2014-05-00; online 2013-12-19]
NGI Uppsala (Uppsala Genome Center)
PubMed DOI Crossref
Protein biomarker validation via proximity ligation assays.
Blokzijl A, Nong R, ..., Landegren U, Kamali-Moghaddam M
Biochim. Biophys. Acta 1844 (5) 933-939 [2014-05-00; online 2013-08-13]
PLA Proteomics
PubMed DOI Crossref
Fish oil and krill oil supplementations differentially regulate lipid catabolic and synthetic pathways in mice.
Tillander V, Bjørndal B, ..., Berge RK, Alexson SE
Nutr Metab (Lond) 11 (-) 20 [2014-04-27; online 2014-04-27]
Bioinformatics and Expression Analysis (BEA)
PubMed DOI Crossref
Analysis of the DNA methylome and transcriptome in granulopoiesis reveals timed changes and dynamic enhancer methylation.
Rönnerblad M, Andersson R, ..., Lennartsson A, FANTOM consortium
Blood 123 (17) e79-e89 [2014-04-24; online 2014-03-29]
Bioinformatics and Expression Analysis (BEA) NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed DOI Crossref
The complete genome of Blastobotrys (Arxula) adeninivorans LS3 - a yeast of biotechnological interest.
Kunze G, Gaillardin C, ..., Scholz U, Neuvéglise C
Biotechnol Biofuels 7 (-) 66 [2014-04-24; online 2014-04-24]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed DOI Crossref
High-throughput transcription profiling identifies putative epigenetic regulators of hematopoiesis.
Prasad P, Rönnerblad M, ..., Ekwall K, FANTOM consortium
Blood 123 (17) e46-e57 [2014-04-24; online 2014-03-29]
Bioinformatics and Expression Analysis (BEA)
PubMed DOI Crossref
Seasonal pattern of lesion development in diseased Fraxinus excelsior infected by Hymenoscyphus pseudoalbidus.
Bengtsson SB, Barklund P, von Brömssen C, Stenlid J
PLoS ONE 9 (4) e76429 [2014-04-23; online 2014-04-23]
NGI Uppsala (Uppsala Genome Center)
PubMed DOI Crossref
Oppositional defiant- and conduct disorder-like problems: neurodevelopmental predictors and genetic background in boys and girls, in a nationwide twin study.
Kerekes N, Lundström S, ..., Nilsson T, Anckarsäter H
PeerJ 2 (-) e359 [2014-04-22; online 2014-04-22]
Mutation Analysis Facility (MAF)
PubMed DOI Crossref
Elucidating the interactions between the human gut microbiota and its host through metabolic modeling.
Shoaie S, Nielsen J
Front Genet 5 (-) 86 [2014-04-22; online 2014-04-22]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed DOI Crossref
Erysipelothrix rhusiopathiae contamination in the poultry house environment during erysipelas outbreaks in organic laying hen flocks.
Eriksson H, Bagge E, ..., Fellström C, Jansson DS
Avian Pathol. 43 (3) 231-237 [2014-04-22; online 2014-03-26]
NGI Uppsala (Uppsala Genome Center)
PubMed DOI Crossref
Systematic design of 18S rRNA gene primers for determining eukaryotic diversity in microbial consortia.
Hugerth LW, Muller EE, ..., Wilmes P, Andersson AF
PLoS ONE 9 (4) e95567 [2014-04-22; online 2014-04-22]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed DOI Crossref
A Drosophila immune response against Ras-induced overgrowth.
Hauling T, Krautz R, ..., Kucerova L, Theopold U
Biol Open 3 (4) 250-260 [2014-04-15; online 2014-03-25]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed DOI Crossref
Clinical and genetic features of pediatric acute lymphoblastic leukemia in Down syndrome in the Nordic countries.
Lundin C, Forestier E, ..., Swedish Cytogenetic Leukemia Study Group (SCLSG) , NOPHO Leukemia Cytogenetic Study Group (NLCSG)
J Hematol Oncol 7 (-) 32 [2014-04-11; online 2014-04-11]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed DOI Crossref
A high-throughput cell-based method to predict the unbound drug fraction in the brain.
Mateus A, Matsson P, Artursson P
J. Med. Chem. 57 (7) 3005-3010 [2014-04-10; online 2014-03-08]
ADME of Therapeutics (UDOPP) Uppsala Drug Optimization and Pharmaceutical Profiling (UDOPP)
PubMed DOI Crossref
Vulnerability of glioblastoma cells to catastrophic vacuolization and death induced by a small molecule.
Kitambi SS, Toledo EM, ..., Hammarström LG, Ernfors P
Cell 157 (2) 313-328 [2014-04-10; online 2014-03-25]
ADME of Therapeutics (UDOPP) Uppsala Drug Optimization and Pharmaceutical Profiling (UDOPP)
PubMed DOI Crossref
MTH1 inhibition eradicates cancer by preventing sanitation of the dNTP pool.
Gad H, Koolmeister T, ..., Berglund UW, Helleday T
Nature 508 (7495) 215-221 [2014-04-10; online 2014-04-04]
ADME of Therapeutics (UDOPP) Biochemical and Cellular Screening Protein Science Facility Uppsala Drug Optimization and Pharmaceutical Profiling (UDOPP)
PubMed DOI Crossref
Autosomal recessive transmission of a rare KRT74 variant causes hair and nail ectodermal dysplasia: allelism with dominant woolly hair/hypotrichosis.
Raykova D, Klar J, ..., Baig SM, Dahl N
PLoS ONE 9 (4) e93607 [2014-04-08; online 2014-04-08]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (Uppsala Genome Center)
PubMed DOI Crossref
ZBED6 modulates the transcription of myogenic genes in mouse myoblast cells.
Jiang L, Wallerman O, ..., Andersson G, Andersson L
PLoS ONE 9 (4) e94187 [2014-04-08; online 2014-04-08]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (Uppsala Genome Center)
PubMed DOI Crossref
RNA- and antibody-based profiling of the human proteome with focus on chromosome 19.
Stadler C, Fagerberg L, ..., Lundberg E, Uhlén M
J. Proteome Res. 13 (4) 2019-2027 [2014-04-04; online 2014-03-04]
Cell Profiling NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed DOI Crossref
Quantitative label-free phosphoproteomics of six different life stages of the late blight pathogen Phytophthora infestans reveals abundant phosphorylation of members of the CRN effector family.
Resjö S, Ali A, ..., Govers F, Andreasson E
J. Proteome Res. 13 (4) 1848-1859 [2014-04-04; online 2014-03-05]
Bioinformatics Short-term Support and Infrastructure (BILS)
PubMed DOI Crossref
Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction.
El-Semman IE, Karlsson FH, ..., Soliman TH, Nielsen J
BMC Syst Biol 8 (-) 41 [2014-04-03; online 2014-04-03]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed DOI Crossref
CDKAL1-related single nucleotide polymorphisms are associated with insulin resistance in a cross-sectional cohort of Greek children.
Rask-Andersen M, Philippot G, ..., Fredriksson R, Schiöth HB
PLoS ONE 9 (4) e93193 [2014-04-02; online 2014-04-02]
NGI Uppsala (SNP&SEQ Technology Platform) NGI Uppsala (Uppsala Genome Center)
PubMed DOI Crossref
WNT5A-mediated β-catenin-independent signalling is a novel regulator of cancer cell metabolism.
Sherwood V, Chaurasiya SK, ..., James P, Andersson T
Carcinogenesis 35 (4) 784-794 [2014-04-00; online 2013-12-03]
Tissue Profiling
PubMed DOI Crossref
DNA methylation changes in genes frequently mutated in sporadic colorectal cancer and in the DNA repair and Wnt/β-catenin signaling pathway genes.
Farkas SA, Vymetalkova V, ..., Vodicka P, Nilsson TK
Epigenomics 6 (2) 179-191 [2014-04-00; online 2014-05-09]
NGI Uppsala (SNP&SEQ Technology Platform)
PubMed DOI Crossref
Disassembly of the divisome in Escherichia coli: evidence that FtsZ dissociates before compartmentalization.
Söderström B, Skoog K, ..., von Heijne G, Daley DO
Mol. Microbiol. 92 (1) 1-9 [2014-04-00; online 2014-02-11]
Advanced Light Microscopy
PubMed DOI Crossref
Temporal profiling of cytokine-induced genes in pancreatic β-cells by meta-analysis and network inference.
Lopes M, Kutlu B, ..., Bontempi G, Eizirik DL
Genomics 103 (4) 264-275 [2014-04-00; online 2014-01-28]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed DOI Crossref
Investigation of molecular alterations of AKT-3 in triple-negative breast cancer.
O'Hurley G, Daly E, ..., Kay EW, Gallagher WM
Histopathology 64 (5) 660-670 [2014-04-00; online 2013-10-22]
Tissue Profiling
PubMed DOI Crossref
A cis-eQTL of HLA-DRB1 and a frameshift mutation of MICA contribute to the pattern of association of HLA alleles with cervical cancer.
Chen D, Gyllensten U
Cancer Med 3 (2) 445-452 [2014-04-00; online 2014-02-13]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (Uppsala Genome Center)
PubMed DOI Crossref
A novel SERPINE1-FOSB fusion gene results in transcriptional up-regulation of FOSB in pseudomyogenic haemangioendothelioma.
Walther C, Tayebwa J, ..., Fletcher CD, Mertens F
J. Pathol. 232 (5) 534-540 [2014-04-00; online 2014-01-01]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed DOI Crossref
A central role for GRB10 in regulation of islet function in man.
Prokopenko I, Poon W, ..., Groop L, Lyssenko V
PLoS Genet. 10 (4) e1004235 [2014-04-00; online 2014-04-03]
NGI Uppsala (SNP&SEQ Technology Platform)
PubMed DOI Crossref
Affinity proteomics reveals elevated muscle proteins in plasma of children with cerebral malaria.
Bachmann J, Burté F, ..., Fernandez-Reyes D, Nilsson P
PLoS Pathog. 10 (4) e1004038 [2014-04-00; online 2014-04-17]
Protein and peptide arrays
PubMed DOI Crossref
Syntheses and biological evaluation of 2-amino-3-acyl-tetrahydrobenzothiophene derivatives; antibacterial agents with antivirulence activity.
Dang HT, Chorell E, ..., Hultgren SJ, Almqvist F
Org. Biomol. Chem. 12 (12) 1942-1956 [2014-03-28; online 2014-02-18]
Laboratories for Chemical Biology Umeå (LCBU)
PubMed DOI Crossref
A replication study of GWAS findings in migraine identifies association in a Swedish case-control sample.
Ran C, Graae L, ..., Olson L, Belin AC
BMC Med. Genet. 15 (-) 38 [2014-03-28; online 2014-03-28]
NGI Uppsala (SNP&SEQ Technology Platform)
PubMed DOI Crossref
Impact of stereospecific intramolecular hydrogen bonding on cell permeability and physicochemical properties.
Over B, McCarren P, ..., Duvall JR, Kihlberg J
J. Med. Chem. 57 (6) 2746-2754 [2014-03-27; online 2014-02-15]
ADME of Therapeutics (UDOPP) Uppsala Drug Optimization and Pharmaceutical Profiling (UDOPP)
PubMed DOI Crossref
High prevalence of pfcrt-CVIET haplotype in isolates from asymptomatic and symptomatic patients in south-central Oromia, Ethiopia.
Golassa L, Enweji N, ..., Aseffa A, Swedberg G
Malar. J. 13 (-) 120 [2014-03-27; online 2014-03-27]
NGI Uppsala (Uppsala Genome Center)
PubMed DOI Crossref
Design, synthesis, crystallographic studies, and preliminary biological appraisal of new substituted triazolo[4,3-b]pyridazin-8-amine derivatives as tankyrase inhibitors.
Liscio P, Carotti A, ..., Pellicciari R, Camaioni E
J. Med. Chem. 57 (6) 2807-2812 [2014-03-27; online 2014-02-18]
Protein Science Facility
PubMed DOI Crossref
Nanoscopic spine localization of Norbin, an mGluR5 accessory protein.
Westin L, Reuss M, ..., Aperia A, Brismar H
BMC Neurosci 15 (-) 45 [2014-03-26; online 2014-03-26]
Advanced Light Microscopy
PubMed DOI Crossref
The novel diagnostic biomarkers for focal segmental glomerulosclerosis.
Nafar M, Kalantari S, ..., Rutishuser D, Zubarev RA
Int J Nephrol 2014 (-) 574261 [2014-03-26; online 2014-03-26]
Advanced Mass Spectrometry Proteomics
PubMed DOI Crossref
Visualization of angiogenesis during cancer development in the polyoma middle T breast cancer model: molecular imaging with (R)-[11C]PAQ.
Samén E, Lu L, ..., Rundqvist H, Stone-Elander S
EJNMMI Res 4 (1) 17 [2014-03-26; online 2014-03-26]
Fluorescence Tissue Profiling
PubMed DOI Crossref
An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge.
Brownstein CA, Beggs AH, ..., Kohane IS, Margulies DM
Genome Biol. 15 (3) R53 [2014-03-25; online 2014-03-25]
Bioinformatics Short-term Support and Infrastructure (BILS) NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed DOI Crossref
Neuronal calcium-binding proteins 1/2 localize to dorsal root ganglia and excitatory spinal neurons and are regulated by nerve injury.
Zhang MD, Tortoriello G, ..., Harkany T, Hökfelt TG
Proc. Natl. Acad. Sci. U.S.A. 111 (12) E1149-E1158 [2014-03-25; online 2014-03-13]
Fluorescence Tissue Profiling
PubMed DOI Crossref
Draft Genome Sequence of Pseudomonas aeruginosa SG17M, an Environmental Isolate Belonging to Clone C, Prevalent in Patients and Aquatic Habitats.
Lee C, Peters V, Melefors O, Römling U
Genome Announc 2 (2) - [2014-03-20; online 2014-03-20]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed
Identification of anticancer drugs for hepatocellular carcinoma through personalized genome-scale metabolic modeling.
Agren R, Mardinoglu A, ..., Uhlen M, Nielsen J
Mol. Syst. Biol. 10 (-) 721 [2014-03-19; online 2014-03-19]
Tissue Profiling
PubMed DOI Crossref
Binding of Pro-Gly-Pro at the active site of leukotriene A4 hydrolase/aminopeptidase and development of an epoxide hydrolase selective inhibitor.
Stsiapanava A, Olsson U, ..., Rinaldo-Matthis A, Haeggström JZ
Proc. Natl. Acad. Sci. U.S.A. 111 (11) 4227-4232 [2014-03-18; online 2014-03-05]
Advanced Mass Spectrometry Proteomics Protein Science Facility
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Comprehensive profiling of the vaginal microbiome in HIV positive women using massive parallel semiconductor sequencing.
Ameur A, Meiring TL, ..., Williamson AL, Gyllensten U
Sci Rep 4 (-) 4398 [2014-03-18; online 2014-03-18]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (Uppsala Genome Center)
PubMed DOI Crossref
Genetic characterization of a novel Iflavirus associated with vomiting disease in the Chinese oak silkmoth Antheraea pernyi.
Geng P, Li W, ..., An L, Terenius O
PLoS ONE 9 (3) e92107 [2014-03-17; online 2014-03-17]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed DOI Crossref
Sequencing degraded RNA addressed by 3' tag counting.
Sigurgeirsson B, Emanuelsson O, Lundeberg J
PLoS ONE 9 (3) e91851 [2014-03-14; online 2014-03-14]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed DOI Crossref
Novel Peptidomimetic Hepatitis C Virus NS3/4A Protease Inhibitors Spanning the P2-P1' Region.
Lampa AK, Bergman SM, ..., Karlén A, Sandström A
ACS Med Chem Lett 5 (3) 249-254 [2014-03-13; online 2013-08-02]
ADME of Therapeutics (UDOPP) Uppsala Drug Optimization and Pharmaceutical Profiling (UDOPP)
PubMed DOI Crossref
Achiral pyrazinone-based inhibitors of the hepatitis C virus NS3 protease and drug-resistant variants with elongated substituents directed toward the S2 pocket.
Gising J, Belfrage AK, ..., Larhed M, Sandström A
J. Med. Chem. 57 (5) 1790-1801 [2014-03-13; online 2013-03-23]
ADME of Therapeutics (UDOPP) Uppsala Drug Optimization and Pharmaceutical Profiling (UDOPP)
PubMed DOI Crossref
Epitope-specific antibody response is controlled by immunoglobulin V(H) polymorphisms.
Raposo B, Dobritzsch D, ..., Schneider G, Holmdahl R
J. Exp. Med. 211 (3) 405-411 [2014-03-10; online 2014-02-19]
Protein Science Facility
PubMed DOI Crossref
A chromosome-centric analysis of antibodies directed toward the human proteome using Antibodypedia.
Alm T, von Feilitzen K, ..., Sivertsson Å, Uhlén M
J. Proteome Res. 13 (3) 1669-1676 [2014-03-07; online 2014-02-19]
Cell Profiling
PubMed DOI Crossref
Whole genome sequencing of the black grouse (Tetrao tetrix): reference guided assembly suggests faster-Z and MHC evolution.
Wang B, Ekblom R, ..., Siitari H, Höglund J
BMC Genomics 15 (-) 180 [2014-03-06; online 2014-03-06]
NGI Uppsala (Uppsala Genome Center)
PubMed DOI Crossref
ZapE is a novel cell division protein interacting with FtsZ and modulating the Z-ring dynamics.
Marteyn BS, Karimova G, ..., Sansonetti PJ, Tang CM
MBio 5 (2) e00022-e00014 [2014-03-04; online 2014-03-04]
Protein Science Facility
PubMed DOI Crossref
A study of embryonic stem cell-related proteins in human astrocytomas: identification of Nanog as a predictor of survival.
Elsir T, Edqvist PH, ..., Nistér M, Smits A
Int. J. Cancer 134 (5) 1123-1131 [2014-03-01; online 2013-09-17]
Tissue Profiling
PubMed DOI Crossref
Molecular- and organelle-based predictive paradigm underlying recovery by left ventricular assist device support.
Liem DA, Nsair A, ..., Ping P, Deng MC
Circ Heart Fail 7 (2) 359-366 [2014-03-01; online 2014-03-20]
Cell Profiling Tissue Profiling
PubMed DOI Crossref
Cancer death is related to high palmitoleic acid in serum and to polymorphisms in the SCD-1 gene in healthy Swedish men.
Byberg L, Kilander L, ..., Michaëlsson K, Vessby B
Am. J. Clin. Nutr. 99 (3) 551-558 [2014-03-00; online 2013-12-26]
NGI Uppsala (SNP&SEQ Technology Platform)
PubMed DOI Crossref
Investigation of a putative melanoma susceptibility locus at chromosome 3q29.
Tuominen R, Jönsson G, ..., Hansson J, Höiom V
Cancer Genet 207 (3) 70-74 [2014-03-00; online 2014-02-21]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed DOI Crossref
MAX mutations status in Swedish patients with pheochromocytoma and paraganglioma tumours.
Crona J, Maharjan R, ..., Hellman P, Björklund P
Fam. Cancer 13 (1) 121-125 [2014-03-00; online 2013-06-08]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed DOI Crossref
Purification, stability, and immunogenicity analyses of five bluetongue virus proteins for use in development of a subunit vaccine that allows differentiation of infected from vaccinated animals.
Anderson J, Bréard E, ..., Valarcher JF, Hägglund S
Clin. Vaccine Immunol. 21 (3) 443-452 [2014-03-00; online 2014-01-24]
Mass Spectrometry-based Proteomics, Uppsala
PubMed DOI Crossref
Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility.
DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) Consortium , Asian Genetic Epidemiology Network Type 2 Diabetes (AGEN-T2D) Consortium , ..., McCarthy MI, Morris AP
Nat. Genet. 46 (3) 234-244 [2014-03-00; online 2014-02-11]
NGI Uppsala (SNP&SEQ Technology Platform)
PubMed DOI Crossref
Feasibility of targeted next-generation sequencing of the TP53 and ATM genes in chronic lymphocytic leukemia.
Mansouri L, Sutton LA, ..., Nilsson M, Rosenquist R
Leukemia 28 (3) 694-696 [2014-03-00; online 2013-11-01]
NGI Uppsala (SNP&SEQ Technology Platform)
PubMed DOI Crossref
Urinary prognostic biomarkers in patients with focal segmental glomerulosclerosis.
Kalantari S, Nafar M, ..., Rutishauser D, Zubarev R
Nephrourol Mon 6 (2) e16806 [2014-03-00; online 2014-03-09]
Advanced Mass Spectrometry Proteomics
PubMed DOI Crossref
Centromeric histone H2B monoubiquitination promotes noncoding transcription and chromatin integrity.
Sadeghi L, Siggens L, Svensson JP, Ekwall K
Nat. Struct. Mol. Biol. 21 (3) 236-243 [2014-03-00; online 2014-02-18]
Bioinformatics and Expression Analysis (BEA)
PubMed DOI Crossref
Antibody performance in western blot applications is context-dependent.
Algenäs C, Agaton C, ..., Ottosson Takanen J, Hober S
Biotechnol J 9 (3) 435-445 [2014-03-00; online 2014-01-10]
Cell Profiling Tissue Profiling
PubMed DOI Crossref
On the biogeography of Centipeda: a species-tree diffusion approach.
Nylinder S, Lemey P, ..., Walsh N, Anderberg AA
Syst. Biol. 63 (2) 178-191 [2014-03-00; online 2013-12-18]
Bioinformatics Short-term Support and Infrastructure (BILS)
PubMed DOI Crossref
Detection of enterovirus in the islet cells of patients with type 1 diabetes: what do we learn from immunohistochemistry?
Hansson SF, Korsgren S, Pontén F, Korsgren O
Diabetologia 57 (3) 645-646 [2014-03-00; online 2013-12-20]
Tissue Profiling
DOI Crossref
Analysis of plasma from prostate cancer patients links decreased carnosine dipeptidase 1 levels to lymph node metastasis
Qundos U, Johannesson H, ..., Nilsson P, Schwenk JM
Translational Proteomics 2 (-) 14-24 [2014-03-00; online 2014-03-00]
Protein and peptide arrays
PubMed DOI Crossref
The Dictyostelium discoideum RNA-dependent RNA polymerase RrpC silences the centromeric retrotransposon DIRS-1 post-transcriptionally and is required for the spreading of RNA silencing signals.
Wiegand S, Meier D, ..., Söderbom F, Hammann C
Nucleic Acids Res. 42 (5) 3330-3345 [2014-03-00; online 2013-12-27]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed DOI Crossref
Functional tradeoffs underpin salinity-driven divergence in microbial community composition.
Dupont CL, Larsson J, ..., Venter JC, Bergman B
PLoS ONE 9 (2) e89549 [2014-02-27; online 2014-02-27]
Bioinformatics Short-term Support and Infrastructure (BILS) NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed DOI Crossref
Robust isolation of malignant plasma cells in multiple myeloma.
Frigyesi I, Adolfsson J, ..., Hansson M, Nilsson B
Blood 123 (9) 1336-1340 [2014-02-27; online 2014-01-05]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed DOI Crossref
Crystal structures of leukotriene C4 synthase in complex with product analogs: implications for the enzyme mechanism.
Niegowski D, Kleinschmidt T, ..., Rinaldo-Matthis A, Haeggström JZ
J. Biol. Chem. 289 (8) 5199-5207 [2014-02-21; online 2013-12-25]
Protein Science Facility
PubMed DOI Crossref
An alternative root for the eukaryote tree of life.
He D, Fiz-Palacios O, ..., Tsai CC, Baldauf SL
Curr. Biol. 24 (4) 465-470 [2014-02-17; online 2014-02-11]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed DOI Crossref
Integrative genome and transcriptome analyses reveal two distinct types of ring chromosome in soft tissue sarcomas.
Nord KH, Macchia G, ..., Mandahl N, Mertens F
Hum. Mol. Genet. 23 (4) 878-888 [2014-02-15; online 2013-09-28]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed DOI Crossref
BET bromodomain inhibition of MYC-amplified medulloblastoma.
Bandopadhayay P, Bergthold G, ..., Beroukhim R, Cho YJ
Clin. Cancer Res. 20 (4) 912-925 [2014-02-15; online 2013-12-04]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed DOI Crossref
Microevolution during an Anthrax outbreak leading to clonal heterogeneity and penicillin resistance.
Ågren J, Finn M, Bengtsson B, Segerman B
PLoS ONE 9 (2) e89112 [2014-02-13; online 2014-02-13]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (SNP&SEQ Technology Platform)
PubMed DOI Crossref
Structural and functional insights into peptidoglycan access for the lytic amidase LytA of Streptococcus pneumoniae.
Mellroth P, Sandalova T, ..., Henriques-Normark B, Achour A
MBio 5 (1) e01120-e01113 [2014-02-11; online 2014-02-11]
Protein Science Facility
PubMed DOI Crossref
Sequential pH-driven dimerization and stabilization of the N-terminal domain enables rapid spider silk formation.
Kronqvist N, Otikovs M, ..., Jaudzems K, Johansson J
Nat Commun 5 (-) 3254 [2014-02-11; online 2014-02-11]
Fluorescence Correlation Spectroscopy
PubMed DOI Crossref
Prognostic polypeptide blood plasma biomarkers of Alzheimer's disease progression.
Yang H, Lyutvinskiy Y, ..., Rutishauser D, Zubarev RA
J. Alzheimers Dis. 40 (3) 659-666 [2014-02-08; online 2014-02-08]
Advanced Mass Spectrometry Proteomics
PubMed DOI Crossref
Identification of novel downstream molecules of tissue factor activation by comparative proteomic analysis.
Kask L, Jorsback A, ..., Bergquist J, Siegbahn A
J. Proteome Res. 13 (2) 477-488 [2014-02-07; online 2013-11-28]
Clinical Biomarkers
PubMed DOI Crossref
Removal of total organic carbon from sewage wastewater using poly(ethylenimine)-functionalized magnetic nanoparticles.
Lakshmanan R, Sanchez-Dominguez M, ..., Wennmalm S, Kuttuva Rajarao G
Langmuir 30 (4) 1036-1044 [2014-02-04; online 2014-01-17]
Fluorescence Correlation Spectroscopy
PubMed DOI Crossref
Visual detection of DNA on paper chips.
Song Y, Gyarmati P, ..., Brumer H, Ståhl PL
Anal. Chem. 86 (3) 1575-1582 [2014-02-04; online 2014-01-05]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed DOI Crossref
Intraclonal variations among Streptococcus pneumoniae isolates influence the likelihood of invasive disease in children.
Browall S, Norman M, ..., Normark S, Henriques-Normark B
J. Infect. Dis. 209 (3) 377-388 [2014-02-01; online 2013-09-07]
Bioinformatics Short-term Support and Infrastructure (BILS) NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed DOI Crossref
Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics.
Fagerberg L, Hallström BM, ..., Ponten F, Uhlén M
Mol. Cell Proteomics 13 (2) 397-406 [2014-02-00; online 2013-12-07]
Cell Profiling NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) Protein and peptide arrays Tissue Profiling
PubMed DOI Crossref
Subtyping of gliomas of various WHO grades by the application of immunohistochemistry.
Popova SN, Bergqvist M, ..., Sooman L, Alafuzoff I
Histopathology 64 (3) 365-379 [2014-02-00; online 2014-01-15]
Tissue Profiling
DOI Crossref
2′-(Z)-Cinnamoylsalicortin: A novel salicinoid isolated from Populus tremula
Keefover-Ring K, Carlsson M, Albrectsen BR
Phytochemistry Letters 7 (-) 212-216 [2014-02-00; online 2014-02-00]
Laboratories for Chemical Biology Umeå (LCBU)
PubMed DOI Crossref
Glioma-derived macrophage migration inhibitory factor (MIF) promotes mast cell recruitment in a STAT5-dependent manner.
Põlajeva J, Bergström T, ..., Forsberg Nilsson K, Tchougounova E
Mol Oncol 8 (1) 50-58 [2014-02-00; online 2013-10-05]
Tissue Profiling
PubMed DOI Crossref
Global DNA methylation patterns through an array-based approach in small intestinal neuroendocrine tumors.
Verdugo AD, Crona J, ..., Hellman P, Björklund P
Endocr. Relat. Cancer 21 (1) L5-L7 [2014-02-00; online 2013-11-07]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed DOI Crossref
A variant upstream of HLA-DRB1 and multiple variants in MICA influence susceptibility to cervical cancer in a Swedish population.
Chen D, Hammer J, ..., Idahl A, Gyllensten U
Cancer Med 3 (1) 190-198 [2014-02-00; online 2014-01-10]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (SNP&SEQ Technology Platform) NGI Uppsala (Uppsala Genome Center)
PubMed DOI Crossref
Collecting and preserving biological samples from challenging environments for DNA analysis.
Buś MM, Allen M
Biopreserv Biobank 12 (1) 17-22 [2014-02-00; online 2014-03-14]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed DOI Crossref
Lipid mediator profiles differ between lung compartments in asthmatic and healthy humans.
Larsson N, Lundström SL, ..., Wheelock CE, Nording ML
Eur. Respir. J. 43 (2) 453-463 [2014-02-00; online 2013-09-17]
Bioinformatics Short-term Support and Infrastructure (BILS)
PubMed DOI Crossref
Rearrangements of chromosome bands 15q12-q21 are secondary to HMGA2 deregulation in conventional lipoma.
Macchia G, Nord KH, ..., Storlazzi CT, Mertens F
Oncol. Rep. 31 (2) 807-811 [2014-02-00; online 2013-12-04]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed DOI Crossref
Product formation controlled by substrate dynamics in leukotriene A4 hydrolase.
Stsiapanava A, Tholander F, ..., Haeggström JZ, Rinaldo-Matthis A
Biochim. Biophys. Acta 1844 (2) 439-446 [2014-02-00; online 2013-12-18]
Protein Science Facility
PubMed DOI Crossref
A possible genetic association with chronic fatigue in primary Sjögren's syndrome: a candidate gene study.
Norheim KB, Le Hellard S, ..., Jonsson R, Omdal R
Rheumatol. Int. 34 (2) 191-197 [2014-02-00; online 2013-09-04]
NGI Uppsala (SNP&SEQ Technology Platform)
PubMed DOI Crossref
The genome of Spironucleus salmonicida highlights a fish pathogen adapted to fluctuating environments.
Xu F, Jerlström-Hultqvist J, ..., Svärd SG, Andersson JO
PLoS Genet. 10 (2) e1004053 [2014-02-00; online 2014-02-06]
NGI Uppsala (SNP&SEQ Technology Platform)
PubMed DOI Crossref
WNT10A mutations account for ¼ of population-based isolated oligodontia and show phenotypic correlations.
Arzoo PS, Klar J, ..., Norderyd J, Dahl N
Am. J. Med. Genet. A 164A (2) 353-359 [2014-02-00; online 2014-01-23]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed DOI Crossref
A prostate cancer susceptibility allele at 6q22 increases RFX6 expression by modulating HOXB13 chromatin binding.
Huang Q, Whitington T, ..., Taipale J, Wei GH
Nat. Genet. 46 (2) 126-135 [2014-02-00; online 2014-01-07]
Karolinska High Throughput Center (KHTC)
PubMed DOI Crossref
Increased alpha-9 human papillomavirus species viral load in human immunodeficiency virus positive women.
Mbulawa ZZ, Johnson LF, ..., Gyllensten U, Williamson AL
BMC Infect. Dis. 14 (-) 51 [2014-01-31; online 2014-01-31]
NGI Uppsala (Uppsala Genome Center)
PubMed DOI Crossref
Trypanosoma cruzi Clone Dm28c Draft Genome Sequence.
Grisard EC, Teixeira SM, ..., Andersson B, de Vasconcelos AT
Genome Announc 2 (1) - [2014-01-30; online 2014-01-30]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed DOI Crossref
Aspirin degradation in surface-charged TEMPO-oxidized mesoporous crystalline nanocellulose.
Carlsson DO, Hua K, Forsgren J, Mihranyan A
Int J Pharm 461 (1-2) 74-81 [2014-01-30; online 2013-12-03]
BioMaterial Interactions (BioMat)
PubMed DOI Crossref
Isolation and characterization of anti-adenoviral secondary metabolites from marine actinobacteria.
Strand M, Carlsson M, ..., Wadell G, Almqvist F
Mar Drugs 12 (2) 799-821 [2014-01-28; online 2014-01-28]
Laboratories for Chemical Biology Umeå (LCBU)
PubMed DOI Crossref
Mycobacteria bypass mucosal NF-kB signalling to induce an epithelial anti-inflammatory IL-22 and IL-10 response.
Lutay N, Håkansson G, ..., Westergren-Thorsson G, Godaly G
PLoS ONE 9 (1) e86466 [2014-01-28; online 2014-01-28]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed DOI Crossref
Metabolic enzyme expression highlights a key role for MTHFD2 and the mitochondrial folate pathway in cancer.
Nilsson R, Jain M, ..., Asplund A, Mootha VK
Nat Commun 5 (-) 3128 [2014-01-24; online 2014-01-24]
Tissue Profiling
PubMed DOI Crossref
BDNF polymorphisms are linked to poorer working memory performance, reduced cerebellar and hippocampal volumes and differences in prefrontal cortex in a Swedish elderly population.
Brooks SJ, Nilsson EK, ..., Lind L, Schiöth HB
PLoS ONE 9 (1) e82707 [2014-01-23; online 2014-01-23]
NGI Uppsala (SNP&SEQ Technology Platform)
PubMed DOI Crossref
Integrative genetic characterization and phenotype correlations in pheochromocytoma and paraganglioma tumours.
Crona J, Nordling M, ..., Hellman P, Björklund P
PLoS ONE 9 (1) e86756 [2014-01-22; online 2014-01-22]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (SNP&SEQ Technology Platform)
PubMed DOI Crossref
Structural basis for binding of fluorinated glucose and galactose to Trametes multicolor pyranose 2-oxidase variants with improved galactose conversion.
Tan TC, Spadiut O, ..., Haltrich D, Divne C
PLoS ONE 9 (1) e86736 [2014-01-21; online 2014-01-21]
Protein Science Facility
PubMed DOI Crossref
Eight new genomes and synthetic controls increase the accessibility of rapid melt-MAMA SNP typing of Coxiella burnetii.
Karlsson E, Macellaro A, ..., Sjödin A, Myrtennäs K
PLoS ONE 9 (1) e85417 [2014-01-21; online 2014-01-21]
NGI Uppsala (SNP&SEQ Technology Platform)
PubMed DOI Crossref
Host-specificity and dynamics in bacterial communities associated with Bloom-forming freshwater phytoplankton.
Bagatini IL, Eiler A, ..., Tessarolli LP, Vieira AA
PLoS ONE 9 (1) e85950 [2014-01-20; online 2014-01-20]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed DOI Crossref
The basic keratin 10-binding domain of the virulence-associated pneumococcal serine-rich protein PsrP adopts a novel MSCRAMM fold.
Schulte T, Löfling J, ..., Henriques-Normark B, Achour A
Open Biol 4 (-) 130090 [2014-01-15; online 2014-01-15]
Protein Science Facility
PubMed DOI Crossref
Dating the diversification of the major lineages of Passeriformes (Aves).
Ericson PG, Klopfstein S, ..., Nguyen JM, Nylander JA
BMC Evol. Biol. 14 (-) 8 [2014-01-15; online 2014-01-15]
Bioinformatics Short-term Support and Infrastructure (BILS)
PubMed DOI Crossref
Transmission of hepatitis C virus among intravenous drug users in the Uppsala region of Sweden.
Danielsson A, Palanisamy N, ..., Sylvan S, Lennerstrand J
Infect Ecol Epidemiol 4 (-) - [2014-01-15; online 2014-01-15]
NGI Uppsala (Uppsala Genome Center)
PubMed DOI Crossref
Genome-scale metabolic modelling of hepatocytes reveals serine deficiency in patients with non-alcoholic fatty liver disease.
Mardinoglu A, Agren R, ..., Uhlen M, Nielsen J
Nat Commun 5 (-) 3083 [2014-01-15; online 2014-01-15]
Tissue Profiling
PubMed DOI Crossref
An N-Terminal Missense Mutation in STX11 Causative of FHL4 Abrogates Syntaxin-11 Binding to Munc18-2.
Müller ML, Chiang SC, ..., Naqvi A, Bryceson YT
Front Immunol 4 (-) 515 [2014-01-14; online 2014-01-14]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed DOI Crossref
Draft Genome Sequence of Saccharopolyspora rectivirgula.
Pettersson BM, Behra PR, ..., Bhattacharya A, Kirsebom LA
Genome Announc 2 (1) - [2014-01-09; online 2014-01-09]
NGI Uppsala (SNP&SEQ Technology Platform)
PubMed DOI Crossref
Assessment of whole genome amplification for sequence capture and massively parallel sequencing.
Hasmats J, Gréen H, ..., Käller M, Lundeberg J
PLoS ONE 9 (1) e84785 [2014-01-07; online 2014-01-07]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed DOI Crossref
Metrics for the Human Proteome Project 2013-2014 and strategies for finding missing proteins.
Lane L, Bairoch A, ..., Lundberg E, Omenn GS
J. Proteome Res. 13 (1) 15-20 [2014-01-03; online 2013-12-25]
Cell Profiling
PubMed DOI Crossref
Dominant mutations in GRHL3 cause Van der Woude Syndrome and disrupt oral periderm development.
Peyrard-Janvid M, Leslie EJ, ..., Kere J, Schutte BC
Am. J. Hum. Genet. 94 (1) 23-32 [2014-01-02; online 2013-12-24]
Mutation Analysis Facility (MAF)
PubMed DOI Crossref
RipD (Rv1566c) from Mycobacterium tuberculosis: adaptation of an NlpC/p60 domain to a non-catalytic peptidoglycan-binding function.
Böth D, Steiner EM, ..., Schneider G, Schnell R
Biochem. J. 457 (1) 33-41 [2014-01-01; online 2013-10-11]
Protein Science Facility
PubMed DOI Crossref
Why time matters: codon evolution and the temporal dynamics of dN/dS.
Mugal CF, Wolf JB, Kaj I
Mol. Biol. Evol. 31 (1) 212-231 [2014-01-00; online 2013-10-17]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed DOI Crossref
HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics.
Branca RM, Orre LM, ..., Käll L, Lehtiö J
Nat. Methods 11 (1) 59-62 [2014-01-00; online 2013-11-19]
Bioinformatics Short-term Support and Infrastructure (BILS) NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed DOI Crossref
Magnetic bead assisted labeling of antibodies at nanogram scale.
Dezfouli M, Vickovic S, ..., Schwenk JM, Ahmadian A
Proteomics 14 (1) 14-18 [2014-01-00; online 2013-12-07]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) Protein and peptide arrays
PubMed DOI Crossref
A systematic analysis of commonly used antibodies in cancer diagnostics.
Gremel G, Bergman J, ..., Micke P, Pontén F
Histopathology 64 (2) 293-305 [2014-01-00; online 2013-12-18]
Tissue Profiling
PubMed DOI Crossref
Detection of the human endogenous retrovirus ERV3-encoded Env-protein in human tissues using antibody-based proteomics.
Fei C, Atterby C, ..., Larsson E, Ryan FP
J R Soc Med 107 (1) 22-29 [2014-01-00; online 2013-11-23]
Tissue Profiling
PubMed DOI Crossref
The maintenance of mitochondrial genetic variation by negative frequency-dependent selection.
Kazancıoğlu E, Arnqvist G
Ecol. Lett. 17 (1) 22-27 [2014-01-00; online 2013-10-19]
NGI Uppsala (Uppsala Genome Center)
PubMed DOI Crossref
Protein biomarkers in vernix with potential to predict the development of atopic eczema in early childhood.
Holm T, Rutishauser D, ..., Alm J, Scheynius A
Allergy 69 (1) 104-112 [2014-01-00; online 2013-11-12]
Advanced Mass Spectrometry Proteomics
PubMed DOI Crossref
Different mutations in PDE4D associated with developmental disorders with mirror phenotypes.
Lindstrand A, Grigelioniene G, ..., Mäkitie O, Nordgren A
J. Med. Genet. 51 (1) 45-54 [2014-01-00; online 2013-11-10]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)
PubMed DOI Crossref
A population-based assessment of germline HOXB13 G84E mutation and prostate cancer risk.
Karlsson R, Aly M, ..., Grönberg H, Wiklund F
Eur. Urol. 65 (1) 169-176 [2014-01-00; online 2012-07-31]
Mutation Analysis Facility (MAF)
PubMed DOI Crossref
SNPs within the GH-signaling pathway are associated with the early IGF1 response to GH replacement therapy in GHD adults.
Glad CA, Barbosa EJ, ..., Svensson PA, Johannsson G
Eur. J. Endocrinol. 170 (1) 101-107 [2014-01-00; online 2013-10-12]
Mutation Analysis Facility (MAF)
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Data processing methods and quality control strategies for label-free LC-MS protein quantification.
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