Publications 2017

An essential regulatory function of the DnaK chaperone dictates the decision between proliferation and maintenance in Caulobacter crescentus

Schramm FD, Heinrich K, Thüring M, Bernhardt J, Jonas K

PLoS Genet. 13 (12) e1007148 [2017-12-27; online 2017-12-27]

Chemical Proteomics & Proteogenomics [Service]

Methylation-based estimated biological age and cardiovascular disease

Lind L, Ingelsson E, Sundström J, Siegbahn A, Lampa E

Eur J Clin Invest - (-) e12872 [2017-12-27; online 2017-12-27]

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

Chemical and microbiological evaluation of novel chemical treatment methods for acid sulfate soils.

Högfors-Rönnholm E, Christel S, Dalhem K, ..., Österholm P, Dopson M

BioProject

Sci. Total Environ. 625 (-) 39-49 [2017-12-26; online 2017-12-26]

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

A family-based genome-wide association study of chronic rhinosinusitis with nasal polyps implicates several genes in the disease pathogenesis

Bohman A, Juodakis J, Oscarsson M, ..., Bende M, Torinsson Naluai Å

PLoS ONE 12 (12) e0185244 [2017-12-18; online 2017-12-18]

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

A chemical screen identifies trifluoperazine as an inhibitor of glioblastoma growth.

Pinheiro T, Otrocka M, Seashore-Ludlow B, ..., Simon A, Kirkham M

Biochem. Biophys. Res. Commun. 494 (3-4) 477-483 [2017-12-16; online 2017-10-21]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Discovery of the fourth mobile sulfonamide resistance gene.

Razavi M, Marathe NP, Gillings MR, ..., Kristiansson E, Joakim Larsson DG

pmc BioProject GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK

Microbiome 5 (1) 160 [2017-12-15; online 2017-12-15]

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

CELSR2 is a candidate susceptibility gene in idiopathic scoliosis

Einarsdottir E, Grauers A, Wang J, ..., Kere J, Gerdhem P

PLoS ONE 12 (12) e0189591 [2017-12-14; online 2017-12-14]

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

NMR study of Rcf2 reveals an unusual dimeric topology in detergent micelles

Zhou S, Pettersson P, Brzezinski P, Ädelroth P, Mäler L

ChemBioChem - (-) - [2017-12-14; online 2017-12-14]

Gene expression and risk of leukemic transformation in myelodysplasia

Shiozawa Y, Malcovati L, Gallì A, ..., Cazzola M, Ogawa S

Blood 130 (24) 2642-2653 [2017-12-14; online 2017-11-02]

Transcriptomics and Targeted Proteomics Analysis to Gain Insights Into the Immune-control Mechanisms of HIV-1 Infected Elite Controllers.

Zhang W, Ambikan AT, Sperk M, ..., Sönnerborg A, Neogi U

BioProject SRA

EBioMedicine - (-) - [2017-12-12; online 2017-12-12]

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

Comparative cell cycle transcriptomics reveals synchronization of developmental transcription factor networks in cancer cells

Boström J, Sramkova Z, Salašová A, ..., Altun M, Andäng M

GEO

PLoS ONE 12 (12) e0188772 [2017-12-11; online 2017-12-11]

Cell Profiling [Collaborative]

Characterization of the Giardia intestinalis secretome during interaction with human intestinal epithelial cells: The impact on host cells

Ma’ayeh SY, Liu J, Peirasmaki D, ..., Bergquist J, Svärd SG

PLoS Negl Trop Dis 11 (12) e0006120 [2017-12-11; online 2017-12-11]

Genomic and phenotypic characteristics of Swedish C. jejuni water isolates.

Nilsson A, Johansson C, Skarp A, ..., Engstrand L, Rautelin H

pmc

PLoS ONE 12 (12) e0189222 [2017-12-07; online 2017-12-07]

A Unique ISR Program Determines Cellular Responses to Chronic Stress.

Guan BJ, van Hoef V, Jobava R, ..., Larsson O, Hatzoglou M

pmc mid GEO

Mol. Cell 68 (5) 885-900.e6 [2017-12-07; online 2017-12-09]

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

Magnesium induces preconditioning of the neonatal brain via profound mitochondrial protection

Koning G, Leverin AL, Nair S, ..., Mallard C, Hagberg H

J Cereb Blood Flow Metab - (-) 0271678X1774613 [2017-12-05; online 2017-12-05]

Metabolome dynamics of diapause in the butterfly Pieris napi: distinguishing maintenance, termination and post-diapause phases

Lehmann P, Pruisscher P, Koštál V, ..., Wheat CW, Gotthard K

Journal of Experimental Biology - (-) - [2017-12-01; online 2017-11-27]

Bioinformatics Long-term Support WABI [Collaborative] Systems Biology [Collaborative]

Metabolome and transcriptome profiling reveal new insights into somatic embryo germination in Norway spruce (Picea abies)

Dobrowolska I, Businge E, Abreu IN, Moritz T, Egertsdotter U

Tree Physiol 37 (12) 1752-1766 [2017-12-01; online 2017-06-28]

The Human Plasma Proteome Draft of 2017: Building on the Human Plasma PeptideAtlas from Mass Spectrometry and Complementary Assays.

Schwenk JM, Omenn GS, Sun Z, ..., Moritz RL, Deutsch EW

pmc mid

J. Proteome Res. 16 (12) 4299-4310 [2017-12-01; online 2017-10-10]

Plasma Profiling [Collaborative]

Reading and editing the Pleurodeles waltl genome reveals novel features of tetrapod regeneration

Elewa A, Wang H, Talavera-López C, ..., Andersson B, Simon A

SRA BioProject

Nat Commun 8 (1) - [2017-12-00; online 2017-12-22]

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

In muro deacetylation of xylan affects lignin properties and improves saccharification of aspen wood

Pawar PMA, Derba-Maceluch M, Chong SL, ..., Jönsson LJ, Mellerowicz EJ

Biotechnol Biofuels 10 (1) - [2017-12-00; online 2017-04-20]

Dog ownership and the risk of cardiovascular disease and death – a nationwide cohort study

Mubanga M, Byberg L, Nowak C, ..., Ingelsson E, Fall T

Sci Rep 7 (1) - [2017-12-00; online 2017-11-17]

Bioinformatics Support and Infrastructure [Service]

Development of an efficient route for combined recycling of PET and cotton from mixed fabrics

Palme A, Peterson A, de la Motte H, Theliander H, Brelid H

Text Cloth Sustain 3 (1) - [2017-12-00; online 2017-02-22]

Mutational and putative neoantigen load predict clinical benefit of adoptive T cell therapy in melanoma

Lauss M, Donia M, Harbst K, ..., Svane IM, Jönsson G

Nat Commun 8 (1) - [2017-12-00; online 2017-11-23]

Bioinformatics Long-term Support WABI [Collaborative]

Comparison of laccase-catalyzed cross-linking of organosolv lignin and lignosulfonates

Gillgren T, Hedenström M, Jönsson LJ

International Journal of Biological Macromolecules 105 (-) 438-446 [2017-12-00; online 2017-12-00]

Overexpression of PaNAC03, a stress induced NAC gene family transcription factor in Norway spruce leads to reduced flavonol biosynthesis and aberrant embryo development

Dalman K, Wind JJ, Nemesio-Gorriz M, ..., Ezcurra I, Elfstrand M

BioProject SRA

BMC Plant Biol. 17 (1) - [2017-12-00; online 2017-01-06]

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

Highly sensitive and specific protein detection via combined capillary isoelectric focusing and proximity ligation

Padhan N, Yan J, Boge A, ..., Claesson-Welsh L, Landegren U

Sci Rep 7 (1) - [2017-12-00; online 2017-05-04]

Transcriptome sequencing in pediatric acute lymphoblastic leukemia identifies fusion genes associated with distinct DNA methylation profiles

Marincevic-Zuniga Y, Dahlberg J, Nilsson S, ..., Nordlund J, Syvänen AC

J Hematol Oncol 10 (1) - [2017-12-00; online 2017-08-14]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

Large meta-analysis of genome-wide association studies identifies five loci for lean body mass

Zillikens MC, Demissie S, Hsu YH, ..., Ohlsson C, Kiel DP

Nat Commun 8 (1) - [2017-12-00; online 2017-07-19]

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

The dynamic dimer structure of the chaperone Trigger Factor

Morgado L, Burmann BM, Sharpe T, Mazur A, Hiller S

Nat Commun 8 (1) - [2017-12-00; online 2017-12-08]

Agonist-induced dimer dissociation as a macromolecular step in G protein-coupled receptor signaling

Petersen J, Wright SC, Rodríguez D, ..., Carlsson J, Schulte G

Nat Commun 8 (1) - [2017-12-00; online 2017-08-09]

Fluorescence Correlation Spectroscopy [Collaborative]

Brassinosteroid signaling-dependent root responses to prolonged elevated ambient temperature

Martins S, Montiel-Jorda A, Cayrel A, ..., Ljung K, Vert G

Nat Commun 8 (1) - [2017-12-00; online 2017-08-21]

Genetic- and Lifestyle-dependent Dental Caries Defined by the Acidic Proline-rich Protein Genes PRH1 and PRH2

Strömberg N, Esberg A, Sheng N, ..., Danielsson K, Källestål C

EBioMedicine 26 (-) 38-46 [2017-12-00; online 2017-12-00]

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

Structural basis for dolichylphosphate mannose biosynthesis

Gandini R, Reichenbach T, Tan TC, Divne C

Nat Commun 8 (1) - [2017-12-00; online 2017-07-25]

Genome-wide standing variation facilitates long-term response to bidirectional selection for antibody response in chickens

Lillie M, Sheng Z, Honaker CF, ..., Siegel PB, Carlborg Ö

SRA SRA SRA SRA SRA

BMC Genomics 18 (1) - [2017-12-00; online 2017-01-18]

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

Drug Target Commons: A Community Effort to Build a Consensus Knowledge Base for Drug-Target Interactions

Tang J, Tanoli ZuR, Ravikumar B, ..., Wennerberg K, Aittokallio T

Cell Chem Biol - (-) - [2017-12-00; online 2017-12-00]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Inflammatory infiltrates in parathyroid tumors.

Haglund F, Hallström BM, Nilsson IL, ..., Juhlin CC, Larsson C

pmc

Eur. J. Endocrinol. 177 (6) 445-453 [2017-12-00; online 2017-08-30]

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

Combined genome and transcriptome sequencing to investigate the plant cell wall degrading enzyme system in the thermophilic fungus Malbranchea cinnamomea

Hüttner S, Nguyen TT, Granchi Z, ..., Thanh VN, Olsson L

Biotechnol Biofuels 10 (1) - [2017-12-00; online 2017-11-13]

Bioinformatics Support and Infrastructure [Collaborative]

Multiple genotypes within aecial clusters in Puccinia graminis and Puccinia coronata: improved understanding of the biology of cereal rust fungi

Berlin A, Samils B, Andersson B

Fungal Biol Biotechnol 4 (1) - [2017-12-00; online 2017-05-03]

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

Mapping of leptin and its syntenic genes to chicken chromosome 1p

Seroussi E, Pitel F, Leroux S, ..., Anderson L, Friedman-Einat M

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

BMC Genet. 18 (1) - [2017-12-00; online 2017-08-09]

RNA-sequence data normalization through in silico prediction of reference genes: the bacterial response to DNA damage as case study

Berghoff BA, Karlsson T, Källman T, Wagner EGH, Grabherr MG

BioData Mining 10 (1) - [2017-12-00; online 2017-09-05]

Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

Draft genome of the brown-rot fungus Fomitopsis pinicola GR9-4

Kancherla RP, Durling MB, Stenlid J, Högberg N

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service]

Data Brief 15 (-) 496-500 [2017-12-00; online 2017-12-00]

Automated Training of Deep Convolutional Neural Networks for Cell Segmentation

Sadanandan SK, Ranefall P, Le Guyader S, Wählby C

Sci Rep 7 (1) - [2017-12-00; online 2017-08-10]

BioImage Informatics [Technology development]

A comprehensive structural, biochemical and biological profiling of the human NUDIX hydrolase family

Carreras-Puigvert J, Zitnik M, Jemth AS, ..., Zupan B, Helleday T

Nat Commun 8 (1) - [2017-12-00; online 2017-11-16]

BioImage Informatics [Collaborative] Drug Discovery and Development (DDD) [Collaborative] Protein Science Facility (PSF) [Service]

Heterogeneous Patterns of Genetic Diversity and Differentiation in European and Siberian Chiffchaff ( Phylloscopus collybita abietinus/P. tristis )

Talla V, Kalsoom F, Shipilina D, Marova I, Backström N

BioProject SRA

G3 (Bethesda) 7 (12) 3983-3998 [2017-12-00; online 2017-10-20]

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

A Drosophila female pheromone elicits species-specific long-range attraction via an olfactory channel with dual specificity for sex and food

Lebreton S, Borrero-Echeverry F, Gonzalez F, ..., Becher PG, Witzgall P

BMC Biol. 15 (1) - [2017-12-00; online 2017-09-29]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Influence of pulsed and continuous substrate inputs on freshwater bacterial community composition and functioning in bioreactors

Ricão Canelhas M, Andersson M, Eiler A, Lindström ES, Bertilsson S

SRA

Environ Microbiol 19 (12) 5078-5087 [2017-12-00; online 2017-12-04]

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

Drift, selection, or migration? Processes affecting genetic differentiation and variation along a latitudinal gradient in an amphibian

Cortázar-Chinarro M, Lattenkamp EZ, Meyer-Lucht Y, ..., Laurila A, Höglund J

BMC Evol. Biol. 17 (1) - [2017-12-00; online 2017-08-14]

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

Novel risk genes for systemic lupus erythematosus predicted by random forest classification

Almlöf JC, Alexsson A, Imgenberg-Kreuz J, ..., Sandling JK, Syvänen AC

Sci Rep 7 (1) - [2017-12-00; online 2017-07-24]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

SNX10 gene mutation leading to osteopetrosis with dysfunctional osteoclasts

Stattin EL, Henning P, Klar J, ..., Wikström J, Lerner UH

Sci Rep 7 (1) - [2017-12-00; online 2017-06-07]

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

Detection of QTL for greasy fleece weight in sheep using a 50 K single nucleotide polymorphism chip

Ebrahimi F, Gholizadeh M, Rahimi-Mianji G, Farhadi A

Trop Anim Health Prod 49 (8) 1657-1662 [2017-12-00; online 2017-08-11]

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

Large-scale suppression of recombination predates genomic rearrangements in Neurospora tetrasperma

Sun Y, Svedberg J, Hiltunen M, Corcoran P, Johannesson H

Nat Commun 8 (1) - [2017-12-00; online 2017-10-26]

Identification of NCAN as a candidate gene for developmental dyslexia

Einarsdottir E, Peyrard-Janvid M, Darki F, ..., Leinonen E, Kere J

Sci Rep 7 (1) - [2017-12-00; online 2017-08-24]

Increasing the permeability of Escherichia coli using MAC13243

Muheim C, Götzke H, Eriksson AU, ..., Nørholm MHH, Daley DO

Sci Rep 7 (1) - [2017-12-00; online 2017-12-15]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Rho-kinase inhibitor Y-27632 and hypoxia synergistically enhance chondrocytic phenotype and modify S100 protein profiles in human chondrosarcoma cells

Piltti J, Bygdell J, Fernández-Echevarría C, Marcellino D, Lammi MJ

Sci Rep 7 (1) - [2017-12-00; online 2017-06-16]

Bioinformatics Support and Infrastructure [Collaborative]

Correspondence on Lovell et al.: identification of chicken genes previously assumed to be evolutionarily lost

Bornelöv S, Seroussi E, Yosefi S, ..., Friedman-Einat M, Andersson L

Genome Biol. 18 (1) - [2017-12-00; online 2017-06-14]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

The cryo-EM structure of hibernating 100S ribosome dimer from pathogenic Staphylococcus aureus

Matzov D, Aibara S, Basu A, ..., Amunts A, Yonath AE

PDB PDB

Nat Commun 8 (1) - [2017-12-00; online 2017-09-28]

Flow Cytometric Measurement of Blood Cells with BCR-ABL1 Fusion Protein in Chronic Myeloid Leukemia

Löf L, Arngården L, Olsson-Strömberg U, ..., Landegren U, Kamali-Moghaddam M

Sci Rep 7 (1) - [2017-12-00; online 2017-04-04]

Lipid Driven Nanodomains in Giant Lipid Vesicles are Fluid and Disordered

Koukalová A, Amaro M, Aydogan G, ..., Hof M, Šachl R

Sci Rep 7 (1) - [2017-12-00; online 2017-07-14]

Common founder effects of hereditary hemochromatosis, Wilson´s disease, the long QT syndrome and autosomal recessive deafness caused by two novel mutations in the WHRN and TMC1 genes

Olsson KS, Wålinder O, Jansson U, ..., Raha-Chowdhury R, Williams R

Hereditas 154 (1) - [2017-12-00; online 2017-12-19]

Clinical Genomics Uppsala [Collaborative]

Lubricin binds cartilage proteins, cartilage oligomeric matrix protein, fibronectin and collagen II at the cartilage surface

Flowers SA, Zieba A, Örnros J, ..., Kamali-Moghaddam M, Karlsson NG

Sci Rep 7 (1) - [2017-12-00; online 2017-10-13]

PLA Proteomics [Collaborative]

Fluorescent CRISPR Adaptation Reporter for rapid quantification of spacer acquisition

Amlinger L, Hoekzema M, Wagner EGH, Koskiniemi S, Lundgren M

Sci Rep 7 (1) - [2017-12-00; online 2017-09-04]

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

Mechanistic Insights into Autoinhibition of the Oncogenic Chromatin Remodeler ALC1

Lehmann LC, Hewitt G, Aibara S, ..., Boulton SJ, Deindl S

Molecular Cell 68 (5) 847-859.e7 [2017-12-00; online 2017-12-00]

Cryo-EM [Service] Protein Science Facility (PSF) [Service]

The oxylipin and endocannabidome responses in acute phase Plasmodium falciparum malaria in children

Surowiec I, Gouveia-Figueira S, Orikiiriza J, ..., Normark J, Trygg J

Malar. J. 16 (1) - [2017-12-00; online 2017-09-08]

Microbial mineralization of cellulose in frozen soils

Segura JH, Nilsson MB, Haei M, ..., Schleucher J, Öquist MG

Nat Commun 8 (1) - [2017-12-00; online 2017-10-27]

Identification and description of three families with familial Alzheimer disease that segregate variants in the SORL1 gene

Thonberg H, Chiang HH, Lilius L, ..., Rönnbäck A, Graff C

Acta Neuropathol Commun 5 (1) - [2017-12-00; online 2017-06-09]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

A short feature vector for image matching: The Log-Polar Magnitude feature descriptor

Matuszewski DJ, Hast A, Wählby C, Sintorn IM

PLoS ONE 12 (11) e0188496 [2017-11-30; online 2017-11-30]

BioImage Informatics [Technology development]

Isolated myelosarcoma is characterized by recurrent NFE2 mutations and concurrent preleukemic clones in the bone marrow.

Lazarevic V, Orsmark-Pietras C, Lilljebjörn H, ..., Juliusson G, Fioretos T

Blood - (-) - [2017-11-30; online 2017-11-30]

Clinical Genomics Lund [Collaborative]

Intra-tumor heterogeneity in breast cancer has limited impact on transcriptomic-based molecular profiling.

Karthik GM, Rantalainen M, Stålhammar G, ..., Bergh J, Hartman J

pmc

BMC Cancer 17 (1) 802 [2017-11-29; online 2017-11-29]

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

Mitogenome evolution in the last surviving woolly mammoth population reveals neutral and functional consequences of small population size

Pečnerová P, Palkopoulou E, Wheat CW, ..., Díez-del-Molino D, Dalén L

Evolution Letters - (-) - [2017-11-28; online 2017-11-28]

Bioinformatics Long-term Support WABI [Service]

STRT-seq-2i: dual-index 5' single cell and nucleus RNA-seq on an addressable microwell array.

Hochgerner H, Lönnerberg P, Hodge R, ..., Zeisel A, Linnarsson S

pmc GEO

Sci Rep 7 (1) 16327 [2017-11-27; online 2017-11-27]

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

Mechanism of peptide binding and cleavage by the human mitochondrial peptidase neurolysin.

Teixeira PF, Masuyer G, Pinho CM, ..., Stenmark P, Glaser E

J. Mol. Biol. - (-) - [2017-11-25; online 2017-11-25]

Chemical Proteomics & Proteogenomics [Service] Clinical Proteomics Mass spectrometry [Service]

A common peptidolytic mechanism for targeting peptide degradation in mitochondria and chloroplasts.

Kmiec B, Branca RMM, Murcha MW, ..., Glaser E, Teixeira PF

Mol Plant - (-) - [2017-11-25; online 2017-11-25]

Chemical Proteomics & Proteogenomics [Service] Clinical Proteomics Mass spectrometry [Service]

Cancer risk susceptibility loci in a Swedish population

Liu W, Jiao X, Thutkawkorapin J, Mahdessian H, Lindblom A

Oncotarget - (-) - [2017-11-25; online 2017-11-25]

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

Regulatory coiled-coil domains promote head-to-head assemblies of AAA+ chaperones essential for tunable activity control

Carroni M, Franke KB, Maurer M, ..., Bukau B, Mogk A

Elife 6 (-) - [2017-11-22; online 2017-11-22]

Cryo-EM [Collaborative]

Activating FGFR1 Mutations in Sporadic Pheochromocytomas.

Welander J, Łysiak M, Brauckhoff M, ..., Söderkvist P, Gimm O

World J Surg - (-) - [2017-11-20; online 2017-11-20]

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

Genome-Based Sexing Provides Clues about Behavior and Social Structure in the Woolly Mammoth.

Pečnerová P, Díez-Del-Molino D, Dussex N, ..., Vartanyan S, Dalén L

BioProject

Curr. Biol. 27 (22) 3505-3510.e3 [2017-11-20; online 2017-11-02]

Bioinformatics Long-term Support WABI [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]

Normalization of mass spectrometry data (NOMAD).

Murie C, Sandri B, Sandberg AS, ..., Wendt C, Larsson O

Adv Biol Regul - (-) - [2017-11-20; online 2017-11-20]

Chemical Proteomics & Proteogenomics [Service] Clinical Proteomics Mass spectrometry [Service]

Multi-omics Reveals the Lifestyle of the Acidophilic, Mineral-Oxidizing Model Species Leptospirillum ferriphilumT

Christel S, Herold M, Bellenberg S, ..., Poetsch A, Dopson M

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service]

Appl Environ Microbiol 84 (3) e02091-17 [2017-11-17; online 2018-01-17]

Combined transcriptome and translatome analyses reveal a role for tryptophan-dependent auxin biosynthesis in the control of DOG1-dependent seed dormancy

Bai B, Novák O, Ljung K, Hanson J, Bentsink L

New Phytol - (-) - [2017-11-15; online 2017-11-15]

Novel KIAA0753 mutations extend the phenotype of skeletal ciliopathies.

Hammarsjö A, Wang Z, Vaz R, ..., Grigelioniene G, Ikegawa S

pmc

Sci Rep 7 (1) 15585 [2017-11-14; online 2017-11-14]

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

Diffusion in Ionic Liquid–Cellulose Solutions during Coagulation in Water: Mass Transport and Coagulation Rate Measurements

Hedlund A, Köhnke T, Theliander H

Macromolecules 50 (21) 8707-8719 [2017-11-14; online 2017-10-17]

Female mice lacking Pald1 exhibit endothelial cell apoptosis and emphysema.

Egaña I, Kaito H, Nitzsche A, ..., Hellström M, German Mouse Clinic Consortium

pmc

Sci Rep 7 (1) 15453 [2017-11-13; online 2017-11-13]

Chemical Proteomics & Proteogenomics [Collaborative] Clinical Proteomics Mass spectrometry [Service]

Antibody Heavy Chain Variable Domains of Different Germline Gene Origins Diversify through Different Paths

Kirik U, Persson H, Levander F, Greiff L, Ohlin M

Front Immunol 8 (-) - [2017-11-13; online 2017-11-13]

Bioinformatics Support and Infrastructure [Collaborative] Drug Discovery and Development (DDD) [Collaborative]

Adipocyte Expression of SLC19A1 Links DNA Hypermethylation to Adipose Tissue Inflammation and Insulin Resistance

Petrus P, Bialesova L, Checa A, ..., Gao H, Rydén M

- - (-) - [2017-11-07; online 2017-11-07]

Genomic Analyses of Pre-European Conquest Human Remains from the Canary Islands Reveal Close Affinity to Modern North Africans.

Rodríguez-Varela R, Günther T, Krzewińska M, ..., Götherström A, Girdland-Flink L

BioProject

Curr. Biol. 27 (21) 3396-3402.e5 [2017-11-06; online 2017-10-26]

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

RNA-Seq de novo assembly and differential transcriptome analysis of the nematode Ascaridia galli in relation to in vivo exposure to flubendazole

Martis MM, Tarbiat B, Tydén E, Jansson DS, Höglund J

Bioinformatics Support and Infrastructure [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

PLoS ONE 12 (11) e0185182 [2017-11-03; online 2017-11-03]

Unique case of cerebrotendinous xanthomatosis revisited: All the mutations responsible for this disease are present in the CYP27A1 gene.

Jiao H, Olin M, Hansson M, ..., Angelin B, Björkhem I

J. Intern. Med. - (-) - [2017-11-02; online 2017-11-02]

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

Deep Convolutional Neural Networks For Detecting Cellular Changes Due To Malignancy

Wieslander H, Forslid G, Bengtsson E, ..., Runow Stark C, Kecheril Sadanandan S

The IEEE International Conference on Computer Vision (ICCV), 2017 - (-) - [2017-11-01; online 2017-09-13]

Cryo-EM reconstruction of the chlororibosome to 3.2 Å resolution within 24 h

Forsberg BO, Aibara S, Kimanius D, ..., Lindahl E, Amunts A

Int Union Crystallogr J IUCr J Int Union Cryst J IUCrJ 4 (6) - [2017-11-01; online 2017-09-22]

Highly HIV-exposed HIV uninfected Kenyan female sex workers display a thick ectocervical epithelium

Röhl M, Lajoie J, Tjernlund A, ..., Fowke KR, Broliden K

HIV&Hepatitis Nordic Conference, Stockholm, 2017-09-27-29 - (-) - [2017-11-01]

Untreated urban waste contaminates Indian river sediments with resistance genes to last resort antibiotics.

Marathe NP, Pal C, Gaikwad SS, ..., Kristiansson E, Larsson DGJ

Water Res. 124 (-) 388-397 [2017-11-01; online 2017-07-25]

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

Spheroid segmentation using multiscale deep adversarial networks

Kecheril Sadanandan S, Karlsson J, Wählby C

The IEEE International Conference on Computer Vision (ICCV), 2017 - (-) 36-41 [2017-11-01; online 2017-09-13]

Brief Report: Rare X Chromosome Abnormalities in Systemic Lupus Erythematosus and Sjögren's Syndrome

Sharma R, Harris VM, Cavett J, ..., Sivils KL, Scofield RH

Arthritis Rheumatol 69 (11) 2187-2192 [2017-11-00; online 2017-10-12]

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

Type B Response Regulators Act As Central Integrators in Transcriptional Control of the Auxin Biosynthesis Enzyme TAA1

Yan Z, Liu X, Ljung K, ..., Wang M, Tao Y

Plant Physiol. 175 (3) 1438-1454 [2017-11-00; online 2017-09-20]

An Expanded Genome-Wide Association Study of Type 2 Diabetes in Europeans

Scott RA, Scott LJ, Mägi R, ..., McCarthy MI, Prokopenko I

Diabetes 66 (11) 2888-2902 [2017-11-00; online 2017-05-31]

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

High abundance and expression of transposases in bacteria from the Baltic Sea.

Vigil-Stenman T, Ininbergs K, Bergman B, Ekman M

pmc

ISME J 11 (11) 2611-2623 [2017-11-00; online 2017-07-21]

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

Genotype-based recall to study metabolic effects of genetic variation: a pilot study of PPARG Pro12Ala carriers.

Kamble PG, Gustafsson S, Pereira MJ, ..., Eriksson JW, Ingelsson E

pmc

Ups. J. Med. Sci. 122 (4) 234-242 [2017-11-00; online 2018-01-05]

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

Proteomic Analysis of Phytophthora infestans Reveals the Importance of Cell Wall Proteins in Pathogenicity

Resjö S, Brus M, Ali A, ..., Grenville-Briggs L, Andreasson E

Mol Cell Proteomics 16 (11) 1958-1971 [2017-11-00; online 2017-09-21]

Bioinformatics Support and Infrastructure [Collaborative]

Ninety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation.

Svartström O, Alneberg J, Terrapon N, ..., Aspeborg H, Andersson AF

pmc mid BioProject

ISME J 11 (11) 2538-2551 [2017-11-00; online 2017-07-21]

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

Integrative studies implicate matrix metalloproteinase-12 as a culprit gene for large-artery atherosclerotic stroke

Mahdessian H, Perisic Matic L, Lengquist M, ..., Mälarstig A, None

J Intern Med 282 (5) 429-444 [2017-11-00; online 2017-08-28]

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

A nonsense mutation in CEP55 defines a new locus for a Meckel-like syndrome, an autosomal recessive lethal fetal ciliopathy.

Bondeson M, Ericson K, Gudmundsson S, ..., Frykholm C, Wilbe M

Clin. Genet. 92 (5) 510-516 [2017-11-00; online 2017-05-03]

Bioinformatics Compute and Storage [Service] Clinical Genomics Uppsala [Collaborative] NGI Uppsala (Uppsala Genome Center) [Service] Tissue Profiling [Collaborative]

SweGen: a whole-genome data resource of genetic variability in a cross-section of the Swedish population.

Ameur A, Dahlberg J, Olason P, ..., Magnusson PK, Gyllensten U

Eur. J. Hum. Genet. 25 (11) 1253-1260 [2017-11-00; online 2017-08-23]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative]

Vitamin and Amino Acid Auxotrophy in Anaerobic Consortia Operating under Methanogenic Conditions

Hubalek V, Buck M, Tan B, ..., Bertilsson S, Eiler A

mSystems 2 (5) e00038-17 [2017-10-31; online 2017-10-31]

Bioinformatics Support and Infrastructure [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

Exome-wide association study of plasma lipids in >300,000 individuals.

Liu DJ, Peloso GM, Yu H, ..., Willer CJ, Kathiresan S

Nat. Genet. - (-) - [2017-10-30; online 2017-10-30]

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

Institutional profile: the national Swedish academic drug discovery & development platform at SciLifeLab.

Arvidsson PI, Sandberg K, Sakariassen KS

Future Sci. OA 3(2), FSO176 (2) - [2017-10-30; online 2017-04-07]

Drug Discovery and Development (DDD) [Technology development]

Shared genetic origin of asthma, hay fever and eczema elucidates allergic disease biology.

Ferreira MA, Vonk JM, Baurecht H, ..., Koppelman GH, Paternoster L

Nat. Genet. - (-) - [2017-10-30; online 2017-10-30]

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

Combined x-ray crystallography and computational modeling approach to investigate the Hsp90 C-terminal peptide binding to FKBP51.

Kumar R, Moche M, Winblad B, Pavlov PF

Sci Rep 7 (1) 14288 [2017-10-27; online 2017-10-27]

Protein Science Facility (PSF) [Collaborative]

Crystal structures of OrfX2 and P47 from a Botulinum neurotoxin OrfX type gene cluster.

Gustafsson R, Berntsson RP, Martínez-Carranza M, ..., Johnson EA, Stenmark P

FEBS Lett. - (-) - [2017-10-25; online 2017-10-25]

Thiol-ene-epoxy thermoset for low-temperature bonding to biofunctionalized microarray surfaces.

Zhou XC, Sjöberg R, Druet A, ..., Haraldsson T, Carlborg CF

Lab Chip 17 (21) 3672-3681 [2017-10-25; online 2017-10-05]

Autoimmunity Profiling [Technology development] Plasma Profiling [Technology development]

Efficient protein production by yeast requires global tuning of metabolism.

Huang M, Bao J, Hallström BM, Petranovic D, Nielsen J

pmc

Nat Commun 8 (1) 1131 [2017-10-25; online 2017-10-25]

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

Polysome-profiling in small tissue samples.

Liang S, Bellato HM, Lorent J, ..., Hajj GNM, Larsson O

BioProject

Nucleic Acids Res. - (-) - [2017-10-23; online 2017-10-23]

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

Below-ground organic matter accumulation along a boreal forest fertility gradient relates to guild interaction within fungal communities

Kyaschenko J, Clemmensen KE, Karltun E, Lindahl BD

Ecol Lett - (-) - [2017-10-22; online 2017-10-22]

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

Proteomic analysis of cell cycle progression in asynchronous cultures, including mitotic subphases, using PRIMMUS

Ly T, Whigham A, Clarke R, ..., Wadsworth P, Lamond AI

Elife 6 (-) - [2017-10-20; online 2017-10-20]

Cell Profiling [Collaborative]

Effects of long-term low oxygen tension in human chondrosarcoma cells

Piltti J, Bygdell J, Qu C, Lammi MJ

J. Cell. Biochem. - (-) - [2017-10-18; online 2017-10-18]

Bioinformatics Support and Infrastructure [Collaborative]

Zebrafish larvae as a model system for high-throughput, image-based screens in diabetes and insulin resistance

Emmanouilidou A, Ranefall P, Bandaru M, ..., Ingelsson E, den Hoed M

ASHG 2017 Annual Meeting - The American Society of Human Genetics - (-) - [2017-10-17; online 2017-10-17]

Zebrafish larvae as a model system for high-throughput, image-based genetic screens in cardiometabolic diseases

den Hoed M, Emmanouilidou A, Bandaru M, ..., Larsson A, Ingelsson E

ASHG 2017 Annual Meeting - The American Society of Human Genetics - (-) - [2017-10-17; online 2017-10-17]

Identifying and characterizing causal genes in GWAS-identified loci for heart rate variability using high-throughput, image-based screens in zebrafish larvae

von der Heyde B, Emmanouilidou A, Klingström T, ..., Allalou A, den Hoed M

ASHG 2017 Annual Meeting - The American Society of Human Genetics - (-) - [2017-10-17; online 2017-10-17]

Glioblastoma and glioblastoma stem cells are dependent on functional MTH1

Pudelko L, Rouhi P, Sanjiv K, ..., Helleday T, Bräutigam L

Oncotarget 8 (49) - [2017-10-17; online 2017-07-20]

Advanced Light Microscopy (ALM) [Collaborative]

Strong impact on plasma protein profiles by precentrifugation delay but not by repeated freeze-thaw cycles, as analyzed using multiplex proximity extension assays.

Shen Q, Björkesten J, Galli J, ..., Tybring G, Landegren U

Clin. Chem. Lab. Med. - (-) - [2017-10-17; online 2017-10-17]

Large-scale validation of zebrafish larvae as a model system for genetic screens in dyslipidaemia, atherosclerosis and coronary artery disease

Bandaru M, Emmanouilidou A, Ranefall P, ..., Ingelsson E, den Hoed M

ASHG 2017 Annual Meeting - The American Society of Human Genetics - (-) - [2017-10-17; online 2017-10-17]

Targeted proteomic analysis of habitual coffee consumption.

Cornelis MC, Gustafsson S, Ärnlöv J, ..., Lind L, Ingelsson E

J. Intern. Med. - (-) - [2017-10-16; online 2017-10-16]

Quantitative high-content/high-throughput microscopy analysis of lipid droplets in subject-specific adipogenesis models

Bombrun M, Gao H, Ranefall P, ..., Arner P, Wählby C

Cytometry - (-) - [2017-10-14; online 2017-10-14]

The downfall of TBA-354 – a possible explanation for its neurotoxicity via mass spectrometric imaging

Ntshangase S, Shobo A, Kruger HG, ..., Govender T, Baijnath S

Xenobiotica - (-) 1-7 [2017-10-13; online 2017-10-13]

Drug Discovery and Development (DDD) [Collaborative]

Entirely enzymatic nanofabrication of DNA–protein conjugates

Bernardinelli G, Högberg B

Nucleic Acids Res 45 (18) e160-e160 [2017-10-13; online 2017-08-16]

De novo design and synthesis of a 30-cistron translation-factor module

Shepherd TR, Du L, Liljeruhm J, ..., Yomo T, Forster AC

Nucleic Acids Res 45 (18) 10895-10905 [2017-10-13; online 2017-09-04]

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

Spatial detection of fetal marker genes expressed at low level in adult human heart tissue.

Asp M, Salmén F, Ståhl PL, ..., Linde C, Lundeberg J

pmc

Sci Rep 7 (1) 12941 [2017-10-11; online 2017-10-11]

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

Chemical Proteomics for Target Discovery of Head-to-Tail Cyclized Mini-Proteins

Hellinger R, Thell K, Vasileva M, ..., Becker CW, Gruber CW

Front. Chem. 5 (-) - [2017-10-11; online 2017-10-11]

Diatoms dominate the eukaryotic metatranscriptome during spring in coastal 'dead zone' sediments.

Broman E, Sachpazidou V, Dopson M, Hylander S

pmc BioProject BioProject

Proc. Biol. Sci. 284 (1864) - [2017-10-11; online 2017-10-06]

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

Exome sequencing reveals NAA15 and PUF60 as candidate genes associated with intellectual disability.

Zhao JJ, Halvardson J, Zander CS, ..., Thuresson AC, Feuk L

Am. J. Med. Genet. B Neuropsychiatr. Genet. - (-) - [2017-10-09; online 2017-10-09]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service]

Demographic inference from whole genome and RAD sequencing data suggests alternating human impacts on goose populations since the Last Ice Age.

Pujolar JM, Dalén L, Hansen MM, Madsen J

BioProject Dryad

Mol. Ecol. - (-) - [2017-10-05; online 2017-10-05]

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

Late presenting atypical severe combined immunodeficiency (SCID) associated with a novel missense mutation in DCLRE1C.

Sundin M, Uhlin M, Gaballa A, ..., Marits P, Nilsson J

Pediatr Allergy Immunol - (-) - [2017-10-05; online 2017-10-05]

Chromatin and Single-Cell RNA-Seq Profiling Reveal Dynamic Signaling and Metabolic Transitions during Human Spermatogonial Stem Cell Development.

Guo J, Grow EJ, Yi C, ..., Hotaling JM, Cairns BR

GEO GEO GEO GEO

Cell Stem Cell 21 (4) 533-546.e6 [2017-10-05; online 2017-10-07]

Protective Effect of Intravitreal Administration of Exosomes Derived from Mesenchymal Stem Cells on Retinal Ischemia

Moisseiev E, Anderson JD, Oltjen S, ..., Nolta JA, Park SS

Current Eye Research 42 (10) 1358-1367 [2017-10-03; online 2017-06-21]

Chemical Proteomics & Proteogenomics [Service]

Molecular profiles of oxyphilic and chief cell parathyroid adenoma.

Lu M, Kjellin H, Fotouhi O, ..., Lehtiö J, Larsson C

Mol. Cell. Endocrinol. - (-) - [2017-10-03; online 2017-10-03]

Chemical Proteomics & Proteogenomics [Service] Clinical Proteomics Mass spectrometry [Service]

Circulating proteins as predictors of incident heart failure in the elderly.

Stenemo M, Nowak C, Byberg L, ..., Fall T, Ärnlöv J

Eur. J. Heart Fail. - (-) - [2017-10-02; online 2017-10-02]

Motivating students with authentic science experiences: changes in motivation for school science

Hellgren JM, Lindberg S

Research in Science & Technological Education 35 (4) 409-426 [2017-10-02; online 2017-05-03]

Chemical Biology Consortium Sweden (CBCS) [Technology development]

Rapid Increase in Genome Size as a Consequence of Transposable Element Hyperactivity in Wood-White (Leptidea) Butterflies.

Talla V, Suh A, Kalsoom F, ..., Wiklund C, Backström N

BioProject GENBANK

Genome Biol Evol 9 (10) 2491-2505 [2017-10-01; online 2017-10-06]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

DNA methylation profiles in red blood cells of adult hens correlate with their rearing conditions

Pértille F, Brantsæter M, Nordgreen J, ..., Jensen P, Guerrero-Bosagna C

J Exp Biol 220 (19) 3579-3587 [2017-10-01; online 2017-08-07]

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

Shaping the Tumor Stroma and Sparking Immune Activation by CD40 and 4-1BB Signaling Induced by an Armed Oncolytic Virus

Eriksson E, Milenova I, Wenthe J, ..., Alemany R, Loskog A

Clin. Cancer Res. 23 (19) 5846-5857 [2017-10-01; online 2017-05-23]

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

The Evolution of Dark Matter in the Mitogenome of Seed Beetles

Sayadi A, Immonen E, Tellgren-Roth C, Arnqvist G

GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK

Genome Biol Evol 9 (10) 2697-2706 [2017-10-01; online 2017-09-27]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative]

A MIR4646 associated methylation locus is hypomethylated in adolescent depression.

Boström AE, Ciuculete DM, Attwood M, ..., Mwinyi J, Schiöth HB

J Affect Disord 220 (-) 117-128 [2017-10-01; online 2017-05-17]

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

The evolutionary history of the DMRT3 ‘Gait keeper ’ haplotype

Staiger EA, Almén MS, Promerová M, ..., Rubin CJ, Andersson L

Anim Genet 48 (5) 551-559 [2017-10-00; online 2017-07-25]

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

Reduced cell surface levels of GPI-linked markers in a new case with PIGG loss of function

Zhao JJ, Halvardson J, Knaus A, ..., Thuresson AC, Feuk L

Human Mutation 38 (10) 1394-1401 [2017-10-00; online 2017-06-12]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service]

Novel genetic loci associated HLA-B*08:01 positive myasthenia gravis

Varade J, Wang N, Lim CK, ..., Xu X, Hammarström L

Journal of Autoimmunity - (-) - [2017-10-00; online 2017-10-00]

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

Quantitative interactions between the biocontrol fungus Phlebiopsis gigantea , the forest pathogen Heterobasidion annosum and the fungal community inhabiting Norway spruce stumps

Oliva J, Messal M, Wendt L, Elfstrand M

Forest Ecology and Management 402 (-) 253-264 [2017-10-00; online 2017-10-00]

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

CRISPR/Cas9 screening using unique molecular identifiers

Schmierer B, Botla SK, Zhang J, ..., Kivioja T, Taipale J

Mol. Syst. Biol. 13 (10) 945 [2017-10-00; online 2017-10-09]

High-throughput Genome Engineering (HTGE) [Technology development]

Cetuximab sensitivity of head and neck squamous cell carcinoma xenografts is associated with treatment-induced reduction in EGFR, pEGFR, and pSrc.

Jedlinski A, Garvin S, Johansson A, ..., Ponten F, Roberg K

J. Oral Pathol. Med. 46 (9) 717-724 [2017-10-00; online 2017-01-28]

Comprehensive analysis of NMR data using advanced line shape fitting

Niklasson M, Otten R, Ahlner A, ..., Petzold K, Lundström P

J Biomol NMR 69 (2) 93-99 [2017-10-00; online 2017-10-17]

Validation of risk stratification models in acute myeloid leukemia using sequencing-based molecular profiling.

Wang M, Lindberg J, Klevebring D, ..., Lehmann S, Grönberg H

pmc

Leukemia 31 (10) 2029-2036 [2017-10-00; online 2017-02-07]

Eosinophil Cationic Protein, Carotid Plaque, and Incidence of Stroke.

Sundström J, Söderholm M, Borné Y, ..., Orho-Melander M, Engström G

Stroke 48 (10) 2686-2692 [2017-10-00; online 2017-09-13]

Multivariate strategy for the sample selection and integration of multi-batch data in metabolomics

Surowiec I, Johansson E, Torell F, ..., Jakobsson PJ, Trygg J

Metabolomics 13 (10) - [2017-10-00; online 2017-08-24]

Swedish Metabolomics Centre (SMC) [Technology development]

NorWood: a gene expression resource for evo-devo studies of conifer wood development.

Jokipii-Lukkari S, Sundell D, Nilsson O, ..., Street NR, Tuominen H

New Phytol. 216 (2) 482-494 [2017-10-00; online 2017-02-10]

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

GDF-15 and TRAIL-R2 are powerful predictors of long-term mortality in patients with acute myocardial infarction.

Skau E, Henriksen E, Wagner P, ..., Siegbahn A, Leppert J

Eur J Prev Cardiol 24 (15) 1576-1583 [2017-10-00; online 2017-08-01]

Breast cancer in young women and prognosis: How important are proliferation markers?

Fredholm H, Magnusson K, Lindström LS, ..., Frisell J, Fredriksson I

Eur. J. Cancer 84 (-) 278-289 [2017-10-00; online 2017-08-29]

N-Acylated Derivatives of Sulfamethoxazole Block Chlamydia Fatty Acid Synthesis and Interact with FabF

Mojica SA, Salin O, Bastidas RJ, ..., Elofsson M, Gylfe Å

Antimicrob. Agents Chemother. 61 (10) e00716-17 [2017-10-00; online 2017-08-07]

Bioinformatory-assisted analysis of next-generation sequencing data for precision medicine in pancreatic cancer.

Malgerud L, Lindberg J, Wirta V, ..., Grönberg H, Matthias Löhr J

pmc

Mol Oncol 11 (10) 1413-1429 [2017-10-00; online 2017-08-08]

The cagE gene sequence as a diagnostic marker to identify JP2 and non-JP2 highly leukotoxic Aggregatibacter actinomycetemcomitans serotype b strains.

Johansson A, Claesson R, Höglund Åberg C, Haubek D, Oscarsson J

GENBANK GENBANK GENBANK GENBANK GENBANK

J. Periodont. Res. 52 (5) 903-912 [2017-10-00; online 2017-04-10]

Bioinformatics Support and Infrastructure [Service]

Alterations of c-di-GMP turnover proteins modulate semi-constitutive rdar biofilm formation in commensal and uropathogenic Escherichia coli.

Cimdins A, Simm R, Li F, ..., Brauner A, Römling U

pmc

Microbiologyopen 6 (5) - [2017-10-00; online 2017-09-15]

Bioinformatics Support and Infrastructure [Service]

Antibody Affinity Against 2009 A/H1N1 Influenza and Pandemrix Vaccine Nucleoproteins Differs Between Childhood Narcolepsy Patients and Controls.

Lind A, Freyhult E, Ramelius A, ..., Elding Larsson H, Lernmark Å

Viral Immunol. 30 (8) 590-600 [2017-10-00; online 2017-08-10]

Bioinformatics Support and Infrastructure [Collaborative]

Detection of Post-Translational Modifications Using Solid-Phase Proximity Ligation Assay

Oliveira FMSd, Mereiter S, Lönn P, ..., Reis CA, Kamali-Moghaddam M

New Biotechnology - (-) - [2017-10-00; online 2017-10-00]

Artificial Selection Response due to Polygenic Adaptation from a Multilocus, Multiallelic Genetic Architecture

Zan Y, Sheng Z, Lillie M, ..., Siegel PB, Carlborg Ö

- 34 (10) 2678-2689 [2017-10-00; online 2017-07-11]

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

Tumor Necrosis Factor Receptor 1 and 2 Are Associated With Risk of Intracerebral Hemorrhage.

Svensson EH, Söderholm M, Abul-Kasim K, Engström G

Stroke 48 (10) 2710-2715 [2017-10-00; online 2017-08-22]

Conflicting results from mitochondrial genomic data challenge current views of Rubiaceae phylogeny

Rydin C, Wikström N, Bremer B

Am. J. Bot. 104 (10) 1522-1532 [2017-10-00; online 2017-10-18]

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

Profiling of in vitro activities of urea-based inhibitors against cysteine synthases from Mycobacterium tuberculosis

Brunner K, Steiner EM, Reshma RS, ..., Schnell R, Schneider G

Bioorganic & Medicinal Chemistry Letters 27 (19) 4582-4587 [2017-10-00; online 2017-10-00]

Identification of the PAK4 interactome reveals PAK4 phosphorylation of N-WASP and promotion of Arp2/3-dependent actin polymerization.

Zhao M, Spiess M, Johansson HJ, ..., Lehtiö J, Strömblad S

pmc

Oncotarget 8 (44) 77061-77074 [2017-09-29; online 2017-08-18]

Chemical Proteomics & Proteogenomics [Service] Clinical Proteomics Mass spectrometry [Service]

Identification of a novel proinsulin-associated SNP and demonstration that proinsulin is unlikely to be a causal factor in subclinical vascular remodelling using Mendelian randomisation.

Strawbridge RJ, Silveira A, Hoed MD, ..., Hamsten A, IMPROVE study group

Atherosclerosis 266 (-) 196-204 [2017-09-28; online 2017-09-28]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

Southern African ancient genomes estimate modern human divergence to 350,000 to 260,000 years ago

Schlebusch CM, Malmström H, Günther T, ..., Lombard M, Jakobsson M

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

Science - (-) eaao6266 [2017-09-28; online 2017-09-28]

Epidemiological characterization of a nosocomial outbreak of extended spectrum β-lactamase Escherichia coli ST-131 confirms the clinical value of core genome multilocus sequence typing

Woksepp H, Ryberg A, Berglind L, Schön T, Söderman J

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

APMIS - (-) - [2017-09-28; online 2017-09-28]

Hormonal contraceptive use affects HIV susceptibility: mechanisms revealed by image analysis

Edfeldt G, Röhl M, Lajoie J, ..., Fowke KR, Broliden K

HIV&Hepatitis Nordic Conference, Stockholm, 2017-09-27-29 - (-) - [2017-09-27]

HIV-infected women have high numbers of CD103-CD8+ T cells residing close to the basal membrane of the ectocervical epithelium

PubMed

Tjernlund A, Gibbs A, Buggert M, ..., Wählby C, Broliden K

HIV&Hepatitis Nordic Conference, Stockholm, 2017-09-27-29 - (-) - [2017-09-27]

Anti-mycobacterial activity correlates with altered DNA methylation pattern in immune cells from BCG-vaccinated subjects.

Verma D, Parasa VR, Raffetseder J, ..., Netea M, Lerm M

pmc

Sci Rep 7 (1) 12305 [2017-09-26; online 2017-09-26]

Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

Validating Missing Proteins in Human Sperm Cells by Targeted Mass-Spectrometry- and Antibody-based Methods.

Carapito C, Duek P, Macron C, ..., Lane L, Pineau C

J. Proteome Res. - (-) - [2017-09-26; online 2017-09-26]

Genetic risk scores and family history as predictors of schizophrenia in Nordic registers.

Lu Y, Pouget JG, Andreassen OA, ..., Werge T, Sullivan PF

Psychol Med - (-) 1-9 [2017-09-25; online 2017-09-25]

Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

The human protein atlas: A spatial map of the human proteome.

Thul PJ, Lindskog C

Protein Sci. - (-) - [2017-09-23; online 2017-09-23]

Tissue Profiling [Technology development]

In situ protein detection with enhanced specificity using DNA-conjugated antibodies and proximity ligation.

Zieba A, Ponten F, Uhlén M, Landegren U

Mod. Pathol. - (-) - [2017-09-22; online 2017-09-22]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] PLA Proteomics [Technology development] Tissue Profiling [Collaborative]

The regulation of hydroxysteroid 17β-dehydrogenase type 1 and 2 gene expression in breast cancer cell lines by estradiol, dihydrotestosterone, microRNAs, and genes related to breast cancer.

Hilborn E, Stål O, Alexeyenko A, Jansson A

pmc

Oncotarget 8 (37) 62183-62194 [2017-09-22; online 2017-07-10]

Bioinformatics Support and Infrastructure [Collaborative]

New oncogenic subtypes in pediatric B-cell precursor acute lymphoblastic leukemia.

Lilljebjörn H, Fioretos T

Blood 130 (12) 1395-1401 [2017-09-21; online 2017-08-04]

Clinical Genomics Lund [Collaborative]

Plasma stem cell factor levels are associated with risk of cardiovascular disease and death

Björkbacka H, Yao Mattisson I, Wigren M, ..., Engström G, Nilsson J

J Intern Med - (-) - [2017-09-21; online 2017-09-21]

Major transcriptional changes observed in the Fulani, an ethnic group less susceptible to malaria.

Quin JE, Bujila I, Chérif M, ..., Nebie I, Östlund Farrants AK

pmc GEO

Elife 6 (-) - [2017-09-19; online 2017-09-19]

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

The complete genome sequence of human adenovirus 84, a highly recombinant new Human mastadenovirus D type with a unique fiber gene.

Kaján GL, Kajon AE, Pinto AC, Bartha D, Arnberg N

Virus Res. 242 (-) 79-84 [2017-09-18; online 2017-09-18]

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

A novel approach using long-read sequencing and ddPCR to investigate gonadal mosaicism and estimate recurrence risk in two families with developmental disorders.

Wilbe M, Gudmundsson S, Johansson J, ..., Frykholm C, Bondeson M

Prenat. Diagn. - (-) - [2017-09-16; online 2017-09-16]

Bioinformatics Compute and Storage [Service] Clinical Genomics Uppsala [Collaborative] NGI Uppsala (Uppsala Genome Center) [Technology development]

Tartrate-resistant acid phosphatase (TRAP/ACP5) promotes metastasis-related properties via TGFβ2/TβR and CD44 in MDA-MB-231 breast cancer cells.

Reithmeier A, Panizza E, Krumpel M, ..., Ek-Rylander B, Andersson G

pmc

BMC Cancer 17 (1) 650 [2017-09-15; online 2017-09-15]

Chemical Proteomics & Proteogenomics [Service] Clinical Proteomics Mass spectrometry [Service]

Effects of tumour necrosis factor α upon the metabolism of the endocannabinoid anandamide in prostate cancer cells

Karlsson J, Gouveia-Figueira S, Alhouayek M, Fowler CJ

PLoS ONE 12 (9) e0185011 [2017-09-14; online 2017-09-14]

Acute doses of caffeine shift nervous system cell expression profiles toward promotion of neuronal projection growth.

Yu NY, Bieder A, Raman A, ..., Daub CO, Kere J

pmc BioProject

Sci Rep 7 (1) 11458 [2017-09-13; online 2017-09-13]

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

Impact of common genetic determinants of Hemoglobin A1c on type 2 diabetes risk and diagnosis in ancestrally diverse populations: A transethnic genome-wide meta-analysis

Wheeler E, Leong A, Liu CT, ..., None , None

PLoS Med. 14 (9) e1002383 [2017-09-12; online 2017-09-12]

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

Mass Cytometry Identifies Distinct Lung CD4(+) T Cell Patterns in Löfgren's Syndrome and Non-Löfgren's Syndrome Sarcoidosis.

Kaiser Y, Lakshmikanth T, Chen Y, ..., Achour A, Grunewald J

pmc

Front Immunol 8 (-) 1130 [2017-09-12; online 2017-09-12]

Mass Cytometry [Collaborative]

Structures of the human mitochondrial ribosome in native states of assembly

Brown A, Rathore S, Kimanius D, ..., Amunts A, Ramakrishnan V

PDB PDB

Nat Struct Mol Biol - (-) - [2017-09-11; online 2017-09-11]

Copper chaperone ATOX1 regulates pluripotency factor OCT4 in preimplantation mouse embryos.

Celauro E, Mukaj A, Fierro-González JC, Wittung-Stafshede P

Biochem. Biophys. Res. Commun. 491 (1) 147-153 [2017-09-09; online 2017-07-12]

Bioinformatics Support and Infrastructure [Service]

A female Viking warrior confirmed by genomics.

Hedenstierna-Jonson C, Kjellström A, Zachrisson T, ..., Götherström A, Storå J

Am. J. Phys. Anthropol. - (-) - [2017-09-08; online 2017-09-08]

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

Auxin minimum triggers the developmental switch from cell division to cell differentiation in theArabidopsisroot

Di Mambro R, De Ruvo M, Pacifici E, ..., Grieneisen VA, Sabatini S

Proc Natl Acad Sci USA 114 (36) E7641-E7649 [2017-09-05; online 2017-08-22]

Metabolism and Whole-Body Fat Oxidation Following Post-Exercise Carbohydrate or Protein Intake

Hall UA, Pettersson S, Edin F, ..., Malmodin D, Madsen K

International Journal of Sport Nutrition and Exercise Metabolism - (-) 1-25 [2017-09-05; online 2017-09-05]

Capturing LTA4hydrolase in action: Insights to the chemistry and dynamics of chemotactic LTB4synthesis

Stsiapanava A, Samuelsson B, Haeggström JZ

Proc Natl Acad Sci USA 114 (36) 9689-9694 [2017-09-05; online 2017-08-21]

Impact of N-methylation of the substance P 1-7 amide on anti-allodynic effect in mice after peripheral administration.

Skogh A, Lesniak A, Gaugaz FZ, ..., Hallberg M, Sandström A

Eur J Pharm Sci 109 (-) 533-540 [2017-09-05; online 2017-09-05]

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

Analysing Microbial Community Composition through Amplicon Sequencing: From Sampling to Hypothesis Testing.

Hugerth LW, Andersson AF

pmc

Front Microbiol 8 (-) 1561 [2017-09-04; online 2017-09-04]

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

A practical guide to build de-novo assemblies for single tissues of non-model organisms: the example of a Neotropical frog

Montero-Mendieta S, Grabherr M, Lantz H, ..., Webster MT, Vilà C

SRA GENBANK BioProject

PeerJ 5 (-) e3702 [2017-09-01; online 2017-09-01]

Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

Retention of seed trees fails to lifeboat ectomycorrhizal fungal diversity in harvested Scots pine forests.

Varenius K, Lindahl BD, Dahlberg A

FEMS Microbiol. Ecol. 93 (9) - [2017-09-01; online 2017-09-29]

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

Multifocus structured illumination microscopy for fast volumetric super-resolution imaging

Abrahamsson S, Blom H, Agostinho A, ..., Heintzmann R, Brismar H

Biomed. Opt. Express 8 (9) 4135 [2017-09-01; online 2017-08-17]

Advanced Light Microscopy (ALM) [Technology development]

The Huperzia selago Shoot Tip Transcriptome Sheds New Light on the Evolution of Leaves.

Evkaikina AI, Berke L, Romanova MA, ..., Pawlowski K, Voitsekhovskaja OV

pmc BioProject

Genome Biol Evol 9 (9) 2444-2460 [2017-09-01; online 2017-09-29]

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

Genome Characterization of Oleaginous Aspergillus oryzae BCC7051: A Potential Fungal-Based Platform for Lipid Production.

Thammarongtham C, Nookaew I, Vorapreeda T, ..., Jeennor S, Laoteng K

Curr. Microbiol. - (-) - [2017-09-01; online 2017-09-01]

The U2AF1S34F mutation induces lineage-specific splicing alterations in myelodysplastic syndromes

Yip BH, Steeples V, Repapi E, ..., Pellagatti A, Boultwood J

- 127 (9) 3557-3557 [2017-09-01; online 2017-09-01]

A CRISPR-Cas9 Generated MDCK Cell Line Expressing Human MDR1 Without Endogenous Canine MDR1 (cABCB1): An Improved Tool for Drug Efflux Studies.

Karlgren M, Simoff I, Backlund M, ..., Oswald S, Artursson P

J Pharm Sci 106 (9) 2909-2913 [2017-09-00; online 2017-04-24]

Bioinformatics Compute and Storage [Service] Chemical Biology Consortium Sweden (CBCS) [Technology development] Drug Discovery and Development (DDD) [Technology development] NGI Uppsala (Uppsala Genome Center) [Service]

Metabolic profiles from two different breakfast meals characterized by 1 H NMR-based metabolomics

Rådjursöga M, Karlsson GB, Lindqvist HM, ..., Ellegård L, Winkvist A

Food Chem 231 (-) 267-274 [2017-09-00; online 2017-09-00]

Genome scale metabolic modeling of cancer

Nilsson A, Nielsen J

Metabolic Engineering 43 (-) 103-112 [2017-09-00; online 2017-09-00]

Systems Biology [Technology development]

Analytically Sensitive Protein Detection in Microtiter Plates by Proximity Ligation with Rolling Circle Amplification

Ebai T, Souza de Oliveira FM, Löf L, ..., Landegren U, Kamali-Moghaddam M

Clinical Chemistry 63 (9) 1497-1505 [2017-09-00; online 2017-06-30]

Serotonin, ATRX, and DAXX Expression in Pituitary Adenomas: Markers in the Differential Diagnosis of Neuroendocrine Tumors of the Sellar Region.

Casar-Borota O, Botling J, Granberg D, ..., Pontén F, Trouillas J

Am. J. Surg. Pathol. 41 (9) 1238-1246 [2017-09-00; online 2017-07-19]

Novel Blood Pressure Locus and Gene Discovery Using Genome-Wide Association Study and Expression Data Sets From Blood and the KidneyNovelty and Significance

Wain LV, Vaez A, Jansen R, ..., None , None

GEO

Hypertension 70 (3) e4-e19 [2017-09-00; online 2017-07-24]

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

Regulation of gene expression is associated with tolerance of the Arctic copepod Calanus glacialis to CO2 -acidified sea water

Bailey A, De Wit P, Thor P, ..., Thompson C, Hop H

BioProject SRA

Ecol Evol 7 (18) 7145-7160 [2017-09-00; online 2017-08-02]

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

Measurement of protein backbone 13CO and 15N relaxation dispersion at high resolution

Mayzel M, Ahlner A, Lundström P, Orekhov VY

J Biomol NMR 69 (1) 1-12 [2017-09-00; online 2017-09-01]

Enhanced Secondary- and Hormone Metabolism in Leaves of Arbuscular Mycorrhizal Medicago truncatula

Adolfsson L, Nziengui H, Abreu IN, ..., Schoefs B, Spetea C

Plant Physiol. 175 (1) 392-411 [2017-09-00; online 2017-07-11]

The relative contribution of DNA methylation and genetic variants on protein biomarkers for human diseases.

Ahsan M, Ek WE, Rask-Andersen M, ..., Gyllensten U, Johansson Å

pmc GEO

PLoS Genet. 13 (9) e1007005 [2017-09-00; online 2017-09-15]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

Proteomics in Hypothermia as Adjunctive Therapy in Patients with ST-Segment Elevation Myocardial Infarction: A CHILL-MI Substudy.

Mohammad MA, Noc M, Lang I, ..., Metzler B, Erlinge D

Ther Hypothermia Temp Manag 7 (3) 152-161 [2017-09-00; online 2017-03-02]

Silencing FLI or targeting CD13/ANPEP lead to dephosphorylation of EPHA2, a mediator of BRAF inhibitor resistance, and induce growth arrest or apoptosis in melanoma cells.

Azimi A, Tuominen R, Costa Svedman F, ..., Hansson J, Egyhazi Brage S

pmc

Cell Death Dis 8 (8) e3029 [2017-08-31; online 2017-08-31]

Chemical Proteomics & Proteogenomics [Service] Clinical Proteomics Mass spectrometry [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service]

Neuroblastoma patient-derived xenograft cells cultured in stem-cell promoting medium retain tumorigenic and metastatic capacities but differentiate in serum.

Persson CU, von Stedingk K, Bexell D, ..., Påhlman S, Wigerup C

pmc

Sci Rep 7 (1) 10274 [2017-08-31; online 2017-08-31]

A genomic exploration identifies mechanisms that may explain adverse cardiovascular effects of COX-2 inhibitors.

Brænne I, Willenborg C, Tragante V, ..., Erdmann J, Schunkert H

pmc

Sci Rep 7 (1) 10252 [2017-08-31; online 2017-08-31]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

Importance of N- and C-terminal residues of substance P 1-7 for alleviating allodynia in mice after peripheral administration.

Skogh A, Lesniak A, Gaugaz FZ, ..., Hallberg M, Sandström A

Eur J Pharm Sci 106 (-) 345-351 [2017-08-30; online 2017-06-03]

Drug Discovery and Development (DDD) [Collaborative]

First de novo whole genome sequencing and assembly of the pink-footed goose.

Pujolar JM, Dalén L, Olsen RA, Hansen MM, Madsen J

BioProject

Genomics - (-) - [2017-08-30; online 2017-08-30]

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

Mass Cytometry and Topological Data Analysis Reveal Immune Parameters Associated with Complications after Allogeneic Stem Cell Transplantation.

Lakshmikanth T, Olin A, Chen Y, ..., Omazic B, Brodin P

Cell Rep 20 (9) 2238-2250 [2017-08-29; online 2017-08-31]

Mass Cytometry [Technology development]

Cerium oxide nanoparticles inhibit differentiation of neural stem cells.

Gliga AR, Edoff K, Caputo F, ..., Ceccatelli S, Fadeel B

pmc

Sci Rep 7 (1) 9284 [2017-08-24; online 2017-08-24]

Advanced Light Microscopy (ALM) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]

Clonal Evolution of Autoreactive Germinal Centers.

Degn SE, van der Poel CE, Firl DJ, ..., Victora GD, Carroll MC

Cell 170 (5) 913-926.e19 [2017-08-24; online 2017-08-26]

Autoimmunity Profiling [Service]

Identification of NCAN as a candidate gene for developmental dyslexia.

Einarsdottir E, Peyrard-Janvid M, Darki F, ..., Leinonen E, Kere J

pmc BioProject

Sci Rep 7 (1) 9294 [2017-08-24; online 2017-08-24]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service]

Nitrogen uptake and assimilation in proliferating embryogenic cultures of Norway spruce—Investigating the specific role of glutamine

Carlsson J, Svennerstam H, Moritz T, Egertsdotter U, Ganeteg U

PLoS ONE 12 (8) e0181785 [2017-08-24; online 2017-08-24]

Genomic correlates of glatiramer acetate adverse cardiovascular effects lead to a novel locus mediating coronary risk

Brænne I, Zeng L, Willenborg C, ..., None , None

PLoS ONE 12 (8) e0182999 [2017-08-22; online 2017-08-22]

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

A specific antibody to detect transcription factor T-Pit: a reliable marker of corticotroph cell differentiation and a tool to improve the classification of pituitary neuroendocrine tumours.

Sjöstedt E, Bollerslev J, Mulder J, ..., Pontén F, Casar-Borota O

Acta Neuropathol. - (-) - [2017-08-19; online 2017-08-19]

A pathology atlas of the human cancer transcriptome.

Uhlen M, Zhang C, Lee S, ..., Mardinoglu A, Ponten F

Science 357 (6352) - [2017-08-18; online 2017-08-19]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] Tissue Profiling [Technology development]

SF3B1-initiating mutations in MDS-RSs target lymphomyeloid hematopoietic stem cells

Mortera-Blanco T, Dimitriou M, Woll PS, ..., Jacobsen SEW, Hellström-Lindberg E

Blood 130 (7) 881-890 [2017-08-17; online 2017-06-20]

Tea and coffee consumption in relation to DNA methylation in four European cohorts.

Ek WE, Tobi EW, Ahsan M, ..., Johansson Å, Epigenome-Wide Association Study Consortium

Hum. Mol. Genet. 26 (16) 3221-3231 [2017-08-15; online 2017-05-24]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

Diverse heterocyclic scaffolds as dCTP pyrophosphatase 1 inhibitors. Part 1: Triazoles, triazolopyrimidines, triazinoindoles, quinoline hydrazones and arylpiperazines.

Llona-Minguez S, Häggblad M, Martens U, ..., Scobie M, Helleday T

Bioorg. Med. Chem. Lett. 27 (16) 3897-3904 [2017-08-15; online 2017-06-16]

Drug Discovery and Development (DDD) [Collaborative]

SubCons: a new ensemble method for improved human subcellular localization predictions.

Salvatore M, Warholm P, Shu N, Basile W, Elofsson A

Bioinformatics 33 (16) 2464-2470 [2017-08-15; online 2017-04-14]

Bioinformatics Support and Infrastructure [Collaborative]

Mucin-Inspired Lubrication on Hydrophobic Surfaces

Käsdorf BT, Weber F, Petrou G, ..., Crouzier T, Lieleg O

Biomacromolecules 18 (8) 2454-2462 [2017-08-14; online 2017-07-03]

The Sydney Heart Bank: improving translational research while eliminating or reducing the use of animal models of human heart disease.

Dos Remedios CG, Lal SP, Li A, ..., Linke W, van der Velden J

pmc

Biophys Rev - (-) - [2017-08-14; online 2017-08-14]

Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life

Spang A, Caceres EF, Ettema TJG

Science 357 (6351) eaaf3883 [2017-08-11; online 2017-08-10]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

High RBM3 expression is associated with an improved survival and oxaliplatin response in patients with metastatic colorectal cancer.

Siesing C, Sorbye H, Dragomir A, ..., Glimelius B, Eberhard J

pmc

PLoS ONE 12 (8) e0182512 [2017-08-11; online 2017-08-11]

Shifts in coastal sediment oxygenation cause pronounced changes in microbial community composition and associated metabolism.

Broman E, Sjöstedt J, Pinhassi J, Dopson M

pmc

Microbiome 5 (1) 96 [2017-08-09; online 2017-08-09]

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

Rho-associated kinase is a therapeutic target in neuroblastoma.

Dyberg C, Fransson S, Andonova T, ..., Johnsen JI, Wickström M

pmc

Proc. Natl. Acad. Sci. U.S.A. 114 (32) E6603-E6612 [2017-08-08; online 2017-07-24]

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

Use of Proteomics To Investigate Kidney Function Decline over 5 Years.

Carlsson AC, Ingelsson E, Sundström J, ..., Lind L, Ärnlöv J

pmc

Clin J Am Soc Nephrol 12 (8) 1226-1235 [2017-08-07; online 2017-07-21]

PLS3 Deletions Lead to Severe Spinal Osteoporosis and Disturbed Bone Matrix Mineralization.

Kämpe AJ, Costantini A, Levy-Shraga Y, ..., Grasemann C, Mäkitie O

J. Bone Miner. Res. - (-) - [2017-08-04; online 2017-08-04]

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

Diverse heterocyclic scaffolds as dCTP pyrophosphatase 1 inhibitors. Part 2: Pyridone- and pyrimidinone-derived systems.

Llona-Minguez S, Häggblad M, Martens U, ..., Scobie M, Helleday T

Bioorg. Med. Chem. Lett. 27 (15) 3219-3225 [2017-08-01; online 2017-06-15]

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

Comparison of four DNA extraction methods for comprehensive assessment of 16S rRNA bacterial diversity in marine biofilms using high-throughput sequencing

Corcoll N, Österlund T, Sinclair L, ..., Backhaus T, Eriksson KM

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

FEMS Microbiol. Lett. 364 (14) - [2017-08-01; online 2017-06-29]

A MUTYH germline mutation is associated with small intestinal neuroendocrine tumors.

Dumanski JP, Rasi C, Björklund P, ..., Hellman P, Tiensuu Janson E

pmc

Endocr. Relat. Cancer 24 (8) 427-443 [2017-08-00; online 2017-06-20]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service]

Low-Frequency Synonymous Coding Variation in CYP2R1 Has Large Effects on Vitamin D Levels and Risk of Multiple Sclerosis

Manousaki D, Dudding T, Haworth S, ..., Timpson NJ, Richards JB

The American Journal of Human Genetics 101 (2) 227-238 [2017-08-00; online 2017-08-00]

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

CKM Glu83Gly Is Associated With Blunted Creatine Kinase Variation, but Not With Myalgia

Siddiqui MK, Veluchamy A, Maroteau C, ..., Chasman DI, Palmer CNA

Circ Cardiovasc Genet 10 (4) e001737 [2017-08-00; online 2017-08-08]

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

Dual herbivore attack and herbivore density affect metabolic profiles of Brassica nigra leaves

Ponzio C, Papazian S, Albrectsen BR, Dicke M, Gols R

Plant, Cell & Environment 40 (8) 1356-1367 [2017-08-00; online 2017-02-24]

Combination of phage and Gram-positive bacterial display of human antibody repertoires enables isolation of functional high affinity binders

Hu FJ, Volk AL, Persson H, ..., Uhlen M, Rockberg J

New Biotechnology - (-) - [2017-08-00; online 2017-08-00]

Drug Discovery and Development (DDD) [Technology development]

Genome-Wide Association Study of Angioedema Induced by Ace Inhibitors or Arbs in Sweden

Wadelius M, Eriksson N, Johansson C, ..., Magnusson PKE, Hallberg P

Clinical Therapeutics 39 (8) e76 [2017-08-00; online 2017-08-00]

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

Regional genetic differentiation in the blue mussel from the Baltic Sea area

Larsson J, Lind EE, Corell H, ..., Smolarz K, Lönn M

Estuarine, Coastal and Shelf Science 195 (-) 98-109 [2017-08-00; online 2017-08-00]

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

Rates of gene flow in a freshwater snail and the evolution of phenotypic plasticity

Hollander J, Ahlgren J, Brönmark C

- 121 (4) 764-770 [2017-08-00; online 2017-06-01]

Investigation of calcium-dependent activity and conformational dynamics of zebra fish 12-lipoxygenase

Mittal M, Hasan M, Balagunaseelan N, ..., Haeggström JZ, Rinaldo-Matthis A

Biochimica et Biophysica Acta (BBA) - General Subjects 1861 (8) 2099-2111 [2017-08-00; online 2017-08-00]

Data on haplotype-supported immunoglobulin germline gene inference.

Kirik U, Greiff L, Levander F, Ohlin M

pmc

Data Brief 13 (-) 620-640 [2017-08-00; online 2017-06-27]

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

Northeast African genomic variation shaped by the continuity of indigenous groups and Eurasian migrations.

Hollfelder N, Schlebusch CM, Günther T, ..., Hassan HY, Jakobsson M

pmc Dryad

PLoS Genet. 13 (8) e1006976 [2017-08-00; online 2017-08-24]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

Genomewide patterns of variation in genetic diversity are shared among populations, species and higher-order taxa

Vijay N, Weissensteiner M, Burri R, ..., Ellegren H, Wolf JBW

Mol Ecol 26 (16) 4284-4295 [2017-08-00; online 2017-06-27]

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

The structure of the tetanus toxin reveals pH‐mediated domain dynamics

Masuyer G, Conrad J, Stenmark P

PDB PDB

EMBO Rep. 18 (8) 1306-1317 [2017-08-00; online 2017-06-23]

Bioinformatic processing of RAD-seq data dramatically impacts downstream population genetic inference

Shafer ABA, Peart CR, Tusso S, ..., Wheat CW, Wolf JBW

BioProject Dryad Dryad

Methods Ecol Evol 8 (8) 907-917 [2017-08-00; online 2016-11-28]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

Differences in genetic and environmental variation in adult BMI by sex, age, time period, and region: an individual-based pooled analysis of 40 twin cohorts

Silventoinen K, Jelenkovic A, Sund R, ..., Sørensen TI, Kaprio J

Am J Clin Nutr 106 (2) 457-466 [2017-08-00; online 2017-07-05]

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

Poorly known microbial taxa dominate the microbiome of permafrost thaw ponds

Wurzbacher C, Nilsson RH, Rautio M, Peura S

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

ISME J 11 (8) 1938-1941 [2017-08-00; online 2017-04-21]

Low temperature, autotrophic microbial denitrification using thiosulfate or thiocyanate as electron donor.

Broman E, Jawad A, Wu X, ..., Sundkvist JE, Dopson M

pmc

Biodegradation 28 (4) 287-301 [2017-08-00; online 2017-06-02]

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

Comprehensive Profiling of the Androgen Receptor in Liquid Biopsies from Castration-resistant Prostate Cancer Reveals Novel Intra-AR Structural Variation and Splice Variant Expression Patterns.

De Laere B, van Dam PJ, Whitington T, ..., Grönberg H, Lindberg J

Eur. Urol. 72 (2) 192-200 [2017-08-00; online 2017-01-16]

Objective automated quantification of fluorescence signal in histological sections of rat lens

Talebizadeh N, Hagström NZ, Yu Z, ..., Söderberg P, Wählby C

Cytometry 91 (8) 815-821 [2017-08-00; online 2017-05-11]

Whole-genome patterns of linkage disequilibrium across flycatcher populations clarify the causes and consequences of fine-scale recombination rate variation in birds

Kawakami T, Mugal CF, Suh A, ..., Smeds L, Ellegren H

BioProject Dryad

Mol Ecol 26 (16) 4158-4172 [2017-08-00; online 2017-07-05]

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

Structural pathway of regulated substrate transfer and threading through an Hsp100 disaggregase

Deville C, Carroni M, Franke KB, ..., Mogk A, Saibil HR

PDB PDB

Sci Adv 3 (8) e1701726 [2017-08-00; online 2017-08-04]

Clofazimine protects against Mycobacterium tuberculosis dissemination in the central nervous system following aerosol challenge in a murine model

Baijnath S, Moodley C, Ngcobo B, ..., Pym A, Govender T

International Journal of Antimicrobial Agents - (-) - [2017-08-00; online 2017-08-00]

Drug Discovery and Development (DDD) [Collaborative]

Genetic differences between willow warbler migratory phenotypes are few and cluster in large haplotype blocks

Lundberg M, Liedvogel M, Larson K, ..., Åkesson S, Bensch S

Evolution Letters 1 (3) 155-168 [2017-08-00; online 2017-06-16]

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

Switchable ionic liquids enable efficient nanofibrillation of wood pulp

Berglund L, Anugwom I, Hedenström M, ..., Mikkola JP, Oksman K

Cellulose 24 (8) 3265-3279 [2017-08-00; online 2017-06-06]

Isoflavones and Rotenoids from the Leaves of Millettia oblata ssp. teitensis

Deyou T, Marco M, Heydenreich M, ..., Yenesew A, Erdélyi M

J. Nat. Prod. 80 (7) 2060-2066 [2017-07-28; online 2017-06-30]

Solution NMR structure of the TRIM21 B-box2 and identification of residues involved in its interaction with the RING domain

Wallenhammar A, Anandapadamanaban M, Lemak A, ..., Wallner B, Sunnerhagen M

PDB

PLoS ONE 12 (7) e0181551 [2017-07-28; online 2017-07-28]

Droplet Barcode Sequencing for targeted linked-read haplotyping of single DNA molecules.

Redin D, Borgström E, He M, ..., Käller M, Ahmadian A

pmc

Nucleic Acids Res. 45 (13) e125 [2017-07-27; online 2017-05-20]

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

Biophysical characterization of the calmodulin-like domain of Plasmodium falciparum calcium dependent protein kinase 3

Andresen C, Niklasson M, Cassman Eklöf S, Wallner B, Lundström P

PLoS ONE 12 (7) e0181721 [2017-07-26; online 2017-07-26]

Protein Science Facility (PSF) [Service] Swedish NMR Centre (SNC) [Service]

PLS3 sequencing in childhood-onset primary osteoporosis identifies two novel disease-causing variants.

Kämpe AJ, Costantini A, Mäkitie RE, ..., Jiao H, Mäkitie O

pmc

Osteoporos Int - (-) - [2017-07-26; online 2017-07-26]

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

Prediction of intracellular exposure bridges the gap between target- and cell-based drug discovery

Mateus A, Gordon LJ, Wayne GJ, ..., Hann MM, Artursson P

Proc Natl Acad Sci USA 114 (30) E6231-E6239 [2017-07-25; online 2017-07-12]

Chemical Biology Consortium Sweden (CBCS) [Technology development]

Untargeted screening for novel autoantibodies with prognostic value in first-episode psychosis.

Zandian A, Wingård L, Nilsson H, ..., Nilsson P, Persson MAA

pmc

Transl Psychiatry 7 (7) e1177 [2017-07-25; online 2017-07-25]

Autoimmunity Profiling [Collaborative] Tissue Profiling [Collaborative]

Recent increased identification and transmission of HIV-1 unique recombinant forms in Sweden.

Neogi U, Siddik AB, Kalaghatgi P, ..., Marrone G, Sönnerborg A

pmc

Sci Rep 7 (1) 6371 [2017-07-25; online 2017-07-25]

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

Combined epigenetic and differentiation-based treatment inhibits neuroblastoma tumor growth and links HIF2α to tumor suppression.

Westerlund I, Shi Y, Toskas K, ..., Schlisio S, Holmberg J

pmc

Proc. Natl. Acad. Sci. U.S.A. 114 (30) E6137-E6146 [2017-07-25; online 2017-07-10]

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

Continuous immunotypes describe human immune variation and predict diverse responses.

Kaczorowski KJ, Shekhar K, Nkulikiyimfura D, ..., Chakraborty AK, Brodin P

pmc

Proc. Natl. Acad. Sci. U.S.A. 114 (30) E6097-E6106 [2017-07-25; online 2017-07-10]

Mass Cytometry [Technology development]

Haploid selection within a single ejaculate increases offspring fitness

Alavioon G, Hotzy C, Nakhro K, ..., Maklakov AA, Immler S

Proc Natl Acad Sci USA 114 (30) 8053-8058 [2017-07-25; online 2017-07-11]

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

Targeted sequencing of tonsillar and base of tongue cancer and human papillomavirus positive unknown primary of the head and neck reveals prognostic effects of mutated FGFR3

Bersani C, Sivars L, Haeggblom L, ..., Ramqvist T, Dalianis T

Oncotarget - (-) - [2017-07-18; online 2017-02-09]

Bioinformatics Support and Infrastructure [Collaborative]

Tuning Metabolome Coverage in Reversed Phase LC–MS Metabolomics of MeOH Extracted Samples Using the Reconstitution Solvent Composition

Lindahl A, Sääf S, Lehtiö J, Nordström A

Anal. Chem. 89 (14) 7356-7364 [2017-07-18; online 2017-06-28]

Chemical Proteomics & Proteogenomics [Service] Clinical Proteomics Mass spectrometry [Service] Swedish Metabolomics Centre (SMC) [Technology development]

Association analyses based on false discovery rate implicate new loci for coronary artery disease

Nelson CP, Goel A, Butterworth AS, ..., Watkins H, Deloukas P

Nat Genet 49 (9) 1385-1391 [2017-07-17; online 2017-07-17]

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

Loss of DIP2C in RKO cells stimulates changes in DNA methylation and epithelial-mesenchymal transition.

Larsson C, Ali MA, Pandzic T, ..., He L, Sjöblom T

pmc

BMC Cancer 17 (1) 487 [2017-07-17; online 2017-07-17]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service]

Transcriptional profiling of the rat nucleus accumbens after modest or high alcohol exposure.

Morud J, Ashouri A, Larsson E, Ericson M, Söderpalm B

pmc GEO

PLoS ONE 12 (7) e0181084 [2017-07-17; online 2017-07-17]

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

Analysis of aquaporins from the euryhaline barnacle Balanus improvisus reveals differential expression in response to changes in salinity.

Lind U, Järvå M, Alm Rosenblad M, ..., Hedfalk K, Blomberg A

pmc GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK

PLoS ONE 12 (7) e0181192 [2017-07-17; online 2017-07-17]

Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service]

Transancestral mapping and genetic load in systemic lupus erythematosus.

Langefeld CD, Ainsworth HC, Cunninghame Graham DS, ..., Gaffney PM, Vyse TJ

pmc

Nat Commun 8 (-) 16021 [2017-07-17; online 2017-07-17]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

Does antifouling paint select for antibiotic resistance?

Flach CF, Pal C, Svensson CJ, ..., Tysklind M, Larsson DG

Sci. Total Environ. 590-591 (-) 461-468 [2017-07-15; online 2017-03-08]

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

Prediction and modeling of pre-analytical sampling errors as a strategy to improve plasma NMR metabolomics data

Brunius C, Pedersen A, Malmodin D, ..., Tybring G, Landberg R

Bioinformatics - (-) - [2017-07-14; online 2017-07-14]

A TRPV1-to-secretagogin regulatory axis controls pancreatic β-cell survival by modulating protein turnover.

Malenczyk K, Girach F, Szodorai E, ..., Groop L, Harkany T

pmc

EMBO J. 36 (14) 2107-2125 [2017-07-14; online 2017-06-21]

Lansoprazole-sulfide, pharmacokinetics of this promising anti-tuberculous agent

Mdanda S, Baijnath S, Shobo A, ..., Naicker T, Govender T

Biomedical Chromatography - (-) e4035 [2017-07-13; online 2017-07-13]

Drug Discovery and Development (DDD) [Collaborative]

Genotype–covariate interaction effects and the heritability of adult body mass index

Robinson MR, English G, Moser G, ..., Cesarini D, Visscher PM

Nat Genet 49 (8) 1174-1181 [2017-07-10; online 2017-07-10]

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

Multipotent peripheral glial cells generate neuroendocrine cells of the adrenal medulla.

Furlan A, Dyachuk V, Kastriti ME, ..., Ernfors P, Adameyko I

Science 357 (6346) - [2017-07-07; online 2017-07-08]

Eukaryotic Single Cell Genomics (ESCG) [Service]

Anti-citrullinated protein antibodies cause arthritis by cross-reactivity to joint cartilage.

Ge C, Tong D, Liang B, ..., Dobritzsch D, Holmdahl R

pmc

JCI Insight 2 (13) - [2017-07-06; online 2017-07-06]

Autoimmunity Profiling [Service] Protein Science Facility (PSF) [Service]

High-Density Serum/Plasma Reverse Phase Protein Arrays.

Hellström C, Dodig-Crnković T, Hong MG, ..., Nilsson P, Sjöberg R

Methods Mol. Biol. 1619 (-) 229-238 [2017-07-05; online 2017-07-05]

Autoimmunity Profiling [Technology development] Plasma Profiling [Technology development]

Bead-Based and Multiplexed Immunoassays for Protein Profiling via Sequential Affinity Capture.

Birgersson E, Schwenk JM, Ayoglu B

Methods Mol. Biol. 1619 (-) 45-54 [2017-07-05; online 2017-07-05]

Plasma Profiling [Technology development]

Detection of Extracellular Vesicles Using Proximity Ligation Assay with Flow Cytometry Readout-ExoPLA.

Löf L, Arngården L, Ebai T, ..., Söderberg O, Kamali-Moghaddam M

Curr Protoc Cytom 81 (-) 4.8.1-4.8.10 [2017-07-05; online 2017-07-05]

Whole mitochondrial genome capture from faecal samples and museum-preserved specimens.

van der Valk T, Lona Durazo F, Dalén L, Guschanski K

Mol Ecol Resour - (-) - [2017-07-04; online 2017-07-04]

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

Mineral Type Structures Soil Microbial Communities

Ahmed E, Hugerth LW, Logue JB, ..., Andersson AF, Holmström SJM

Geomicrobiology Journal - (-) 1-8 [2017-07-03; online 2016-08-25]

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

Isoelectric point-based fractionation by HiRIEF coupled to LC-MS allows for in-depth quantitative analysis of the phosphoproteome.

Panizza E, Branca RMM, Oliviusson P, Orre LM, Lehtiö J

pmc

Sci Rep 7 (1) 4513 [2017-07-03; online 2017-07-03]

Chemical Proteomics & Proteogenomics [Service] Clinical Proteomics Mass spectrometry [Service]

Niche-mediated depletion of the normal hematopoietic stem cell reservoir by Flt3-ITD-induced myeloproliferation.

Mead AJ, Neo WH, Barkas N, ..., Nerlov C, Jacobsen SEW

pmc

J. Exp. Med. 214 (7) 2005-2021 [2017-07-03; online 2017-06-21]

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

Paternal personality and social status influence offspring activity in zebrafish.

Zajitschek S, Herbert-Read JE, Abbasi NM, Zajitschek F, Immler S

pmc

BMC Evol. Biol. 17 (1) 157 [2017-07-03; online 2017-07-03]

Genome Engineering Zebrafish [Service]

Genetics of phenotypic plasticity and biomass traits in hybrid willows across contrasting environments and years

Berlin S, Hallingbäck HR, Beyer F, ..., Weih M, Rönnberg-Wästljung AC

- 120 (1) 87-100 [2017-07-01; online 2017-04-25]

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

Interspecific Plastome Recombination Reflects Ancient Reticulate Evolution in Picea (Pinaceae).

Sullivan AR, Schiffthaler B, Thompson SL, Street NR, Wang XR

pmc

Mol. Biol. Evol. 34 (7) 1689-1701 [2017-07-01; online 2017-04-07]

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

Stability of Proteins in Dried Blood Spot Biobanks

Björkesten J, Enroth S, Shen Q, ..., Kamali-Moghaddam M, Landegren U

Mol Cell Proteomics 16 (7) 1286-1296 [2017-07-00; online 2017-05-13]

Integrative Genomics Identifies the Molecular Basis of Resistance to Azacitidine Therapy in Myelodysplastic Syndromes

Unnikrishnan A, Papaemmanuil E, Beck D, ..., Campbell PJ, Pimanda JE

Cell Rep 20 (3) 572-585 [2017-07-00; online 2017-07-00]

A Low-Frequency Inactivating AKT2 Variant Enriched in the Finnish Population Is Associated With Fasting Insulin Levels and Type 2 Diabetes Risk.

Manning A, Highland HM, Gasser J, ..., Gloyn AL, Lindgren CM

pmc mid

Diabetes 66 (7) 2019-2032 [2017-07-00; online 2017-03-24]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

EGR2 mutations define a new clinically aggressive subgroup of chronic lymphocytic leukemia

Young E, Noerenberg D, Mansouri L, ..., Rosenquist R, Damm F

Leukemia 31 (7) 1547-1554 [2017-07-00; online 2017-01-03]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

Relations between lipoprotein(a) concentrations, LPA genetic variants, and the risk of mortality in patients with established coronary heart disease: a molecular and genetic association study

Zewinger S, Kleber ME, Tragante V, ..., März W, Speer T

The Lancet Diabetes & Endocrinology 5 (7) 534-543 [2017-07-00; online 2017-07-00]

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

Wholegrain oat diet changes the expression of genes associated with intestinal bile acid transport.

Andersson KE, Chawade A, Thuresson N, ..., Olsson O, Hellstrand P

Mol Nutr Food Res 61 (7) - [2017-07-00; online 2017-03-30]

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

Blood transcriptomes and de novo identification of candidate loci for mating success in lekking great snipe (Gallinago media)

Höglund J, Wang B, Saether SA, ..., Kålås JA, Ekblom R

Mol Ecol 26 (13) 3458-3471 [2017-07-00; online 2017-04-28]

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

2b-RAD genotyping for population genomic studies of Chagas disease vectors: Rhodnius ecuadoriensis in Ecuador.

Hernandez-Castro LE, Paterno M, Villacís AG, ..., Grijalva MJ, Llewellyn MS

pmc

PLoS Negl Trop Dis 11 (7) e0005710 [2017-07-00; online 2017-07-19]

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

Parallel antibody germline gene and haplotype analyses support the validity of immunoglobulin germline gene inference and discovery.

Kirik U, Greiff L, Levander F, Ohlin M

Mol. Immunol. 87 (-) 12-22 [2017-07-00; online 2017-04-04]

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

Reaching the limits of prognostication in non-small cell lung cancer: an optimized biomarker panel fails to outperform clinical parameters.

Grinberg M, Djureinovic D, Brunnström HR, ..., Rahnenführer J, Micke P

Mod. Pathol. 30 (7) 964-977 [2017-07-00; online 2017-03-10]

Design and synthesis of potent inhibitors of the mono(ADP-ribosyl)transferase, PARP14

Upton K, Meyers M, Thorsell AG, ..., Schüler H, Ferraris D

Bioorganic & Medicinal Chemistry Letters 27 (13) 2907-2911 [2017-07-00; online 2017-07-00]

Genomewide analysis of admixture and adaptation in the Africanized honeybee.

Nelson RM, Wallberg A, Simões ZLP, Lawson DJ, Webster MT

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service]

Mol. Ecol. 26 (14) 3603-3617 [2017-07-00; online 2017-04-24]

Close Encounters – Probing Proximal Proteins in Live or Fixed Cells

Lönn P, Landegren U

Trends in Biochemical Sciences 42 (7) 504-515 [2017-07-00; online 2017-07-00]

Primary familial brain calcification linked to deletion of 5' noncoding region of SLC20A2.

Pasanen P, Mäkinen J, Myllykangas L, ..., Pöyhönen M, Baumann P

Acta Neurol. Scand. 136 (1) 59-63 [2017-07-00; online 2016-10-10]

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

Moderate nucleotide diversity in the Atlantic herring is associated with a low mutation rate

Feng C, Pettersson M, Lamichhaney S, ..., Folkvord A, Andersson L

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

Elife 6 (-) - [2017-06-30; online 2017-06-30]

The wolf reference genome sequence (Canis lupus lupus) and its implications for Canis spp. population genomics.

Gopalakrishnan S, Samaniego Castruita JA, Sinding MS, ..., Dalén L, Gilbert MTP

pmc

BMC Genomics 18 (1) 495 [2017-06-29; online 2017-06-29]

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

Halogen Bonding: A Powerful Tool for Modulation of Peptide Conformation

Danelius E, Andersson H, Jarvoll P, ..., Gräfenstein J, Erdélyi M

Biochemistry 56 (25) 3265-3272 [2017-06-27; online 2017-06-12]

Identification of a Sjögren's syndrome susceptibility locus at OAS1 that influences isoform switching, protein expression, and responsiveness to type I interferons

Li H, Reksten TR, Ice JA, ..., Sivils KL, None

PLoS Genet. 13 (6) e1006820 [2017-06-22; online 2017-06-22]

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

Identification of novel small molecules that inhibit STAT3-dependent transcription and function

Kolosenko I, Yu Y, Busker S, ..., Page BDG, Grander D

PLoS ONE 12 (6) e0178844 [2017-06-21; online 2017-06-21]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Identifying Bird Remains Using Ancient DNA Barcoding

Dalén L, Lagerholm V, Nylander J, ..., Irestedt M, Stewart J

Genes 8 (6) 169 [2017-06-21; online 2017-06-21]

Bioinformatics Support and Infrastructure [Collaborative]

U-CAN: a prospective longitudinal collection of biomaterials and clinical information from adult cancer patients in Sweden.

Glimelius B, Melin B, Enblad G, ..., Palmqvist R, Sjöblom T

Acta Oncol - (-) 1-8 [2017-06-20; online 2017-06-20]

Leucine Biosynthesis Is Involved in Regulating High Lipid Accumulation in Yarrowia lipolytica.

Kerkhoven EJ, Kim YM, Wei S, ..., Metz TO, Nielsen J

pmc

MBio 8 (3) - [2017-06-20; online 2017-06-20]

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

Global Kinetic Mechanism of Microsomal Glutathione Transferase 1 and Insights into Dynamic Enzyme Activation.

Spahiu L, Ålander J, Ottosson-Wadlund A, ..., Armstrong RN, Morgenstern R

Biochemistry 56 (24) 3089-3098 [2017-06-20; online 2017-06-09]

Drug Discovery and Development (DDD) [Collaborative]

Systems Biology of Metabolism

Nielsen J

Annu. Rev. Biochem. 86 (1) 245-275 [2017-06-20; online 2017-06-20]

Systems Biology [Technology development]

Combining Flow and Mass Cytometry in the Search for Biomarkers in Chronic Graft-versus-Host Disease.

Stikvoort A, Chen Y, Rådestad E, ..., Brodin P, Uhlin M

pmc

Front Immunol 8 (-) 717 [2017-06-19; online 2017-06-19]

Mass Cytometry [Collaborative]

Establishment of photosynthesis is controlled by two distinct regulatory phases

Dubreuil C, Jin X, Barajas-López JdD, ..., Small ID, Strand A

Plant Physiol. - (-) pp.00435.2017 [2017-06-16; online 2017-06-16]

Cryo-EM [Service] Swedish Metabolomics Centre (SMC) [Service]

Protein expression in tension wood formation monitored at high tissue resolution in Populus

Bygdell J, Srivastava V, Obudulu O, ..., Mellerowicz EJ, Wingsle G

- 68 (13) 3405-3417 [2017-06-15; online 2017-06-13]

Bioinformatics Support and Infrastructure [Collaborative]

Microbial Community Structure in a Serpentine-Hosted Abiotic Gas Seepage at the Chimaera Ophiolite, Turkey.

Neubeck A, Sun L, Müller B, ..., Broman C, Schnürer A

pmc

Appl. Environ. Microbiol. 83 (12) - [2017-06-15; online 2017-05-31]

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

Ranking and characterization of established BMI and lipid associated loci as candidates for gene-environment interactions

Shungin D, Deng WQ, Varga TV, ..., Franks PW, None

PLoS Genet. 13 (6) e1006812 [2017-06-14; online 2017-06-14]

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

Genetic loci associated with heart rate variability and their effects on cardiac disease risk.

Nolte IM, Munoz ML, Tragante V, ..., Snieder H, de Geus EJC

pmc

Nat Commun 8 (-) 15805 [2017-06-14; online 2017-06-14]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

Stimulated Emission Depletion Microscopy

Blom H, Widengren J

Chem. Rev. 117 (11) 7377-7427 [2017-06-14; online 2017-03-06]

Advanced Light Microscopy (ALM) [Technology development]

Four simple recommendations to encourage best practices in research software

Jiménez RC, Kuzak M, Alhamdoosh M, ..., Watson-Haigh NS, Crouch S

F1000Res 6 (-) 876 [2017-06-13; online 2017-06-13]

Bioinformatics Support and Infrastructure [Technology development]

Structural basis for ligand binding to an enzyme by a conformational selection pathway

Kovermann M, Grundström C, Sauer-Eriksson AE, Sauer UH, Wolf-Watz M

Proc Natl Acad Sci USA 114 (24) 6298-6303 [2017-06-13; online 2017-05-30]

A community proposal to integrate proteomics activities in ELIXIR

Vizcaíno JA, Walzer M, Jiménez RC, ..., Martens L, Kohlbacher O

F1000Res 6 (-) 875 [2017-06-13; online 2017-06-13]

Bioinformatics Support and Infrastructure [Technology development]

Functional and Compositional Stability of Bacterial Metacommunities in Response to Salinity Changes

Berga M, Zha Y, Székely AJ, Langenheder S

Front Microbiol 8 (-) - [2017-06-08; online 2017-06-08]

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

Fast and general tests of genetic interaction for genome-wide association studies

Frånberg M, Strawbridge RJ, Hamsten A, ..., Sennblad B, None

PLoS Comput. Biol. 13 (6) e1005556 [2017-06-06; online 2017-06-06]

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

Mast Cell Infiltration in Human Brain Metastases Modulates the Microenvironment and Contributes to the Metastatic Potential.

Roy A, Libard S, Weishaupt H, ..., Alafuzoff I, Tchougounova E

pmc

Front Oncol 7 (-) 115 [2017-06-02; online 2017-06-02]

Genome Sequence of Roseovarius mucosus Strain SMR3, Isolated from a Culture of the Diatom Skeletonema marinoi.

Töpel M, Pinder MIM, Johansson ON, ..., Godhe A, Clarke AK

pmc

Genome Announc 5 (22) - [2017-06-01; online 2017-06-01]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service]

Injury Leads to the Appearance of Cells with Characteristics of Both Microglia and Astrocytes in Mouse and Human Brain.

Wilhelmsson U, Andersson D, de Pablo Y, ..., Pekny M, Pekna M

Cereb. Cortex 27 (6) 3360-3377 [2017-06-01; online 2017-04-12]

Methylation of HPA axis related genes in men with hypersexual disorder

Jokinen J, Boström AE, Chatzittofis A, ..., Arver S, Schiöth HB

Psychoneuroendocrinology 80 (-) 67-73 [2017-06-00; online 2017-06-00]

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

Identification and characterization of inhibitors of UDP-glucose and UDP-sugar pyrophosphorylases for in vivo studies

Decker D, Öberg C, Kleczkowski LA

Plant J 90 (6) 1093-1107 [2017-06-00; online 2017-04-13]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

An automated method measures variability in P-glycoprotein and ABCG2 densities across brain regions and brain matter.

Kannan P, Schain M, Kretzschmar WW, ..., Hall MD, Mulder J

J. Cereb. Blood Flow Metab. - (-) 271678X16660984 [2017-06-00; online 2016-08-05]

Fluorescence Tissue Profiling [Technology development]

Draft genome of the oomycete pathogen Phytophthora cactorum strain LV007 isolated from European beech (Fagus sylvatica).

Grenville-Briggs LJ, Kushwaha SK, Cleary MR, ..., Chawade A, Vetukuri RR

pmc

Genom Data 12 (-) 155-156 [2017-06-00; online 2017-05-12]

Bioinformatics Support and Infrastructure [Collaborative]

Levels of oxylipins, endocannabinoids and related lipids in plasma before and after low-level exposure to acrolein in healthy individuals and individuals with chemical intolerance

Claeson AS, Gouveia-Figueira S, Häggström J, Fowler CJ, Nording ML

Prostaglandins, Leukotrienes and Essential Fatty Acids (PLEFA) 121 (-) 60-67 [2017-06-00; online 2017-06-00]

The effects of thawing on the plasma metabolome: evaluating differences between thawed plasma and multi-organ samples

Torell F, Bennett K, Rännar S, ..., Lundstedt T, Trygg J

Metabolomics 13 (6) - [2017-06-00; online 2017-04-17]

Methylation of HPA axis related genes in men with hypersexual disorder.

Jokinen J, Boström AE, Chatzittofis A, ..., Arver S, Schiöth HB

Psychoneuroendocrinology 80 (-) 67-73 [2017-06-00; online 2017-03-10]

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

Metabolite quantification by NMR and LC-MS/MS reveals differences between unstimulated, stimulated, and pure parotid saliva

Figueira J, Gouveia-Figueira S, Öhman C, ..., Nording ML, Öhman A

Journal of Pharmaceutical and Biomedical Analysis 140 (-) 295-300 [2017-06-00; online 2017-06-00]

Swedish Metabolomics Centre (SMC) [Service] Swedish NMR Centre (SNC) [Collaborative]

A DNA methylation site within the KLF13 gene is associated with orexigenic processes based on neural responses and ghrelin levels.

Wiemerslage L, Islam R, van der Kamp C, ..., Benedict C, Schiöth HB

Int J Obes (Lond) 41 (6) 990-994 [2017-06-00; online 2017-02-14]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

No evidence for MHC class II-based non-random mating at the gametic haplotype in Atlantic salmon

Promerová M, Alavioon G, Tusso S, Burri R, Immler S

Heredity 118 (6) 563-567 [2017-06-00; online 2017-01-18]

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

Chemisorption of air CO2 on cellulose: an overlooked feature of the cellulose/NaOH(aq) dissolution system

Gunnarsson M, Theliander H, Hasani M

Cellulose 24 (6) 2427-2436 [2017-06-00; online 2017-04-12]

A missense variant in ITPR1 provides evidence for autosomal recessive SCA29 with asymptomatic cerebellar hypoplasia in carriers

Klar J, Ali Z, Farooq M, ..., Baig SM, Dahl N

Eur J Hum Genet 25 (7) 848-853 [2017-06-00; online 2017-05-10]

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

Gene flow, ancient polymorphism, and ecological adaptation shape the genomic landscape of divergence among Darwin's finches

Han F, Lamichhaney S, Grant BR, ..., Andersson L, Webster MT

Genome Res. 27 (6) 1004-1015 [2017-06-00; online 2017-04-25]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

Large-Scale Identification of Common Trait and Disease Variants Affecting Gene Expression

Hauberg ME, Zhang W, Giambartolomei C, ..., Domenici E, Devlin B

The American Journal of Human Genetics 100 (6) 885-894 [2017-06-00; online 2017-06-00]

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

Downregulation of RWA genes in hybrid aspen affects xylan acetylation and wood saccharification

Pawar PMA, Ratke C, Balasubramanian VK, ..., Jönsson LJ, Mellerowicz EJ

New Phytol 214 (4) 1491-1505 [2017-06-00; online 2017-03-03]

Synthetic approaches to radiochemical probes for imaging of bacterial infections

Dutta J, Naicker T, Ebenhan T, ..., Arvidsson PI, Govender T

European Journal of Medicinal Chemistry 133 (-) 287-308 [2017-06-00; online 2017-06-00]

Drug Discovery and Development (DDD) [Collaborative]

Tumoral cubilin is a predictive marker for treatment of renal cancer patients with sunitinib and sorafenib.

Niinivirta M, Enblad G, Edqvist PH, ..., Dragomir A, Ullenhag GJ

pmc

J. Cancer Res. Clin. Oncol. 143 (6) 961-970 [2017-06-00; online 2017-03-04]

Separating the effects of forage source and field microbiota on silage fermentation quality and aerobic stability

Mogodiniyai Kasmaei K, Dicksved J, Spörndly R, Udén P

Grass Forage Sci - (-) - [2017-06-00; online 2016-06-06]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Service]

The transcriptome of the avian malaria parasite Plasmodium ashfordi displays host-specific gene expression.

Videvall E, Cornwallis CK, Ahrén D, ..., Valkiūnas G, Hellgren O

Mol. Ecol. 26 (11) 2939-2958 [2017-06-00; online 2017-04-08]

Bioinformatics Support and Infrastructure [Collaborative]

Lower inflammatory markers in women with antenatal depression brings the M1/M2 balance into focus from a new direction

Edvinsson Å, Bränn E, Hellgren C, ..., Cunningham JL, Sundström-Poromaa I

Psychoneuroendocrinology 80 (-) 15-25 [2017-06-00; online 2017-06-00]

Bioinformatics Support and Infrastructure [Collaborative] Clinical Biomarkers [Service] PLA Proteomics [Collaborative]

Affinity Proteomics Exploration of Melanoma Identifies Proteins in Serum with Associations to T-Stage and Recurrence.

Byström S, Fredolini C, Edqvist PH, ..., Pontén F, Schwenk JM

pmc

Transl Oncol 10 (3) 385-395 [2017-06-00; online 2017-04-20]

Plasma Profiling [Collaborative] Tissue Profiling [Collaborative]

Contribution of different bacterial dispersal sources to lakes: Population and community effects in different seasons

Comte J, Berga M, Severin I, Logue JB, Lindström ES

Environ Microbiol 19 (6) 2391-2404 [2017-06-00; online 2017-05-05]

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

Genetic susceptibility to cardiovascular disease and risk of dementia

Karlsson IK, Ploner A, Song C, ..., Pedersen NL, Hägg S

Transl Psychiatry 7 (5) e1142 [2017-05-30; online 2017-05-30]

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

A subcellular map of the human proteome.

Thul PJ, Åkesson L, Wiking M, ..., Uhlén M, Lundberg E

Science 356 (6340) - [2017-05-26; online 2017-05-11]

Bioinformatics Compute and Storage [Service] Cell Profiling [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]

Draft Genome Sequence of the Mycoparasitic Oomycete Pythium oligandrum Strain CBS 530.74.

Kushwaha SK, Vetukuri RR, Grenville-Briggs LJ

pmc

Genome Announc 5 (21) - [2017-05-25; online 2017-05-25]

Bioinformatics Support and Infrastructure [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]

Piperazin-1-ylpyridazine Derivatives Are a Novel Class of Human dCTP Pyrophosphatase 1 Inhibitors

Llona-Minguez S, Höglund A, Ghassemian A, ..., Scobie M, Helleday T

J. Med. Chem. 60 (10) 4279-4292 [2017-05-25; online 2017-05-16]

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

Type 2 diabetes and obesity induce similar transcriptional reprogramming in human myocytes.

Väremo L, Henriksen TI, Scheele C, ..., Pedersen BK, Nielsen J

pmc

Genome Med 9 (1) 47 [2017-05-25; online 2017-05-25]

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

Absolute Quantification of Protein and mRNA Abundances Demonstrate Variability in Gene-Specific Translation Efficiency in Yeast.

Lahtvee P, Sánchez BJ, Smialowska A, ..., Gatto F, Nielsen J

Cell Syst 4 (5) 495-504.e5 [2017-05-24; online 2017-03-29]

Bioinformatics Support and Infrastructure [Collaborative]

Genome-wide association meta-analysis of 78,308 individuals identifies new loci and genes influencing human intelligence

Sniekers S, Stringer S, Watanabe K, ..., van Duijn CM, Posthuma D

Nat Genet 49 (7) 1107-1112 [2017-05-22; online 2017-05-22]

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

Neuroproteomic Profiling of Cerebrospinal Fluid (CSF) by Multiplexed Affinity Arrays.

Häggmark-Månberg A, Nilsson P, Schwenk JM

Methods Mol. Biol. 1598 (-) 247-254 [2017-05-17; online 2017-05-17]

Autoimmunity Profiling [Technology development] Plasma Profiling [Technology development]

ProQ3D: improved model quality assessments using deep learning.

Uziela K, Menéndez Hurtado D, Shu N, Wallner B, Elofsson A

Bioinformatics 33 (10) 1578-1580 [2017-05-15; online 2017-01-06]

Bioinformatics Support and Infrastructure [Collaborative]

Genome Sequence of a Bovine Rhinitis B Virus Identified in Cattle in Sweden

Blomström AL, Oma V, Khatri M, ..., Berg M, Myrmel M

Genome Announc 5 (19) e00172-17 [2017-05-11; online 2017-05-11]

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

Whole blood gene expression in adolescent chronic fatigue syndrome: an exploratory cross-sectional study suggesting altered B cell differentiation and survival.

Nguyen CB, Alsøe L, Lindvall JM, ..., Nilsen H, Wyller VB

pmc ClinicalTrials.gov ClinicalTrials.gov

J Transl Med 15 (1) 102 [2017-05-11; online 2017-05-11]

Bioinformatics Support and Infrastructure [Collaborative]

TIDDIT, an efficient and comprehensive structural variant caller for massive parallel sequencing data.

Eisfeldt J, Vezzi F, Olason P, Nilsson D, Lindstrand A

pmc

F1000Res 6 (-) 664 [2017-05-10; online 2017-05-10]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Clinical Genomics Stockholm [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]

Reproducible diagnostic metabolites in plasma from typhoid fever patients in Asia and Africa

Näsström E, Parry CM, Vu Thieu NT, ..., Antti H, Baker S

Elife 6 (-) - [2017-05-09; online 2017-05-09]

Spatially resolved transcriptome profiling in model plant species.

Giacomello S, Salmén F, Terebieniec BK, ..., Street NR, Lundeberg J

NPLANTS 3 (-) 17061 [2017-05-08; online 2017-05-08]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]

Regulation of PfEMP1-VAR2CSA translation by a Plasmodium translation-enhancing factor.

Chan S, Frasch A, Mandava CS, ..., Sanyal S, Wahlgren M

Nat Microbiol 2 (-) 17068 [2017-05-08; online 2017-05-08]

Bioinformatics Compute and Storage [Service] Chemical Proteomics & Proteogenomics [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]

Screening and Validation of Novel Biomarkers in Osteoarticular Pathologies by Comprehensive Combination of Protein Array Technologies.

Sierra-Sánchez Á, Garrido-Martín D, Lourido L, ..., Blanco F, Fuentes M

J. Proteome Res. 16 (5) 1890-1899 [2017-05-05; online 2017-04-17]

Autoimmunity Profiling [Collaborative]

Impact of cytosine methylation on DNA binding specificities of human transcription factors

Yin Y, Morgunova E, Jolma A, ..., Vinson C, Taipale J

Science 356 (6337) eaaj2239 [2017-05-05; online 2017-05-04]

Regulating plant physiology with organic electronics

Poxson DJ, Karady M, Gabrielsson R, ..., Simon DT, Berggren M

Proc Natl Acad Sci USA 114 (18) 4597-4602 [2017-05-02; online 2017-04-18]

Apoptotic Bax at Oxidatively Stressed Mitochondrial Membranes: Lipid Dynamics and Permeabilization

Dingeldein APG, Pokorná Š, Lidman M, ..., Hof M, Gröbner G

Biophysical Journal 112 (10) 2147-2158 [2017-05-00; online 2017-05-00]

Two extended haplotype blocks are associated with adaptation to high altitude habitats in East African honey bees.

Wallberg A, Schöning C, Webster MT, Hasselmann M

pmc BioProject Dryad

PLoS Genet. 13 (5) e1006792 [2017-05-00; online 2017-05-25]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

Contrasting patterns of cytokinins between years in senescing aspen leaves

Edlund E, Novak O, Karady M, Ljung K, Jansson S

Plant, Cell & Environment 40 (5) 622-634 [2017-05-00; online 2017-03-27]

Transcriptomics and methylomics of CD4-positive T cells in arsenic-exposed women.

Engström K, Wojdacz TK, Marabita F, ..., Vahter M, Broberg K

pmc

Arch. Toxicol. 91 (5) 2067-2078 [2017-05-00; online 2016-11-12]

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

Immune Biomarkers on the Radar—Comprehensive “Immunograms” for Multimodal Treatment Prediction

Botling J, Sandelin M

Journal of Thoracic Oncology 12 (5) 770-772 [2017-05-00; online 2017-05-00]

Clinical Genomics Uppsala [Collaborative]

Further evidence for specific IFIH1 mutation as a cause of Singleton-Merten syndrome with phenotypic heterogeneity.

Pettersson M, Bergendal B, Norderyd J, ..., Nordgren A, Lindstrand A

Am. J. Med. Genet. A 173 (5) 1396-1399 [2017-05-00; online 2017-03-20]

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

On the bridge over the translational valley of death: interview with Per I Arvidsson

Arvidsson PI

Future Science OA 3 (2) FSO183 [2017-05-00; online 2017-05-00]

Drug Discovery and Development (DDD) [Technology development]

Bayesian Inference of Allele-Specific Gene Expression Indicates Abundant Cis-Regulatory Variation in Natural Flycatcher Populations

Wang M, Uebbing S, Ellegren H

Genome Biol Evol 9 (5) 1266-1279 [2017-05-00; online 2017-05-01]

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

Genomic repertoire of the Woeseiaceae/JTB255, cosmopolitan and abundant core members of microbial communities in marine sediments.

Mußmann M, Pjevac P, Krüger K, Dyksma S

pmc

ISME J 11 (5) 1276-1281 [2017-05-00; online 2017-01-06]

Microbial Single Cell Genomics [Service]

Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications.

Weissensteiner MH, Pang AWC, Bunikis I, ..., Suh A, Wolf JBW

pmc

Genome Res. 27 (5) 697-708 [2017-05-00; online 2017-03-30]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative]

Discrimination of pancreatic cancer and pancreatitis by LC-MS metabolomics

Lindahl A, Heuchel R, Forshed J, ..., Löhr M, Nordström A

Metabolomics 13 (5) - [2017-05-00; online 2017-04-01]

Chemical Proteomics & Proteogenomics [Service] Clinical Proteomics Mass spectrometry [Service] Swedish Metabolomics Centre (SMC) [Service]

Induction of functional dopamine neurons from human astrocytes in vitro and mouse astrocytes in a Parkinson's disease model.

Rivetti di Val Cervo P, Romanov RA, Spigolon G, ..., Fisone G, Arenas E

Nat. Biotechnol. 35 (5) 444-452 [2017-05-00; online 2017-04-10]

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

The chloroplast genome of Ephedra foeminea (Ephedraceae, Gnetales), an entomophilous gymnosperm endemic to the Mediterranean area.

Hou C, Wikström N, Rydin C

Mitochondrial DNA A DNA Mapp Seq Anal 28 (3) 330-331 [2017-05-00; online 2015-12-29]

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

QTL mapping of stress related gene expression in a cross between domesticated chickens and ancestral red junglefowl

Fallahsharoudi A, de Kock N, Johnsson M, ..., Wright D, Jensen P

Molecular and Cellular Endocrinology 446 (-) 52-58 [2017-05-00; online 2017-05-00]

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

Inflammatory markers in late pregnancy in association with postpartum depression—A nested case-control study

Bränn E, Papadopoulos F, Fransson E, ..., Sundström-Poromaa I, Skalkidou A

Psychoneuroendocrinology 79 (-) 146-159 [2017-05-00; online 2017-05-00]

Clinical Biomarkers [Service] PLA Proteomics [Collaborative]

The effect of temperature and substrate quality on the carbon use efficiency of saprotrophic decomposition

Öquist MG, Erhagen B, Haei M, ..., Schleucher J, Nilsson MB

Plant Soil 414 (1-2) 113-125 [2017-05-00; online 2016-11-26]

FADD, Caspase-3, and Caspase-8 and Incidence of Coronary Events.

Xue L, Borné Y, Mattisson IY, ..., Nilsson J, Engström G

Arterioscler. Thromb. Vasc. Biol. 37 (5) 983-989 [2017-05-00; online 2017-03-16]

Comparative genomics and expression levels of hydrophobins from eight mycorrhizal genomes.

Rineau F, Lmalem H, Ahren D, ..., Martin F, Colpaert JV

Mycorrhiza 27 (4) 383-396 [2017-05-00; online 2017-01-09]

Bioinformatics Support and Infrastructure [Collaborative]

Loss of chromosome Y (LOY) in blood cells is associated with increased risk for disease and mortality in aging men

Forsberg LA

Hum Genet 136 (5) 657-663 [2017-05-00; online 2017-04-19]

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

Brodie vs Hummers graphite oxides for preparation of multi-layered materials

Talyzin AV, Mercier G, Klechikov A, ..., Opitz A, Moons E

Carbon 115 (-) 430-440 [2017-05-00; online 2017-05-00]

Genetic Profile of Ductal Adenocarcinoma of the Prostate.

Seipel AH, Whitington T, Delahunt B, ..., Lindberg J, Egevad L

Hum. Pathol. - (-) - [2017-04-27; online 2017-04-27]

Does the sex of one's co-twin affect height and BMI in adulthood? A study of dizygotic adult twins from 31 cohorts.

Bogl LH, Jelenkovic A, Vuoksimaa E, ..., Silventoinen K, Kaprio J

pmc

Biol Sex Differ 8 (-) 14 [2017-04-27; online 2017-04-27]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

Genome-wide meta-analysis of 241,258 adults accounting for smoking behaviour identifies novel loci for obesity traits

Justice AE, Winkler TW, Feitosa MF, ..., North KE, Cupples LA

Nat Commun 8 (-) 14977 [2017-04-26; online 2017-04-26]

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

Corrigendum: MTH1 inhibition eradicates cancer by preventing sanitation of the dNTP pool.

Gad H, Koolmeister T, Jemth AS, ..., Scobie M, Ulrika Warpman Berglund &Thomas Helleday

Nature 544 (7651) 508 [2017-04-26; online 2017-04-28]

Drug Discovery and Development (DDD) [Service]

Comprehensive mapping of the effects of azacitidine on DNA methylation, repressive/permissive histone marks and gene expression in primary cells from patients with MDS and MDS-related disease.

Tobiasson M, Abdulkadir H, Lennartsson A, ..., Hellström-Lindberg E, Ungerstedt J

pmc

Oncotarget 8 (17) 28812-28825 [2017-04-25; online 2017-04-22]

Bioinformatics Support and Infrastructure [Collaborative]

Parallel adaptive evolution of geographically distant herring populations on both sides of the North Atlantic Ocean

Lamichhaney S, Fuentes-Pardo AP, Rafati N, ..., Ruzzante DE, Andersson L

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

Proc Natl Acad Sci USA 114 (17) E3452-E3461 [2017-04-25; online 2017-04-07]

Genomic analyses identify hundreds of variants associated with age at menarche and support a role for puberty timing in cancer risk

Day FR, Thompson DJ, Helgason H, ..., Ong KK, Perry JRB

Nat Genet 49 (6) 834-841 [2017-04-24; online 2017-04-24]

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

The Influence of Hydroxyapatite Nanoparticle Morphology on Embryonic Development in a Zebrafish Exposure Model.

Pujari-Palmer S, Lu X, Karlsson Ott M

pmc

Nanomaterials (Basel) 7 (4) - [2017-04-22; online 2017-04-22]

Genome Engineering Zebrafish [Service]

Persistent Effects of Developmental Exposure to 17α-Ethinylestradiol on the Zebrafish (Danio rerio) Brain Transcriptome and Behavior

Porseryd T, Volkova K, Reyhanian Caspillo N, ..., Dinnetz P, Porsh Hällström I

Front. Behav. Neurosci. 11 (-) - [2017-04-20; online 2017-04-20]

Bioinformatics Support and Infrastructure [Collaborative] NGI Uppsala (Uppsala Genome Center) [Service]

Gain-of-function SAMD9L mutations cause a syndrome of cytopenia, immunodeficiency, MDS, and neurological symptoms

Tesi B, Davidsson J, Voss M, ..., Cammenga J, Bryceson YT

Blood 129 (16) 2266-2279 [2017-04-20; online 2017-02-15]

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

Respiratory chain complex III deficiency due to mutated BCS1L: a novel phenotype with encephalomyopathy, partially phenocopied in a Bcs1l mutant mouse model.

Tegelberg S, Tomašić N, Kallijärvi J, ..., Eklund EA, Fellman V

pmc

Orphanet J Rare Dis 12 (1) 73 [2017-04-20; online 2017-04-20]

Large-scale analyses of common and rare variants identify 12 new loci associated with atrial fibrillation

Christophersen IE, Rienstra M, Roselli C, ..., Lubitz SA, Ellinor PT

Nat Genet 49 (6) 946-952 [2017-04-17; online 2017-04-17]

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

Oriented clonal cell dynamics enables accurate growth and shaping of vertebrate cartilage

Kaucka M, Zikmund T, Tesarova M, ..., Fried K, Adameyko I

Elife 6 (-) - [2017-04-17; online 2017-04-17]

Advanced Light Microscopy (ALM) [Collaborative]

Adaptation to infectious disease exposure in indigenous Southern African populations

Owers KA, Sjödin P, Schlebusch CM, ..., Soodyall H, Jakobsson M

Proc. R. Soc. B 284 (1852) 20170226 [2017-04-12; online 2017-04-05]

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

Anaerobic Methanotrophic Archaea of the ANME-2d Cluster Are Active in a Low-sulfate, Iron-rich Freshwater Sediment.

Weber HS, Habicht KS, Thamdrup B

pmc

Front Microbiol 8 (-) 619 [2017-04-12; online 2017-04-12]

SnoN Stabilizes the SMAD3/SMAD4 Protein Complex

Walldén K, Nyman T, Hällberg BM

Sci Rep 7 (-) 46370 [2017-04-11; online 2017-04-11]

Protein Science Facility (PSF) [Collaborative]

Serglycin as a potential biomarker for glioma: association of serglycin expression, extent of mast cell recruitment and glioblastoma progression.

Roy A, Attarha S, Weishaupt H, ..., Pontén F, Tchougounova E

pmc

Oncotarget 8 (15) 24815-24827 [2017-04-11; online 2017-04-28]

Multi-label prediction of subcellular localization in confocal images using deep neural networks

Winsnes CF, Sullivan DP, Smith K, Lundberg E

Molecular Biology of the Cell 27 (-) - [2017-04-10; online 2017-04-10]

Large-scale genome-wide analysis identifies genetic variants associated with cardiac structure and function

Wild PS, Felix JF, Schillert A, ..., Vasan RS, Dörr M

- 127 (5) 1798-1812 [2017-04-10; online 2017-04-10]

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

Genome-wide identification of physically clustered genes suggests chromatin-level co-regulation in male reproductive development in Arabidopsis thaliana

Reimegård J, Kundu S, Pendle A, ..., Sundström JF, Emanuelsson O

Nucleic Acids Res 45 (6) 3253-3265 [2017-04-07; online 2017-02-08]

Bioinformatics Long-term Support WABI [Collaborative]

SPlinted Ligation Adapter Tagging (SPLAT), a novel library preparation method for whole genome bisulphite sequencing

Raine A, Manlig E, Wahlberg P, Syvänen AC, Nordlund J

Nucleic Acids Res 45 (6) e36-e36 [2017-04-07; online 2016-11-29]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Technology development]

Draft Genome Sequences of Six Strains of Streptococcus pneumoniae from Serotypes 5, 6A, 6B, 18C, 19A, and 23F.

Jakobsson HE, Salvà-Serra F, Thorell K, ..., Kristiansson E, Moore ER

pmc

Genome Announc 5 (14) - [2017-04-06; online 2017-04-06]

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

Complete Genome Sequences of the Xylose-Fermenting Candida intermedia Strains CBS 141442 and PYCC 4715

Moreno AD, Tellgren-Roth C, Soler L, ..., Olsson L, Geijer C

Genome Announc 5 (14) e00138-17 [2017-04-06; online 2017-04-06]

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

dUTPase inhibition augments replication defects of 5-Fluorouracil.

Hagenkort A, Paulin CBJ, Desroses M, ..., Scobie M, Helleday T

pmc

Oncotarget 8 (14) 23713-23726 [2017-04-04; online 2017-04-21]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Global analysis of biosynthetic gene clusters reveals vast potential of secondary metabolite production in Penicillium species.

Nielsen JC, Grijseels S, Prigent S, ..., Workman M, Nielsen J

Nat Microbiol 2 (-) 17044 [2017-04-03; online 2017-04-03]

Bioinformatics Support and Infrastructure [Collaborative]

Sulfonimidamides in Medicinal and Agricultural Chemistry

Chinthakindi PK, Naicker T, Thota N, ..., Kruger HG, Arvidsson PI

Angew. Chem. Int. Ed. 56 (15) 4100-4109 [2017-04-03; online 2017-02-23]

Drug Discovery and Development (DDD) [Technology development]

Interactions of Freshwater Cyanobacteria with Bacterial Antagonists

Osman OA, Beier S, Grabherr M, Bertilsson S

Appl. Environ. Microbiol. 83 (7) e02634-16 [2017-04-01; online 2017-01-23]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

Membrane-Depolarizing Channel Blockers Induce Selective Glioma Cell Death by Impairing Nutrient Transport and Unfolded Protein/Amino Acid Responses.

Niklasson M, Maddalo G, Sramkova Z, ..., Enger PØ, Andäng M

Cancer Res. 77 (7) 1741-1752 [2017-04-01; online 2017-01-13]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Identification and quantification of even and odd chained 5-n alkylresorcinols, branched chain-alkylresorcinols and methylalkylresorcinols in Quinoa (Chenopodium quinoa).

Ross AB, Svelander C, Karlsson G, Savolainen OI

Food Chem 220 (-) 344-351 [2017-04-01; online 2016-10-05]

Somatic Ephrin Receptor Mutations Are Associated with Metastasis in Primary Colorectal Cancer

Mathot L, Kundu S, Ljungström V, ..., Nilsson M, Sjöblom T

Cancer Res 77 (7) 1730-1740 [2017-04-01; online 2017-01-20]

Clinical Genomics Uppsala [Collaborative]

Green listed—a CRISPR screen tool

Panda SK, Boddul SV, Jiménez-Andrade GY, ..., Fernandez-Ricaud L, Wermeling F

- 33 (7) 1099-1100 [2017-04-01; online 2016-12-19]

Bioinformatics Support and Infrastructure [Collaborative]

Epigenome-wide DNA methylation study of IgE concentration in relation to self-reported allergies.

Ek WE, Ahsan M, Rask-Andersen M, ..., Gyllensten U, Johansson Å

Epigenomics 9 (4) 407-418 [2017-04-00; online 2017-03-21]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

Porosity investigation of yttria-stabilized zirconia topcoats using NMR cryoporometry

Ekberg J, Nordstierna L, Klement U

Surface and Coatings Technology 315 (-) 468-474 [2017-04-00; online 2017-04-00]

Induction of Apoptosis in Intestinal Toxicity to a Histone Deacetylase Inhibitor in a Phase I Study with Pelvic Radiotherapy.

Kalanxhi E, Risberg K, Barua IS, ..., Flatmark K, Ree AH

Cancer Res Treat 49 (2) 374-386 [2017-04-00; online 2016-08-05]

Bioinformatics Support and Infrastructure [Collaborative]

Lipid response patterns in acute phase paediatric Plasmodium falciparum malaria

Orikiiriza J, Surowiec I, Lindquist E, ..., Trygg J, Normark J

Metabolomics 13 (4) - [2017-04-00; online 2017-02-23]

Combined immunodeficiency and hypoglycemia associated with mutations in hypoxia upregulated 1.

Haapaniemi EM, Fogarty CL, Keskitalo S, ..., Seppänen M, Kere J

J. Allergy Clin. Immunol. 139 (4) 1391-1393.e11 [2017-04-00; online 2016-12-04]

Bioinformatics Compute and Storage [Service]

Mapping of 79 loci for 83 plasma protein biomarkers in cardiovascular disease.

Folkersen L, Fauman E, Sabater-Lleal M, ..., Hamsten A, Mälarstig A

pmc

PLoS Genet. 13 (4) e1006706 [2017-04-00; online 2017-04-03]

Bioinformatics Compute and Storage [Service] Clinical Biomarkers [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

A Large Inversion Involving GNAS Exon A/B and All Exons Encoding Gsα Is Associated With Autosomal Dominant Pseudohypoparathyroidism Type Ib (PHP1B).

Grigelioniene G, Nevalainen PI, Reyes M, ..., Mäkitie O, Jüppner H

pmc mid

J. Bone Miner. Res. 32 (4) 776-783 [2017-04-00; online 2017-02-24]

Bioinformatics Compute and Storage [Service] Clinical Genomics Stockholm [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]

Effects of dietary inclusion of the yeasts Saccharomyces cerevisiae and Wickerhamomyces anomalus on gut microbiota of rainbow trout

Huyben D, Nyman A, Vidaković A, ..., Dicksved J, Lundh T

Aquaculture 473 (-) 528-537 [2017-04-00; online 2017-04-00]

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

Genomic analysis reveals the presence of a class D beta-lactamase with broad substrate specificity in animal bite associated Capnocytophaga species.

Zangenah S, Andersson AF, Özenci V, Bergman P

pmc

Eur. J. Clin. Microbiol. Infect. Dis. 36 (4) 657-662 [2017-04-00; online 2016-12-03]

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

HRDetect is a predictor of BRCA1 and BRCA2 deficiency based on mutational signatures.

Davies H, Glodzik D, Morganella S, ..., Stratton MR, Nik-Zainal S

Nat. Med. 23 (4) 517-525 [2017-04-00; online 2017-03-13]

Clinical Genomics Lund [Collaborative]

Shift in fungal communities and associated enzyme activities along an age gradient of managed Pinus sylvestris stands

Kyaschenko J, Clemmensen KE, Hagenbo A, Karltun E, Lindahl BD

ISME J 11 (4) 863-874 [2017-04-00; online 2017-01-13]

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

Neonatal Cord Blood Oxylipins and Exposure to Particulate Matter in the Early-Life Environment: An ENVIRONAGE Birth Cohort Study.

Martens DS, Gouveia S, Madhloum N, ..., Nording M, Nawrot TS

pmc

Environ. Health Perspect. 125 (4) 691-698 [2017-04-00; online 2016-11-05]

Whole-Genome Bisulfite Sequencing of Human Pancreatic Islets Reveals Novel Differentially Methylated Regions in Type 2 Diabetes Pathogenesis

Volkov P, Bacos K, Ofori JK, ..., Rönn T, Ling C

Diabetes 66 (4) 1074-1085 [2017-04-00; online 2017-01-04]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

The anti-inflammatory compound palmitoylethanolamide inhibits prostaglandin and hydroxyeicosatetraenoic acid production by a macrophage cell line

Gabrielsson L, Gouveia-Figueira S, Häggström J, Alhouayek M, Fowler CJ

Pharmacol Res Perspect 5 (2) e00300 [2017-04-00; online 2017-02-27]

Gene co-expression network connectivity is an important determinant of selective constraint.

Mähler N, Wang J, Terebieniec BK, ..., Street NR, Hvidsten TR

pmc

PLoS Genet. 13 (4) e1006402 [2017-04-00; online 2017-04-13]

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

Frequent low-level mutations of protein kinase D2 in angiolipoma

Hofvander J, Arbajian E, Stenkula KG, ..., Hornick JL, Mertens F

J. Pathol 241 (5) 578-582 [2017-04-00; online 2017-02-27]

Bioinformatics Support and Infrastructure [Collaborative]

FZD10-Gα13 signalling axis points to a role of FZD10 in CNS angiogenesis.

Hot B, Valnohova J, Arthofer E, ..., Mulder J, Schulte G

Cell. Signal. 32 (-) 93-103 [2017-04-00; online 2017-01-24]

Genomic structure of the horse major histocompatibility complex class II region resolved using PacBio long-read sequencing technology

Viļuma A, Mikko S, Hahn D, ..., Andersson G, Bergström TF

Sci Rep 7 (-) 45518 [2017-03-31; online 2017-03-31]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Service] NGI Uppsala (Uppsala Genome Center) [Service]

Improvement of identification methods for honeybee specific Lactic Acid Bacteria; future approaches.

Lamei S, Hu YO, Olofsson TC, ..., Forsgren E, Vásquez A

pmc

PLoS ONE 12 (3) e0174614 [2017-03-27; online 2017-03-27]

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

Draft Genome Sequence of the Mycoparasitic Oomycete Pythium periplocum Strain CBS 532.74.

Kushwaha SK, Vetukuri RR, Grenville-Briggs LJ

pmc

Genome Announc 5 (12) - [2017-03-23; online 2017-03-23]

Bioinformatics Support and Infrastructure [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]

Potential for hydrogen-oxidizing chemolithoautotrophic and diazotrophic populations to initiate biofilm formation in oligotrophic, deep terrestrial subsurface waters.

Wu X, Pedersen K, Edlund J, ..., Bertilsson S, Dopson M

pmc

Microbiome 5 (1) 37 [2017-03-23; online 2017-03-23]

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

NEArender: an R package for functional interpretation of 'omics' data via network enrichment analysis.

Jeggari A, Alexeyenko A

pmc

BMC Bioinformatics 18 (Suppl 5) 118 [2017-03-23; online 2017-03-23]

Bioinformatics Support and Infrastructure [Collaborative]

A Preliminary Report: Radical Surgery and Stem Cell Transplantation for the Treatment of Patients With Pancreatic Cancer.

Omazic B, Ayoglu B, Löhr M, ..., Maeurer MJ, Ringden O

J. Immunother. - (-) - [2017-03-23; online 2017-03-23]

Autoimmunity Profiling [Collaborative] Plasma Profiling [Collaborative]

The evolutionary and phylogeographic history of woolly mammoths: a comprehensive mitogenomic analysis.

Chang D, Knapp M, Enk J, ..., Hofreiter M, Shapiro B

pmc

Sci Rep 7 (-) 44585 [2017-03-22; online 2017-03-22]

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

Atrophin controls developmental signaling pathways via interactions with Trithorax-like

Yeung K, Boija A, Karlsson E, ..., Mannervik M, McNeill H

Elife 6 (-) - [2017-03-22; online 2017-03-22]

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

Proteogenomics produces comprehensive and highly accurate protein-coding gene annotation in a complete genome assembly of Malassezia sympodialis.

Zhu Y, Engström PG, Tellgren-Roth C, ..., Scheynius A, Lehtiö J

pmc

Nucleic Acids Res. 45 (5) 2629-2643 [2017-03-17; online 2017-01-20]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Chemical Proteomics & Proteogenomics [Technology development] Clinical Proteomics Mass spectrometry [Technology development] NGI Uppsala (Uppsala Genome Center) [Collaborative]

PATZ1 down-regulates FADS1 by binding to rs174557 and is opposed by SP1/SREBP1c.

Pan G, Ameur A, Enroth S, ..., Gyllensten U, Wadelius C

pmc

Nucleic Acids Res. 45 (5) 2408-2422 [2017-03-17; online 2016-12-10]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Technology development] NGI Uppsala (Uppsala Genome Center) [Service]

Chromosome and Megaplasmid Sequences of Borrelia anserina (Sakharoff 1891), the Agent of Avian Spirochetosis and Type Species of the Genus

Elbir H, Sitlani P, Bergström S, Barbour AG

Genome Announc 5 (11) e00018-17 [2017-03-16; online 2017-03-16]

Altered expression of maize PLASTOCHRON1 enhances biomass and seed yield by extending cell division duration

Sun X, Cahill J, Van Hautegem T, ..., Inzé D, Nelissen H

Nat Commun 8 (-) 14752 [2017-03-16; online 2017-03-16]

Revertant mosaicism repairs skin lesions in a patient with keratitis-ichthyosis-deafness syndrome by second-site mutations in connexin 26

Gudmundsson S, Wilbe M, Ekvall S, ..., Törmä H, Bondeson ML

- 26 (6) 1070-1077 [2017-03-15; online 2017-02-01]

Bioinformatics Compute and Storage [Service] Clinical Genomics Uppsala [Collaborative] NGI Uppsala (Uppsala Genome Center) [Collaborative] PLA Proteomics [Service]

Microbial community assembly and evolution in subseafloor sediment

Starnawski P, Bataillon T, Ettema TJG, ..., Schramm A, Kjeldsen KU

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

Proc Natl Acad Sci USA 114 (11) 2940-2945 [2017-03-14; online 2017-02-27]

Identification of Triazolothiadiazoles as Potent Inhibitors of the dCTP Pyrophosphatase 1.

Llona-Minguez S, Höglund A, Wiita E, ..., Scobie M, Helleday T

J. Med. Chem. 60 (5) 2148-2154 [2017-03-09; online 2017-02-15]

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

Discovery of circulating proteins associated to knee radiographic osteoarthritis.

Lourido L, Ayoglu B, Fernández-Tajes J, ..., Nilsson P, Blanco FJ

pmc

Sci Rep 7 (1) 137 [2017-03-09; online 2017-03-09]

Plasma Profiling [Collaborative]

Diverse origin of mitochondrial lineages in Iron Age Black Sea Scythians.

Juras A, Krzewińska M, Nikitin AG, ..., Dabert M, Götherström A

pmc

Sci Rep 7 (-) 43950 [2017-03-07; online 2017-03-07]

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

Method to Visualize and Analyze Membrane Interacting Proteins by Transmission Electron Microscopy

B. Kumar R, Zhu L, Hebert H, Jegerschöld C

J Vis Exp - (121) - [2017-03-05; online 2017-03-05]

Antibody Validation by Immunoprecipitation Followed by Mass Spectrometry Analysis.

Persson H, Preger C, Marcon E, Lengqvist J, Gräslund S

Methods Mol. Biol. 1575 (-) 175-187 [2017-03-04; online 2017-03-04]

Drug Discovery and Development (DDD) [Service]

Whole-Proteome Peptide Microarrays for Profiling Autoantibody Repertoires within Multiple Sclerosis and Narcolepsy.

Zandian A, Forsström B, Häggmark-Månberg A, ..., Nilsson P, Ayoglu B

J. Proteome Res. 16 (3) 1300-1314 [2017-03-03; online 2017-02-09]

Autoimmunity Profiling [Technology development]

Mating Changes Sexually Dimorphic Gene Expression in the Seed Beetle Callosobruchus maculatus.

Immonen E, Sayadi A, Bayram H, Arnqvist G

Genome Biol Evol 9 (3) 677-699 [2017-03-01; online 2017-04-10]

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

Towards a whole-genome sequence for rye (Secale cereale L.).

Bauer E, Schmutzer T, Barilar I, ..., Schön CC, Scholz U

GENBANK GENBANK GENBANK

Plant J. 89 (5) 853-869 [2017-03-00; online 2016-11-27]

Bioinformatics Support and Infrastructure [Collaborative]

Damaged reward areas in human alcoholics: neuronal proportion decline and astrocyte activation.

Sarkisyan D, Bazov I, Watanabe H, ..., Yakovleva T, Bakalkin G

Acta Neuropathol. 133 (3) 485-487 [2017-03-00; online 2017-01-17]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

Antibody-encoding repertoires of bone marrow and peripheral blood-a focus on IgE.

Levin M, Levander F, Palmason R, Greiff L, Ohlin M

J. Allergy Clin. Immunol. 139 (3) 1026-1030 [2017-03-00; online 2016-08-09]

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

Reducing VEGF-B Signaling Ameliorates Renal Lipotoxicity and Protects against Diabetic Kidney Disease

Falkevall A, Mehlem A, Palombo I, ..., Nash A, Eriksson U

Cell Metabolism 25 (3) 713-726 [2017-03-00; online 2017-03-00]

DNA methylation profiling of pediatric B-cell lymphoblastic leukemia with KMT2A rearrangement identifies hypomethylation at enhancer sites.

Bergmann AK, Castellano G, Alten J, ..., Schrappe M, Siebert R

Pediatr Blood Cancer 64 (3) - [2017-03-00; online 2016-10-28]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Technology development]

Development of [(11)C]/[(3)H]THK-5351 - A potential novel carbon-11 tau imaging PET radioligand.

Stepanov V, Svedberg M, Jia Z, ..., Nordberg A, Halldin C

Nucl. Med. Biol. 46 (-) 50-53 [2017-03-00; online 2016-12-26]

A genetic risk score is significantly associated with statin therapy response in the elderly population.

Ciuculete DM, Bandstein M, Benedict C, ..., Schiöth HB, Mwinyi J

Clin. Genet. 91 (3) 379-385 [2017-03-00; online 2016-12-13]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

Inferring Individual Inbreeding and Demographic History from Segments of Identity by Descent in Ficedula Flycatcher Genome Sequences

Kardos M, Qvarnström A, Ellegren H

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

Genetics 205 (3) 1319-1334 [2017-03-00; online 2017-01-18]

Phylogenetic analysis of Monascus and new species from honey, pollen and nests of stingless bees

Barbosa RN, Leong SL, Vinnere-Pettersson O, ..., Oliveira NT, Houbraken J

Studies in Mycology 86 (-) 29-51 [2017-03-00; online 2017-03-00]

NGI Uppsala (Uppsala Genome Center) [Collaborative]

Tracing Cellular Origin of Human Exosomes Using Multiplex Proximity Extension Assays

Larssen P, Wik L, Czarnewski P, ..., Gabrielsson S, Kamali-Moghaddam M

Mol Cell Proteomics 16 (3) 502-511 [2017-03-00; online 2017-01-22]

Bioinformatics Support and Infrastructure [Collaborative] PLA Proteomics [Technology development]

Binding and processing of β-lactam antibiotics by the transpeptidase LdtMt2fromMycobacterium tuberculosis

Steiner EM, Schneider G, Schnell R

FEBS J 284 (5) 725-741 [2017-03-00; online 2017-02-08]

Metapopulation theory identifies biogeographical patterns among core and satellite marine bacteria scaling from tens to thousands of kilometers.

Lindh MV, Sjöstedt J, Ekstam B, ..., Legrand C, Pinhassi J

Environ. Microbiol. 19 (3) 1222-1236 [2017-03-00; online 2017-02-06]

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

High GC content causes orphan proteins to be intrinsically disordered.

Basile W, Sachenkova O, Light S, Elofsson A

pmc

PLoS Comput. Biol. 13 (3) e1005375 [2017-03-00; online 2017-03-29]

Bioinformatics Support and Infrastructure [Collaborative]

Discovery of new biomarkers for atrial fibrillation using a custom-made proteomics chip.

Lind L, Sundström J, Stenemo M, Hagström E, Ärnlöv J

Heart 103 (5) 377-382 [2017-03-00; online 2016-09-10]

Genomic Variation in IbA10G2 and Other Patient-Derived Cryptosporidium hominis Subtypes

Sikora P, Andersson S, Winiecka-Krusnell J, ..., Beser J, Arrighi RBG

J. Clin. Microbiol. 55 (3) 844-858 [2017-03-00; online 2016-12-21]

Clinical Genomics Gothenburg [Collaborative]

Use of a proximity extension assay proteomics chip to discover new biomarkers associated with albuminuria.

Carlsson AC, Sundström J, Carrero JJ, ..., Lind L, Ärnlöv J

Eur J Prev Cardiol 24 (4) 340-348 [2017-03-00; online 2016-10-28]

Stool frequency is associated with gut microbiota composition.

Hadizadeh F, Walter S, Belheouane M, ..., Franke A, D'Amato M

Gut 66 (3) 559-560 [2017-03-00; online 2016-05-20]

Clinical Genomics Stockholm [Collaborative]

Assessing the Ability of Spectroscopic Methods to Determine the Difference in the Folding Propensities of Highly Similar β-Hairpins

Andersson H, Danelius E, Jarvoll P, ..., Brath U, Erdélyi M

ACS Omega 2 (2) 508-516 [2017-02-28; online 2017-02-13]

Measuring true localization accuracy in super resolution microscopy with DNA-origami nanostructures

Reuss M, Fördős F, Blom H, ..., Högberg B, Brismar H

New J. Phys. 19 (2) 025013 [2017-02-27; online 2017-02-27]

Advanced Light Microscopy (ALM) [Technology development]

Characterization of the Ruler Protein Interaction Interface on the Substrate Specificity Switch Protein in theYersiniaType III Secretion System

Ho O, Rogne P, Edgren T, ..., Login FH, Wolf-Watz M

J. Biol. Chem. 292 (8) 3299-3311 [2017-02-24; online 2016-12-30]

Protein Science Facility (PSF) [Service] Swedish NMR Centre (SNC) [Service]

Epitopes of anti-RIFIN antibodies and characterization of rif-expressing Plasmodium falciparum parasites by RNA sequencing.

Ch'ng JH, Sirel M, Zandian A, ..., Qundos U, Wahlgren M

pmc

Sci Rep 7 (-) 43190 [2017-02-24; online 2017-02-24]

Autoimmunity Profiling [Service]

Flavonoids fromErythrina schliebenii

Nyandoro SS, Munissi JJE, Kombo M, ..., Rissanen K, Erdélyi M

J. Nat. Prod. 80 (2) 377-383 [2017-02-24; online 2017-01-23]

Evaluating Variant Calling Tools for Non-Matched Next-Generation Sequencing Data.

Sandmann S, de Graaf AO, Karimi M, ..., Jansen JH, Dugas M

pmc

Sci Rep 7 (-) 43169 [2017-02-24; online 2017-02-24]

Clinical Genomics Uppsala [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]

Structural Basis for Potency and Promiscuity in Poly(ADP-ribose) Polymerase (PARP) and Tankyrase Inhibitors

Thorsell AG, Ekblad T, Karlberg T, ..., Cohen MS, Schüler H

J. Med. Chem. 60 (4) 1262-1271 [2017-02-23; online 2016-12-21]

Defining the human copper proteome and analysis of its expression variation in cancers.

Blockhuys S, Celauro E, Hildesjö C, ..., Fierro-González JC, Wittung-Stafshede P

Metallomics 9 (2) 112-123 [2017-02-22; online 2016-12-13]

Bioinformatics Support and Infrastructure [Service]

Clonal reversal of ageing-associated stem cell lineage bias via a pluripotent intermediate.

Wahlestedt M, Erlandsson E, Kristiansen T, ..., Martin-Gonzalez J, Bryder D

pmc

Nat Commun 8 (-) 14533 [2017-02-22; online 2017-02-22]

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

Intracellular drug bioavailability: a new predictor of system dependent drug disposition.

Mateus A, Treyer A, Wegler C, ..., Matsson P, Artursson P

pmc

Sci Rep 7 (-) 43047 [2017-02-22; online 2017-02-22]

Drug Discovery and Development (DDD) [Service]

Covariation in levels of nucleotide diversity in homologous regions of the avian genome long after completion of lineage sorting

Dutoit L, Vijay N, Mugal CF, ..., Wolf J, Ellegren H

Proc. R. Soc. B 284 (1849) 20162756 [2017-02-22; online 2017-02-15]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

RhoA knockout fibroblasts lose tumor-inhibitory capacity in vitro and promote tumor growth in vivo.

Alkasalias T, Alexeyenko A, Hennig K, ..., Gad AK, Pavlova T

pmc

Proc. Natl. Acad. Sci. U.S.A. 114 (8) E1413-E1421 [2017-02-21; online 2017-02-07]

Bioinformatics Support and Infrastructure [Collaborative] Cell Profiling [Collaborative]

Three Chalconoids and a Pterocarpene from the Roots of Tephrosia aequilata

Atilaw Y, Duffy S, Heydenreich M, ..., Erdélyi M, Yenesew A

Molecules 22 (2) 318 [2017-02-20; online 2017-02-20]

Methane Production in Dairy Cows Correlates with Rumen Methanogenic and Bacterial Community Structure.

Danielsson R, Dicksved J, Sun L, ..., Schnürer A, Bertilsson J

pmc

Front Microbiol 8 (-) 226 [2017-02-17; online 2017-02-17]

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

Comparison of whole genome amplification techniques for human single cell exome sequencing.

Borgström E, Paterlini M, Mold JE, Frisen J, Lundeberg J

pmc

PLoS ONE 12 (2) e0171566 [2017-02-16; online 2017-02-16]

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

The mitochondrial genome sequences of the round goby and the sand goby reveal patterns of recent evolution in gobiid fish.

Adrian-Kalchhauser I, Svensson O, Kutschera VE, ..., Blomberg A, Burkhardt-Holm P

pmc

BMC Genomics 18 (1) 177 [2017-02-16; online 2017-02-16]

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

Driver GW, Huang Y, Laaksonen A, ..., Wang Y, Westlund P

Phys Chem Chem Phys 19 (7) 4975-4988 [2017-02-15; online 2017-01-12]

Genome-wide Association for Major Depression Through Age at Onset Stratification: Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium.

Power RA, Tansey KE, Buttenschøn HN, ..., Breen G, Lewis CM

pmc

Biol. Psychiatry 81 (4) 325-335 [2017-02-15; online 2016-08-16]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

Distinct Anaerobic Bacterial Consumers of Cellobiose-Derived Carbon in Boreal Fens with Different CO2/CH4 Production Ratios

Juottonen H, Eiler A, Biasi C, ..., Yrjälä K, Fritze H

SRA

Appl. Environ. Microbiol. 83 (4) e02533-16 [2017-02-15; online 2016-12-02]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

Crystal Structure of the Emerging Cancer Target MTHFD2 in Complex with a Substrate-Based Inhibitor.

Gustafsson R, Jemth A, Gustafsson NMS, ..., Helleday T, Stenmark P

Cancer Res. 77 (4) 937-948 [2017-02-15; online 2016-12-03]

Drug Discovery and Development (DDD) [Collaborative]

The Baltic Sea Virome: Diversity and Transcriptional Activity of DNA and RNA Viruses.

Zeigler Allen L, McCrow JP, Ininbergs K, ..., Bergman B, Venter JC

pmc

mSystems 2 (1) - [2017-02-14; online 2017-02-14]

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

A novel RNA sequencing data analysis method for cell line authentication.

Fasterius E, Raso C, Kennedy S, ..., Uhlén M, Al-Khalili Szigyarto C

pmc

PLoS ONE 12 (2) e0171435 [2017-02-13; online 2017-02-13]

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

Detection of Somatic Mutations in Gastroenteropancreatic Neuroendocrine Tumors Using Targeted Deep Sequencing

BACKMAN S, NORLÉN O, ERIKSSON B, ..., STÅLBERG P, CRONA J

AR 37 (2) 705-712 [2017-02-10; online 2017-02-10]

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

microRNAs with AAGUGC seed motif constitute an integral part of an oncogenic signaling network.

Zhou Y, Frings O, Branca RM, ..., Agami R, Orre LM

pmc

Oncogene 36 (6) 731-745 [2017-02-09; online 2016-08-01]

Bioinformatics Support and Infrastructure [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]

Rare and low-frequency coding variants alter human adult height.

Marouli E, Graff M, Medina-Gomez C, ..., Deloukas P, Lettre G

pmc mid

Nature 542 (7640) 186-190 [2017-02-09; online 2017-02-01]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

Photochemically Induced Aryl Azide Rearrangement: Solution NMR Spectroscopic Identification of the Rearrangement Product

Andersson H, Gräfenstein J, Isobe M, Erdélyi M, Sydnes MO

J. Org. Chem. 82 (3) 1812-1816 [2017-02-03; online 2017-01-23]

Seasonal Variation in Abundance and Diversity of Bacterial Methanotrophs in Five Temperate Lakes

Samad MS, Bertilsson S

Front Microbiol 8 (-) - [2017-02-03; online 2017-02-03]

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

A Synthesis of “Dual Warhead” β-Aryl Ethenesulfonyl Fluorides and One-Pot Reaction to β-Sultams

Chinthakindi PK, Govender KB, Kumar AS, ..., Naicker T, Arvidsson PI

Org. Lett. 19 (3) 480-483 [2017-02-03; online 2017-01-11]

Drug Discovery and Development (DDD) [Technology development]

The Arabidopsis bZIP11 transcription factor links low-energy signalling to auxin-mediated control of primary root growth

Weiste C, Pedrotti L, Selvanayagam J, ..., Hanson J, Dröge-Laser W

PLoS Genet. 13 (2) e1006607 [2017-02-03; online 2017-02-03]

Posttranscriptional Regulation in Adenovirus Infected Cells

Zhao H, Konzer A, Mi J, ..., Pettersson U, Lind SB

J. Proteome Res. 16 (2) 872-888 [2017-02-03; online 2016-12-13]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

Massive parallel sequencing questions the pathogenic role of missense variants in dilated cardiomyopathy.

Dalin MG, Engström PG, Ivarsson EG, ..., Andersson B, Bergo MO

Int. J. Cardiol. 228 (-) 742-748 [2017-02-01; online 2016-11-26]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]

Metabolic and functional characterization of effects of developmental temperature in Drosophila melanogaster.

Schou MF, Kristensen TN, Pedersen A, ..., Loeschcke V, Malmendal A

pmc

Am. J. Physiol. Regul. Integr. Comp. Physiol. 312 (2) R211-R222 [2017-02-01; online 2016-12-09]

Causal Effect of Genetic Variants Associated With Body Mass Index on Multiple Sclerosis Susceptibility.

Gianfrancesco MA, Glymour MM, Walter S, ..., Alfredsson L, Barcellos LF

pmc

Am. J. Epidemiol. 185 (3) 162-171 [2017-02-01; online 2017-01-12]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

The Human Adrenal Gland Proteome Defined by Transcriptomics and Antibody-Based Profiling.

Bergman J, Botling J, Fagerberg L, ..., Uhlén M, Pontén F

Endocrinology 158 (2) 239-251 [2017-02-01; online 2016-12-03]

Bioinformatics Compute and Storage [Service] Clinical Genomics Uppsala [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] Tissue Profiling [Technology development]

Evidence for three genetic loci involved in both anorexia nervosa risk and variation of body mass index.

Hinney A, Kesselmeier M, Jall S, ..., Müller TD, Hebebrand J

pmc mid

Mol. Psychiatry 22 (2) 192-201 [2017-02-00; online 2016-05-18]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

Distinct global binding patterns of the Wilms tumor gene 1 (WT1) -KTS and +KTS isoforms in leukemic cells.

Ullmark T, Järvstråt L, Sandén C, ..., Nilsson B, Gullberg U

pmc

Haematologica 102 (2) 336-345 [2017-02-00; online 2016-09-11]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

A meta-analysis of reflux genome-wide association studies in 6750 Northern Europeans from the general population.

Bonfiglio F, Hysi PG, Ek W, ..., Schmidt PT, D'Amato M

Neurogastroenterol. Motil. 29 (2) - [2017-02-00; online 2016-08-04]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

Effects of microbe- and mussel-based diets on the gut microbiota in Arctic charr ( Salvelinus alpinus )

Nyman A, Huyben D, Lundh T, Dicksved J

Aquaculture Reports 5 (-) 34-40 [2017-02-00; online 2017-02-00]

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

Novel seminal fluid proteins in the seed beetleCallosobruchus maculatusidentified by a proteomic and transcriptomic approach

Bayram H, Sayadi A, Goenaga J, Immonen E, Arnqvist G

Insect Mol Biol 26 (1) 58-73 [2017-02-00; online 2016-10-24]

Bioinformatics Compute and Storage [Service] Mass Spectrometry-based Proteomics, Uppsala [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

Molecular interrogation of hypothalamic organization reveals distinct dopamine neuronal subtypes.

Romanov RA, Zeisel A, Bakker J, ..., Horvath TL, Harkany T

Nat. Neurosci. 20 (2) 176-188 [2017-02-00; online 2016-12-20]

Whole-Genome Sequencing of Cytogenetically Balanced Chromosome Translocations Identifies Potentially Pathological Gene Disruptions and Highlights the Importance of Microhomology in the Mechanism of Formation.

Nilsson D, Pettersson M, Gustavsson P, ..., Carvalho CMB, Lindstrand A

pmc mid

Hum. Mutat. 38 (2) 180-192 [2017-02-00; online 2016-12-05]

Bioinformatics Compute and Storage [Service] Clinical Genomics Stockholm [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]

Associations of defect mismatch repair genes with prognosis and heredity in sporadic colorectal cancer.

Ghanipour L, Jirström K, Sundström M, Glimelius B, Birgisson H

Eur J Surg Oncol 43 (2) 311-321 [2017-02-00; online 2016-11-12]

Tissue Profiling [Service]

Evolution of bird genomes-a transposon's-eye view.

Kapusta A, Suh A

Ann. N. Y. Acad. Sci. 1389 (1) 164-185 [2017-02-00; online 2016-12-20]

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

Genetic and Targeted eQTL Mapping Reveals Strong Candidate Genes Modulating the Stress Response During Chicken Domestication

Fallahsharoudi A, de Kock N, Johnsson M, ..., Wright D, Jensen P

G3 (Bethesda) 7 (2) 497-504 [2017-02-00; online 2016-12-14]

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

Defense Responses in Aspen with Altered Pectin Methylesterase Activity Reveal the Hormonal Inducers of Tyloses

Leśniewska J, Öhman D, Krzesłowska M, ..., Moritz T, Mellerowicz EJ

Plant Physiol. 173 (2) 1409-1419 [2017-02-00; online 2016-12-06]

Identification of new TRIP12 variants and detailed clinical evaluation of individuals with non-syndromic intellectual disability with or without autism.

Bramswig NC, Lüdecke HJ, Pettersson M, ..., Kleefstra T, Wieczorek D

Hum. Genet. 136 (2) 179-192 [2017-02-00; online 2016-11-15]

Bioinformatics Compute and Storage [Service] Clinical Genomics Stockholm [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service]

Activation of myeloid and endothelial cells by CD40L gene therapy supports T-cell expansion and migration into the tumor microenvironment

Eriksson E, Moreno R, Milenova I, ..., Alemany R, Loskog A

Gene Ther 24 (2) 92-103 [2017-02-00; online 2016-12-01]

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

The in silico identification and characterization of a bread wheat/Triticum militinae introgression line.

Abrouk M, Balcárková B, Šimková H, ..., Doležel J, Valárik M

pmc

Plant Biotechnol. J. 15 (2) 249-256 [2017-02-00; online 2016-08-12]

Bioinformatics Support and Infrastructure [Collaborative]

PCSK9 genetic variants and risk of type 2 diabetes: a mendelian randomisation study.

Schmidt AF, Swerdlow DI, Holmes MV, ..., UCLEB consortium , Sattar N

pmc

Lancet Diabetes Endocrinol 5 (2) 97-105 [2017-02-00; online 2016-12-03]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

Meta-omic analyses of Baltic Sea cyanobacteria: diversity, community structure and salt acclimation.

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

Environ. Microbiol. 19 (2) 673-686 [2017-02-00; online 2017-01-27]

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

Opioid precursor protein isoform is targeted to the cell nuclei in the human brain.

Kononenko O, Bazov I, Watanabe H, ..., Yakovleva T, Bakalkin G

pmc mid

Biochim. Biophys. Acta 1861 (2) 246-255 [2017-02-00; online 2016-11-14]

Towards encoded particles for highly multiplexed colorimetric point of care autoantibody detection.

Svedberg G, Jeong Y, Na H, ..., Gantelius J, Svahn HA

Lab Chip 17 (3) 549-556 [2017-01-31; online 2017-01-20]

Autoimmunity Profiling [Service]

Genomic analysis reveals major determinants ofcis-regulatory variation inCapsella grandiflora

Steige KA, Laenen B, Reimegård J, Scofield DG, Slotte T

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

Proc Natl Acad Sci USA 114 (5) 1087-1092 [2017-01-31; online 2017-01-17]

Model communities hint to promiscuous metabolic linkages between ubiquitous free-living freshwater bacteria

Garcia SL, Buck M, Hamilton JJ, ..., Warnecke F, Eiler A

- - (-) - [2017-01-28; online 2017-01-28]

Bioinformatics Support and Infrastructure [Collaborative]

Polyoxygenated Cyclohexenes and Other Constituents of Cleistochlamys kirkii Leaves

Nyandoro SS, Munissi JJE, Gruhonjic A, ..., Rissanen K, Erdélyi M

J. Nat. Prod. 80 (1) 114-125 [2017-01-27; online 2016-12-21]

Draft Genome Sequences of Semiconstitutive Red, Dry, and Rough Biofilm-Forming Commensal and Uropathogenic Escherichia coli Isolates.

Cimdins A, Lüthje P, Li F, ..., Brauner A, Römling U

pmc

Genome Announc 5 (4) - [2017-01-26; online 2017-01-26]

Bioinformatics Support and Infrastructure [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service]

About structural changes of lignin during kraft cooking and the kinetics of delignification

Mattsson C, Hasani M, Dang B, Mayzel M, Theliander H

- 71 (7-8) - [2017-01-26; online 2017-01-01]

Early onset of inflammation during ontogeny of bipolar disorder: the NLRP2 inflammasome gene distinctly differentiates between patients and healthy controls in the transition between iPS cell and neural stem cell stages

Vizlin-Hodzic D, Zhai Q, Illes S, ..., Ågren H, Funa K

Transl Psychiatry 7 (1) e1010 [2017-01-24; online 2017-01-24]

Bioinformatics Support and Infrastructure [Collaborative]

Analysis of the distribution of CD103 on CD8 T cells in blood and genital mucosa of HIV-infected female sex workers

Gibbs A, Buggert M, Ranefall P, ..., Broliden K, Tjernlund A

AIDS Research and Human Retroviruses 32 (S1) 307 [2017-01-24]

Vimentin Levels and Serine 71 Phosphorylation in the Control of Cell-Matrix Adhesions, Migration Speed, and Shape of Transformed Human Fibroblasts

Terriac E, Coceano G, Mavajian Z, ..., Lautenschläger F, Gad A

Cells 6 (1) 2 [2017-01-22; online 2017-01-22]

Advanced Light Microscopy (ALM) [Service]

Meta-Analysis of Genome-Wide Association Studies for Abdominal Aortic Aneurysm Identifies Four New Disease-Specific Risk Loci.

Jones GT, Tromp G, Kuivaniemi H, ..., Samani NJ, Bown MJ

pmc mid

Circ. Res. 120 (2) 341-353 [2017-01-20; online 2016-12-03]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

Novel genetic loci associated with hippocampal volume.

Hibar DP, Adams HH, Jahanshad N, ..., Thompson PM, Ikram MA

pmc

Nat Commun 8 (-) 13624 [2017-01-18; online 2017-01-18]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

Perivascular PDGFR-β is an independent marker for prognosis in renal cell carcinoma.

Frödin M, Mezheyeuski A, Corvigno S, ..., Johansson M, Östman A

pmc

Br. J. Cancer 116 (2) 195-201 [2017-01-17; online 2016-12-09]

Tissue Profiling [Service]

A methylome-wide mQTL analysis reveals associations of methylation sites with GAD1 and HDAC3 SNPs and a general psychiatric risk score.

Ciuculete DM, Boström AE, Voisin S, ..., Mwinyi J, Schiöth HB

pmc

Transl Psychiatry 7 (1) e1002 [2017-01-17; online 2017-01-17]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

NLK-mediated phosphorylation of HDAC1 negatively regulates Wnt signaling.

Masoumi KC, Daams R, Sime W, ..., Levander F, Massoumi R

pmc

Mol. Biol. Cell 28 (2) 346-355 [2017-01-15; online 2016-11-30]

Bioinformatics Support and Infrastructure [Collaborative]

Identification of endoribonuclease specific cleavage positions reveals novel targets of RNase III inStreptococcus pyogenes

Le Rhun A, Lécrivain AL, Reimegård J, ..., Della Beffa C, Charpentier E

Nucleic Acids Res - (-) gkw1316 [2017-01-12; online 2017-01-12]

Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support and Infrastructure [Service]

Asgard archaea illuminate the origin of eukaryotic cellular complexity

Zaremba-Niedzwiedzka K, Caceres EF, Saw JH, ..., Spang A, Ettema TJG

BioProject GENBANK GENBANK BioProject GENBANK BioProject GENBANK GENBANK GENBANK GENBANK GENBANK

Nature 541 (7637) 353-358 [2017-01-11; online 2017-01-11]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

Targeting SAMHD1 with the Vpx protein to improve cytarabine therapy for hematological malignancies

Herold N, Rudd SG, Ljungblad L, ..., Helleday T, Schaller T

Nat Med 23 (2) 256-263 [2017-01-09; online 2017-01-09]

Chemical Biology Consortium Sweden (CBCS) [Collaborative] Protein Science Facility (PSF) [Service]

Identification of a Novel Autoimmune Peptide Epitope of Prostein in Prostate Cancer.

Pin E, Henjes F, Hong MG, ..., Nilsson P, Schwenk JM

J. Proteome Res. 16 (1) 204-216 [2017-01-06; online 2016-10-05]

Autoimmunity Profiling [Collaborative]

Antibody Validation in Bioimaging Applications Based on Endogenous Expression of Tagged Proteins.

Skogs M, Stadler C, Schutten R, ..., Uhlén M, Lundberg E

J. Proteome Res. 16 (1) 147-155 [2017-01-06; online 2016-10-12]

Cell Profiling [Technology development]

Single-Cell Analysis Reveals a Close Relationship between Differentiating Dopamine and Subthalamic Nucleus Neuronal Lineages.

Kee N, Volakakis N, Kirkeby A, ..., Parmar M, Perlmann T

Cell Stem Cell 20 (1) 29-40 [2017-01-05; online 2016-10-27]

Bioinformatics Long-term Support WABI [Collaborative]

Mapping eQTLs with RNA-seq reveals novel susceptibility genes, non-coding RNAs and alternative-splicing events in systemic lupus erythematosus

Odhams CA, Cortini A, Chen L, ..., Vyse TJ, Cunninghame Graham DS

Hum. Mol. Genet. - (-) ddw417 [2017-01-05; online 2017-01-05]

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

Imputation-Based Fine-Mapping Suggests That Most QTL in an Outbred Chicken Advanced Intercross Body Weight Line Are Due to Multiple, Linked Loci.

Brandt M, Ahsan M, Honaker CF, Siegel PB, Carlborg Ö

pmc

G3 (Bethesda) 7 (1) 119-128 [2017-01-05; online 2017-01-05]

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

A systematic search strategy identifies cubilin as independent prognostic marker for renal cell carcinoma.

Gremel G, Djureinovic D, Niinivirta M, ..., Stewart GD, Pontén F

pmc

BMC Cancer 17 (1) 9 [2017-01-04; online 2017-01-04]

Tissue Profiling [Technology development]

Genome-wide association study with additional genetic and post-transcriptional analyses reveals novel regulators of plasma factor XI levels

Sennblad B, Basu S, Mazur J, ..., Trégouët DA, Sabater-Lleal M

Hum. Mol. Genet. - (-) ddw401 [2017-01-04; online 2017-01-04]

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

Mitochondrial genome of the North African Sahara Honeybee, Apis mellifera sahariensis (Hymenoptera: Apidae)

Haddad N, Adjlane N, Loucif-Ayad W, ..., Al-Nakeeb K, Sicheritz-Ponten T

Mitochondrial DNA Part B 2 (2) 548-549 [2017-01-02; online 2017-08-22]

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

Epigenetic changes as prognostic predictors in endometrial carcinomas.

Farkas SA, Sorbe BG, Nilsson TK

pmc

Epigenetics 12 (1) 19-26 [2017-01-02; online 2016-11-23]

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

Small Molecule Microarray Based Discovery of PARP14 Inhibitors

Peng B, Thorsell AG, Karlberg T, Schüler H, Yao SQ

Angew. Chem. Int. Ed. 56 (1) 248-253 [2017-01-02; online 2016-12-05]

Comprehensive RNA sequencing of healthy human endometrium at two time points of the menstrual cycle.

Sigurgeirsson B, Åmark H, Jemt A, ..., Lundeberg J, Gidlöf S

GEO

Biol. Reprod. 96 (1) 24-33 [2017-01-01; online 2017-04-11]

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

Expression of Transient Receptor Potential Channels in the Purified Human Pancreatic β-Cells.

Marabita F, Islam MS

Pancreas 46 (1) 97-101 [2017-01-00; online 2016-07-29]

Bioinformatics Support and Infrastructure [Collaborative]

Emerging microbiota during cold storage and temperature abuse of ready-to-eat salad

Söderqvist K, Ahmed Osman O, Wolff C, ..., Vågsholm I, Boqvist S

Infect Ecol Epidemiol 7 (1) 1328963 [2017-01-00; online 2017-06-06]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

A combined large-scale meta-analysis identifies COG6 as a novel shared risk locus for rheumatoid arthritis and systemic lupus erythematosus.

Márquez A, Vidal-Bralo L, Rodríguez-Rodríguez L, ..., Alarcón-Riquelme ME, Martín J

Ann. Rheum. Dis. 76 (1) 286-294 [2017-01-00; online 2016-05-20]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

Expression of possible targets for new proteasome inhibitors in diffuse large B-cell lymphoma.

Delforoush M, Berglund M, Edqvist PH, ..., Gullbo J, Enblad G

Eur. J. Haematol. 98 (1) 52-56 [2017-01-00; online 2016-07-12]

Deep Fish: Deep Learning–Based Classification of Zebrafish Deformation for High-Throughput Screening

Ishaq O, Sadanandan SK, Wählby C

SLAS DISCOVERY: Advancing Life Sciences R&D 22 (1) 102-107 [2017-01-00; online 2016-09-26]

BioImage Informatics [Technology development]

Evolutionary engineering reveals divergent paths when yeast is adapted to different acidic environments.

Fletcher E, Feizi A, Bisschops MM, ..., Siewers V, Nielsen J

Metab. Eng. 39 (-) 19-28 [2017-01-00; online 2016-11-02]

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

Evolutionary engineering reveals divergent paths when yeast is adapted to different acidic environments

Fletcher E, Feizi A, Bisschops MMM, ..., Siewers V, Nielsen J

Metabolic Engineering 39 (-) 19-28 [2017-01-00; online 2017-01-00]

cis-Cinnamic Acid Is a Novel, Natural Auxin Efflux Inhibitor That Promotes Lateral Root Formation

Steenackers W, Klíma P, Quareshy M, ..., Boerjan W, Vanholme B

Plant Physiol. 173 (1) 552-565 [2017-01-00; online 2016-11-11]

Both maternal and offspring Elovl2 genotypes determine systemic DHA levels in perinatal mice.

Pauter AM, Trattner S, Gonzalez-Bengtsson A, ..., Dethlefsen O, Jacobsson A

pmc

J. Lipid Res. 58 (1) 111-123 [2017-01-00; online 2016-11-20]

Bioinformatics Support and Infrastructure [Collaborative]

Association of Body Mass Index with DNA Methylation and Gene Expression in Blood Cells and Relations to Cardiometabolic Disease: A Mendelian Randomization Approach.

Mendelson MM, Marioni RE, Joehanes R, ..., Levy D, Deary IJ

pmc

PLoS Med. 14 (1) e1002215 [2017-01-00; online 2017-01-17]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

A multi-step peptidolytic cascade for amino acid recovery in chloroplasts

Teixeira PF, Kmiec B, Branca RMM, ..., Lehtiö J, Glaser E

Nat Chem Biol 13 (1) 15-17 [2017-01-00; online 2016-10-31]

Chemical Proteomics & Proteogenomics [Collaborative] Clinical Proteomics Mass spectrometry [Collaborative] Swedish Metabolomics Centre (SMC) [Service]

Multiethnic genome-wide meta-analysis of ectopic fat depots identifies loci associated with adipocyte development and differentiation.

Chu AY, Deng X, Fisher VA, ..., Steinhauser ML, Fox CS

Nat. Genet. 49 (1) 125-130 [2017-01-00; online 2016-12-06]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

Epigenetic Patterns in Blood Associated With Lipid Traits Predict Incident Coronary Heart Disease Events and Are Enriched for Results From Genome-Wide Association Studies.

Hedman ÅK, Mendelson MM, Marioni RE, ..., Levy D, Ingelsson E

pmc mid

Circ Cardiovasc Genet 10 (1) - [2017-01-00; online 2017-02-19]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

SHADE AVOIDANCE 4 Is Required for Proper Auxin Distribution in the Hypocotyl

Ge Y, Yan F, Zourelidou M, ..., Schwechheimer C, Tao Y

Plant Physiol. 173 (1) 788-800 [2017-01-00; online 2016-11-21]

Genetic and methylation variation in the CYP2B6 gene is related to circulating p,p'-dde levels in a population-based sample.

Lind L, Ng E, Ingelsson E, ..., Morris AP, Lind PM

pmc

Environ Int 98 (-) 212-218 [2017-01-00; online 2016-11-15]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

Rye B chromosomes encode a functional Argonaute-like protein with in vitro slicer activities similar to its A chromosome paralog.

Ma W, Gabriel TS, Martis MM, ..., Banaei-Moghaddam AM, Houben A

New Phytol. 213 (2) 916-928 [2017-01-00; online 2016-07-29]

Bioinformatics Support and Infrastructure [Collaborative]

P1.02-063 Mutation Profiling by Targeted Next-Generation Sequencing of an Unselected NSCLC Cohort

La Fleur L, Falk-Sorqvist E, Smeds P, ..., Moens L, Botling J

Journal of Thoracic Oncology 12 (1) S526-S527 [2017-01-00; online 2017-01-00]

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

Investigating kinship of Neolithic post-LBK human remains from Krusza Zamkowa, Poland using ancient DNA.

Juras A, Chyleński M, Krenz-Niedbała M, ..., Jakobsson M, Dabert M

GENBANK GENBANK GENBANK GENBANK

Forensic Sci Int Genet 26 (-) 30-39 [2017-01-00; online 2016-10-25]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

Identification of two distinct mesenchymal stromal cell populations in human malignant glioma.

Svensson A, Ramos-Moreno T, Eberstål S, Scheding S, Bengzon J

pmc

J. Neurooncol. 131 (2) 245-254 [2017-01-00; online 2016-10-18]

Clinical Genomics Lund [Service]

Mitochondrial genome divergence between beluga whales in Baffin Bay and the Sea of Okhotsk

Skovrind M, Samaniego Castruita JA, Heide-Jørgensen MP, Dalén L, Lorenzen E

Mitochondrial DNA Part B 2 (1) 257-258 [2017-01-00; online 2017-04-28]

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

Meta-GWAS Accuracy and Power (MetaGAP) Calculator Shows that Hiding Heritability Is Partially Due to Imperfect Genetic Correlations across Studies.

de Vlaming R, Okbay A, Rietveld CA, ..., Thurik AR, Koellinger PD

pmc

PLoS Genet. 13 (1) e1006495 [2017-01-00; online 2017-01-17]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

Elevated levels of circulating CDH5 and FABP1 in association with human drug-induced liver injury.

Mikus M, Drobin K, Gry M, ..., Nilsson P, Schuppe-Koistinen I

pmc

Liver Int. 37 (1) 132-140 [2017-01-00; online 2016-05-26]

Plasma Profiling [Collaborative]

Contribution of different dispersal sources to the metabolic response of lake bacterioplankton following a salinity change.

Comte J, Langenheder S, Berga M, Lindström ES

SRA

Environ. Microbiol. 19 (1) 251-260 [2017-01-00; online 2016-11-22]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

Complete mitochondrial genome of the Oriental Hornet, Vespa orientalis F. (Hymenoptera: Vespidae)

Haddad NJ, Al-Nakeeb K, Petersen B, ..., Blom N, Sicheritz-Pontén T

Mitochondrial DNA Part B 2 (1) 139-140 [2017-01-00; online 2017-03-00]

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

VAV1 regulates experimental autoimmune arthritis and is associated with anti-CCP negative rheumatoid arthritis

Guerreiro-Cacais AO, None , Norin U, ..., Kockum I, Padyukov L

Genes Immun 18 (1) 48-56 [2017-01-00; online 2017-01-05]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

Lysozyme's lectin-like characteristics facilitates its immune defense function

Zhang R, Wu L, Eckert T, ..., Nifantiev NE, Siebert HC

Quart. Rev. Biophys. 50 (-) - [2017-00-00; online 2017-05-30]

Structure–metabolism-relationships in the microsomal clearance of piperazin-1-ylpyridazines

Llona-Minguez S, Ghassemian A, Baranczewski P, ..., Scobie M, Helleday T

Med. Chem. Commun. 8 (7) 1553-1560 [2017-00-00; online 2017-00-00]

Drug Discovery and Development (DDD) [Collaborative]

A Fast Low Rank Hankel Matrix Factorization Reconstruction Method for Non-Uniformly Sampled Magnetic Resonance Spectroscopy

Guo D, Lu H, Qu X

IEEE Access 5 (-) 16033-16039 [2017-00-00; online 2017-00-00]

Synthesis of phenanthridine spiropyrans and studies of their effects on G-quadruplex DNA

Livendahl M, Jamroskovic J, Hedenström M, ..., Sabouri N, Chorell E

Org. Biomol. Chem. 15 (15) 3265-3275 [2017-00-00; online 2017-00-00]

124 CHANGES IN GENE EXPRESSION FOLLOWING EXPOSURE OF BOVINE ENDOMETRIAL EPITHELIAL CELLS (bEEC) TO ESCHERICHIA COLI LPS; THEIR POSSIBLE EFFECT ON IMPLANTATION

Guo Y, Jahmat N, Van Shaik T, ..., Andersson G, Humblot P

Reprod. Fertil. Dev. 29 (1) 170 [2017-00-00; online 2017-00-00]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

High-affinity recognition of the human C-reactive protein independent of phosphocholine

Yang J, Gustavsson AL, Haraldsson M, ..., Norberg T, Baltzer L

Org. Biomol. Chem. 15 (21) 4644-4654 [2017-00-00; online 2017-00-00]

Chemical Biology Consortium Sweden (CBCS) [Collaborative] Swedish NMR Centre (SNC) [Service]

The 15N NMR chemical shift in the characterization of weak halogen bonding in solution

Hakkert SB, Gräfenstein J, Erdelyi M

Faraday Discuss. 203 (-) 333-346 [2017-00-00; online 2017-00-00]

Decoding Gene Expression in 2D and 3D

Bombrun M, Ranefall P, Lindblad J, ..., Nilsson M, Wählby C

Scandinavian Conference on Image Analysis 2017 - (-) 257-268 [2017-00-00; online 2017-05-19]

Differential Neuroprotective Effects of Interleukin-1 Receptor Antagonist on Spinal Cord Neurons after Excitotoxic Injury

Schizas N, Perry S, Andersson B, ..., Kullander K, Hailer NP

Neuroimmunomodulation 24 (4-5) 220-230 [2017-00-00; online 2018-01-26]

BioImage Informatics [Service]

Achieving enhanced ionic mobility in nanoporous silica by controlled surface interactions

Garaga MN, Aguilera L, Yaghini N, ..., Persson M, Martinelli A

Phys. Chem. Chem. Phys. 19 (8) 5727-5736 [2017-00-00; online 2017-00-00]

Synthesis and characterization of poly-3-((2,5-hydroquinone)vinyl)-1H-pyrrole: investigation on backbone/pendant interactions in a conducting redox polymer

Huang H, Karlsson C, Strømme M, Gogoll A, Sjödin M

Phys. Chem. Chem. Phys. 19 (16) 10427-10435 [2017-00-00; online 2017-00-00]

Low Rank Enhanced Matrix Recovery of Hybrid Time and Frequency Data in Fast Magnetic Resonance Spectroscopy

Lu H, Zhang X, Qiu T, ..., Chen Z, Qu X

IEEE Trans. Biomed. Eng. - (-) 1-1 [2017-00-00; online 2017-00-00]

Favored surface-limited oxidation of cellulose with Oxone® in water

Ruan CQ, Strømme M, Mihranyan A, Lindh J

RSC Adv. 7 (64) 40600-40607 [2017-00-00; online 2017-00-00]