Publications 2017

Mineral Type Structures Soil Microbial Communities

Ahmed E, Hugerth LW, ..., Andersson AF, Holmström SJM

Geomicrobiology Journal - (-) 1-8 [2017-07-03; online 2016-08-25]

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

An automated method measures variability in P-glycoprotein and ABCG2 densities across brain regions and brain matter.

Kannan P, Schain M, ..., Hall MD, Mulder J

J. Cereb. Blood Flow Metab. - (-) 271678X16660984 [2017-06-00; online 2016-08-05]

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

Spatially resolved transcriptome profiling in model plant species

Giacomello S, Salmén F, ..., Street NR, Lundeberg J

NPLANTS 3 (6) 17061 [2017-05-08; online 2017-05-08]

Transcriptomics and methylomics of CD4-positive T cells in arsenic-exposed women.

Engström K, Wojdacz TK, ..., Vahter M, Broberg K

Arch. Toxicol. 91 (5) 2067-2078 [2017-05-00; online 2016-11-12]

Bioinformatics Compute and Storage (UPPNEX) Bioinformatics Short-term Support and Infrastructure (BILS) NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

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]

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

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]

Swedish NMR Centre (SNC)

Induction of Apoptosis in Intestinal Toxicity to a Histone Deacetylase Inhibitor in a Phase I Study with Pelvic Radiotherapy.

Kalanxhi E, Risberg K, ..., Flatmark K, Ree AH

Cancer Res Treat 49 (2) 374-386 [2017-04-00; online 2016-08-05]

Bioinformatics Short-term Support and Infrastructure (BILS)

Combined immunodeficiency and hypoglycemia associated with mutations in hypoxia upregulated 1.

Haapaniemi EM, Fogarty CL, ..., Seppänen M, Kere J

J. Allergy Clin. Immunol. 139 (4) 1391-1393.e11 [2017-04-00; online 2016-12-04]

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

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

Eur. J. Clin. Microbiol. Infect. Dis. 36 (4) 657-662 [2017-04-00; online 2016-12-03]

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

Neonatal Cord Blood Oxylipins and Exposure to Particulate Matter in the Early-Life Environment: An ENVIRONAGE Birth Cohort Study.

Martens DS, Gouveia S, ..., Nording M, Nawrot TS

Environ. Health Perspect. 125 (4) 691-698 [2017-04-00; online 2016-11-05]

PATZ1 down-regulates FADS1 by binding to rs174557 and is opposed by SP1/SREBP1c.

Pan G, Ameur A, ..., Gyllensten U, Wadelius C

Nucleic Acids Res. 45 (5) 2408-2422 [2017-03-17; online 2016-12-10]

NGI Uppsala (SNP&SEQ Technology Platform) NGI Uppsala (Uppsala Genome Center)

Towards a whole-genome sequence for rye (Secale cereale L.).

Bauer E, Schmutzer T, ..., Schön CC, Scholz U

Plant J. 89 (5) 853-869 [2017-03-00; online 2016-11-27]

Bioinformatics Short-term Support and Infrastructure (BILS)

Antibody-encoding repertoires of bone marrow and peripheral blood-a focus on IgE.

Levin M, Levander F, ..., Greiff L, Ohlin M

J. Allergy Clin. Immunol. 139 (3) 1026-1030 [2017-03-00; online 2016-08-16]

Bioinformatics Compute and Storage (UPPNEX) Bioinformatics Short-term Support and Infrastructure (BILS) NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

DNA methylation profiling of pediatric B-cell lymphoblastic leukemia with KMT2A rearrangement identifies hypomethylation at enhancer sites.

Bergmann AK, Castellano G, ..., Schrappe M, Siebert R

Pediatr Blood Cancer 64 (3) - [2017-03-00; online 2016-10-28]

Bioinformatics Compute and Storage (UPPNEX) NGI Uppsala (SNP&SEQ Technology Platform)

Development of [(11)C]/[(3)H]THK-5351 - A potential novel carbon-11 tau imaging PET radioligand.

Stepanov V, Svedberg M, ..., 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, ..., Schiöth HB, Mwinyi J

Clin. Genet. 91 (3) 379-385 [2017-03-00; online 2016-12-13]

Discovery of new biomarkers for atrial fibrillation using a custom-made proteomics chip.

Lind L, Sundström J, ..., Hagström E, Ärnlöv J

Heart 103 (5) 377-382 [2017-03-00; online 2016-09-10]

Clinical Biomarkers

Use of a proximity extension assay proteomics chip to discover new biomarkers associated with albuminuria.

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

Eur J Prev Cardiol 24 (4) 340-348 [2017-03-00; online 2016-11-01]

Clinical Biomarkers

Stool frequency is associated with gut microbiota composition.

Hadizadeh F, Walter S, ..., Franke A, D'Amato M

Gut 66 (3) 559-560 [2017-03-00; online 2016-05-20]

Clinical Genomics

Driver GW, Huang Y, ..., Wang Y, Westlund P

Phys Chem Chem Phys 19 (7) 4975-4988 [2017-02-15; online 2017-01-12]

Swedish NMR Centre (SNC)

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, ..., Breen G, Lewis CM

Biol. Psychiatry 81 (4) 325-335 [2017-02-15; online 2016-08-16]

Bioinformatics Compute and Storage (UPPNEX) NGI Uppsala (SNP&SEQ Technology Platform)

Distinct Anaerobic Bacterial Consumers of Cellobiose-Derived Carbon in Boreal Fens with Different CO2/CH4 Production Ratios.

Juottonen H, Eiler A, ..., Yrjälä K, Fritze H

Appl. Environ. Microbiol. 83 (4) - [2017-02-15; online 2016-12-04]

Bioinformatics Compute and Storage (UPPNEX) NGI Uppsala (SNP&SEQ Technology Platform)

Crystal Structure of the Emerging Cancer Target MTHFD2 in Complex with a Substrate-Based Inhibitor.

Gustafsson R, Jemth AS, ..., Helleday T, Stenmark P

Cancer Res. 77 (4) 937-948 [2017-02-15; online 2016-12-03]

Medicinal Chemistry – Hit2Lead Protein Expression and Characterization

microRNAs with AAGUGC seed motif constitute an integral part of an oncogenic signaling network.

Zhou Y, Frings O, ..., Agami R, Orre LM

Oncogene 36 (6) 731-745 [2017-02-09; online 2016-08-02]

Bioinformatics Short-term Support and Infrastructure (BILS) NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

Massive parallel sequencing questions the pathogenic role of missense variants in dilated cardiomyopathy.

Dalin MG, Engström PG, ..., Andersson B, Bergo MO

Int. J. Cardiol. 228 (-) 742-748 [2017-02-01; online 2016-11-26]

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

Metabolic and functional characterization of effects of developmental temperature in Drosophila melanogaster.

Schou MF, Kristensen TN, ..., Loeschcke V, Malmendal A

Am. J. Physiol. Regul. Integr. Comp. Physiol. 312 (2) R211-R222 [2017-02-01; online 2016-12-09]

Swedish NMR Centre (SNC)

The Human Adrenal Gland Proteome Defined by Transcriptomics and Antibody-Based Profiling.

Bergman J, Botling J, ..., Uhlén M, Pontén F

Endocrinology 158 (2) 239-251 [2017-02-01; online 2016-12-03]

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

Evidence for three genetic loci involved in both anorexia nervosa risk and variation of body mass index.

Hinney A, Kesselmeier M, ..., Müller TD, Hebebrand J

Mol. Psychiatry 22 (2) 192-201 [2017-02-00; online 2016-05-18]

Bioinformatics Compute and Storage (UPPNEX) NGI Uppsala (SNP&SEQ Technology Platform)

Distinct global binding patterns of the Wilms tumor gene 1 (WT1) -KTS and +KTS isoforms in leukemic cells.

Ullmark T, Järvstråt L, ..., Nilsson B, Gullberg U

Haematologica 102 (2) 336-345 [2017-02-00; online 2016-09-11]

A meta-analysis of reflux genome-wide association studies in 6750 Northern Europeans from the general population.

Bonfiglio F, Hysi PG, ..., Schmidt PT, D'Amato M

Neurogastroenterol. Motil. 29 (2) - [2017-02-00; online 2016-08-04]

Bioinformatics Compute and Storage (UPPNEX) NGI Uppsala (SNP&SEQ Technology Platform)

Novel seminal fluid proteins in the seed beetle Callosobruchus maculatus identified by a proteomic and transcriptomic approach.

Bayram H, Sayadi A, ..., Immonen E, Arnqvist G

Insect Mol. Biol. 26 (1) 58-73 [2017-02-00; online 2016-10-24]

Mass Spectrometry-based Proteomics, Uppsala

Molecular interrogation of hypothalamic organization reveals distinct dopamine neuronal subtypes.

Romanov RA, Zeisel A, ..., 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, ..., Carvalho CM, Lindstrand A

Hum. Mutat. 38 (2) 180-192 [2017-02-00; online 2016-11-20]

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

Associations of defect mismatch repair genes with prognosis and heredity in sporadic colorectal cancer.

Ghanipour L, Jirström K, ..., Glimelius B, Birgisson H

Eur J Surg Oncol 43 (2) 311-321 [2017-02-00; online 2016-11-12]

Tissue Profiling

Identification of new TRIP12 variants and detailed clinical evaluation of individuals with non-syndromic intellectual disability with or without autism.

Bramswig NC, Lüdecke HJ, ..., Kleefstra T, Wieczorek D

Hum. Genet. 136 (2) 179-192 [2017-02-00; online 2016-11-17]

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

The in silico identification and characterization of a bread wheat/Triticum militinae introgression line.

Abrouk M, Balcárková B, ..., Doležel J, Valárik M

Plant Biotechnol. J. 15 (2) 249-256 [2017-02-00; online 2016-08-12]

Bioinformatics Short-term Support and Infrastructure (BILS)

PCSK9 genetic variants and risk of type 2 diabetes: a mendelian randomisation study.

Schmidt AF, Swerdlow DI, ..., UCLEB consortium , Sattar N

Lancet Diabetes Endocrinol 5 (2) 97-105 [2017-02-00; online 2016-12-03]

Bioinformatics Compute and Storage (UPPNEX) NGI Uppsala (SNP&SEQ Technology Platform)

Meta-omic analyses of Baltic Sea cyanobacteria: diversity, community structure and salt acclimation.

Celepli N, Sundh J, ..., Bergman B, Ininbergs K

Environ. Microbiol. 19 (2) 673-686 [2017-02-00; online 2016-11-22]

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

Opioid precursor protein isoform is targeted to the cell nuclei in the human brain.

Kononenko O, Bazov I, ..., Yakovleva T, Bakalkin G

Biochim. Biophys. Acta 1861 (2) 246-255 [2017-02-00; online 2016-11-14]

Genomic analysis reveals major determinants ofcis-regulatory variation inCapsella grandiflora

Steige KA, Laenen B, ..., Scofield DG, Slotte T

Proc Natl Acad Sci USA 114 (5) 1087-1092 [2017-01-31; online 2017-01-17]

Meta-Analysis of Genome-Wide Association Studies for Abdominal Aortic Aneurysm Identifies Four New Disease-Specific Risk Loci.

Jones GT, Tromp G, ..., Samani NJ, Bown MJ

Circ. Res. 120 (2) 341-353 [2017-01-20; online 2016-12-03]

Proteogenomics produces comprehensive and highly accurate protein-coding gene annotation in a complete genome assembly ofMalassezia sympodialis

Zhu Y, Engström PG, ..., Scheynius A, Lehtiö J

Nucleic Acids Res - (-) gkx006 [2017-01-18; online 2017-01-18]

Perivascular PDGFR-β is an independent marker for prognosis in renal cell carcinoma.

Frödin M, Mezheyeuski A, ..., Johansson M, Östman A

Br. J. Cancer 116 (2) 195-201 [2017-01-17; online 2016-12-09]

Tissue Profiling

Identification of a Novel Autoimmune Peptide Epitope of Prostein in Prostate Cancer.

Pin E, Henjes F, ..., Nilsson P, Schwenk JM

J. Proteome Res. 16 (1) 204-216 [2017-01-06; online 2016-10-05]

Protein and peptide arrays

Antibody Validation in Bioimaging Applications Based on Endogenous Expression of Tagged Proteins.

Skogs M, Stadler C, ..., Uhlén M, Lundberg E

J. Proteome Res. 16 (1) 147-155 [2017-01-06; online 2016-10-12]

Cell Profiling

Single-Cell Analysis Reveals a Close Relationship between Differentiating Dopamine and Subthalamic Nucleus Neuronal Lineages.

Kee N, Volakakis N, ..., Parmar M, Perlmann T

Cell Stem Cell 20 (1) 29-40 [2017-01-05; online 2016-10-27]

Epigenetic changes as prognostic predictors in endometrial carcinomas.

Farkas SA, Sorbe BG, Nilsson TK

Epigenetics 12 (1) 19-26 [2017-01-02; online 2016-11-23]

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 Short-term Support and Infrastructure (BILS)

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, ..., Alarcón-Riquelme ME, Martín J

Ann. Rheum. Dis. 76 (1) 286-294 [2017-01-00; online 2016-05-20]

Bioinformatics Compute and Storage (UPPNEX) NGI Uppsala (SNP&SEQ Technology Platform)

Expression of possible targets for new proteasome inhibitors in diffuse large B-cell lymphoma.

Delforoush M, Berglund M, ..., Gullbo J, Enblad G

Eur. J. Haematol. 98 (1) 52-56 [2017-01-00; online 2016-06-16]

Tissue Profiling

Both maternal and offspring Elovl2 genotypes determine systemic DHA levels in perinatal mice.

Pauter AM, Trattner S, ..., Dethlefsen O, Jacobsson A

J. Lipid Res. 58 (1) 111-123 [2017-01-00; online 2016-11-20]

Bioinformatics Short-term Support and Infrastructure (BILS)

A multi-step peptidolytic cascade for amino acid recovery in chloroplasts.

Teixeira PF, Kmiec B, ..., Lehtiö J, Glaser E

Nat. Chem. Biol. 13 (1) 15-17 [2017-01-00; online 2016-10-31]

Clinical Proteomics Mass spectrometry Swedish Metabolomics Centre

Multiethnic genome-wide meta-analysis of ectopic fat depots identifies loci associated with adipocyte development and differentiation.

Chu AY, Deng X, ..., Steinhauser ML, Fox CS

Nat. Genet. 49 (1) 125-130 [2017-01-00; online 2016-12-06]

Bioinformatics Compute and Storage (UPPNEX) NGI Uppsala (SNP&SEQ Technology Platform)

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, ..., Morris AP, Lind PM

Environ Int 98 (-) 212-218 [2017-01-00; online 2016-11-15]

Bioinformatics Compute and Storage (UPPNEX) NGI Uppsala (SNP&SEQ Technology Platform)

Rye B chromosomes encode a functional Argonaute-like protein with in vitro slicer activities similar to its A chromosome paralog.

Ma W, Gabriel TS, ..., Banaei-Moghaddam AM, Houben A

New Phytol. 213 (2) 916-928 [2017-01-00; online 2016-07-29]

Bioinformatics Short-term Support and Infrastructure (BILS)

Investigating kinship of Neolithic post-LBK human remains from Krusza Zamkowa, Poland using ancient DNA.

Juras A, Chyleński M, ..., Jakobsson M, Dabert M

Forensic Sci Int Genet 26 (-) 30-39 [2017-01-00; online 2016-10-25]

Bioinformatics Compute and Storage (UPPNEX) NGI Uppsala (SNP&SEQ Technology Platform)

Elevated levels of circulating CDH5 and FABP1 in association with human drug-induced liver injury.

Mikus M, Drobin K, ..., Nilsson P, Schuppe-Koistinen I

Liver Int. 37 (1) 132-140 [2017-01-00; online 2016-05-26]

Plasma Profiling

Contribution of different dispersal sources to the metabolic response of lake bacterioplankton following a salinity change.

Comte J, Langenheder S, Berga M, Lindström ES

Environ. Microbiol. 19 (1) 251-260 [2017-01-00; online 2016-11-22]

Contribution of copy number variants to schizophrenia from a genome-wide study of 41,321 subjects.

CNV and Schizophrenia Working Groups of the Psychiatric Genomics Consortium , Psychosis Endophenotypes International Consortium

Nat. Genet. 49 (1) 27-35 [2017-01-00; online 2016-11-22]