Publications 2016

Bacterial associations reveal spatial population dynamics in Anopheles gambiae mosquitoes

Buck M, Nilsson LKJ, Brunius C, ..., Hopkins R, Terenius O

Sci Rep 6 (1) - [2016-09-00; online 2016-03-10]

Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]

Autoantibody targets in vaccine-associated narcolepsy.

Häggmark-Månberg A, Zandian A, Forsström B, ..., Olsson T, Nilsson P

Autoimmunity 49 (6) 421-433 [2016-09-00; online 2016-05-20]

Autoimmunity and Serology Profiling [Collaborative]

Approach for Identifying Human Leukocyte Antigen (HLA)-DR Bound Peptides from Scarce Clinical Samples.

Heyder T, Kohler M, Tarasova NK, ..., Grunewald J, Ytterberg AJ

Mol. Cell Proteomics 15 (9) 3017-3029 [2016-09-00; online 2016-07-24]

Advanced Mass Spectrometry Proteomics [Collaborative]

Advancing the global proteome survey platform by using an oriented single chain antibody fragment immobilization approach

Säll A, Persson H, Ohlin M, Borrebaeck CAK, Wingren C

New Biotechnology 33 (5) 503-513 [2016-09-00; online 2016-09-00]

Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]

ATM mutations in major stereotyped subsets of chronic lymphocytic leukemia: enrichment in subset #2 is associated with markedly short telomeres.

Navrkalova V, Young E, Baliakas P, ..., Rosenquist R, Trbusek M

Haematologica 101 (9) e369-e373 [2016-09-00; online 2016-08-02]

Clinical Genomics Uppsala [Service]

A genetic variant in proximity to the gene LYPLAL1 is associated with lower hunger feelings and increased weight loss following Roux-en-Y gastric bypass surgery.

Bandstein M, Mwinyi J, Ernst B, ..., Schultes B, Schiöth HB

Scand. J. Gastroenterol. 51 (9) 1050-1055 [2016-09-00; online 2016-05-18]

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

A Role for the Chromatin-Remodeling Factor BAZ1A in Neurodevelopment.

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

Hum. Mutat. 37 (9) 964-975 [2016-09-00; online 2016-07-08]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

A Rickettsiales symbiont of amoebae with ancient features.

Schulz F, Martijn J, Wascher F, ..., Ettema TJ, Horn M

Environ. Microbiol. 18 (8) 2326-2342 [2016-09-00; online 2015-04-25]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

A Genetic Risk Score Is Associated with Weight Loss Following Roux-en Y Gastric Bypass Surgery.

Bandstein M, Voisin S, Nilsson EK, ..., Mwinyi J, Schiöth HB

Obes Surg 26 (9) 2183-2189 [2016-09-00; online 2016-02-03]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

The Adipose Transcriptional Response to Insulin Is Determined by Obesity, Not Insulin Sensitivity.

Rydén M, Hrydziuszko O, Mileti E, ..., Daub CO, Arner P

Cell Rep 16 (9) 2317-2326 [2016-08-30; online 2016-08-23]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Cystatin C and Cardiovascular Disease: A Mendelian Randomization Study.

van der Laan SW, Fall T, Soumaré A, ..., Holmes MV, Asselbergs FW

J. Am. Coll. Cardiol. 68 (9) 934-945 [2016-08-30; online 2016-08-27]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Phosphorylation of Leukotriene C4 Synthase at Serine 36 Impairs Catalytic Activity.

Ahmad S, Ytterberg AJ, Thulasingam M, ..., Rinaldo-Matthis A, Haeggström JZ

J. Biol. Chem. 291 (35) 18410-18418 [2016-08-26; online 2016-06-30]

Advanced Mass Spectrometry Proteomics [Collaborative]

One-night sleep deprivation induces changes in the DNA methylation and serum activity indices of stearoyl-CoA desaturase in young healthy men.

Skuladottir GV, Nilsson EK, Mwinyi J, Schiöth HB

Lipids Health Dis 15 (1) 137 [2016-08-26; online 2016-08-26]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Factors regulating capillary remodeling in a reversible model of inflammatory corneal angiogenesis.

Mukwaya A, Peebo B, Xeroudaki M, ..., Jensen L, Lagali N

Sci Rep 6 (1) 32137 [2016-08-26; online 2016-08-26]

Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]

Enantioselective Organocatalyzed Transformations of β-Ketoesters.

Govender T, Arvidsson PI, Maguire GE, Kruger HG, Naicker T

Chem. Rev. 116 (16) 9375-9437 [2016-08-24; online 2016-07-28]

Drug Discovery and Development (DDD) [Collaborative]

Oxidation and cyclization of casbene in the biosynthesis of Euphorbia factors from mature seeds of Euphorbia lathyris L.

Luo D, Callari R, Hamberger B, ..., Staerk D, Hamberger B

Proc. Natl. Acad. Sci. U.S.A. 113 (34) E5082-E5089 [2016-08-23; online 2016-08-11]

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

Identification of Multiple QTLs Linked to Neuropathology in the Engrailed-1 Heterozygous Mouse Model of Parkinson's Disease.

Kurowska Z, Jewett M, Brattås PL, ..., Brundin P, Swanberg M

Sci Rep 6 (-) 31701 [2016-08-23; online 2016-08-23]

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

Effects of wastewater treatment plant effluent inputs on planktonic metabolic rates and microbial community composition in the Baltic Sea

Vaquer-Sunyer R, Reader HE, Muthusamy S, ..., Conley DJ, Kritzberg ES

Biogeosciences 13 (16) 4751-4765 [2016-08-23; online 2016-08-23]

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

Single base resolution analysis of 5-hydroxymethylcytosine in 188 human genes: implications for hepatic gene expression.

Ivanov M, Kals M, Lauschke V, ..., Milani L, Ingelman-Sundberg M

Nucleic Acids Res. 44 (14) 6756-6769 [2016-08-19; online 2016-04-29]

Bioinformatics Support for Computational Resources [Service] Clinical Proteomics Mass spectrometry [Collaborative] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]

Cardiometabolic risk loci share downstream cis- and trans-gene regulation across tissues and diseases.

Franzén O, Ermel R, Cohain A, ..., Schadt EE, Björkegren JL

Science 353 (6301) 827-830 [2016-08-19; online 2016-08-20]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Structural origin of proton mobility in a protic ionic liquid/imidazole mixture: insights from computational and experimental results.

Yaghini N, Gómez-González V, Varela LM, Martinelli A

Phys Chem Chem Phys 18 (33) 23195-23206 [2016-08-17; online 2016-08-09]

Multifunctional Hyaluronic Acid and Chondroitin Sulfate Nanoparticles: Impact of Glycosaminoglycan Presentation on Receptor Mediated Cellular Uptake and Immune Activation.

Oommen OP, Duehrkop C, Nilsson B, Hilborn J, Varghese OP

ACS Appl Mater Interfaces 8 (32) 20614-20624 [2016-08-17; online 2016-07-29]

Cinobufagin Modulates Human Innate Immune Responses and Triggers Antibacterial Activity.

Xie S, Spelmink L, Codemo M, ..., Henriques-Normark B, Olliver M

PLoS ONE 11 (8) e0160734 [2016-08-16; online 2016-08-16]

Mass Spectrometry-based Proteomics, Uppsala [Service]

Chondroitin sulfate derived theranostic nanoparticles for targeted drug delivery.

Varghese OP, Liu J, Sundaram K, Hilborn J, Oommen OP

Biomater Sci 4 (9) 1310-1313 [2016-08-16; online 2016-07-20]

Cellular Barcoding Links B-1a B Cell Potential to a Fetal Hematopoietic Stem Cell State at the Single-Cell Level.

Kristiansen TA, Jaensson Gyllenbäck E, Zriwil A, ..., Bryder D, Yuan J

Immunity 45 (2) 346-357 [2016-08-16; online 2016-08-18]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Metastasis Stimulation by Hypoxia and Acidosis-Induced Extracellular Lipid Uptake Is Mediated by Proteoglycan-Dependent Endocytosis.

Menard JA, Christianson HC, Kucharzewska P, ..., Johansson MC, Belting M

Cancer Res. 76 (16) 4828-4840 [2016-08-15; online 2016-05-19]

Substituent Effects on the [N-I-N](+) Halogen Bond.

Carlsson AC, Mehmeti K, Uhrbom M, ..., Rissanen K, Erdélyi M

J. Am. Chem. Soc. 138 (31) 9853-9863 [2016-08-10; online 2016-06-17]

Large-scale ligand-based predictive modelling using support vector machines.

Alvarsson J, Lampa S, Schaal W, ..., Wikberg JE, Spjuth O

J Cheminform 8 (-) 39 [2016-08-10; online 2016-08-10]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

The genome-scale DNA-binding profile of BarR, a β-alanine responsive transcription factor in the archaeon Sulfolobus acidocaldarius.

Liu H, Wang K, Lindås AC, Peeters E

BMC Genomics 17 (-) 569 [2016-08-08; online 2016-08-08]

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

Stromal Hedgehog signalling is downregulated in colon cancer and its restoration restrains tumour growth.

Gerling M, Büller NV, Kirn LM, ..., van den Brink GR, Toftgård R

Nat Commun 7 (-) 12321 [2016-08-05; online 2016-08-05]

Bioinformatics and Expression Analysis (BEA) [Service]

Inconsistent results in the analysis of ALK rearrangements in non-small cell lung cancer.

Mattsson JS, Brunnström H, Jabs V, ..., Micke P, Svensson MA

BMC Cancer 16 (-) 603 [2016-08-05; online 2016-08-05]

Clinical Genomics Uppsala [Service] Tissue Profiling [Collaborative]

The genetic architecture of type 2 diabetes.

Fuchsberger C, Flannick J, Teslovich TM, ..., Altshuler D, McCarthy MI

Nature 536 (7614) 41-47 [2016-08-04; online 2016-07-11]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]

Rapid and specific hypomethylation of enhancers in endothelial cells during adaptation to cell culturing.

Magnusson M, Larsson P, Lu EX, ..., Carén H, Jern S

Epigenetics 11 (8) 614-624 [2016-08-02; online 2016-06-14]

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

Mutation-Induced Population Shift in the MexR Conformational Ensemble Disengages DNA Binding: A Novel Mechanism for MarR Family Derepression.

Anandapadamanaban M, Pilstål R, Andresen C, ..., Wallner B, Sunnerhagen M

Structure 24 (8) 1311-1321 [2016-08-02; online 2016-07-14]

Protein Science Facility (PSF) [Collaborative]

Compounds from the marine sponge Cribrochalina vasculum offer a way to target IGF-1R mediated signaling in tumor cells

Zovko A, Novak M, Hååg P, ..., Lewensohn R, Viktorsson K

Oncotarget 7 (31) 50258-50276 [2016-08-02; online 2016-07-01]

Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]

ω-3 Polyunsaturated Fatty Acid Biomarkers and Coronary Heart Disease: Pooling Project of 19 Cohort Studies.

Del Gobbo LC, Imamura F, Aslibekyan S, ..., Mozaffarian D, Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Fatty Acids and Outcomes Research Consortium (FORCe)

JAMA Intern Med 176 (8) 1155-1166 [2016-08-01; online 2016-07-01]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Simultaneous imaging of multiple neurotransmitters and neuroactive substances in the brain by desorption electrospray ionization mass spectrometry.

Shariatgorji M, Strittmatter N, Nilsson A, ..., Goodwin RJ, Andren PE

Neuroimage 136 (-) 129-138 [2016-08-01; online 2016-05-04]

Spatial Mass Spectrometry [Technology development]

Profilin connects actin assembly with microtubule dynamics.

Nejedla M, Sadi S, Sulimenko V, ..., Aspenström P, Karlsson R

Mol. Biol. Cell 27 (15) 2381-2393 [2016-08-01; online 2016-06-17]

Integrated Microscopy Technologies Stockholm [Collaborative]

On the reversibility of parasitism: adaptation to a free-living lifestyle via gene acquisitions in the diplomonad Trepomonas sp. PC1.

Xu F, Jerlström-Hultqvist J, Kolisko M, ..., Svärd SG, Andersson JO

BMC Biol. 14 (-) 62 [2016-08-01; online 2016-08-01]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

MetLab: An In Silico Experimental Design, Simulation and Analysis Tool for Viral Metagenomics Studies.

Norling M, Karlsson-Lindsjö OE, Gourlé H, Bongcam-Rudloff E, Hayer J

PLoS ONE 11 (8) e0160334 [2016-08-01; online 2016-08-01]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Kinetic investigation of human 5-lipoxygenase with arachidonic acid.

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

Bioorg. Med. Chem. Lett. 26 (15) 3547-3551 [2016-08-01; online 2016-06-11]

Tuning fresh: radiation through rewiring of central metabolism in streamlined bacteria.

Eiler A, Mondav R, Sinclair L, ..., Woyke T, Bertilsson S

ISME J 10 (8) 1902-1914 [2016-08-00; online 2016-01-19]

Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training Microbial Single Cell Genomics [Collaborative]

Transcriptomic analysis reveals how a lack of potassium ions increases Sulfolobus acidocaldarius sensitivity to pH changes.

Buetti-Dinh A, Dethlefsen O, Friedman R, Dopson M

Microbiology (Reading, Engl.) 162 (8) 1422-1434 [2016-08-00; online 2016-05-28]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Spondyloocular Syndrome: Novel Mutations in XYLT2 Gene and Expansion of the Phenotypic Spectrum.

Taylan F, Costantini A, Coles N, ..., Tüysüz B, Mäkitie O

J. Bone Miner. Res. 31 (8) 1577-1585 [2016-08-00; online 2016-03-19]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Serum nuclear magnetic resonance-based metabolomics and outcome in diffuse large B-cell lymphoma patients - a pilot study.

Stenson M, Pedersen A, Hasselblom S, ..., Pinto R, Andersson PO

Leuk. Lymphoma 57 (8) 1814-1822 [2016-08-00; online 2016-02-17]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Swedish NMR Centre (SNC) [Collaborative]

SATB2 is expressed in Merkel cell carcinoma.

Fukuhara M, Agnarsdóttir M, Edqvist PH, Coter A, Ponten F

Arch. Dermatol. Res. 308 (6) 449-454 [2016-08-00; online 2016-06-04]

Tissue Profiling [Technology development]

Remnants of marine bacterial communities can be retrieved from deep sediments in lakes of marine origin.

Langenheder S, Comte J, Zha Y, ..., Eiler A, Lindström ES

Environ Microbiol Rep 8 (4) 479-485 [2016-08-00; online 2016-03-02]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Rapid Evolution of Genomic Imprinting in Two Species of the Brassicaceae.

Hatorangan MR, Laenen B, Steige KA, Slotte T, Köhler C

Plant Cell 28 (8) 1815-1827 [2016-08-00; online 2016-07-29]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Postprandial alterations in whole-blood DNA methylation are mediated by changes in white blood cell composition.

Rask-Andersen M, Bringeland N, Nilsson EK, ..., Benedict C, Schiöth HB

Am. J. Clin. Nutr. 104 (2) 518-525 [2016-08-00; online 2016-07-08]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Phytophthora infestans Argonaute 1 binds microRNA and small RNAs from effector genes and transposable elements.

Åsman AK, Fogelqvist J, Vetukuri RR, Dixelius C

New Phytol. 211 (3) 993-1007 [2016-08-00; online 2016-03-25]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Novel regulatory variant detected on the VKORC1 haplotype that is associated with warfarin dose.

Cavalli M, Pan G, Nord H, ..., Wadelius C, Wadelius M

Pharmacogenomics 17 (12) 1305-1314 [2016-08-00; online 2016-02-06]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Neuroprotective potential of Linezolid: a quantitative and distribution study via mass spectrometry.

Baijnath S, Shobo A, Bester LA, ..., Naicker T, Govender T

J. Mol. Histol. 47 (4) 429-435 [2016-08-00; online 2016-06-22]

Drug Discovery and Development (DDD) [Collaborative]

Meta-analysis of 375,000 individuals identifies 38 susceptibility loci for migraine.

Gormley P, Anttila V, Winsvold BS, ..., Nyholt DR, Palotie A

Nat. Genet. 48 (8) 856-866 [2016-08-00; online 2016-06-21]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Intra-tumour IgA1 is common in cancer and is correlated with poor prognosis in bladder cancer.

Welinder C, Jirström K, Lehn S, ..., Danielsson L, Jansson B

Heliyon 2 (8) e00143 [2016-08-00; online 2016-08-16]

In quest for the optimal delignification of lignocellulosic biomass using hydrated, SO2 switched DBU MEASIL switchable ionic liquid

Anugwom I, Rujana L, Wärnå J, Hedenström M, Mikkola JP

Chemical Engineering Journal 297 (-) 256-264 [2016-08-00; online 2016-08-00]

Impact of ocean acidification on antimicrobial activity in gills of the blue mussel (Mytilus edulis).

Hernroth B, Baden S, Tassidis H, ..., Bergström Lind S, Bergquist J

Fish Shellfish Immunol. 55 (-) 452-459 [2016-08-00; online 2016-06-08]

Mass Spectrometry-based Proteomics, Uppsala [Collaborative]

Genome-wide association meta-analysis in Chinese and European individuals identifies ten new loci associated with systemic lupus erythematosus.

Morris DL, Sheng Y, Zhang Y, ..., Cui Y, Vyse TJ

Nat. Genet. 48 (8) 940-946 [2016-08-00; online 2016-07-12]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Genetic determinants of warfarin maintenance dose and time in therapeutic treatment range: a RE-LY genomics substudy.

Eriksson N, Wallentin L, Berglund L, ..., Yusuf S, Wadelius M

Pharmacogenomics 17 (13) 1425-1439 [2016-08-00; online 2016-08-04]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]

Genetic and environmental effects on body mass index from infancy to the onset of adulthood: an individual-based pooled analysis of 45 twin cohorts participating in the COllaborative project of Development of Anthropometrical measures in Twins (CODATwins) study.

Silventoinen K, Jelenkovic A, Sund R, ..., Boomsma DI, Kaprio J

Am. J. Clin. Nutr. 104 (2) 371-379 [2016-08-00; online 2016-07-15]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Developmental exposure to progestins causes male bias and precocious puberty in zebrafish (Danio rerio).

Svensson J, Mustafa A, Fick J, Schmitz M, Brunström B

Aquat. Toxicol. 177 (-) 316-323 [2016-08-00; online 2016-06-14]

Genome Engineering Zebrafish [Service]

Assessing the taxonomic status of Osmoderma cristinae (Coleoptera: Scarabaeidae), endemic to Sicily, by genetic, morphological and pheromonal analyses

Zauli A, Carpaneto GM, Chiari S, ..., Bologna MA, Svensson GP

J Zool Syst Evol Res 54 (3) 206-214 [2016-08-00; online 2016-02-12]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Analysis of neural crest-derived clones reveals novel aspects of facial development.

Kaucka M, Ivashkin E, Gyllborg D, ..., Hellander A, Adameyko I

Sci Adv 2 (8) e1600060 [2016-08-00; online 2016-08-03]

Integrated Microscopy Technologies Stockholm [Collaborative]

Adaptation to different types of stress converge on mitochondrial metabolism

Lahtvee PJ, Kumar R, Hallström BM, Nielsen J

Mol. Biol. Cell 27 (15) 2505-2514 [2016-08-00; online 2016-08-00]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

A novel splicing mutation in the IQSEC2 gene that modulates the phenotype severity in a family with intellectual disability.

Madrigal I, Alvarez-Mora MI, Rosell J, ..., Syvänen AC, Mila M

Eur. J. Hum. Genet. 24 (8) 1117-1123 [2016-08-00; online 2016-01-07]

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

A new class of fatty acid allene oxide formed by the DOX-P450 fusion proteins of human and plant pathogenic fungi, C. immitis and Z. tritici.

Oliw EH, Aragó M, Chen Y, Jernerén F

J. Lipid Res. 57 (8) 1518-1528 [2016-08-00; online 2016-06-11]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Inhibitors of the Cysteine Synthase CysM with Antibacterial Potency against Dormant Mycobacterium tuberculosis.

Brunner K, Maric S, Reshma RS, ..., Schnell R, Schneider G

J. Med. Chem. 59 (14) 6848-6859 [2016-07-28; online 2016-07-13]

Chemical Biology Consortium Sweden (CBCS) [Collaborative] Protein Science Facility (PSF) [Service]

Delineating the conformational flexibility of trisaccharides from NMR spectroscopy experiments and computer simulations.

Yang M, Angles d'Ortoli T, Säwén E, ..., Widmalm G, MacKerell AD

Phys Chem Chem Phys 18 (28) 18776-18794 [2016-07-28; online 2016-06-27]

The De Novo Transcriptome and Its Functional Annotation in the Seed Beetle Callosobruchus maculatus.

Sayadi A, Immonen E, Bayram H, Arnqvist G

PLoS ONE 11 (7) e0158565 [2016-07-21; online 2016-07-21]

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

Short Chain Fatty Acids (SCFA) Reprogram Gene Expression in Human Malignant Epithelial and Lymphoid Cells.

Astakhova L, Ngara M, Babich O, ..., Ernberg I, Matskova L

PLoS ONE 11 (7) e0154102 [2016-07-21; online 2016-07-21]

Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]

Metabolic Profiling of Systemic Lupus Erythematosus and Comparison with Primary Sjögren's Syndrome and Systemic Sclerosis.

Bengtsson AA, Trygg J, Wuttge DM, ..., Rännar S, Lundstedt T

PLoS ONE 11 (7) e0159384 [2016-07-21; online 2016-07-21]

Systematic Analysis Reveals that Cancer Mutations Converge on Deregulated Metabolism of Arachidonate and Xenobiotics.

Gatto F, Schulze A, Nielsen J

Cell Rep 16 (3) 878-895 [2016-07-19; online 2016-07-12]

Bioinformatics Support, Infrastructure and Training [Technology development] Systems Biology [Technology development]

Horizontal Cells, the Odd Ones Out in the Retina, Give Insights into Development and Disease.

Boije H, Shirazi Fard S, Edqvist PH, Hallböök F

Front Neuroanat 10 (-) 77 [2016-07-19; online 2016-07-19]

DNA Content in Extracellular Vesicles Isolated from Porcine Coronary Venous Blood Directly after Myocardial Ischemic Preconditioning.

Svennerholm K, Rodsand P, Hellman U, ..., Ronquist G, Haney M

PLoS ONE 11 (7) e0159105 [2016-07-19; online 2016-07-19]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Peroxisome Proliferator-activated Receptor γ Coactivator-1 α Isoforms Selectively Regulate Multiple Splicing Events on Target Genes.

Martínez-Redondo V, Jannig PR, Correia JC, ..., Dahlman-Wright K, Ruas JL

J. Biol. Chem. 291 (29) 15169-15184 [2016-07-15; online 2016-05-28]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Direct imaging of elemental distributions in tissue sections by laser ablation mass spectrometry.

Shariatgorji M, Nilsson A, Bonta M, ..., Limbeck A, Andrén PE

Methods 104 (-) 86-92 [2016-07-15; online 2016-06-02]

Spatial Mass Spectrometry [Technology development]

Abstract 2688: A forward genetics screen of murine brain tumors identifies novel candidate genes involved in gliomagenesis

Cancer M, Weishaupt H, Rosen G, ..., Ameur A, Swartling FJ

Cancer Res 76 (14 Supplement) 2688-2688 [2016-07-15; online 2016-07-22]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

Abstract 2473: Combined BET-bromodomain and CDK2 inhibition in MYC-driven medulloblastoma

Bolin S, Borgenvik A, Persson C, ..., Weishaupt H, Swartling FJ

Cancer Res 76 (14 Supplement) 2473-2473 [2016-07-15; online 2016-07-22]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Cloche is a bHLH-PAS transcription factor that drives haemato-vascular specification.

Reischauer S, Stone OA, Villasenor A, ..., Andersson O, Stainier DY

Nature 535 (7611) 294-298 [2016-07-14; online 2016-07-15]

Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

A C2HC zinc finger is essential for the RING-E2 interaction of the ubiquitin ligase RNF125.

Bijlmakers MJ, Teixeira JM, Boer R, ..., Pons M, Crosas B

Sci Rep 6 (-) 29232 [2016-07-14; online 2016-07-14]

Rosette-Disrupting Effect of an Anti-Plasmodial Compound for the Potential Treatment of Plasmodium falciparum Malaria Complications.

Ch'ng JH, Moll K, Quintana Mdel P, ..., Eriksson AB, Wahlgren M

Sci Rep 6 (-) 29317 [2016-07-11; online 2016-07-11]

Integrative functional genomics identifies regulatory mechanisms at coronary artery disease loci.

Miller CL, Pjanic M, Wang T, ..., Björkegren JL, Quertermous T

Nat Commun 7 (-) 12092 [2016-07-08; online 2016-07-08]

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

Dysregulated signaling hubs of liver lipid metabolism reveal hepatocellular carcinoma pathogenesis.

Lee S, Mardinoglu A, Zhang C, Lee D, Nielsen J

Nucleic Acids Res. 44 (12) 5529-5539 [2016-07-08; online 2016-05-25]

Bioinformatics Support, Infrastructure and Training [Technology development] Systems Biology [Technology development]

Profiling cancer testis antigens in non-small-cell lung cancer.

Djureinovic D, Hallström BM, Horie M, ..., Uhlén M, Micke P

JCI Insight 1 (10) e86837 [2016-07-07; online 2016-07-07]

Bioinformatics Support for Computational Resources [Service] Clinical Genomics Uppsala [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Tissue Profiling [Collaborative]

Large Deletions at the SHOX Locus in the Pseudoautosomal Region Are Associated with Skeletal Atavism in Shetland Ponies.

Rafati N, Andersson LS, Mikko S, ..., Lindgren G, Rubin CJ

G3 (Bethesda) 6 (7) 2213-2223 [2016-07-07; online 2016-07-07]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Exome sequencing in pooled DNA samples to identify maternal pre-eclampsia risk variants.

Kaartokallio T, Wang J, Heinonen S, ..., Kere J, Laivuori H

Sci Rep 6 (-) 29085 [2016-07-07; online 2016-07-07]

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Diversity and Expression of Bacterial Metacaspases in an Aquatic Ecosystem.

Asplund-Samuelsson J, Sundh J, Dupont CL, ..., Ininbergs K, Ekman M

Front Microbiol 7 (-) 1043 [2016-07-06; online 2016-07-06]

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Survival-associated heterogeneity of marker-defined perivascular cells in colorectal cancer.

Mezheyeuski A, Bradic Lindh M, Guren TK, ..., Sorbye H, Östman A

Oncotarget 7 (27) 41948-41958 [2016-07-05; online 2016-06-02]

Fluorescence Tissue Profiling [Collaborative] Tissue Profiling [Collaborative]

Pooled analysis of genome-wide association studies of cervical intraepithelial neoplasia 3 (CIN3) identifies a new susceptibility locus.

Chen D, Enroth S, Liu H, ..., Xu S, Gyllensten U

Oncotarget 7 (27) 42216-42224 [2016-07-05; online 2016-06-11]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Long-term genetic stability and a high-altitude East Asian origin for the peoples of the high valleys of the Himalayan arc.

Jeong C, Ozga AT, Witonsky DB, ..., Di Rienzo A, Warinner C

Proc. Natl. Acad. Sci. U.S.A. 113 (27) 7485-7490 [2016-07-05; online 2016-06-20]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics.

Ståhl PL, Salmén F, Vickovic S, ..., Lundeberg J, Frisén J

Science 353 (6294) 78-82 [2016-07-01; online 2016-07-02]

Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] Fluorescence Tissue Profiling [Collaborative] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Tissue Profiling [Collaborative]

The epidermis coordinates auxin-induced stem growth in response to shade.

Procko C, Burko Y, Jaillais Y, ..., Long JA, Chory J

Genes Dev. 30 (13) 1529-1541 [2016-07-01; online 2016-07-13]

Genome-wide association study identifies multiple susceptibility loci for multiple myeloma.

Mitchell JS, Li N, Weinhold N, ..., Nilsson B, Houlston RS

Nat Commun 7 (-) 12050 [2016-07-01; online 2016-07-01]

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

Establishing a Proteomics-Based Monocyte Assay To Assess Differential Innate Immune Activation Responses.

Tarasova NK, Ytterberg AJ, Lundberg K, ..., Harris RA, Zubarev RA

J. Proteome Res. 15 (7) 2337-2345 [2016-07-01; online 2016-06-03]

Advanced Mass Spectrometry Proteomics [Collaborative] Chemical Proteomics [Technology development]

Dinosaur: A Refined Open-Source Peptide MS Feature Detector.

Teleman J, Chawade A, Sandin M, Levander F, Malmström J

J. Proteome Res. 15 (7) 2143-2151 [2016-07-01; online 2016-05-26]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Whole genome duplication in coast redwood (Sequoia sempervirens) and its implications for explaining the rarity of polyploidy in conifers.

Scott AD, Stenz NW, Ingvarsson PK, Baum DA

New Phytol. 211 (1) 186-193 [2016-07-00; online 2016-03-22]

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

Variation in Linked Selection and Recombination Drive Genomic Divergence during Allopatric Speciation of European and American Aspens.

Wang J, Street NR, Scofield DG, Ingvarsson PK

Mol. Biol. Evol. 33 (7) 1754-1767 [2016-07-00; online 2016-03-18]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

The role of germline alterations in the DNA damage response genes BRIP1 and BRCA2 in melanoma susceptibility.

Tuominen R, Engström PG, Helgadottir H, ..., Hansson J, Höiom V

Genes Chromosomes Cancer 55 (7) 601-611 [2016-07-00; online 2016-04-14]

Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

The genetic landscape of paediatric de novo acute myeloid leukaemia as defined by single nucleotide polymorphism array and exon sequencing of 100 candidate genes.

Olsson L, Zettermark S, Biloglav A, ..., Paulsson K, Johansson B

Br. J. Haematol. 174 (2) 292-301 [2016-07-00; online 2016-03-31]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

The Human Protein Atlas - an important resource for basic and clinical research.

Lindskog C

Expert Rev Proteomics 13 (7) 627-629 [2016-07-00; online 2016-06-22]

Tissue Profiling [Technology development]

Super-resolution structured illumination fluorescence microscopy of the lateral wall of the cochlea: the Connexin26/30 proteins are separately expressed in man.

Liu W, Edin F, Blom H, ..., Laurell G, Rask-Andersen H

Cell Tissue Res. 365 (1) 13-27 [2016-07-00; online 2016-03-05]

Integrated Microscopy Technologies Stockholm [Collaborative]

Prevention of apoptosis averts glomerular tubular disconnection and podocyte loss in proteinuric kidney disease.

Burlaka I, Nilsson LM, Scott L, ..., Brismar H, Aperia A

Kidney Int. 90 (1) 135-148 [2016-07-00; online 2016-05-25]

Integrated Microscopy Technologies Stockholm [Collaborative]

Multi-platform metabolomics assays for human lung lavage fluids in an air pollution exposure study.

Surowiec I, Karimpour M, Gouveia-Figueira S, ..., Trygg J, Nording ML

Anal Bioanal Chem 408 (17) 4751-4764 [2016-07-00; online 2016-04-25]

Increasing the power of genome wide association studies in natural populations using repeated measures - evaluation and implementation.

Rönnegård L, McFarlane SE, Husby A, ..., Ellegren H, Qvarnström A

Methods Ecol Evol 7 (7) 792-799 [2016-07-00; online 2016-02-05]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Identification of Inhibitors of Pseudomonas aeruginosa Exotoxin-S ADP-Ribosyltransferase Activity.

Pinto AF, Ebrahimi M, Saleeb M, ..., Elofsson M, Schüler H

J Biomol Screen 21 (6) 590-595 [2016-07-00; online 2016-02-05]

Distinct transcription factor complexes act on a permissive chromatin landscape to establish regionalized gene expression in CNS stem cells.

Hagey DW, Zaouter C, Combeau G, ..., Huss M, Muhr J

Genome Res. 26 (7) 908-917 [2016-07-00; online 2016-05-02]

Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Combined structural, biochemical and cellular evidence demonstrates that both FGDF motifs in alphavirus nsP3 are required for efficient replication.

Schulte T, Liu L, Panas MD, ..., Achour A, McInerney GM

Open Biol 6 (7) - [2016-07-00; online 2016-07-08]

An Integrative Genomic Analysis of Formalin Fixed Paraffin-Embedded Archived Serous Ovarian Carcinoma Comparing Long-term and Short-term Survivors.

Stålberg K, Crona J, Razmara M, ..., Skogseid B, Stålberg P

Int. J. Gynecol. Cancer 26 (6) 1027-1032 [2016-07-00; online 2016-05-14]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

A draft fur seal genome provides insights into factors affecting SNP validation and how to mitigate them.

Humble E, Martinez-Barrio A, Forcada J, ..., Wolf JB, Hoffman JI

Mol Ecol Resour 16 (4) 909-921 [2016-07-00; online 2015-12-20]

Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Gene-Expression Profiling Suggests Impaired Signaling via the Interferon Pathway in Cstb-/- Microglia.

Körber I, Katayama S, Einarsdottir E, ..., Lehesjoki AE, Joensuu T

PLoS ONE 11 (6) e0158195 [2016-06-29; online 2016-06-29]

Bioinformatics and Expression Analysis (BEA) [Service]

Conserved 33-kb haplotype in the MHC class III region regulates chronic arthritis.

Yau AC, Tuncel J, Haag S, ..., Padyukov L, Holmdahl R

Proc. Natl. Acad. Sci. U.S.A. 113 (26) E3716-E3724 [2016-06-28; online 2016-06-16]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

PRECOG: a tool for automated extraction and visualization of fitness components in microbial growth phenomics.

Fernandez-Ricaud L, Kourtchenko O, Zackrisson M, Warringer J, Blomberg A

BMC Bioinformatics 17 (-) 249 [2016-06-23; online 2016-06-23]

Bioinformatics Support and Infrastructure [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development]

Genetic and environmental influences on height from infancy to early adulthood: An individual-based pooled analysis of 45 twin cohorts.

Jelenkovic A, Sund R, Hur YM, ..., Kaprio J, Silventoinen K

Sci Rep 6 (-) 28496 [2016-06-23; online 2016-06-23]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Cryptosporidium as a testbed for single cell genome characterization of unicellular eukaryotes.

Troell K, Hallström B, Divne AM, ..., Beser J, Bertilsson S

BMC Genomics 17 (-) 471 [2016-06-23; online 2016-06-23]

Bioinformatics Support for Computational Resources [Service] Microbial Single Cell Genomics [Technology development] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

The Aquaporin Splice Variant NbXIP1;1α Is Permeable to Boric Acid and Is Phosphorylated in the N-terminal Domain.

Ampah-Korsah H, Anderberg HI, Engfors A, ..., Kjellbom P, Johanson U

Front Plant Sci 7 (-) 862 [2016-06-16; online 2016-06-16]

Effects of Fluoxetine on Human Embryo Development.

Kaihola H, Yaldir FG, Hreinsson J, ..., Åkerud H, Sundström-Poromaa I

Front Cell Neurosci 10 (-) 160 [2016-06-16; online 2016-06-16]

Mass Spectrometry-based Proteomics, Uppsala [Collaborative]

Draft Genome Sequence of Moraxella catarrhalis Type Strain CCUG 353T.

Jakobsson HE, Salvà-Serra F, Thorell K, ..., Kristiansson E, Moore ERB

Genome Announc 4 (3) e00552-16 [2016-06-16; online 2016-06-16]

Clinical Genomics Gothenburg [Collaborative] Clinical Genomics Stockholm [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Read-based phasing of related individuals.

Garg S, Martin M, Marschall T

Bioinformatics 32 (12) i234-i242 [2016-06-15; online 2016-06-17]

Bioinformatics Long-term Support WABI [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development]

Parental epigenetic asymmetry of PRC2-mediated histone modifications in the Arabidopsis endosperm.

Moreno-Romero J, Jiang H, Santos-González J, Köhler C

EMBO J. 35 (12) 1298-1311 [2016-06-15; online 2016-04-27]

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

Tumor acidosis enhances cytotoxic effects and autophagy inhibition by salinomycin on cancer cell lines and cancer stem cells.

Pellegrini P, Dyczynski M, Sbrana FV, ..., Kharaziha P, De Milito A

Oncotarget 7 (24) 35703-35723 [2016-06-14; online 2016-06-02]

Chemical Biology Consortium Sweden (CBCS) [Service]

Evolution and expression of the phosphodiesterase 6 genes unveils vertebrate novelty to control photosensitivity.

Lagman D, Franzén IE, Eggert J, Larhammar D, Abalo XM

BMC Evol. Biol. 16 (1) 124 [2016-06-13; online 2016-06-13]

Genome Engineering Zebrafish [Technology development]

Structural Analysis of a Complex between Small Ubiquitin-like Modifier 1 (SUMO1) and the ZZ Domain of CREB-binding Protein (CBP/p300) Reveals a New Interaction Surface on SUMO.

Diehl C, Akke M, Bekker-Jensen S, ..., Streicher W, Wikström M

J. Biol. Chem. 291 (24) 12658-12672 [2016-06-10; online 2016-04-25]

Regulation of Bone Morphogenetic Protein Signaling by ADP-ribosylation

Watanabe Y, Papoutsoglou P, Maturi V, ..., Heldin CH, Moustakas A

J. Biol. Chem. 291 (24) 12706-12723 [2016-06-10; online 2016-04-21]

Affinity Proteomics Uppsala [Service] PLA and Single Cell Proteomics [Service]

Oligodendrocyte heterogeneity in the mouse juvenile and adult central nervous system.

Marques S, Zeisel A, Codeluppi S, ..., Linnarsson S, Castelo-Branco G

Science 352 (6291) 1326-1329 [2016-06-10; online 2016-06-11]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Recommendations on e-infrastructures for next-generation sequencing.

Spjuth O, Bongcam-Rudloff E, Dahlberg J, ..., Vezzi F, Korpelainen E

Gigascience 5 (-) 26 [2016-06-07; online 2016-06-07]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Technology development] National Genomics Infrastructure [Technology development]

Identification of ETV6-RUNX1-like and DUX4-rearranged subtypes in paediatric B-cell precursor acute lymphoblastic leukaemia.

Lilljebjörn H, Henningsson R, Hyrenius-Wittsten A, ..., Fontes M, Fioretos T

Nat Commun 7 (-) 11790 [2016-06-06; online 2016-06-06]

Clinical Genomics Lund [Collaborative]

Elevated levels of FN1 and CCL2 in bronchoalveolar lavage fluid from sarcoidosis patients.

Hamsten C, Wiklundh E, Grönlund H, ..., Grunewald J, Häggmark-Månberg A

Respir. Res. 17 (1) 69 [2016-06-04; online 2016-06-04]

Affinity Proteomics Stockholm [Collaborative]

Guidance Molecule SEMA3A Restricts Tumor Growth by Differentially Regulating the Proliferation of Tumor-Associated Macrophages.

Wallerius M, Wallmann T, Bartish M, ..., Andersson J, Rolny C

Cancer Res. 76 (11) 3166-3178 [2016-06-01; online 2016-04-06]

Aerobic exercise augments muscle transcriptome profile of resistance exercise.

Lundberg TR, Fernandez-Gonzalo R, Tesch PA, Rullman E, Gustafsson T

Am. J. Physiol. Regul. Integr. Comp. Physiol. 310 (11) R1279-R1287 [2016-06-01; online 2016-04-13]

Bioinformatics and Expression Analysis (BEA) [Service]

The oxidized phospholipid PazePC promotes permeabilization of mitochondrial membranes by Bax.

Lidman M, Pokorná Š, Dingeldein AP, ..., Hof M, Gröbner G

Biochim. Biophys. Acta 1858 (6) 1288-1297 [2016-06-00; online 2016-03-04]

Somatic, positive and negative domains of the Center for Epidemiological Studies Depression (CES-D) scale: a meta-analysis of genome-wide association studies.

Demirkan A, Lahti J, Direk N, ..., van Duijn CM, Räikkönen K

Psychol Med 46 (8) 1613-1623 [2016-06-00; online 2016-03-22]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Single Chain Antibodies as Tools to Study transforming growth factor-β-Regulated SMAD Proteins in Proximity Ligation-Based Pharmacological Screens.

Blokzijl A, Zieba A, Hust M, ..., Dübel S, Landegren U

Mol. Cell Proteomics 15 (6) 1848-1856 [2016-06-00; online 2016-03-02]

Affinity Proteomics Uppsala [Technology development] PLA and Single Cell Proteomics [Technology development]

Scolytus multistriatus associated with Dutch elm disease on the island of Gotland: phenology and communities of vectored fungi

Menkis A, Östbrant IL, Davydenko K, ..., Balalaikins M, Vasaitis R

Mycol Progress 15 (6) - [2016-06-00; online 2016-05-26]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Mosaic Loss of Chromosome Y in Blood Is Associated with Alzheimer Disease

Dumanski JP, Lambert JC, Rasi C, ..., Lind L, Forsberg LA

The American Journal of Human Genetics 98 (6) 1208-1219 [2016-06-00; online 2016-06-00]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

High density of REC8 constrains sister chromatid axes and prevents illegitimate synaptonemal complex formation.

Agostinho A, Manneberg O, van Schendel R, ..., Brismar H, Höög C

EMBO Rep. 17 (6) 901-913 [2016-06-00; online 2016-05-14]

Integrated Microscopy Technologies Stockholm [Collaborative]

Genetic variants associated with subjective well-being, depressive symptoms, and neuroticism identified through genome-wide analyses.

Okbay A, Baselmans BM, De Neve JE, ..., Bartels M, Cesarini D

Nat. Genet. 48 (6) 624-633 [2016-06-00; online 2016-04-19]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Genetic variants associated with antithyroid drug-induced agranulocytosis: a genome-wide association study in a European population.

Hallberg P, Eriksson N, Ibañez L, ..., Wadelius M, EuDAC collaborators

Lancet Diabetes Endocrinol 4 (6) 507-516 [2016-06-00; online 2016-05-10]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]

GPR44 is a pancreatic protein restricted to the human beta cell.

Hellström-Lindahl E, Danielsson A, Ponten F, ..., Johansson L, Eriksson O

Acta Diabetol 53 (3) 413-421 [2016-06-00; online 2015-10-14]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Tissue Profiling [Collaborative]

Epigenomics of Total Acute Sleep Deprivation in Relation to Genome-Wide DNA Methylation Profiles and RNA Expression.

Nilsson EK, Boström AE, Mwinyi J, Schiöth HB

OMICS 20 (6) 334-342 [2016-06-00; online 2016-06-17]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Epigenome-wide DNA methylation patterns associated with fatigue in primary Sjögren's syndrome.

Brække Norheim K, Imgenberg-Kreuz J, Jonsdottir K, ..., Nordmark G, Omdal R

Rheumatology (Oxford) 55 (6) 1074-1082 [2016-06-00; online 2016-03-12]

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

Disruptive selection without genome-wide evolution across a migratory divide.

von Rönn JA, Shafer AB, Wolf JB

Mol. Ecol. 25 (11) 2529-2541 [2016-06-00; online 2016-01-11]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Detection of Biomarkers with Solid-Phase Proximity Ligation Assay in Patients with Colorectal Cancer

Ghanipour L, Darmanis S, Landegren U, ..., Påhlman L, Birgisson H

Transl Oncol 9 (3) 251-255 [2016-06-00; online 2016-06-00]

Affinity Proteomics Uppsala [Collaborative] PLA and Single Cell Proteomics [Collaborative] Tissue Profiling [Service]

Coxsackievirus counters the host innate immune response by blocking type III interferon expression.

Lind K, Svedin E, Domsgen E, ..., Moll M, Flodström-Tullberg M

J. Gen. Virol. 97 (6) 1-12 [2016-06-00; online 2016-03-02]

Common and Rare Genetic Variation in CCR2, CCR5, or CX3CR1 and Risk of Atherosclerotic Coronary Heart Disease and Glucometabolic Traits.

Golbus JR, Stitziel NO, Zhao W, ..., Reilly MP, CARDIoGRAMplusC4D, Myocardial Infarction Genetics (MIGen), Exome Sequencing Project and Early-Onset Myocardial Infarction (ESP EOMI), and the Pakistan Risk of Myocardial Infarction Study (PROMIS) Consortia*

Circ Cardiovasc Genet 9 (3) 250-258 [2016-06-00; online 2016-03-26]

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

Allele-specific transcription factor binding in liver and cervix cells unveils many likely drivers of GWAS signals.

Cavalli M, Pan G, Nord H, ..., Wallerman O, Wadelius C

Genomics 107 (6) 248-254 [2016-06-00; online 2016-04-30]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Variants within the SP110 nuclear body protein modify risk of canine degenerative myelopathy.

Ivansson EL, Megquier K, Kozyrev SV, ..., Coates JR, Lindblad-Toh K

Proc. Natl. Acad. Sci. U.S.A. 113 (22) E3091-E3100 [2016-05-31; online 2016-05-18]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

The POU/Oct Transcription Factor Pdm1/nub Is Necessary for a Beneficial Gut Microbiota and Normal Lifespan of Drosophila.

Dantoft W, Lundin D, Esfahani SS, Engström Y

J Innate Immun 8 (4) 412-426 [2016-05-28; online 2016-05-28]

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

Thermotolerant yeasts selected by adaptive evolution express heat stress response at 30 °C.

Caspeta L, Chen Y, Nielsen J

Sci Rep 6 (-) 27003 [2016-05-27; online 2016-05-27]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Genome-wide association study identifies 74 loci associated with educational attainment.

Okbay A, Beauchamp JP, Fontana MA, ..., Cesarini D, Benjamin DJ

Nature 533 (7604) 539-542 [2016-05-26; online 2016-05-11]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Targeting Serglycin Prevents Metastasis in Murine Mammary Carcinoma.

Roy A, Femel J, Huijbers EJ, ..., Olsson AK, Åbrink M

PLoS ONE 11 (5) e0156151 [2016-05-25; online 2016-05-25]

Array and Analysis Facility [Service]

New technologies for DNA analysis--a review of the READNA Project.

McGinn S, Bauer D, Brefort T, ..., Willcocks JP, Gut IG

N Biotechnol 33 (3) 311-330 [2016-05-25; online 2015-10-26]

Clinical Genomics Uppsala [Collaborative]

Glycosaminoglycan Profiling in Patients' Plasma and Urine Predicts the Occurrence of Metastatic Clear Cell Renal Cell Carcinoma.

Gatto F, Volpi N, Nilsson H, ..., Basso U, Nielsen J

Cell Rep 15 (8) 1822-1836 [2016-05-24; online 2016-05-18]

Bioinformatics Support, Infrastructure and Training [Technology development] Systems Biology [Technology development]

Chroman-4-one and chromone based somatostatin β-turn mimetics.

Fridén-Saxin M, Seifert T, Malo M, ..., Grøtli M, Luthman K

Eur J Med Chem 114 (-) 59-64 [2016-05-23; online 2016-02-21]

Metagenomic Analysis of the Indian Ocean Picocyanobacterial Community: Structure, Potential Function and Evolution.

Díez B, Nylander JA, Ininbergs K, ..., Rusch DB, Bergman B

PLoS ONE 11 (5) e0155757 [2016-05-19; online 2016-05-19]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

A Population Shift between Sparsely Populated Folding Intermediates Determines Amyloidogenicity.

Karamanos TK, Pashley CL, Kalverda AP, ..., Orekhov VY, Radford SE

J. Am. Chem. Soc. 138 (19) 6271-6280 [2016-05-18; online 2016-05-06]

Pseudomonas aeruginosa elastase cleaves a C-terminal peptide from human thrombin that inhibits host inflammatory responses.

van der Plas MJ, Bhongir RK, Kjellström S, ..., Mörgelin M, Schmidtchen A

Nat Commun 7 (-) 11567 [2016-05-16; online 2016-05-16]

Effects of Dispersal and Initial Diversity on the Composition and Functional Performance of Bacterial Communities.

Zha Y, Berga M, Comte J, Langenheder S

PLoS ONE 11 (5) e0155239 [2016-05-16; online 2016-05-16]

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Multiplexed MALDI-MS arrays for screening of MIP solid phase extraction materials.

Jagadeesan KK, Wierzbicka C, Laurell T, ..., Shinde S, Ekström S

Journal of Chromatography B 1021 (-) 213-220 [2016-05-15; online 2015-10-30]

Minimal selective concentrations of tetracycline in complex aquatic bacterial biofilms.

Lundström SV, Östman M, Bengtsson-Palme J, ..., Flach CF, Larsson DG

Sci. Total Environ. 553 (-) 587-595 [2016-05-15; online 2016-03-05]

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Microwell-Based Live Cell Imaging of NK Cell Dynamics to Assess Heterogeneity in Motility and Cytotoxic Response.

Vanherberghen B, Frisk T, Forslund E, ..., Guldevall K, Önfelt B

Methods Mol. Biol. 1441 (-) 87-106 [2016-05-15; online 2016-05-15]

Integrated Microscopy Technologies Stockholm [Technology development]

Inclusion of dyad-repeat pattern improves topology prediction of transmembrane β-barrel proteins.

Hayat S, Peters C, Shu N, Tsirigos KD, Elofsson A

Bioinformatics 32 (10) 1571-1573 [2016-05-15; online 2016-01-23]

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Detection of signal recognition particle (SRP) RNAs in the nuclear ribosomal internal transcribed spacer 1 (ITS1) of three lineages of ectomycorrhizal fungi (Agaricomycetes, Basidiomycota)

Nilsson RH, Alm Rosenblad M, Martín MP, ..., Wurzbacher C, Abarenkov K

MycoKeys 13 (-) 21-33 [2016-05-13; online 2016-05-13]

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A combined computational and structural model of the full-length human prolactin receptor.

Bugge K, Papaleo E, Haxholm GW, ..., Lindorff-Larsen K, Kragelund BB

Nat Commun 7 (-) 11578 [2016-05-13; online 2016-05-13]

Diversity of Pico- to Mesoplankton along the 2000 km Salinity Gradient of the Baltic Sea.

Hu YO, Karlson B, Charvet S, Andersson AF

Front Microbiol 7 (-) 679 [2016-05-12; online 2016-05-12]

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Inflammatory Serum Protein Profiling of Patients with Lumbar Radicular Pain One Year after Disc Herniation.

Moen A, Lind AL, Thulin M, ..., Gjerstad J, Gordh T

Int J Inflam 2016 (-) 3874964 [2016-05-11; online 2016-05-11]

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Divergent non-heme iron enzymes in the nogalamycin biosynthetic pathway.

Siitonen V, Selvaraj B, Niiranen L, ..., Schneider G, Metsä-Ketelä M

Proc. Natl. Acad. Sci. U.S.A. 113 (19) 5251-5256 [2016-05-10; online 2016-04-25]

Determining breast cancer histological grade from RNA-sequencing data.

Wang M, Klevebring D, Lindberg J, ..., Grönberg H, Rantalainen M

Breast Cancer Res. 18 (1) 48 [2016-05-10; online 2016-05-10]

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Unscrambling Cyanobacteria Community Dynamics Related to Environmental Factors.

Bertos-Fortis M, Farnelid HM, Lindh MV, ..., Pinhassi J, Legrand C

Front Microbiol 7 (-) 625 [2016-05-09; online 2016-05-09]

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Asp-ase Activity of the Opossum Granzyme B Supports the Role of Granzyme B as Part of Anti-Viral Immunity Already during Early Mammalian Evolution.

Fu Z, Thorpe M, Akula S, Hellman L

PLoS ONE 11 (5) e0154886 [2016-05-06; online 2016-05-06]

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The Effects of High Steady State Auxin Levels on Root Cell Elongation in Brachypodium.

Pacheco-Villalobos D, Díaz-Moreno SM, van der Schuren A, ..., Bulone V, Hardtke CS

Plant Cell - (-) - [2016-05-05; online 2016-05-05]

Changes in variation at the MHC class II DQA locus during the final demise of the woolly mammoth.

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

Sci Rep 6 (-) 25274 [2016-05-04; online 2016-05-04]

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The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing.

Martinez Barrio A, Lamichhaney S, Fan G, ..., Xu X, Andersson L

Elife 5 (-) - [2016-05-03; online 2016-05-03]

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Sister Chromatid Cohesion Establishment Factor ESCO1 Operates by Substrate-Assisted Catalysis.

Kouznetsova E, Kanno T, Karlberg T, ..., Sjögren C, Schüler H

Structure 24 (5) 789-796 [2016-05-03; online 2016-04-21]

Schizophrenia and subsequent neighborhood deprivation: revisiting the social drift hypothesis using population, twin and molecular genetic data.

Sariaslan A, Fazel S, D'Onofrio BM, ..., Kuja-Halkola R, Lichtenstein P

Transl Psychiatry 6 (-) e796 [2016-05-03; online 2016-05-03]

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Epigenetic silencing of miR-26A1 in chronic lymphocytic leukemia and mantle cell lymphoma: Impact on EZH2 expression.

Kopparapu PK, Bhoi S, Mansouri L, ..., Rosenquist R, Kanduri M

Epigenetics 11 (5) 335-343 [2016-05-03; online 2016-04-08]

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mRNA GPR162 changes are associated with decreased food intake in rat, and its human genetic variants with impairments in glucose homeostasis in two Swedish cohorts.

Caruso V, Sreedharan S, Carlini VP, ..., Fredriksson R, Schiöth HB

Gene 581 (2) 139-145 [2016-05-01; online 2016-02-02]

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High-Density Genetic Mapping Identifies New Susceptibility Variants in Sarcoidosis Phenotypes and Shows Genomic-driven Phenotypic Differences.

Rivera NV, Ronninger M, Shchetynsky K, ..., Padyukov L, Grunewald J

Am. J. Respir. Crit. Care Med. 193 (9) 1008-1022 [2016-05-01; online 2015-12-15]

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Evidence for Genetic Overlap Between Schizophrenia and Age at First Birth in Women.

Mehta D, Tropf FC, Gratten J, ..., Weiser M, Wu JQ

JAMA Psychiatry 73 (5) 497-505 [2016-05-01; online 2016-03-24]

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nanoCAGE reveals 5' UTR features that define specific modes of translation of functionally related MTOR-sensitive mRNAs.

Gandin V, Masvidal L, Hulea L, ..., Larsson O, Topisirovic I

Genome Res. 26 (5) 636-648 [2016-05-00; online 2016-03-18]

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Whole-genome resequencing of extreme phenotypes in collared flycatchers highlights the difficulty of detecting quantitative trait loci in natural populations.

Kardos M, Husby A, McFarlane SE, Qvarnström A, Ellegren H

Mol Ecol Resour 16 (3) 727-741 [2016-05-00; online 2015-12-10]

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Utilizing the Dog Genome in the Search for Novel Candidate Genes Involved in Glioma Development-Genome Wide Association Mapping followed by Targeted Massive Parallel Sequencing Identifies a Strongly Associated Locus.

Truvé K, Dickinson P, Xiong A, ..., Bannasch D, Lindblad-Toh K

PLoS Genet. 12 (5) e1006000 [2016-05-00; online 2016-05-12]

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Synchronous genetic turnovers across Western Eurasia in Late Pleistocene collared lemmings.

Palkopoulou E, Baca M, Abramson NI, ..., Stankovic A, Dalén L

Glob Chang Biol 22 (5) 1710-1721 [2016-05-00; online 2016-02-27]

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Regulating retrotransposon activity through the use of alternative transcription start sites.

Persson J, Steglich B, Smialowska A, ..., Nielsen O, Ekwall K

EMBO Rep. 17 (5) 753-768 [2016-05-00; online 2016-02-22]

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Reduced mitochondrial malate dehydrogenase activity has a strong effect on photorespiratory metabolism as revealed by 13C labelling.

Lindén P, Keech O, Stenlund H, Gardeström P, Moritz T

J. Exp. Bot. 67 (10) 3123-3135 [2016-05-00; online 2016-02-19]

Swedish Metabolomics Centre (SMC) [Collaborative]

Molecular Characterization of Three Canine Models of Human Rare Bone Diseases: Caffey, van den Ende-Gupta, and Raine Syndromes.

Hytönen MK, Arumilli M, Lappalainen AK, ..., Drögemüller C, Lohi H

PLoS Genet. 12 (5) e1006037 [2016-05-00; online 2016-05-17]

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Microbial metagenomes from three aquifers in the Fennoscandian shield terrestrial deep biosphere reveal metabolic partitioning among populations.

Wu X, Holmfeldt K, Hubalek V, ..., Bertilsson S, Dopson M

ISME J 10 (5) 1192-1203 [2016-05-00; online 2015-10-21]

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Metabolomics study of fatigue in patients with rheumatoid arthritis naïve to biological treatment.

Surowiec I, Gjesdal CG, Jonsson G, ..., Trygg J, Omdal R

Rheumatol. Int. 36 (5) 703-711 [2016-05-00; online 2016-01-25]

High-Resolution Mapping of Crossover and Non-crossover Recombination Events by Whole-Genome Re-sequencing of an Avian Pedigree.

Smeds L, Mugal CF, Qvarnström A, Ellegren H

PLoS Genet. 12 (5) e1006044 [2016-05-00; online 2016-05-24]

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Genetic risk variants in the CDKN2A/B, RTEL1 and EGFR genes are associated with somatic biomarkers in glioma.

Ghasimi S, Wibom C, Dahlin AM, ..., Andersson U, Melin B

J. Neurooncol. 127 (3) 483-492 [2016-05-00; online 2016-02-04]

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Genetic loci on chromosome 5 are associated with circulating levels of interleukin-5 and eosinophil count in a European population with high risk for cardiovascular disease.

McLeod O, Silveira A, Valdes-Marquez E, ..., Strawbridge RJ, IMPROVE Study Group

Cytokine 81 (-) 1-9 [2016-05-00; online 2016-01-29]

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Functionalized silk assembled from a recombinant spider silk fusion protein (Z-4RepCT) produced in the methylotrophic yeast Pichia pastoris.

Jansson R, Lau CH, Ishida T, ..., Sandgren M, Hedhammar M

Biotechnol J 11 (5) 687-699 [2016-05-00; online 2016-03-04]

Mass Spectrometry-based Proteomics, Uppsala [Collaborative]

Divergence in gene expression within and between two closely related flycatcher species.

Uebbing S, Künstner A, Mäkinen H, ..., Searle SM, Ellegren H

Mol. Ecol. 25 (9) 2015-2028 [2016-05-00; online 2016-03-02]

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Distinct temporal changes in host cell lncRNA expression during the course of an adenovirus infection.

Zhao H, Chen M, Lind SB, Pettersson U

Virology 492 (-) 242-250 [2016-05-00; online 2016-03-24]

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Displacement of US-1 clonal lineage by a new lineage ofPhytophthora infestanson potato in Kenya and Uganda

Njoroge AW, Tusiime G, Forbes GA, Yuen JE

Plant Pathol 65 (4) 587-592 [2016-05-00; online 2015-09-16]

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Details in the catalytic mechanism of mammalian thioredoxin reductase 1 revealed using point mutations and juglone-coupled enzyme activities.

Xu J, Cheng Q, Arnér ES

Free Radic. Biol. Med. 94 (-) 110-120 [2016-05-00; online 2016-02-17]

Mass Spectrometry-based Proteomics, Uppsala [Service]

DNA-metabarcoding uncovers the diversity of soil-inhabiting fungi in the tropical island of Puerto Rico

Urbina H, Scofield DG, Cafaro M, Rosling A

Mycoscience 57 (3) 217-227 [2016-05-00; online 2016-05-00]

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Biotin and Thiamine Responsive Basal Ganglia Disease--A vital differential diagnosis in infants with severe encephalopathy.

Ygberg S, Naess K, Eriksson M, ..., Wedell A, Wickström R

Eur. J. Paediatr. Neurol. 20 (3) 457-461 [2016-05-00; online 2016-03-16]

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Association mapping in Salix viminalis L. (Salicaceae) - identification of candidate genes associated with growth and phenology.

Hallingbäck HR, Fogelqvist J, Powers SJ, ..., Berlin S, Rönnberg-Wästljung AC

Glob Change Biol Bioenergy 8 (3) 670-685 [2016-05-00; online 2015-07-29]

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Antigen arrays for profiling autoantibody repertoires.

Ayoglu B, Schwenk JM, Nilsson P

Bioanalysis 8 (10) 1105-1126 [2016-05-00; online 2016-04-22]

Autoimmunity and Serology Profiling [Technology development]

An obesity-associated risk allele within the FTO gene affects human brain activity for areas important for emotion, impulse control and reward in response to food images.

Wiemerslage L, Nilsson EK, Solstrand Dahlberg L, ..., Brooks SJ, Schiöth HB

Eur. J. Neurosci. 43 (9) 1173-1180 [2016-05-00; online 2016-01-23]

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Allele-specific transcription factor binding to common and rare variants associated with disease and gene expression.

Cavalli M, Pan G, Nord H, ..., Lindblad Toh K, Wadelius C

Hum. Genet. 135 (5) 485-497 [2016-05-00; online 2016-03-20]

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A Systematic Characterization of Aquaporin-9 Expression in Human Normal and Pathological Tissues.

Lindskog C, Asplund A, Catrina A, Nielsen S, Rützler M

J. Histochem. Cytochem. 64 (5) 287-300 [2016-05-00; online 2016-03-29]

TOR Signaling and Nutrient Sensing.

Dobrenel T, Caldana C, Hanson J, ..., Veit B, Meyer C

Annu Rev Plant Biol 67 (-) 261-285 [2016-04-29; online 2016-02-26]

The Bee Microbiome: Impact on Bee Health and Model for Evolution and Ecology of Host-Microbe Interactions.

Engel P, Kwong WK, McFrederick Q, ..., vanEngelsdorp D, Dainat B

MBio 7 (2) e02164-e02115 [2016-04-26; online 2016-04-26]

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Elevated Levels of SOX10 in Serum from Vitiligo and Melanoma Patients, Analyzed by Proximity Ligation Assay

Blokzijl A, Chen LE, Gustafsdottir SM, ..., Kamali-Moghaddam M, Hedstrand H

PLoS ONE 11 (4) e0154214 [2016-04-25; online 2016-04-25]

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Longitudinal genome-wide methylation study of Roux-en-Y gastric bypass patients reveals novel CpG sites associated with essential hypertension.

Boström AE, Mwinyi J, Voisin S, ..., Zhang K, Schiöth HB

BMC Med Genomics 9 (-) 20 [2016-04-22; online 2016-04-22]

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A beak size locus in Darwin's finches facilitated character displacement during a drought.

Lamichhaney S, Han F, Berglund J, ..., Grant PR, Andersson L

Science 352 (6284) 470-474 [2016-04-22; online 2016-04-23]

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Spatio-Temporal Interdependence of Bacteria and Phytoplankton during a Baltic Sea Spring Bloom.

Bunse C, Bertos-Fortis M, Sassenhagen I, ..., Pinhassi J, Legrand C

Front Microbiol 7 (-) 517 [2016-04-21; online 2016-04-21]

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Associations between a locus downstream DRD1 gene and cerebrospinal fluid dopamine metabolite concentrations in psychosis.

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

Neurosci. Lett. 619 (-) 126-130 [2016-04-21; online 2016-03-10]

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Hypoxia regulates global membrane protein endocytosis through caveolin-1 in cancer cells.

Bourseau-Guilmain E, Menard JA, Lindqvist E, ..., Welinder C, Belting M

Nat Commun 7 (-) 11371 [2016-04-20; online 2016-04-20]

msIQuant--Quantitation Software for Mass Spectrometry Imaging Enabling Fast Access, Visualization, and Analysis of Large Data Sets.

Källback P, Nilsson A, Shariatgorji M, Andrén PE

Anal. Chem. 88 (8) 4346-4353 [2016-04-19; online 2016-04-05]

Spatial Mass Spectrometry [Technology development]

Mutations in histone modulators are associated with prolonged survival during azacitidine therapy.

Tobiasson M, McLornan DP, Karimi M, ..., Mufti GJ, Hellström-Lindberg E

Oncotarget 7 (16) 22103-22115 [2016-04-19; online 2016-03-10]

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EPH/ephrin profile and EPHB2 expression predicts patient survival in breast cancer.

Husa AM, Magić Ž, Larsson M, Fornander T, Pérez-Tenorio G

Oncotarget 7 (16) 21362-21380 [2016-04-19; online 2016-02-13]

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Improved topology prediction using the terminal hydrophobic helices rule.

Peters C, Tsirigos KD, Shu N, Elofsson A

Bioinformatics 32 (8) 1158-1162 [2016-04-15; online 2015-12-09]

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Cytosolic splice isoform of Hsp70 nucleotide exchange factor Fes1 is required for the degradation of misfolded proteins in yeast.

Gowda NK, Kaimal JM, Masser AE, ..., Friedländer MR, Andréasson C

Mol. Biol. Cell 27 (8) 1210-1219 [2016-04-15; online 2016-02-26]

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A role for PDGF-C/PDGFRα signaling in the formation of the meningeal basement membranes surrounding the cerebral cortex.

Andrae J, Gouveia L, Gallini R, ..., Eriksson U, Betsholtz C

Biol Open 5 (4) 461-474 [2016-04-15; online 2016-04-15]

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Using an Inbred Horse Breed in a High Density Genome-Wide Scan for Genetic Risk Factors of Insect Bite Hypersensitivity (IBH).

Velie BD, Shrestha M, Franҫois L, ..., Buys N, Lindgren G

PLoS ONE 11 (4) e0152966 [2016-04-12; online 2016-04-12]

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Immunostimulatory AdCD40L gene therapy combined with low-dose cyclophosphamide in metastatic melanoma patients.

Loskog A, Maleka A, Mangsbo S, ..., Tötterman TH, Ullenhag G

Br. J. Cancer 114 (8) 872-880 [2016-04-12; online 2016-03-31]

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Tissue and Serum miRNA Profile in Locally Advanced Breast Cancer (LABC) in Response to Neo-Adjuvant Chemotherapy (NAC) Treatment.

Al-Khanbashi M, Caramuta S, Alajmi AM, ..., Lui WO, Al-Moundhri MS

PLoS ONE 11 (4) e0152032 [2016-04-11; online 2016-04-11]

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The Mycobacterium phlei Genome: Expectations and Surprises.

Das S, Pettersson BM, Behra PR, ..., Bhattacharya A, Kirsebom LA

Genome Biol Evol 8 (4) 975-985 [2016-04-08; online 2016-03-05]

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Identification and Characterization of IgdE, a Novel IgG-degrading Protease of Streptococcus suis with Unique Specificity for Porcine IgG.

Spoerry C, Seele J, Valentin-Weigand P, Baums CG, von Pawel-Rammingen U

J. Biol. Chem. 291 (15) 7915-7925 [2016-04-08; online 2016-02-11]

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Modifications of the 7-Hydroxyl Group of the Transthyretin Ligand Luteolin Provide Mechanistic Insights into Its Binding Properties and High Plasma Specificity.

Nilsson L, Larsson A, Begum A, ..., Sauer-Eriksson AE, Olofsson A

PLoS ONE 11 (4) e0153112 [2016-04-06; online 2016-04-06]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Microchip Screening Platform for Single Cell Assessment of NK Cell Cytotoxicity.

Guldevall K, Brandt L, Forslund E, ..., Uhlin M, Önfelt B

Front Immunol 7 (-) 119 [2016-04-05; online 2016-04-05]

Integrated Microscopy Technologies Stockholm [Technology development]

Markers of fibroblast-rich tumor stroma and perivascular cells in serous ovarian cancer: Inter- and intra-patient heterogeneity and impact on survival.

Corvigno S, Wisman GB, Mezheyeuski A, ..., Östman A, Dahlstrand H

Oncotarget 7 (14) 18573-18584 [2016-04-05; online 2016-02-27]

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Transcriptomics resources of human tissues and organs.

Uhlén M, Hallström BM, Lindskog C, ..., Pontén F, Nielsen J

Mol. Syst. Biol. 12 (4) 862 [2016-04-04; online 2016-04-04]

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Label-Free Fluctuation Spectroscopy Based on Coherent Anti-Stokes Raman Scattering from Bulk Water Molecules.

Rabasovic MD, Sisamakis E, Wennmalm S, Widengren J

Chemphyschem 17 (7) 1025-1033 [2016-04-04; online 2016-01-29]

Fluorescence Correlation Spectroscopy [Technology development] Integrated Microscopy Technologies Stockholm

Structural Studies of Lipopolysaccharide-defective Mutants from Brucella melitensis Identify a Core Oligosaccharide Critical in Virulence.

Fontana C, Conde-Álvarez R, Ståhle J, ..., Moriyón I, Widmalm G

J. Biol. Chem. 291 (14) 7727-7741 [2016-04-01; online 2016-02-11]

Sex-dependent expression of anti-Müllerian hormone (amh) and amh receptor 2 during sex organ differentiation and characterization of the Müllerian duct development in Xenopus tropicalis.

Jansson E, Mattsson A, Goldstone J, Berg C

Gen. Comp. Endocrinol. 229 (-) 132-144 [2016-04-01; online 2016-03-19]

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Na+-K+-ATPase, a new class of plasma membrane receptors.

Aperia A, Akkuratov EE, Fontana JM, Brismar H

Am. J. Physiol., Cell Physiol. 310 (7) C491-C495 [2016-04-01; online 2016-01-23]

Integrated Microscopy Technologies Stockholm [Collaborative]

Genome-wide association and Mendelian randomization study of NT-proBNP in patients with acute coronary syndrome.

Johansson Å, Eriksson N, Lindholm D, ..., Wallentin L, PLATO Investigators

Hum. Mol. Genet. 25 (7) 1447-1456 [2016-04-01; online 2016-02-26]

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CopyNumber450kCancer: baseline correction for accurate copy number calling from the 450k methylation array.

Marzouka NA, Nordlund J, Bäcklin CL, ..., Syvänen AC, Carlsson Almlöf J

Bioinformatics 32 (7) 1080-1082 [2016-04-01; online 2015-11-09]

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Whole-body fat oxidation increases more by prior exercise than overnight fasting in elite endurance athletes.

Andersson Hall U, Edin F, Pedersen A, Madsen K

Appl Physiol Nutr Metab 41 (4) 430-437 [2016-04-00; online 2015-12-17]

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Solution structure of the calmodulin-like C-terminal domain of Entamoeba α-actinin2.

Karlsson G, Persson C, Mayzel M, Hedenström M, Backman L

Proteins 84 (4) 461-466 [2016-04-00; online 2016-02-05]

Single-cell transcriptome analysis of endometrial tissue.

Krjutškov K, Katayama S, Saare M, ..., Salumets A, Kere J

Hum. Reprod. 31 (4) 844-853 [2016-04-00; online 2016-02-13]

Bioinformatics and Expression Analysis (BEA) [Service]

Replacement of the European wheat yellow rust population by new races from the centre of diversity in the near-Himalayan region

Hovmøller MS, Walter S, Bayles RA, ..., Ali S, de Vallavieille-Pope C

Plant Pathol 65 (3) 402-411 [2016-04-00; online 2015-07-20]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Reduced oxidative stress in primary human cells by antioxidant released from nanoporous alumina.

Pujari-Palmer S, Pujari-Palmer M, Karlsson Ott M

J. Biomed. Mater. Res. Part B Appl. Biomater. 104 (3) 568-575 [2016-04-00; online 2015-05-09]

BioMaterial Interactions (BioMat)

RNA transcript sequencing reveals inorganic sulfur compound oxidation pathways in the acidophile Acidithiobacillus ferrivorans.

Christel S, Fridlund J, Buetti-Dinh A, ..., Watkin EL, Dopson M

FEMS Microbiol. Lett. 363 (7) - [2016-04-00; online 2016-03-10]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

PGC-1α Coordinates Mitochondrial Respiratory Capacity and Muscular Fatty Acid Uptake via Regulation of VEGF-B.

Mehlem A, Palombo I, Wang X, ..., Eriksson U, Falkevall A

Diabetes 65 (4) 861-873 [2016-04-00; online 2016-01-30]

One CNV Discordance in NRXN1 Observed Upon Genome-wide Screening in 38 Pairs of Adult Healthy Monozygotic Twins.

Magnusson PK, Lee D, Chen X, ..., Feuk L, Pawitan Y

Twin Res Hum Genet 19 (2) 97-103 [2016-04-00; online 2016-02-22]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Novel technologies applied to the nucleotide sequencing and comparative sequence analysis of the genomes of infectious agents in veterinary medicine.

Granberg F, Bálint Á, Belák S

Rev. - Off. Int. Epizoot. 35 (1) 25-42 [2016-04-00; online 2016-05-25]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Novel mode of inhibition by D-tagatose 6-phosphate through a Heyns rearrangement in the active site of transaldolase B variants.

Stellmacher L, Sandalova T, Schneider S, ..., Sprenger GA, Samland AK

Acta Crystallogr D Struct Biol 72 (Pt 4) 467-476 [2016-04-00; online 2016-03-24]

Neuroproteomic profiling of human body fluids.

Häggmark A, Schwenk JM, Nilsson P

Proteomics Clin Appl 10 (4) 485-502 [2016-04-00; online 2015-10-12]

Autoimmunity and Serology Profiling [Technology development]

Multiplexed protein profiling by sequential affinity capture.

Ayoglu B, Birgersson E, Mezger A, ..., Nilsson P, Schwenk JM

Proteomics 16 (8) 1251-1256 [2016-04-00; online 2016-03-31]

Affinity Proteomics Stockholm [Technology development]

Multi-platform mass spectrometry analysis of the CSF and plasma metabolomes of rigorously matched amyotrophic lateral sclerosis, Parkinson's disease and control subjects.

Wuolikainen A, Jonsson P, Ahnlund M, ..., Andersen PM, Trupp M

Mol Biosyst 12 (4) 1287-1298 [2016-04-00; online 2016-02-18]

Identification of Drug-Like Inhibitors of Insulin-Regulated Aminopeptidase Through Small-Molecule Screening.

Engen K, Rosenström U, Axelsson H, ..., Lundbäck T, Larhed M

Assay Drug Dev Technol 14 (3) 180-193 [2016-04-00; online 2016-04-15]

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

High-Throughput Screening Using a Whole-Cell Virus Replication Reporter Gene Assay to Identify Inhibitory Compounds against Rift Valley Fever Virus Infection.

Islam MK, Baudin M, Eriksson J, ..., Ahlm C, Evander M

J Biomol Screen 21 (4) 354-362 [2016-04-00; online 2016-01-15]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Global gray-level thresholding based on object size.

Ranefall P, Wählby C

Cytometry A 89 (4) 385-390 [2016-04-00; online 2016-01-23]

BioImage Informatics [Technology development]

Global genome splicing analysis reveals an increased number of alternatively spliced genes with aging.

Rodríguez SA, Grochová D, McKenna T, ..., Erdos MR, Eriksson M

Aging Cell 15 (2) 267-278 [2016-04-00; online 2015-12-22]

Bioinformatics Support and Infrastructure Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Gene regulatory mechanisms underpinning prostate cancer susceptibility.

Whitington T, Gao P, Song W, ..., Wei GH, Wiklund F

Nat. Genet. 48 (4) 387-397 [2016-04-00; online 2016-03-08]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Fish from Head to Tail: The 9th European Zebrafish Meeting in Oslo.

Griffiths G, Müller F, Ledin J, ..., Press CM, Aleström P

Zebrafish 13 (2) 132-137 [2016-04-00; online 2016-02-09]

Genome Engineering Zebrafish [Collaborative]

Fatal acquisition of vanD gene during vancomycin treatment of septicaemia caused by Enterococcus faecium.

Starlander G, Tellgren-Roth C, Melhus Å

J. Hosp. Infect. 92 (4) 409-410 [2016-04-00; online 2016-02-16]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Engineering a thermostable Halothermothrix orenii β-glucosidase for improved galacto-oligosaccharide synthesis.

Hassan N, Geiger B, Gandini R, ..., Divne C, Tan TC

Appl. Microbiol. Biotechnol. 100 (8) 3533-3543 [2016-04-00; online 2015-12-02]

Protein Science Facility (PSF)

Effect of PTPN22 Gene Variant R620W on Type I Interferon Production Stimulated by Different Toll-like Receptor 7 Agonists: Comment on the Article by Wang et al.

Berggren O, Rönnblom L, Eloranta ML

Arthritis & rheumatology (Hoboken, N.J.) 68 (4) 1045 [2016-04-00; online 2016-01-11]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Digital image analysis outperforms manual biomarker assessment in breast cancer.

Stålhammar G, Fuentes Martinez N, Lippert M, ..., Grunkin M, Hartman J

Mod. Pathol. 29 (4) 318-329 [2016-04-00; online 2016-02-27]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

DeMix-Q: Quantification-Centered Data Processing Workflow.

Zhang B, Käll L, Zubarev RA

Mol. Cell Proteomics 15 (4) 1467-1478 [2016-04-00; online 2016-01-04]

Chemical Proteomics [Technology development]

Connective Auxin Transport in the Shoot Facilitates Communication between Shoot Apices.

Bennett T, Hines G, van Rongen M, ..., Ljung K, Leyser O

PLoS Biol. 14 (4) e1002446 [2016-04-00; online 2016-04-27]

Binding to and Inhibition of Insulin-Regulated Aminopeptidase by Macrocyclic Disulfides Enhances Spine Density.

Diwakarla S, Nylander E, Grönbladh A, ..., Chai SY, Hallberg M

Mol. Pharmacol. 89 (4) 413-424 [2016-04-00; online 2016-01-16]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

An Ouzo emulsion of toluene in water characterized by NMR diffusometry and static multiple light scattering

Tehrani-Bagha AR, Viladot A, Holmberg K, Nordstierna L

Colloids and Surfaces A: Physicochemical and Engineering Aspects 494 (-) 81-86 [2016-04-00; online 2016-04-00]

Adaptive major histocompatibility complex (MHC) and neutral genetic variation in two native Baltic Sea fishes (perch Perca fluviatilis and zander Sander lucioperca) with comparisons to an introduced and disease susceptible population in Australia (P. fluviatilis): assessing the risk of disease epidemics.

Faulks LK, Östman Ö

J. Fish Biol. 88 (4) 1564-1583 [2016-04-00; online 2016-03-05]

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

A saposin-lipoprotein nanoparticle system for membrane proteins.

Frauenfeld J, Löving R, Armache JP, ..., Cheng Y, Nordlund P

Nat. Methods 13 (4) 345-351 [2016-04-00; online 2016-03-07]

Super-resolution microscopy reveals γ-secretase at both sides of the neuronal synapse.

Schedin-Weiss S, Caesar I, Winblad B, Blom H, Tjernberg LO

Acta Neuropathol Commun 4 (-) 29 [2016-03-31; online 2016-03-31]

Integrated Microscopy Technologies Stockholm [Collaborative]

A Facile Synthesis of NODASA-Functionalized Peptide

Naicker T, Albericio F, Dutta J, ..., Kruger H, Govender T

Synlett 27 (11) 1685-1688 [2016-03-30; online 2016-03-30]

Drug Discovery and Development (DDD) [Collaborative]

Pseudomonas aeruginosa N-3-oxo-dodecanoyl-homoserine Lactone Elicits Changes in Cell Volume, Morphology, and AQP9 Characteristics in Macrophages

Holm A, Magnusson KE, Vikström E

Front. Cell. Infect. Microbiol. 6 (-) - [2016-03-24; online 2016-03-24]

Integrated Microscopy Technologies Stockholm [Service]

Draft Genome Sequence of Streptococcus gordonii Type Strain CCUG 33482T.

Salvà-Serra F, Jakobsson HE, Thorell K, ..., Kristiansson E, Moore ER

Genome Announc 4 (2) e00175-16 [2016-03-24; online 2016-03-24]

Bioinformatics Support for Computational Resources [Service] Clinical Genomics Gothenburg [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

CETSA screening identifies known and novel thymidylate synthase inhibitors and slow intracellular activation of 5-fluorouracil.

Almqvist H, Axelsson H, Jafari R, ..., Lundbäck T, Nordlund P

Nat Commun 7 (-) 11040 [2016-03-24; online 2016-03-24]

Chemical Biology Consortium Sweden (CBCS) [Collaborative] Protein Science Facility (PSF) [Service]

VEGFR2 pY949 signalling regulates adherens junction integrity and metastatic spread.

Li X, Padhan N, Sjöström EO, ..., Jansson L, Claesson-Welsh L

Nat Commun 7 (-) 11017 [2016-03-23; online 2016-03-23]

Bioinformatics Support and Infrastructure [Service] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

The chemosensory receptors of codling moth Cydia pomonella-expression in larvae and adults.

Walker WB, Gonzalez F, Garczynski SF, Witzgall P

Sci Rep 6 (-) 23518 [2016-03-23; online 2016-03-23]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

System-wide Clinical Proteomics of Breast Cancer Reveals Global Remodeling of Tissue Homeostasis.

Pozniak Y, Balint-Lahat N, Rudolph JD, ..., Barshack I, Geiger T

Cell Syst 2 (3) 172-184 [2016-03-23; online 2016-03-03]

Metagenomic analysis of bloodstream infections in patients with acute leukemia and therapy-induced neutropenia.

Gyarmati P, Kjellander C, Aust C, ..., Öhrmalm L, Giske CG

Sci Rep 6 (-) 23532 [2016-03-21; online 2016-03-21]

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

Local auxin metabolism regulates environment-induced hypocotyl elongation

Zheng Z, Guo Y, Novák O, ..., Noel JP, Chory J

NPLANTS 2 (4) 16025 [2016-03-21; online 2016-03-21]

On-Water Synthesis of Biaryl Sulfonyl Fluorides.

Chinthakindi PK, Kruger HG, Govender T, Naicker T, Arvidsson PI

J. Org. Chem. 81 (6) 2618-2623 [2016-03-18; online 2016-02-24]

Drug Discovery and Development (DDD) [Collaborative]

PopulationProfiler: A Tool for Population Analysis and Visualization of Image-Based Cell Screening Data.

Matuszewski DJ, Wählby C, Puigvert JC, Sintorn IM

PLoS ONE 11 (3) e0151554 [2016-03-17; online 2016-03-17]

BioImage Informatics [Service]

Metagenomic Analysis from the Interior of a Speleothem in Tjuv-Ante's Cave, Northern Sweden.

Zepeda Mendoza ML, Lundberg J, Ivarsson M, ..., Sallstedt T, Dalen L

PLoS ONE 11 (3) e0151577 [2016-03-17; online 2016-03-17]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

In Situ Staining and Laser Capture Microdissection of Lymph Node Residing SIV Gag-Specific CD8+ T cells--A Tool to Interrogate a Functional Immune Response Ex Vivo.

Tjernlund A, Burgener A, Lindvall JM, ..., McElrath MJ, Corey L

PLoS ONE 11 (3) e0149907 [2016-03-17; online 2016-03-17]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

The role of transposable elements for gene expression in Capsella hybrids and allopolyploids

Steige K, Reimegård J, Rebernig CA, ..., Scofield DG, Slotte T

bioRxiv - (-) - [2016-03-16; online 2016-03-16]

Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

The Intestinal Eukaryotic Virome in Healthy and Diarrhoeic Neonatal Piglets.

Karlsson OE, Larsson J, Hayer J, Berg M, Jacobson M

PLoS ONE 11 (3) e0151481 [2016-03-16; online 2016-03-16]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

The FAIR Guiding Principles for scientific data management and stewardship.

Wilkinson MD, Dumontier M, Aalbersberg IJ, ..., Zhao J, Mons B

Sci Data 3 (-) 160018 [2016-03-15; online 2016-03-15]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Transition from Bioinert to Bioactive Material by Tailoring the Biological Cell Response to Carboxylated Nanocellulose.

Hua K, Rocha I, Zhang P, ..., Mihranyan A, Ferraz N

Biomacromolecules 17 (3) 1224-1233 [2016-03-14; online 2016-03-01]

BioMaterial Interactions (BioMat) [Collaborative]

Luminescent Nanocellulose Platform: From Controlled Graft Block Copolymerization to Biomarker Sensing.

Navarro JR, Wennmalm S, Godfrey J, Breitholtz M, Edlund U

Biomacromolecules 17 (3) 1101-1109 [2016-03-14; online 2016-01-21]

Fluorescence Correlation Spectroscopy [Collaborative] Integrated Microscopy Technologies Stockholm

Thiazolino 2-Pyridone Amide Inhibitors of Chlamydia trachomatis Infectivity.

Good JA, Silver J, Núñez-Otero C, ..., Bergström S, Almqvist F

J. Med. Chem. 59 (5) 2094-2108 [2016-03-10; online 2016-02-22]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Kinetically Selective Inhibitors of Human Carbonic Anhydrase Isozymes I, II, VII, IX, XII, and XIII.

Talibov VO, Linkuvienė V, Matulis D, Danielson UH

J. Med. Chem. 59 (5) 2083-2093 [2016-03-10; online 2016-01-26]

Drug Discovery and Development (DDD) [Collaborative]

Evolutionary history of host use, rather than plant phylogeny, determines gene expression in a generalist butterfly.

Celorio-Mancera Mde L, Wheat CW, Huss M, ..., Nylin S, Janz N

BMC Evol. Biol. 16 (-) 59 [2016-03-08; online 2016-03-08]

Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Collaborative] National Genomics Infrastructure [Service]

Crystal Structures of Type-II Inositol Polyphosphate 5-Phosphatase INPP5B with Synthetic Inositol Polyphosphate Surrogates Reveal New Mechanistic Insights for the Inositol 5-Phosphatase Family.

Mills SJ, Silvander C, Cozier G, ..., Nordlund P, Potter BV

Biochemistry 55 (9) 1384-1397 [2016-03-08; online 2016-02-29]

Whole genome sequencing identifies a novel species of the genus Capnocytophaga isolated from dog and cat bite wounds in humans.

Zangenah S, Abbasi N, Andersson AF, Bergman P

Sci Rep 6 (-) 22919 [2016-03-07; online 2016-03-07]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Multifunctional Antioxidants: Regenerable Radical-Trapping and Hydroperoxide-Decomposing Ebselenols.

Kumar S, Yan J, Poon JF, ..., Engman L, Kumar S

Angew. Chem. Int. Ed. Engl. 55 (11) 3729-3733 [2016-03-07; online 2016-02-16]

BioMaterial Interactions (BioMat) [Collaborative]

Monitoring polydispersity by NMR diffusometry with tailored norm regularisation and moving-frame processing.

Urbańczyk M, Bernin D, Czuroń A, Kazimierczuk K

Analyst 141 (5) 1745-1752 [2016-03-07; online 2016-01-30]

Swedish NMR Centre (SNC) [Technology development]

Mechanistic investigation of the on-surface enzymatic digestion (oSED) protein adsorption detection method using targeted mass spectrometry.

Undin T, Dahlin A, Hörnaeus K, Bergquist J, Lind SB

Analyst 141 (5) 1714-1720 [2016-03-07; online 2016-02-13]

Mass Spectrometry-based Proteomics, Uppsala [Collaborative]

Local coordination and dynamics of a protic ammonium based ionic liquid immobilized in nano-porous silica micro-particles probed by Raman and NMR spectroscopy.

Garaga MN, Persson M, Yaghini N, Martinelli A

Soft Matter 12 (9) 2583-2592 [2016-03-07; online 2016-02-03]

Lesion Size Is Exacerbated in Hypoxic Rats Whereas Hypoxia-Inducible Factor-1 Alpha and Vascular Endothelial Growth Factor Increase in Injured Normoxic Rats: A Prospective Cohort Study of Secondary Hypoxia in Focal Traumatic Brain Injury.

Thelin EP, Frostell A, Mulder J, ..., Morganti-Kossmann MC, Bellander BM

Front Neurol 7 (-) 23 [2016-03-07; online 2016-03-07]

Fluorescence Tissue Profiling [Collaborative]

Analysis of the Cerebrospinal Fluid Proteome in Alzheimer's Disease.

Khoonsari PE, Häggmark A, Lönnberg M, ..., Kultima K, Shevchenko G

PLoS ONE 11 (3) e0150672 [2016-03-07; online 2016-03-07]

Affinity Proteomics Stockholm [Collaborative]

Disruption of POGZ Is Associated with Intellectual Disability and Autism Spectrum Disorders.

Stessman HA, Willemsen MH, Fenckova M, ..., Eichler EE, Kleefstra T

Am. J. Hum. Genet. 98 (3) 541-552 [2016-03-03; online 2016-03-05]

Clinical Genomics Stockholm [Service]

Systematic analysis of overall survival and interactions between tumor mutations and drug treatment.

Gatto F, Nielsen J

J Hematol Oncol 9 (-) 15 [2016-03-02; online 2016-03-02]

Bioinformatics Support, Infrastructure and Training [Technology development] Systems Biology [Technology development]

Fast, accurate, and lightweight analysis of BS-treated reads with ERNE 2.

Prezza N, Vezzi F, Käller M, Policriti A

BMC Bioinformatics 17 Suppl 4 (-) 69 [2016-03-02; online 2016-03-02]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Collaborative] National Genomics Infrastructure [Service]

Cells release subpopulations of exosomes with distinct molecular and biological properties.

Willms E, Johansson HJ, Mäger I, ..., Wood MJ, Vader P

Sci Rep 6 (-) 22519 [2016-03-02; online 2016-03-02]

Clinical Proteomics Mass spectrometry [Technology development]

Visible-Light-Mediated Photocatalytic Difunctionalization of Olefins by Radical Acylarylation and Tandem Acylation/Semipinacol Rearrangement.

Bergonzini G, Cassani C, Lorimer-Olsson H, Hörberg J, Wallentin CJ

Chemistry 22 (10) 3292-3295 [2016-03-01; online 2016-02-02]

The MHC Class I Cancer-Associated Neoepitope Trh4 Linked with Impaired Peptide Processing Induces a Unique Noncanonical TCR Conformer.

Hafstrand I, Doorduijn EM, Duru AD, ..., van Hall T, Achour A

J. Immunol. 196 (5) 2327-2334 [2016-03-01; online 2016-01-22]

mRNA and microRNA transcriptomics analyses in a murine model of dystrophin loss and therapeutic restoration.

Roberts TC, Blomberg KE, Smith CI, El Andaloussi S, Wood MJ

Genom Data 7 (-) 88-89 [2016-03-00; online 2015-12-02]

Bioinformatics and Expression Analysis (BEA) [Service]

The transcriptional coregulator MAML1 affects DNA methylation and gene expression patterns in human embryonic kidney cells.

Putnik M, Brodin D, Wojdacz TK, ..., Dahlman-Wright K, Wallberg AE

Mol. Biol. Rep. 43 (3) 141-150 [2016-03-00; online 2016-02-08]

Bioinformatics and Expression Analysis (BEA) [Service]

The structure and catalytic mechanism of human sphingomyelin phosphodiesterase like 3a--an acid sphingomyelinase homologue with a novel nucleotide hydrolase activity.

Lim SM, Yeung K, Trésaugues L, Ling TH, Nordlund P

FEBS J. 283 (6) 1107-1123 [2016-03-00; online 2016-02-05]

The influence of population structure on gene expression and flowering time variation in the ubiquitous weed Capsella bursa-pastoris (Brassicaceae).

Kryvokhyzha D, Holm K, Chen J, ..., Lagercrantz U, Lascoux M

Mol. Ecol. 25 (5) 1106-1121 [2016-03-00; online 2016-01-23]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

T-cell receptor-HLA-DRB1 associations suggest specific antigens in pulmonary sarcoidosis.

Grunewald J, Kaiser Y, Ostadkarampour M, ..., Ronninger M, Eklund A

Eur. Respir. J. 47 (3) 898-909 [2016-03-00; online 2015-11-19]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Collaborative] National Genomics Infrastructure [Collaborative]

Reclassification of Wolbachia persica as Francisella persica comb. nov. and emended description of the family Francisellaceae.

Larson MA, Nalbantoglu U, Sayood K, ..., Sjöstedt A, Hinrichs SH

Int. J. Syst. Evol. Microbiol. 66 (3) 1200-1205 [2016-03-00; online 2016-01-10]

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

Rat Prostate Tumor Cells Progress in the Bone Microenvironment to a Highly Aggressive Phenotype.

Bergström SH, Rudolfsson SH, Bergh A

Neoplasia 18 (3) 152-161 [2016-03-00; online 2016-03-20]

Rapid and straightforward transesterification of sulfonyl carbamates

Isaksson R, Kumpiņa I, Larhed M, Wannberg J

Tetrahedron Letters 57 (13) 1476-1478 [2016-03-00; online 2016-03-00]

Drug Discovery and Development (DDD) [Collaborative]

Quantitative Auxin Metabolite Profiling Using Stable Isotope Dilution UHPLC-MS/MS.

Novák O, Pěnčík A, Blahoušek O, Ljung K

Curr Protoc Plant Biol 1 (2) 419-430 [2016-03-00; online 2016-03-01]

PSMC analysis of effective population sizes in molecular ecology and its application to black-and-white Ficedula flycatchers.

Nadachowska-Brzyska K, Burri R, Smeds L, Ellegren H

Mol. Ecol. 25 (5) 1058-1072 [2016-03-00; online 2016-01-23]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Oncogene-Induced Senescence in Pituitary Adenomas--an Immunohistochemical Study.

Manojlovic-Gacic E, Skender-Gazibara M, Popovic V, ..., Pontén F, Casar-Borota O

Endocr. Pathol. 27 (1) 1-11 [2016-03-00; online 2015-11-18]

Natural Selection and Recombination Rate Variation Shape Nucleotide Polymorphism Across the Genomes of Three Related Populus Species.

Wang J, Street NR, Scofield DG, Ingvarsson PK

Genetics 202 (3) 1185-1200 [2016-03-00; online 2016-01-02]

Bioinformatics Support and Infrastructure Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Meta-analysis of Genome-Wide Association Studies for Extraversion: Findings from the Genetics of Personality Consortium.

van den Berg SM, de Moor MH, Verweij KJ, ..., Martin NG, Boomsma DI

Behav. Genet. 46 (2) 170-182 [2016-03-00; online 2015-09-13]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Innovation in the prognostication of chronic lymphocytic leukemia: how far beyond TP53 gene analysis can we go?

Pospisilova S, Sutton LA, Malcikova J, ..., Ghia P, European Research Initiative on CLL (ERIC)

Haematologica 101 (3) 263-265 [2016-03-00; online 2016-03-02]

Clinical Genomics Uppsala [Service]

Immune Adaptation to Environmental Influence: The Case of NK Cells and HCMV.

Rölle A, Brodin P

Trends Immunol. 37 (3) 233-243 [2016-03-00; online 2016-02-09]

Cellular Immunomonitoring [Technology development]

Genetic influences on schizophrenia and subcortical brain volumes: large-scale proof of concept.

Franke B, Stein JL, Ripke S, ..., Medland SE, Sullivan PF

Nat. Neurosci. 19 (3) 420-431 [2016-03-00; online 2016-02-09]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Estimation of copy number aberrations: Comparison of exome sequencing data with SNP microarrays identifies homozygous deletions of 19q13.2 and CIC in neuroblastoma.

Fransson S, Östensson M, Djos A, ..., Kogner P, Martinsson T

Int. J. Oncol. 48 (3) 1103-1116 [2016-03-00; online 2016-01-23]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Ectomycorrhizal fungi decompose soil organic matter using oxidative mechanisms adapted from saprotrophic ancestors.

Shah F, Nicolás C, Bentzer J, ..., Persson P, Tunlid A

New Phytol. 209 (4) 1705-1719 [2016-03-00; online 2015-11-04]

Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Coordinated Changes in Gene Expression Throughout Encystation of Giardia intestinalis.

Einarsson E, Troell K, Hoeppner MP, ..., Ribacke U, Svärd SG

PLoS Negl Trop Dis 10 (3) e0004571 [2016-03-00; online 2016-03-25]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Comprehensive Proteomic Analysis of Mesenchymal Stem Cell Exosomes Reveals Modulation of Angiogenesis via Nuclear Factor-KappaB Signaling.

Anderson JD, Johansson HJ, Graham CS, ..., Lehtiö J, Nolta JA

Stem Cells 34 (3) 601-613 [2016-03-00; online 2016-02-19]

Clinical Proteomics Mass spectrometry [Collaborative] Global Proteomics and Proteogenomics [Collaborative]

Characterization of genetic variation in TLR8 in relation to allergic rhinitis.

Henmyr V, Lind-Halldén C, Carlberg D, ..., Säll T, Cardell LO

Allergy 71 (3) 333-341 [2016-03-00; online 2015-11-12]

Mutation Analysis Facility (MAF)

Biochemical Conversion of Torrefied Norway Spruce After Pretreatment with Acid or Ionic Liquid

Normark M, Pommer L, Gräsvik J, ..., Winestrand S, Jönsson LJ

Bioenerg. Res. 9 (1) 355-368 [2016-03-00; online 2015-11-26]

Altered DNA methylation of glycolytic and lipogenic genes in liver from obese and type 2 diabetic patients.

Kirchner H, Sinha I, Gao H, ..., Dahlman-Wright K, Zierath JR

Mol Metab 5 (3) 171-183 [2016-03-00; online 2016-01-02]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Bacterial community composition and fhs profiles of low- and high-ammonia biogas digesters reveal novel syntrophic acetate-oxidising bacteria.

Müller B, Sun L, Westerholm M, Schnürer A

Biotechnol Biofuels 9 (-) 48 [2016-02-27; online 2016-02-27]

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

Mechanistic Modeling of Pitavastatin Disposition in Sandwich-Cultured Human Hepatocytes: A Proteomics-Informed Bottom-Up Approach

Vildhede A, Mateus A, Khan EK, ..., Artursson P, Kjellsson MC

Drug Metab. Dispos. 44 (4) 505-516 [2016-02-26; online 2016-02-03]

Chemical Biology Consortium Sweden (CBCS) [Technology development]

Whole-exome sequencing in relapsing chronic lymphocytic leukemia: clinical impact of recurrent RPS15 mutations.

Ljungström V, Cortese D, Young E, ..., Sjöblom T, Rosenquist R

Blood 127 (8) 1007-1016 [2016-02-25; online 2015-12-18]

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

Bioelectric and Morphological Response of Liquid-Covered Human Airway Epithelial Calu-3 Cell Monolayer to Periodic Deposition of Colloidal 3-Mercaptopropionic-Acid Coated CdSe-CdS/ZnS Core-Multishell Quantum Dots.

Turdalieva A, Solandt J, Shambetova N, ..., Zelenina M, Fu Y

PLoS ONE 11 (2) e0149915 [2016-02-25; online 2016-02-25]

Integrated Microscopy Technologies Stockholm [Collaborative]

Association between plasma concentrations of linoleic acid-derived oxylipins and the perceived pain scores in an exploratory study in women with chronic neck pain.

Hellström F, Gouveia-Figueira S, Nording ML, Björklund M, Fowler CJ

BMC Musculoskelet Disord 17 (-) 103 [2016-02-25; online 2016-02-25]

A Multiplex Protein Panel Applied to Cerebrospinal Fluid Reveals Three New Biomarker Candidates in ALS but None in Neuropathic Pain Patients

Lind AL, Wu D, Freyhult E, ..., Landegren U, Kamali-Moghaddam M

PLoS ONE 11 (2) e0149821 [2016-02-25; online 2016-02-25]

Affinity Proteomics Uppsala [Technology development] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] PLA and Single Cell Proteomics [Technology development]

Efficient Isotope Editing of Proteins for Site-Directed Vibrational Spectroscopy.

Peuker S, Andersson H, Gustavsson E, ..., Erdelyi M, Westenhoff S

J. Am. Chem. Soc. 138 (7) 2312-2318 [2016-02-24; online 2016-02-10]

An Efficient Protecting-Group-Free Synthesis of Vinylic Sulfoximines via Horner–Wadsworth–Emmons Reaction

Naicker T, Arvidsson P, Chinthakindi P, ..., Govender T, Kruger H

Synlett 27 (09) 1423-1427 [2016-02-24; online 2016-02-24]

Drug Discovery and Development (DDD) [Collaborative]

Anoctamin 2 identified as an autoimmune target in multiple sclerosis.

Ayoglu B, Mitsios N, Kockum I, ..., Olsson T, Nilsson P

Proc. Natl. Acad. Sci. U.S.A. 113 (8) 2188-2193 [2016-02-23; online 2016-02-09]

Autoimmunity and Serology Profiling [Collaborative] Fluorescence Tissue Profiling [Collaborative]

Microwave Promoted Transcarbamylation Reaction of Sulfonylcarbamates under Continuous-Flow Conditions

Kumpiņa I, Isaksson R, Sävmarker J, Wannberg J, Larhed M

Org. Process Res. Dev. 20 (2) 440-445 [2016-02-19; online 2016-01-05]

Drug Discovery and Development (DDD) [Collaborative]

The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea.

Olsen JL, Rouzé P, Verhelst B, ..., Reusch TB, Van de Peer Y

Nature 530 (7590) 331-335 [2016-02-18; online 2016-01-28]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Quantitative proteomics reveals protein profiles underlying major transitions in aspen wood development.

Obudulu O, Bygdell J, Sundberg B, ..., Trygg J, Wingsle G

BMC Genomics 17 (-) 119 [2016-02-18; online 2016-02-18]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Swedish Metabolomics Centre (SMC) [Service]

Postprandial metabolomics: A pilot mass spectrometry and NMR study of the human plasma metabolome in response to a challenge meal.

Karimpour M, Surowiec I, Wu J, ..., Zivkovic AM, Nording ML

Anal. Chim. Acta 908 (-) 121-131 [2016-02-18; online 2016-01-31]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Swedish Metabolomics Centre (SMC) [Service]

GeneiASE: Detection of condition-dependent and static allele-specific expression from RNA-seq data without haplotype information.

Edsgärd D, Iglesias MJ, Reilly SJ, ..., Odeberg J, Emanuelsson O

Sci Rep 6 (-) 21134 [2016-02-18; online 2016-02-18]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Resting-State Brain and the FTO Obesity Risk Allele: Default Mode, Sensorimotor, and Salience Network Connectivity Underlying Different Somatosensory Integration and Reward Processing between Genotypes.

Olivo G, Wiemerslage L, Nilsson EK, ..., Brooks SJ, Schiöth HB

Front Hum Neurosci 10 (-) 52 [2016-02-17; online 2016-02-17]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Species identification of Swedish mosquitoes through DNA metabarcoding

Lilja T, Nylander JAA, Troell K, Lindström A

JOURNAL OF THE EUROPEAN MOSQUITO CONTROL ASSOCIATION 35 (-) 1-9 [2016-02-16; online 2016-02-16]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Genomic comparison of Escherichia coli serotype O103:H2 isolates with and without verotoxin genes: implications for risk assessment of strains commonly found in ruminant reservoirs.

Söderlund R, Hurel J, Jinnerot T, ..., Eriksson E, Bongcam-Rudloff E

Infect Ecol Epidemiol 6 (-) 30246 [2016-02-16; online 2016-02-16]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Genomic inference of the metabolism of cosmopolitan subsurface Archaea, Hadesarchaea.

Baker BJ, Saw JH, Lind AE, ..., Teske AP, Ettema TJG

Nat Microbiol 1 (-) 16002 [2016-02-15; online 2016-02-15]

Microbial Single Cell Genomics [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Genome-wide DNA methylation study identifies genes associated with the cardiovascular biomarker GDF-15.

Ek WE, Hedman ÅK, Enroth S, ..., Lind L, Johansson Å

Hum. Mol. Genet. 25 (4) 817-827 [2016-02-15; online 2015-12-19]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Exome sequencing in one family with gastric- and rectal cancer.

Thutkawkorapin J, Picelli S, Kontham V, ..., Nilsson D, Lindblom A

BMC Genet. 17 (-) 41 [2016-02-13; online 2016-02-13]

Bioinformatics Support for Computational Resources [Service] Clinical Genomics Stockholm [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Discovery of the First Potent and Selective Inhibitors of Human dCTP Pyrophosphatase 1.

Llona-Minguez S, Höglund A, Jacques SA, ..., Scobie M, Helleday T

J. Med. Chem. 59 (3) 1140-1148 [2016-02-11; online 2016-01-27]

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

Aurora kinase inhibitor nanoparticles target tumors with favorable therapeutic index in vivo.

Ashton S, Song YH, Nolan J, ..., Jewsbury PJ, Barry ST

Sci Transl Med 8 (325) 325ra17 [2016-02-10; online 2016-02-13]

Spatial Mass Spectrometry [Service]

Genome-wide profiling of histone H3 lysine 27 and lysine 4 trimethylation in multiple myeloma reveals the importance of Polycomb gene targeting and highlights EZH2 as a potential therapeutic target.

Agarwal P, Alzrigat M, Párraga AA, ..., Kalushkova A, Jernberg-Wiklund H

Oncotarget 7 (6) 6809-6823 [2016-02-09; online 2016-01-13]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Stereoselective synthesis towards unnatural proline based amino acids

S.Makhathini S, Das SK, Singh T, ..., Govender T, Naicker T

ARKIVOC 2016 (3) 134-144 [2016-02-07; online 2016-02-07]

Drug Discovery and Development (DDD) [Collaborative]

Targeted Proteomics Approach for Precision Plant Breeding.

Chawade A, Alexandersson E, Bengtsson T, Andreasson E, Levander F

J. Proteome Res. 15 (2) 638-646 [2016-02-05; online 2015-12-26]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Systems Proteomics View of the Endogenous Human Claudin Protein Family.

Liu F, Koval M, Ranganathan S, ..., Kelleher NL, Baker MS

J. Proteome Res. 15 (2) 339-359 [2016-02-05; online 2016-01-12]

Spatial Proteomics [Service]

Structure and Interactions of a Dimeric Variant of sHIP, a Novel Virulence Determinant of Streptococcus pyogenes.

Diehl C, Wisniewska M, Frick IM, ..., Malmström J, Wikström M

Front Microbiol 7 (-) 95 [2016-02-05; online 2016-02-05]

Elucidating the Molecular Composition of Cartilage by Proteomics.

Hsueh MF, Khabut A, Kjellström S, Önnerfjord P, Kraus VB

J. Proteome Res. 15 (2) 374-388 [2016-02-05; online 2016-01-15]

Xenacoelomorpha is the sister group to Nephrozoa.

Cannon JT, Vellutini BC, Smith J, ..., Jondelius U, Hejnol A

Nature 530 (7588) 89-93 [2016-02-04; online 2016-02-06]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Proteome-wide survey of the autoimmune target repertoire in autoimmune polyendocrine syndrome type 1

Landegren N, Sharon D, Freyhult E, ..., Snyder M, Kämpe O

Sci Rep 6 (1) 20104 [2016-02-01; online 2016-02-01]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Tissue Profiling [Collaborative]

New loci for body fat percentage reveal link between adiposity and cardiometabolic disease risk

Lu Y, Day FR, Gustafsson S, ..., Kilpeläinen TO, Loos RJF

Nat Commun 7 (1) 10495 [2016-02-01; online 2016-02-01]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Genome-wide meta-analysis uncovers novel loci influencing circulating leptin levels.

Kilpeläinen TO, Carli JF, Skowronski AA, ..., Leibel RL, Loos RJ

Nat Commun 7 (-) 10494 [2016-02-01; online 2016-02-01]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Cellular High-Energy Cavitation Trauma - Description of a Novel In Vitro Trauma Model in Three Different Cell Types.

Cao Y, Risling M, Malm E, ..., Bolling MF, Sköld MK

Front Neurol 7 (-) 10 [2016-02-01; online 2016-02-01]

Bioinformatics and Expression Analysis (BEA) [Service]

Worldwide population structure of the wheat rust fungus Puccinia striiformis in the past.

Thach T, Ali S, de Vallavieille-Pope C, Justesen AF, Hovmøller MS

Fungal Genet. Biol. 87 (-) 1-8 [2016-02-00; online 2016-01-03]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Transcriptome profiling of immune tissues reveals habitat-specific gene expression between lake and river sticklebacks.

Huang Y, Chain FJ, Panchal M, ..., Milinski M, Feulner PG

Mol. Ecol. 25 (4) 943-958 [2016-02-00; online 2016-01-11]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Tissue sample stability: thawing effect on multi-organ samples

Torell F, Bennett K, Cereghini S, ..., Trygg J, Lundstedt T

Metabolomics 12 (2) - [2016-02-00; online 2015-12-31]

The Role of Lipids in Regulation of Programmed Cell Death

Lidman M, Dingeldein A, Pokorná Š, ..., Hof M, Gröbner G

Biophysical Journal 110 (3) 473a [2016-02-00; online 2016-02-00]

The C repressor of the P2 bacteriophage.

Massad T, Papadopolos E, Stenmark P, Damberg P

J. Biomol. NMR 64 (2) 175-180 [2016-02-00; online 2015-12-22]

Six Novel Loci Associated with Circulating VEGF Levels Identified by a Meta-analysis of Genome-Wide Association Studies.

Choi SH, Ruggiero D, Sorice R, ..., Seshadri S, Ciullo M

PLoS Genet. 12 (2) e1005874 [2016-02-00; online 2016-02-24]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Segmentation and Track-Analysis in Time-Lapse Imaging of Bacteria

Sadanandan SK, Baltekin O, Magnusson KEG, ..., Elf J, Wahlby C

IEEE J. Sel. Top. Signal Process. 10 (1) 174-184 [2016-02-00; online 2016-02-00]

BioImage Informatics [Technology development]

Replacement of two amino acids of 9R-dioxygenase-allene oxide synthase of Aspergillus niger inverts the chirality of the hydroperoxide and the allene oxide.

Sooman L, Wennman A, Hamberg M, Hoffmann I, Oliw EH

Biochim. Biophys. Acta 1861 (2) 108-118 [2016-02-00; online 2015-11-26]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Regulatory mutations in TBX3 disrupt asymmetric hair pigmentation that underlies Dun camouflage color in horses.

Imsland F, McGowan K, Rubin CJ, ..., Barsh GS, Andersson L

Nat. Genet. 48 (2) 152-158 [2016-02-00; online 2015-12-23]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Numerous Genes in Loci Associated With Body Fat Distribution Are Linked to Adipose Function.

Dahlman I, Rydén M, Brodin D, ..., Strawbridge RJ, Arner P

Diabetes 65 (2) 433-437 [2016-02-00; online 2016-01-23]

Bioinformatics and Expression Analysis (BEA) [Service]

Genome-Wide Association Analysis of Young-Onset Stroke Identifies a Locus on Chromosome 10q25 Near HABP2.

Cheng YC, Stanne TM, Giese AK, ..., Saleheen D, Mitchell BD

Stroke 47 (2) 307-316 [2016-02-00; online 2016-01-07]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Fuzzy regions in an intrinsically disordered protein impair protein-protein interactions.

Gruet A, Dosnon M, Blocquel D, ..., Longhi S, Bignon C

FEBS J. 283 (4) 576-594 [2016-02-00; online 2016-01-12]

Exemplifying the Screening Power of Mass Spectrometry Imaging over Label-Based Technologies for Simultaneous Monitoring of Drug and Metabolite Distributions in Tissue Sections.

Goodwin RJA, Nilsson A, Mackay CL, ..., Andrén PE, Iverson SL

J Biomol Screen 21 (2) 187-193 [2016-02-00; online 2015-12-23]

Spatial Mass Spectrometry

Ex Vivo Assessment of Drug Activity in Patient Tumor Cells as a Basis for Tailored Cancer Therapy.

Blom K, Nygren P, Alvarsson J, Larsson R, Andersson CR

J Lab Autom 21 (1) 178-187 [2016-02-00; online 2015-08-05]

Drug Discovery and Development (DDD) [Service]

Epigenetic profiling in CD4+ and CD8+ T cells from Graves' disease patients reveals changes in genes associated with T cell receptor signaling.

Limbach M, Saare M, Tserel L, ..., Milani L, Peterson P

J. Autoimmun. 67 (-) 46-56 [2016-02-00; online 2015-10-16]

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

Dynamical and Structural Alterations withing Lipid-Protein Assemblies Control Apoptotic Pore Formation - A Solid State NMR Study

Dingeldein APG, Lidman M, Sparrman T, Gröbner G

Biophysical Journal 110 (3) 59a-60a [2016-02-00; online 2016-02-00]

Direct Measurement of Intracellular Compound Concentration by RapidFire Mass Spectrometry Offers Insights into Cell Permeability

Gordon LJ, Allen M, Artursson P, ..., Wayne GJ, West A

J Biomol Screen 21 (2) 156-164 [2016-02-00; online 2015-09-03]

Chemical Biology Consortium Sweden (CBCS) [Technology development]

Diffusion-Controlled Drug Release From the Mesoporous Magnesium Carbonate Upsalite(®).

Zhang P, Zardán Gómez de la Torre T, Forsgren J, Bergström CA, Strømme M

J Pharm Sci 105 (2) 657-663 [2016-02-00; online 2015-06-20]

BioMaterial Interactions (BioMat)

Decreased levels of stem cell factor in subjects with incident coronary events.

Wigren M, Rattik S, Hultman K, ..., Gonçalves I, Nilsson J

J. Intern. Med. 279 (2) 180-191 [2016-02-00; online 2015-10-14]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

Crystal structure of the flavoenzyme PA4991 from Pseudomonas aeruginosa.

Jacewicz A, Schnell R, Lindqvist Y, Schneider G

Acta Crystallogr F Struct Biol Commun 72 (Pt 2) 105-111 [2016-02-00; online 2016-01-22]

Complete Knockout of Endogenous Mdr1 ( Abcb1 ) in MDCK Cells by CRISPR-Cas9

Simoff I, Karlgren M, Backlund M, ..., Matsson P, Artursson P

Journal of Pharmaceutical Sciences 105 (2) 1017-1021 [2016-02-00; online 2016-02-00]

Chemical Biology Consortium Sweden (CBCS) [Technology development] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Biobanking multifocal breast carcinomas: sample adequacy with regard to histology and DNA content.

Pekar G, Davies H, Lukacs AP, ..., Dumanski J, Tot T

Histopathology 68 (3) 411-421 [2016-02-00; online 2015-06-18]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Association analysis of copy numbers of FC-gamma receptor genes for rheumatoid arthritis and other immune-mediated phenotypes.

Franke L, el Bannoudi H, Jansen DT, ..., Toes RE, Zhernakova A

Eur. J. Hum. Genet. 24 (2) 263-270 [2016-02-00; online 2015-05-15]

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

Are freshwater bacterioplankton indifferent to variable types of amino acid substrates?

Ricão Canelhas M, Eiler A, Bertilsson S

FEMS Microbiol. Ecol. 92 (2) - [2016-02-00; online 2016-01-08]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Analysis of hepatitis C NS5A resistance associated polymorphisms using ultra deep single molecule real time (SMRT) sequencing.

Bergfors A, Leenheer D, Bergqvist A, Ameur A, Lennerstrand J

Antiviral Res. 126 (-) 81-89 [2016-02-00; online 2015-12-19]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Analyses of the ash dieback pathogen,Hymenoscyphus fraxineus, suggest role of tree species diversity on colonization and population structure differentiation

Nguyen DT, Cleary MR, Enderle R, Berlin A, Stenlid J

For. Path. 46 (1) 82-84 [2016-02-00; online 2015-10-28]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

A novel phenotype in N-glycosylation disorders: Gillessen-Kaesbach–Nishimura skeletal dysplasia due to pathogenic variants in ALG9

Tham E, Eklund EA, Hammarsjö A, ..., Nishimura G, Grigelioniene G

Eur J Hum Genet 24 (2) 198-207 [2016-02-00; online 2015-05-13]

Clinical Genomics Stockholm

The Story of a Hitchhiker: Population Genetic Patterns in the Invasive Barnacle Balanus(Amphibalanus) improvisus Darwin 1854.

Wrange AL, Charrier G, Thonig A, ..., Jonsson PR, André C

PLoS ONE 11 (1) e0147082 [2016-01-28; online 2016-01-28]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

High levels of cathepsin D and cystatin B are associated with increased risk of coronary events.

Gonçalves I, Hultman K, Dunér P, ..., Nilsson J, Bengtsson E

Open Heart 3 (1) e000353 [2016-01-27; online 2016-01-27]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

High Plasma Levels of Galectin-3 Are Associated with Increased Risk for Stroke after Carotid Endarterectomy.

Edsfeldt A, Bengtsson E, Asciutto G, ..., Nilsson J, Goncalves I

Cerebrovasc Dis 41 (3-4) 199-203 [2016-01-27; online 2016-01-27]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

Genomic sequencing of a dyslexia susceptibility haplotype encompassing ROBO1.

Massinen S, Wang J, Laivuori K, ..., Jiao H, Kere J

J Neurodev Disord 8 (-) 4 [2016-01-27; online 2016-01-27]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

A dynamic Asp-Arg interaction is essential for catalysis in microsomal prostaglandin E2 synthase.

Brock JS, Hamberg M, Balagunaseelan N, ..., Rinaldo-Matthis A, Haeggström JZ

Proc. Natl. Acad. Sci. U.S.A. 113 (4) 972-977 [2016-01-26; online 2016-01-11]

Genomic Evidence Establishes Anatolia as the Source of the European Neolithic Gene Pool.

Omrak A, Günther T, Valdiosera C, ..., Jakobsson M, Götherström A

Curr. Biol. 26 (2) 270-275 [2016-01-25; online 2015-12-31]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Metabolites in Blood for Prediction of Bacteremic Sepsis in the Emergency Room.

Kauppi AM, Edin A, Ziegler I, ..., Strålin K, Johansson A

PLoS ONE 11 (1) e0147670 [2016-01-22; online 2016-01-22]

Genetic associations at 53 loci highlight cell types and biological pathways relevant for kidney function.

Pattaro C, Teumer A, Gorski M, ..., Kao WH, Fox CS

Nat Commun 7 (1) 10023 [2016-01-21; online 2016-01-21]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Backbone Assignment of the MALT1 Paracaspase by Solution NMR.

Unnerståle S, Nowakowski M, Baraznenok V, ..., Orekhov V, Agback T

PLoS ONE 11 (1) e0146496 [2016-01-20; online 2016-01-20]

Reconstructing ecosystem functions of the active microbial community of the Baltic Sea oxygen depleted sediments.

Thureborn P, Franzetti A, Lundin D, Sjöling S

PeerJ 4 (-) e1593 [2016-01-19; online 2016-01-19]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Geographical distribution of genetic diversity in Secale landrace and wild accessions.

Hagenblad J, Oliveira HR, Forsberg NE, Leino MW

BMC Plant Biol. 16 (-) 23 [2016-01-19; online 2016-01-19]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Genetic Determinants of Thrombin Generation and Their Relation to Venous Thrombosis: Results from the GAIT-2 Project.

Martin-Fernandez L, Ziyatdinov A, Carrasco M, ..., Souto JC, Soria JM

PLoS ONE 11 (1) e0146922 [2016-01-19; online 2016-01-19]

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

Chondroitin sulfate coated gold nanoparticles: a new strategy to resolve multidrug resistance and thromboinflammation.

Gurav D, Varghese OP, Hamad OA, ..., Hilborn J, Oommen OP

Chem. Commun. (Camb.) 52 (5) 966-969 [2016-01-18; online 2015-11-21]

Using Whole-Exome Sequencing to Identify Genetic Markers for Carboplatin and Gemcitabine-Induced Toxicities.

Gréen H, Hasmats J, Kupershmidt I, ..., Peterson C, Lundeberg J

Clin. Cancer Res. 22 (2) 366-373 [2016-01-15; online 2015-09-16]

Bioinformatics Support and Infrastructure [Service] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Phytoconstituents with Radical Scavenging and Cytotoxic Activities from Diospyros shimbaensis

Aronsson P, Munissi J, Gruhonjic A, ..., Nyandoro S, Erdelyi M

Diseases 4 (1) 3 [2016-01-15; online 2016-01-15]

A meta-analysis of 120 246 individuals identifies 18 new loci for fibrinogen concentration.

de Vries PS, Chasman DI, Sabater-Lleal M, ..., Strachan DP, Dehghan A

Hum. Mol. Genet. 25 (2) 358-370 [2016-01-15; online 2015-11-10]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Cryptochromes Interact Directly with PIFs to Control Plant Growth in Limiting Blue Light.

Pedmale UV, Huang SS, Zander M, ..., Ecker JR, Chory J

Cell 164 (1-2) 233-245 [2016-01-14; online 2016-01-05]

The protein kinase LKB1 negatively regulates bone morphogenetic protein receptor signaling.

Raja E, Tzavlaki K, Vuilleumier R, ..., Heldin CH, Moustakas A

Oncotarget 7 (2) 1120-1143 [2016-01-12; online 2015-12-25]

Clinical Genomics Uppsala [Collaborative]

Spatial sexual dimorphism of X and Y homolog gene expression in the human central nervous system during early male development.

Johansson MM, Lundin E, Qian X, ..., Nilsson M, Jazin E

Biol Sex Differ 7 (-) 5 [2016-01-12; online 2016-01-12]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Simultaneous Multiplexed Measurement of RNA and Proteins in Single Cells.

Darmanis S, Gallant CJ, Marinescu VD, ..., Westermark B, Landegren U

Cell Rep 14 (2) 380-389 [2016-01-12; online 2016-01-11]

Affinity Proteomics Uppsala [Technology development] PLA and Single Cell Proteomics [Technology development]

Genome-wide identification of Wig-1 mRNA targets by RIP-Seq analysis.

Bersani C, Huss M, Giacomello S, ..., Lui WO, Wiman KG

Oncotarget 7 (2) 1895-1911 [2016-01-12; online 2015-12-18]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

BMP Sustains Embryonic Stem Cell Self-Renewal through Distinct Functions of Different Krüppel-like Factors.

Morikawa M, Koinuma D, Mizutani A, ..., Heldin CH, Miyazono K

Stem Cell Reports 6 (1) 64-73 [2016-01-12; online 2016-01-16]

Genome Engineering Zebrafish [Collaborative]

Serum Trimethylamine-N-Oxide Is Strongly Related to Renal Function and Predicts Outcome in Chronic Kidney Disease.

Missailidis C, Hällqvist J, Qureshi AR, ..., Stenvinkel P, Bergman P

PLoS ONE 11 (1) e0141738 [2016-01-11; online 2016-01-11]

Swedish Metabolomics Centre (SMC) [Collaborative]

Whole-Genome Sequencing of a Canine Family Trio Reveals a FAM83G Variant Associated with Hereditary Footpad Hyperkeratosis.

Sayyab S, Viluma A, Bergvall K, ..., Andersson G, Bergström TF

G3 (Bethesda) 6 (3) 521-527 [2016-01-08; online 2016-01-08]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

The 5300-year-old Helicobacter pylori genome of the Iceman.

Maixner F, Krause-Kyora B, Turaev D, ..., Rattei T, Zink A

Science 351 (6269) 162-165 [2016-01-08; online 2016-01-09]

Clinical Genomics Stockholm [Collaborative]

Identifying Novel Gene Variants in Coronary Artery Disease and Shared Genes With Several Cardiovascular Risk Factors.

LeBlanc M, Zuber V, Andreassen BK, ..., Dale AM, Andreassen OA

Circ. Res. 118 (1) 83-94 [2016-01-08; online 2015-10-22]

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

PGSB PlantsDB: updates to the database framework for comparative plant genome research.

Spannagl M, Nussbaumer T, Bader KC, ..., Gundlach H, Mayer KF

Nucleic Acids Res. 44 (D1) D1141-D1147 [2016-01-04; online 2015-11-04]

Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Characterization and Expression of the Zebrafish qki Paralogs.

Radomska KJ, Sager J, Farnsworth B, ..., Jazin E, Emilsson LS

PLoS ONE 11 (1) e0146155 [2016-01-04; online 2016-01-04]

Genome Engineering Zebrafish [Service]

CRISPRz: a database of zebrafish validated sgRNAs.

Varshney GK, Zhang S, Pei W, ..., Sood R, Burgess SM

Nucleic Acids Res. 44 (D1) D822-D826 [2016-01-04; online 2015-10-04]

Genome Engineering Zebrafish [Technology development]

Protein Detection Using the Multiplexed Proximity Extension Assay (PEA) from Plasma and Vaginal Fluid Applied to the Indicating FTA Elute Micro Card™.

Berggrund M, Ekman D, Gustavsson I, ..., Enroth S, Gyllensten U

Journal of Circulating Biomarkers 5 (-) 9 [2016-01-01; online 2016-01-01]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

Ionic liquid mediated technology for synthesis of cellulose acetates using different co-solvents.

Jogunola O, Eta V, Hedenström M, ..., Salmi T, Mikkola JP

Carbohydr Polym 135 (-) 341-348 [2016-01-01; online 2015-09-02]

Changes in the drug release pattern of fresh and set simvastatin-loaded brushite cement.

Mestres G, Kugiejko K, Pastorino D, ..., Ginebra MP, Persson C

Mater Sci Eng C Mater Biol Appl 58 (-) 88-96 [2016-01-01; online 2015-08-14]

BioMaterial Interactions (BioMat)

The WD40 Domain Protein MSI1 Functions in a Histone Deacetylase Complex to Fine-Tune Abscisic Acid Signaling.

Mehdi S, Derkacheva M, Ramström M, ..., Bergquist J, Hennig L

Plant Cell 28 (1) 42-54 [2016-01-00; online 2015-12-24]

Mass Spectrometry-based Proteomics, Uppsala [Collaborative]

Super-resolution stimulated emission depletion imaging of slit diaphragm proteins in optically cleared kidney tissue.

Unnersjö-Jess D, Scott L, Blom H, Brismar H

Kidney Int. 89 (1) 243-247 [2016-01-00; online 2015-10-08]

Integrated Microscopy Technologies Stockholm [Technology development]

Structural genomic changes underlie alternative reproductive strategies in the ruff (Philomachus pugnax).

Lamichhaney S, Fan G, Widemo F, ..., Liu X, Andersson L

Nat. Genet. 48 (1) 84-88 [2016-01-00; online 2015-11-17]

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

Protein Biomarkers for Insulin Resistance and Type 2 Diabetes Risk in Two Large Community Cohorts.

Nowak C, Sundström J, Gustafsson S, ..., Ingelsson E, Fall T

Diabetes 65 (1) 276-284 [2016-01-00; online 2015-09-29]

Affinity Proteomics Uppsala [Service] Bioinformatics Support for Computational Resources [Service] Clinical Biomarkers NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service] PLA and Single Cell Proteomics [Service]

Pathogenenic variant in the COL2A1 gene is associated with Spondyloepiphyseal dysplasia type Stanescu.

Hammarsjö A, Nordgren A, Lagerstedt-Robinson K, ..., Nishimura G, Grigelioniene G

Am. J. Med. Genet. A 170A (1) 266-269 [2016-01-00; online 2015-10-01]

Bioinformatics Support for Computational Resources [Service] Clinical Genomics Stockholm [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

PAX5-ESRRB is a recurrent fusion gene in B-cell precursor pediatric acute lymphoblastic leukemia.

Marincevic-Zuniga Y, Zachariadis V, Cavelier L, ..., Syvänen AC, Nordlund J

Haematologica 101 (1) e20-e23 [2016-01-00; online 2015-10-22]

Bioinformatics Support for Computational Resources [Service] Clinical Genomics Uppsala [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]

Oxylipins, endocannabinoids, and related compounds in human milk: Levels and effects of storage conditions.

Wu J, Gouveia-Figueira S, Domellöf M, Zivkovic AM, Nording ML

Prostaglandins Other Lipid Mediat. 122 (-) 28-36 [2016-01-00; online 2015-12-15]

Mutations in FLVCR2 associated with Fowler syndrome and survival beyond infancy.

Kvarnung M, Taylan F, Nilsson D, ..., Nordgren A, Syk Lundberg E

Clin. Genet. 89 (1) 99-103 [2016-01-00; online 2015-02-14]

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

Increased lanosterol turnover: a metabolic burden for daunorubicin-resistant leukemia cells.

Stäubert C, Krakowsky R, Bhuiyan H, ..., Broom O, Nordström A

Med. Oncol. 33 (1) 6 [2016-01-00; online 2015-12-23]

G×E Interaction Influences Trajectories of Hand Grip Strength.

Petersen I, Pedersen NL, Rantanen T, ..., Krueger RF, Reynolds C

Behav. Genet. 46 (1) 20-30 [2016-01-00; online 2015-09-01]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Genetic heterogeneity in rhabdomyosarcoma revealed by SNP array analysis.

Walther C, Mayrhofer M, Nilsson J, ..., Gisselsson D, Mertens F

Genes Chromosomes Cancer 55 (1) 3-15 [2016-01-00; online 2015-10-20]

Array and Analysis Facility [Collaborative]

Gene-Environment Interplay in Physical, Psychological, and Cognitive Domains in Mid to Late Adulthood: Is APOE a Variability Gene?

Reynolds CA, Gatz M, Christensen K, ..., Pedersen NL, Interplay of Genes and Environment across Multiple Studies (IGEMS) consortium

Behav. Genet. 46 (1) 4-19 [2016-01-00; online 2015-11-06]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

GREM1 and POLE variants in hereditary colorectal cancer syndromes.

Rohlin A, Eiengård F, Lundstam U, ..., Björk J, Nordling M

Genes Chromosomes Cancer 55 (1) 95-106 [2016-01-00; online 2015-10-23]

Fat intake and breast milk fatty acid composition in farming and nonfarming women and allergy development in the offspring.

Jonsson K, Barman M, Moberg S, ..., Wold AE, Sandberg AS

Pediatr. Res. 79 (1-1) 114-123 [2016-01-00; online 2015-09-21]

Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]

F11 is associated with recurrent VTE in women. A prospective cohort study.

Bruzelius M, Ljungqvist M, Bottai M, ..., Lärfars G, Odeberg J

Thromb. Haemost. 115 (2) 406-414 [2016-01-00; online 2015-10-02]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Exome and genome sequencing: a revolution for the discovery and diagnosis of monogenic disorders.

Stranneheim H, Wedell A

J. Intern. Med. 279 (1) 3-15 [2016-01-00; online 2015-08-08]

Clinical Genomics Stockholm [Service]

Development of single-tube nested real-time PCR assays with long internally quenched probes for detection of norovirus genogroup II.

Xia H, Gravelsina S, Öhrmalm C, Ottoson J, Blomberg J

BioTechniques 60 (1) 28-34 [2016-01-00; online 2016-01-01]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Composition of human faecal microbiota in resistance to Campylobacter infection.

Kampmann C, Dicksved J, Engstrand L, Rautelin H

Clin. Microbiol. Infect. 22 (1) 61.e1-61.e8 [2016-01-00; online 2015-09-16]

Clinical Genomics Stockholm [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

An Immunochip-based interaction study of contrasting interaction effects with smoking in ACPA-positive versus ACPA-negative rheumatoid arthritis.

Jiang X, Källberg H, Chen Z, ..., Padyukov L, Alfredsson L

Rheumatology (Oxford) 55 (1) 149-155 [2016-01-00; online 2015-08-15]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Adaptive radiation of Darwin's finches revisited using whole genome sequencing.

Almén MS, Lamichhaney S, Berglund J, ..., Webster MT, Andersson L

Bioessays 38 (1) 14-20 [2016-01-00; online 2015-11-26]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Overexpression of Trypanosoma rangeli trypanothione reductase increases parasite survival under oxidative stress

BELTRAME-BOTELHO IT, STOCO PH, STEINDEL M, ..., GADELHA FR, GRISARD EC

Parasitology Open 2 (-) - [2016-00-00; online 2016-11-14]

NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Organocatalyzed Mannich reactions on minocycline: Towards novel tetracycline antibiotics

CHIWUNZE TE, Azumah R, Ramtahal M, ..., Govender T, Naicker T

S.Afr.j.chem. 69 (-) - [2016-00-00; online 2016-00-00]

Drug Discovery and Development (DDD) [Collaborative]

NMR analysis of the human saliva metabolome distinguishes dementia patients from matched controls

Figueira J, Jonsson P, Nordin Adolfsson A, ..., Nyberg L, Öhman A

Mol. BioSyst. 12 (8) 2562-2571 [2016-00-00; online 2016-00-00]

Feature Augmented Deep Neural Networks for Segmentation of Cells

Sadanandan SK, Ranefall P, Wählby C

- - (-) 231-243 [2016-00-00; online 2016-09-18]

BioImage Informatics [Technology development]