Search publications

Bax to the future - A novel, high-yielding approach for purification and expression of full-length Bax protein for structural studies.

Dingeldein APG, Lindberg MJ, Ådén J, ..., Stoll R, Gröbner G

Protein Expression and Purification 158 (-) 20-26 [2019-06-00; online 2019-02-06]

Single-Cell RNA Sequencing of the T Helper Cell Response to House Dust Mites Defines a Distinct Gene Expression Signature in Airway Th2 Cells

Tibbitt CA, Stark JM, Martens L, ..., Saeys Y, Coquet JM

Immunity 51 (1) 169-184.e5 [2019-06-00; online 2019-06-00]

Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

A targeted proteomics approach reveals a serum protein signature as diagnostic biomarker for resectable gastric cancer.

Shen Q, Polom K, Williams C, ..., Roviello F, Kamali-Moghaddam M

EBioMedicine 44 (-) 322-333 [2019-06-00; online 2019-05-28]

Affinity Proteomics Uppsala [Technology development] Bioinformatics Support for Computational Resources [Service] Clinical Biomarkers [Service] Glycoproteomics and MS Proteomics [Collaborative] PLA and Single Cell Proteomics [Technology development]

Identification of DNA methylation patterns predisposing for an efficient response to BCG vaccination in healthy BCG-naïve subjects.

Das J, Verma D, Gustafsson M, Lerm M

Epigenetics 14 (6) 589-601 [2019-06-00; online 2019-04-22]

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

A novel RAD21 p.(Gln592del) variant expands the clinical description of Cornelia de Lange syndrome type 4 - Review of the literature.

Gudmundsson S, Annerén G, Marcos-Alcalde Í, ..., Gómez-Puertas P, Bondeson ML

Eur J Med Genet 62 (6) 103526 [2019-06-00; online 2018-08-17]

Bioinformatics Support for Computational Resources [Service] Clinical Genomics [Collaborative] Clinical Genomics Uppsala [Collaborative]

Circulating mast cell progenitors correlate with reduced lung function in allergic asthma.

Salomonsson M, Malinovschi A, Kalm-Stephens P, ..., Alving K, Hallgren J

Clin Exp Allergy 49 (6) 874-882 [2019-06-00; online 2019-03-21]

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

Lipopolysaccharide-induced alteration of mitochondrial morphology induces a metabolic shift in microglia modulating the inflammatory response in vitro and in vivo.

Nair S, Sobotka KS, Joshi P, ..., Mallard C, Hagberg H

Glia 67 (6) 1047-1061 [2019-06-00; online 2019-01-13]

Integrated Microscopy Technologies Gothenburg [Service]

Barcoded Consortium Infections Resolve Cell Type-Dependent Salmonella enterica Serovar Typhimurium Entry Mechanisms.

Di Martino ML, Ek V, Hardt WD, Eriksson J, Sellin ME

MBio 10 (3) - [2019-05-21; online 2019-05-21]

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

Biomarkers of blood cadmium and incidence of cardiovascular events in non-smokers: results from a population-based proteomics study.

Borné Y, Fagerberg B, Sallsten G, ..., Barregard L, Engström G

Clin Proteomics 16 (1) 21 [2019-05-15; online 2019-05-15]

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

Adult Neural Progenitor Cells Transplanted into Spinal Cord Injury Differentiate into Oligodendrocytes, Enhance Myelination, and Contribute to Recovery.

Sankavaram SR, Hakim R, Covacu R, ..., Svensson M, Brundin L

Stem Cell Reports 12 (5) 950-966 [2019-05-14; online 2019-04-25]

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

Automated Cell Processing for Mass Cytometry Experiments.

Mikes J, Olin A, Lakshmikanth T, Chen Y, Brodin P

Methods Mol. Biol. 1989 (-) 111-123 [2019-05-12; online 2019-05-12]

Bioinformatics Support for Computational Resources [Service] Cellular Immunomonitoring [Technology development]

Wnt5a is a TLR2/4-ligand that induces tolerance in human myeloid cells.

Mehmeti M, Bergenfelz C, Källberg E, ..., André I, Leandersson K

Commun Biol 2 (1) 176 [2019-05-09; online 2019-05-09]

Mass Cytometry Identifies Distinct Subsets of Regulatory T Cells and Natural Killer Cells Associated With High Risk for Type 1 Diabetes.

Barcenilla H, Åkerman L, Pihl M, Ludvigsson J, Casas R

Front Immunol 10 (-) 982 [2019-05-03; online 2019-05-03]

Cellular Immunomonitoring [Service]

Prompt apoptotic response to high glucose in SGLT-expressing renal cells.

Nilsson LM, Zhang L, Bondar A, ..., Scott L, Aperia A

Am. J. Physiol. Renal Physiol. 316 (5) F1078-F1089 [2019-05-01; online 2019-03-13]

Bioinformatics Support for Computational Resources [Service] Integrated Microscopy Technologies Stockholm [Service]

Gene expression profile of extraocular muscles following resection strabismus surgery.

Rodríguez MA, Sandgren Hochhard K, Vicente A, Liu JX, Pedrosa Domellöf F

Exp. Eye Res. 182 (-) 182-193 [2019-05-00; online 2019-04-03]

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

Elevated circulating effector memory T cells but similar levels of regulatory T cells in patients with type 2 diabetes mellitus and cardiovascular disease.

Rattik S, Engelbertsen D, Wigren M, ..., Nilsson J, Björkbacka H

Diabetes and Vascular Disease Research 16 (3) 270-280 [2019-05-00; online 2018-12-21]

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

Endocytosis, intracellular fate, accumulation, and agglomeration of titanium dioxide (TiO 2) nanoparticles in the rainbow trout liver cell line RTL-W1.

Lammel T, Mackevica A, Johansson BR, Sturve J

Environ Sci Pollut Res 26 (15) 15354-15372 [2019-05-00; online 2019-03-31]

Integrated Microscopy Technologies Gothenburg [Service]

Molecular orientation distribution of regenerated cellulose fibers investigated with rotor synchronized solid state NMR spectroscopy

Svenningsson L, Sparrman T, Bialik E, Bernin D, Nordstierna L

Cellulose 26 (8) 4681-4692 [2019-05-00; online 2019-04-17]

AdipoR1 and AdipoR2 maintain membrane fluidity in most human cell types and independently of adiponectin.

Ruiz M, Ståhlman M, Borén J, Pilon M

J. Lipid Res. 60 (5) 995-1004 [2019-05-00; online 2019-03-19]

Integrated Microscopy Technologies Gothenburg [Service]

PKCζ facilitates lymphatic metastatic spread of prostate cancer cells in a mice xenograft model

Zang G, Mu Y, Gao L, Bergh A, Landström M

Oncogene 38 (22) 4215-4231 [2019-05-00; online 2019-01-31]

Bioinformatics (NBIS) [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Spatial proteomics: a powerful discovery tool for cell biology.

Lundberg E, Borner GHH

Nat Rev Mol Cell Biol 20 (5) 285-302 [2019-05-00; online 2019-01-20]

Spatial Proteomics [Collaborative]

An Atlas of Vagal Sensory Neurons and Their Molecular Specialization

Kupari J, Häring M, Agirre E, Castelo-Branco G, Ernfors P

Cell Rep 27 (8) 2508-2523.e4 [2019-05-00; online 2019-05-00]

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

Preeclampsia is Associated with Sex-Specific Transcriptional and Proteomic Changes in Fetal Erythroid Cells.

Masoumi Z, Maes GE, Herten K, ..., Familari M, Hansson SR

Int J Mol Sci 20 (8) - [2019-04-25; online 2019-04-25]

PAD2-Mediated Citrullination Contributes to Efficient Oligodendrocyte Differentiation and Myelination.

Falcão AM, Meijer M, Scaglione A, ..., Casaccia P, Castelo-Branco G

Cell Rep 27 (4) 1090-1102.e10 [2019-04-23; online 2019-04-25]

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

The complex barnacle perfume: identification of waterborne pheromone homologues in Balanus improvisus and their differential expression during settlement

Abramova A, Lind U, Blomberg A, Rosenblad MA

Biofouling 35 (4) 416-428 [2019-04-21; online 2019-05-30]

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

A proton T1-nuclear magnetic resonance dispersion study of water motion in snowflakes and hexagonal ice

Westlund PO

Molecular Physics 117 (7-8) 960-967 [2019-04-18; online 2018-10-30]

SAMURAI (Solid-phase Assisted Mutagenesis by Uracil Restriction for Accurate Integration) for antibody affinity maturation and paratope mapping.

Hu FJ, Lundqvist M, Uhlén M, Rockberg J

Nucleic Acids Res. 47 (6) e34 [2019-04-08; online 2019-02-05]

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

The 1H NMR serum metabolomics response to a two meal challenge: a cross-over dietary intervention study in healthy human volunteers.

Rådjursöga M, Lindqvist HM, Pedersen A, ..., Ellegård L, Winkvist A

Nutr J 18 (1) 25 [2019-04-08; online 2019-04-08]

Exploring the Arctic Charr Intestinal Glycome: Evidence of Increased N-Glycolylneuraminic Acid Levels and Changed Host-Pathogen Interactions in Response to Inflammation.

Venkatakrishnan V, Padra JT, Sundh H, ..., Karlsson NG, Lindén SK

J. Proteome Res. 18 (4) 1760-1773 [2019-04-05; online 2019-03-19]

High-Quality Library Preparation for NGS-Based Immunoglobulin Germline Gene Inference and Repertoire Expression Analysis.

Vázquez Bernat N, Corcoran M, Hardt U, ..., Martin M, Karlsson Hedestam GB

Front Immunol 10 (-) 660 [2019-04-05; online 2019-04-05]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative]

Mesenchymal stem cells transplanted into spinal cord injury adopt immune cell-like characteristics.

Hakim R, Covacu R, Zachariadis V, ..., Brundin L, Svensson M

Stem Cell Res Ther 10 (1) 115 [2019-04-03; online 2019-04-03]

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

B cell profiling in malaria reveals expansion and remodelling of CD11c+ B cell subsets.

Sundling C, Rönnberg C, Yman V, ..., Persson KE, Färnert A

JCI Insight 5 (-) - [2019-04-02; online 2019-04-02]

Bioinformatics Support for Computational Resources [Service] Cellular Immunomonitoring [Collaborative]

Dynamics of Resistance Plasmids in Extended-Spectrum-β-Lactamase-Producing Enterobacteriaceae during Postinfection Colonization.

Brolund A, Rajer F, Giske CG, ..., Titelman E, Sandegren L

Antimicrob. Agents Chemother. 63 (4) - [2019-04-00; online 2019-03-27]

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

Mutation patterns in a population-based non-small cell lung cancer cohort and prognostic impact of concomitant mutations in KRAS and TP53 or STK11.

La Fleur L, Falk-Sörqvist E, Smeds P, ..., Moens L, Botling J

Lung Cancer 130 (-) 50-58 [2019-04-00; online 2019-01-09]

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

The biology of the cell - insights from mass cytometry.

Brodin P

FEBS J. 286 (8) 1514-1522 [2019-04-00; online 2018-11-26]

Bioinformatics Support for Computational Resources [Service] Cellular Immunomonitoring [Technology development]

Novel fibronectin mutations and expansion of the phenotype in spondylometaphyseal dysplasia with "corner fractures".

Costantini A, Valta H, Baratang NV, ..., Mäkitie O, Campeau PM

Bone 121 (-) 163-171 [2019-04-00; online 2018-12-30]

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

Placing RNA in context and space - methods for spatially resolved transcriptomics.

Strell C, Hilscher MM, Laxman N, ..., Yokota C, Nilsson M

FEBS J. 286 (8) 1468-1481 [2019-04-00; online 2018-03-31]

In Situ Sequencing (ISS) [Technology development]

Backbone 1H, 13C, and 15N resonance assignments of BoMan26A, a β-mannanase of the glycoside hydrolase family 26 from the human gut bacterium Bacteroides ovatus.

Wernersson S, Bågenholm V, Persson C, ..., Stålbrand H, Akke M

Biomol NMR Assign 13 (1) 213-218 [2019-04-00; online 2019-02-07]

High Serum sCD40 and a Distinct Colonic T Cell Profile in Ulcerative Colitis Associated With Primary Sclerosing Cholangitis.

Lampinen M, Vessby J, Fredricsson A, ..., Rorsman F, Carlson M

J Crohns Colitis 13 (3) 341-350 [2019-03-26; online 2018-11-02]

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

Corticosteroids protect infected cells against mycobacterial killing in vitro.

Tükenmez H, Edström I, Kalsum S, ..., Elofsson M, Larsson C

Biochem. Biophys. Res. Commun. 511 (1) 117-121 [2019-03-26; online 2019-02-14]

Chemical Biology Consortium Sweden (CBCS) [Collaborative] Swedish NMR Centre (SNC) [Service]

A novel human in vitro papillomavirus type 16 positive tonsil cancer cell line with high sensitivity to radiation and cisplatin.

Forslund O, Sugiyama N, Wu C, ..., Wennerberg J, Ekblad L

BMC Cancer 19 (1) 265 [2019-03-25; online 2019-03-25]

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

Helicase/SUMO-targeted ubiquitin ligase Uls1 interacts with the Holliday junction resolvase Yen1.

Bauer SL, Chen J, Åström SU

PLoS ONE 14 (3) e0214102 [2019-03-21; online 2019-03-21]

Bioinformatics (NBIS) [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Service]

Current Status and Future Prospects of Clinically Exploiting Cancer-specific Metabolism-Why Is Tumor Metabolism Not More Extensively Translated into Clinical Targets and Biomarkers?

Muthu M, Nordström A

Int J Mol Sci 20 (6) 1385 [2019-03-19; online 2019-03-19]

Interaction of toluene with polar stationary phases under conditions typical of hydrophilic interaction chromatography probed by saturation transfer difference nuclear magnetic resonance spectroscopy.

Shamshir A, Dinh NP, Jonsson T, ..., Ashiq MJ, Irgum K

Journal of Chromatography A 1588 (-) 58-67 [2019-03-15; online 2018-12-13]

Surveillance of cell wall diffusion barrier integrity modulates water and solute transport in plants.

Wang P, Calvo-Polanco M, Reyt G, ..., Boursiac Y, Salt DE

Sci Rep 9 (1) 4227 [2019-03-12; online 2019-03-12]

Single-Cell RNA-Seq Reveals Cellular Heterogeneity of Pluripotency Transition and X Chromosome Dynamics during Early Mouse Development.

Cheng S, Pei Y, He L, ..., Jing N, Deng Q

Cell Rep 26 (10) 2593-2607.e3 [2019-03-05; online 2019-03-07]

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

Oxygen induces the expression of invasion and stress response genes in the anaerobic salmon parasite Spironucleus salmonicida.

Stairs CW, Kokla A, Ástvaldsson Á, ..., Svärd S, Ettema TJG

BMC Biol. 17 (1) 19 [2019-03-01; online 2019-03-01]

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

A radical switch in clonality reveals a stem cell niche in the epiphyseal growth plate.

Newton PT, Li L, Zhou B, ..., Sävendahl L, Chagin AS

Nature 567 (7747) 234-238 [2019-03-00; online 2019-02-27]

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

Proteomic Analysis of Endothelial Cells Exposed to Ultrasmall Nanoparticles Reveals Disruption in Paracellular and Transcellular Transport.

Kuruvilla J, Bayat N, Cristobal S

Proteomics 19 (5) e1800228 [2019-03-00; online 2019-02-25]

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

Spontaneous calcium activity in metanephric mesenchymal cells regulates branching morphogenesis in the embryonic kidney.

Fontana JM, Khodus GR, Unnersjö-Jess D, ..., Aperia A, Brismar H

FASEB J. 33 (3) 4089-4096 [2019-03-00; online 2018-11-29]

Integrated Microscopy Technologies Stockholm [Service]

Recombinant Glycoprotein E of Varicella Zoster Virus Contains Glycan-Peptide Motifs That Modulate B Cell Epitopes into Discrete Immunological Signatures.

Nordén R, Nilsson J, Samuelsson E, ..., Olofsson S, Bergström T

Int J Mol Sci 20 (4) - [2019-02-22; online 2019-02-22]

A Quantitative Analysis of Colonic Mucosal Oxylipins and Endocannabinoids in Treatment-Naïve and Deep Remission Ulcerative Colitis Patients and the Potential Link With Cytokine Gene Expression.

Diab J, Al-Mahdi R, Gouveia-Figueira S, ..., Florholmen J, Forsdahl G

Inflamm Bowel Dis 25 (3) 490-497 [2019-02-21; online 2018-11-27]

Prediction of response to anti-cancer drugs becomes robust via network integration of molecular data.

Franco M, Jeggari A, Peuget S, ..., Selivanova G, Alexeyenko A

Sci Rep 9 (1) 2379 [2019-02-20; online 2019-02-20]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative]

Immune-informed mucin hydrogels evade fibrotic foreign body response in vivo

Yan H, Seignez C, Hjorth M, ..., Phillipson M, Crouzier T

- - (-) - [2019-02-19; online 2019-02-19]

Spatial Proteomics [Service]

Mass cytometry identifies distinct CD4+ T cell clusters distinguishing HIV-1-infected patients according to antiretroviral therapy initiation.

Bekele Y, Lakshmikanth T, Chen Y, ..., Brodin P, Chiodi F

JCI Insight 4 (3) - [2019-02-07; online 2019-02-07]

Bioinformatics Support for Computational Resources [Service] Cellular Immunomonitoring [Collaborative]

Exploring the genetics of trotting racing ability in horses using a unique Nordic horse model.

Velie BD, Lillie M, Fegraeus KJ, ..., Strand E, Lindgren G

BMC Genomics 20 (1) 104 [2019-02-04; online 2019-02-04]

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

Introgression of resistance to Rhopalosiphum padi L. from wild barley into cultivated barley facilitated by doubled haploid and molecular marker techniques.

Åhman I, Bengtsson T

Theor. Appl. Genet. - (-) - [2019-02-02; online 2019-02-02]

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

A Chemical Screen Identifies Compounds Limiting the Toxicity of C9ORF72 Dipeptide Repeats

Corman A, Jung B, Häggblad M, ..., Carreras-Puigvert J, Fernandez-Capetillo O

Cell Chem Biol 26 (2) 235-243.e5 [2019-02-00; online 2019-02-00]

Chemical Biology Consortium Sweden (CBCS) [Service] Spatial Proteomics [Service]

Spatial and temporal heterogeneity of mouse and human microglia at single-cell resolution.

Masuda T, Sankowski R, Staszewski O, ..., Stadelmann C, Prinz M

Nature 566 (7744) 388-392 [2019-02-00; online 2019-02-13]

B cell alterations during BAFF inhibition with belimumab in SLE.

Ramsköld D, Parodis I, Lakshmikanth T, ..., Gunnarsson I, Malmström V

EBioMedicine 40 (-) 517-527 [2019-02-00; online 2018-12-26]

Recognition of Amino Acid Motifs, Rather Than Specific Proteins, by Human Plasma Cell-Derived Monoclonal Antibodies to Posttranslationally Modified Proteins in Rheumatoid Arthritis.

Steen J, Forsström B, Sahlström P, ..., Klareskog L, Malmström V

Arthritis & rheumatology (Hoboken, N.J.) 71 (2) 196-209 [2019-02-00; online 2018-08-29]

Autoimmunity and Serology Profiling [Collaborative] Bioinformatics Support for Computational Resources [Service]

Drug sensitivity testing on patient-derived sarcoma cells predicts patient response to treatment and identifies c-Sarc inhibitors as active drugs for translocation sarcomas.

Brodin BA, Wennerberg K, Lidbrink E, ..., Kallioniemi O, Stragliotto CL

Br. J. Cancer 120 (4) 435-443 [2019-02-00; online 2019-02-12]

Clinical Genomics [Collaborative] Clinical Genomics Uppsala [Collaborative]

CD99 expression is strongly associated with clinical outcome in children with B-cell precursor acute lymphoblastic leukaemia.

Chen D, Camponeschi A, Wu Q, ..., Fogelstrand L, Mårtensson IL

Br. J. Haematol. 184 (3) 418-423 [2019-02-00; online 2018-11-28]

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

Low Molecular Mass Myocardial Hyaluronan in Human Hypertrophic Cardiomyopathy.

Lorén CE, Dahl CP, Do L, ..., Mörner S, Hellman U

Cells 8 (2) 97 [2019-01-29; online 2019-01-29]

Photoactivated Colibactin Probes Induce Cellular DNA Damage.

Moodie LWK, Hubert M, Zhou X, ..., Wanrooij S, Hedberg C

Angew. Chem. Int. Ed. Engl. 58 (5) 1417-1421 [2019-01-28; online 2018-12-27]

Integrated Microscopy Technologies Umeå [Service]

Peri-arterial specification of vascular mural cells from naïve mesenchyme requires Notch signaling.

Ando K, Wang W, Peng D, ..., Mochizuki N, Betsholtz C

Development 146 (2) dev165589 [2019-01-25; online 2019-01-25]

Differential Expression Patterns of Glycolytic Enzymes and Mitochondria-Dependent Apoptosis in PCOS Patients with Endometrial Hyperplasia, an Early Hallmark of Endometrial Cancer, In Vivo and the Impact of Metformin In Vitro.

Wang T, Zhang J, Hu M, ..., Shao LR, Billig H

Int. J. Biol. Sci. 15 (3) 714-725 [2019-01-24; online 2019-01-24]

Integrated Microscopy Technologies Gothenburg [Service]

Transformation of mature mouse B cells into malignant plasma cells in vitro via introduction of defined genetic elements.

Högstrand K, Lindvall JM, Sundblad A, Grandien A

Eur. J. Immunol. - (-) - [2019-01-21; online 2019-01-21]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Complement Activation Occurs at the Surface of Platelets Activated by Streptococcal M1 Protein and This Results in Phagocytosis of Platelets.

Palm F, Sjöholm K, Malmström J, Shannon O

J. Immunol. 202 (2) 503-513 [2019-01-15; online 2018-12-12]

Structural Proteomics [Collaborative]

The bile salt glycocholate induces global changes in gene and protein expression and activates virulence in enterotoxigenic Escherichia coli.

Joffre E, Nicklasson M, Álvarez-Carretero S, ..., Zhu B, Sjöling Å

Sci Rep 9 (1) 108 [2019-01-14; online 2019-01-14]

Fecal pollution can explain antibiotic resistance gene abundances in anthropogenically impacted environments.

Karkman A, Pärnänen K, Larsson DGJ

Nat Commun 10 (1) 80 [2019-01-08; online 2019-01-08]

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

Effect of CTLA4-Ig (abatacept) treatment on T cells and B cells in peripheral blood of patients with polymyositis and dermatomyositis.

Tang Q, Ramsköld D, Krystufkova O, ..., Lundberg IE, Malmström V

Scand. J. Immunol. 89 (1) e12732 [2019-01-00; online 2018-12-09]

Bioinformatics Support for Computational Resources [Service] Cellular Immunomonitoring [Collaborative]

Exploring rare and low-frequency variants in the Saguenay-Lac-Saint-Jean population identified genes associated with asthma and allergy traits.

Morin A, Madore AM, Kwan T, ..., Pastinen T, Laprise C

Eur. J. Hum. Genet. 27 (1) 90-101 [2019-01-00; online 2018-09-11]

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

Cryo-EM structure of the yeast respiratory supercomplex.

Rathore S, Berndtsson J, Marin-Buera L, ..., Brzezinski P, Ott M

Nat. Struct. Mol. Biol. 26 (1) 50-57 [2019-01-00; online 2018-12-31]

Cryo-EM [Collaborative]

An integrated transcriptome analysis in T-cell acute lymphoblastic leukemia links DNA methylation subgroups to dysregulated TAL1 and ANTP homeobox gene expression.

Haider Z, Larsson P, Landfors M, ..., Hultdin M, Degerman S

Cancer Med 8 (1) 311-324 [2019-01-00; online 2018-12-21]

Clinical Genomics [Collaborative] Clinical Genomics Umeå [Collaborative]

ZBED6 negatively regulates insulin production, neuronal differentiation, and cell aggregation in MIN6 cells.

Wang X, Jiang L, Wallerman O, ..., Welsh N, Andersson L

FASEB J. 33 (1) 88-100 [2019-01-00; online 2018-06-29]

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

Understanding the mechanism of low temperature deactivation of Cu/SAPO-34 exposed to various amounts of water vapor in the NH3-SCR reaction

Woo J, Bernin D, Ahari H, ..., Zammit M, Olsson L

Catal. Sci. Technol. 9 (14) 3623-3636 [2019-00-00; online 2019-00-00]

Sensitive ADAR editing reporter in cancer cells enables high-throughput screening of small molecule libraries

Fritzell K, Xu LD, Otrocka M, Andréasson C, Öhman M

Nucleic Acids Res - (-) - [2018-12-22; online 2018-12-22]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Carbon's Three-Center, Four-Electron Tetrel Bond, Treated Experimentally.

Karim A, Schulz N, Andersson H, ..., Keller S, Erdélyi M

J. Am. Chem. Soc. 140 (50) 17571-17579 [2018-12-19; online 2018-12-07]

Targeted Delivery of Stk25 Antisense Oligonucleotides to Hepatocytes Protects Mice Against Nonalcoholic Fatty Liver Disease.

Cansby E, Nuñez-Durán E, Magnusson E, ..., Aghajan M, Mahlapuu M

Cellular and Molecular Gastroenterology and Hepatology 7 (3) 597-618 [2018-12-19; online 2018-12-19]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Systems Biology [Collaborative]

Red Fluorescent Chlamydia trachomatis Applied to Live Cell Imaging and Screening for Antibacterial Agents.

Mojica SA, Eriksson AU, Davis RA, ..., Elofsson M, Gylfe Å

Front Microbiol 9 (-) 3151 [2018-12-18; online 2018-12-18]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Rainbow Trout Maintain Intestinal Transport and Barrier Functions Following Exposure to Polystyrene Microplastics.

Ašmonaitė G, Sundh H, Asker N, Carney Almroth B

Environ. Sci. Technol. 52 (24) 14392-14401 [2018-12-18; online 2018-12-05]

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Significantly altered peripheral blood cell DNA methylation profile as a result of immediate effect of metformin use in healthy individuals.

Elbere I, Silamikelis I, Ustinova M, ..., Schiöth HB, Klovins J

Clin Epigenetics 10 (1) 156 [2018-12-13; online 2018-12-13]

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Transcriptional landscape of B cell precursor acute lymphoblastic leukemia based on an international study of 1,223 cases.

Li JF, Dai YT, Lilljebjörn H, ..., Chen SJ, Huang JY

Proc. Natl. Acad. Sci. U.S.A. 115 (50) E11711-E11720 [2018-12-11; online 2018-11-28]

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Porous Cellulose Nanofiber-Based Microcapsules for Biomolecular Sensing.

Paulraj T, Wennmalm S, Riazanova AV, ..., Crespo GA, Svagan AJ

ACS Appl Mater Interfaces 10 (48) 41146-41154 [2018-12-05; online 2018-11-26]

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Spatially and functionally distinct subclasses of breast cancer-associated fibroblasts revealed by single cell RNA sequencing.

Bartoschek M, Oskolkov N, Bocci M, ..., Björklund Å, Pietras K

Nat Commun 9 (1) 5150 [2018-12-04; online 2018-12-04]

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Analysis of porcine body size variation using re-sequencing data of miniature and large pigs

Reimer C, Rubin CJ, Sharifi AR, ..., Schlather M, Simianer H

BMC Genomics 19 (1) - [2018-12-00; online 2018-09-19]

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RNA-sequencing reveals long-term effects of silver nanoparticles on human lung cells

Gliga AR, Di Bucchianico S, Lindvall J, Fadeel B, Karlsson HL

Sci Rep 8 (1) - [2018-12-00; online 2018-04-27]

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A drug screening assay on cancer cells chronically adapted to acidosis

Pellegrini P, Serviss JT, Lundbäck T, ..., Linder S, De Milito A

Cancer Cell Int 18 (1) - [2018-12-00; online 2018-09-25]

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Targeting PFKFB3 radiosensitizes cancer cells and suppresses homologous recombination

Gustafsson NMS, Färnegårdh K, Bonagas N, ..., Olin T, Helleday T

Nat Commun 9 (1) - [2018-12-00; online 2018-09-24]

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Stereocilin gene variants associated with episodic vertigo: expansion of the DFNB16 phenotype.

Frykholm C, Klar J, Tomanovic T, Ameur A, Dahl N

Eur. J. Hum. Genet. 26 (12) 1871-1874 [2018-12-00; online 2018-09-24]

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Somatic mutagenesis in satellite cells associates with human skeletal muscle aging

Franco I, Johansson A, Olsson K, ..., Fischer H, Eriksson M

Nat Commun 9 (1) - [2018-12-00; online 2018-02-23]

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Image-Based Detection of Patient-Specific Drug-Induced Cell-Cycle Effects in Glioblastoma.

Matuszewski DJ, Wählby C, Krona C, Nelander S, Sintorn IM

SLAS DISCOVERY: Advancing Life Sciences R&D 23 (10) 1030-1039 [2018-12-00; online 2018-08-03]

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Extracellular nanovesicles released from the commensal yeast Malassezia sympodialis are enriched in allergens and interact with cells in human skin

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Sci Rep 8 (1) - [2018-12-00; online 2018-06-15]

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Exploring benzimidazole resistance in Haemonchus contortus by next generation sequencing and droplet digital PCR

Baltrušis P, Halvarsson P, Höglund J

International Journal for Parasitology: Drugs and Drug Resistance 8 (3) 411-419 [2018-12-00; online 2018-12-00]

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The gut microbiome participates in transgenerational inheritance of low-temperature responses in Drosophila melanogaster.

Zare A, Johansson AM, Karlsson E, Delhomme N, Stenberg P

FEBS Lett. 592 (24) 4078-4086 [2018-12-00; online 2018-11-15]

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Publisher Correction: A DHODH inhibitor increases p53 synthesis and enhances tumor cell killing by p53 degradation blockage

Ladds MJGW, van Leeuwen IMM, Drummond CJ, ..., McCormack E, Laín S

Nat Commun 9 (1) - [2018-12-00; online 2018-05-22]

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Linking FOXO3, NCOA3, and TCF7L2 to Ras pathway phenotypes through a genome-wide forward genetic screen in human colorectal cancer cells

Kundu S, Ali MA, Handin N, ..., Hellström M, Sjöblom T

Genome Med 10 (1) - [2018-12-00; online 2018-01-04]

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The Mutant p53-Targeting Compound APR-246 Induces ROS-Modulating Genes in Breast Cancer Cells.

Synnott NC, Madden SF, Bykov VJN, ..., Wiman KG, Duffy MJ

Transl Oncol 11 (6) 1343-1349 [2018-12-00; online 2018-09-06]

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Gene expression correlated with delay in shell formation in larval Pacific oysters (Crassostrea gigas) exposed to experimental ocean acidification provides insights into shell formation mechanisms

De Wit P, Durland E, Ventura A, Langdon CJ

BMC Genomics 19 (1) - [2018-12-00; online 2018-02-22]

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Structure of a functional obligate complex III 2IV2 respiratory supercomplex from Mycobacterium smegmatis.

Wiseman B, Nitharwal RG, Fedotovskaya O, ..., Brzezinski P, Högbom M

Nat. Struct. Mol. Biol. 25 (12) 1128-1136 [2018-12-00; online 2018-12-05]

Using High Content Imaging to Quantify Target Engagement in Adherent Cells.

Axelsson H, Almqvist H, Seashore-Ludlow B

J Vis Exp - (141) - [2018-11-29; online 2018-11-29]

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Metabolic control of PPAR activity by aldehyde dehydrogenase regulates invasive cell behavior and predicts survival in hepatocellular and renal clear cell carcinoma.

Andrejeva D, Kugler JM, Nguyen HT, ..., Loya AC, Cohen SM

BMC Cancer 18 (1) 1180 [2018-11-28; online 2018-11-28]

Cell-free DNA profiling of metastatic prostate cancer reveals microsatellite instability, structural rearrangements and clonal hematopoiesis.

Mayrhofer M, De Laere B, Whitington T, ..., Grönberg H, Lindberg J

Genome Med 10 (1) 85 [2018-11-21; online 2018-05-11]

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Quantitative Interpretation of Intracellular Drug Binding and Kinetics Using the Cellular Thermal Shift Assay

Seashore-Ludlow B, Axelsson H, Almqvist H, ..., Jonsson M, Lundbäck T

Biochemistry - (-) - [2018-11-19; online 2018-11-19]

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Expression profiling and in situ screening of circular RNAs in human tissues.

Zaghlool A, Ameur A, Wu C, ..., Nilsson M, Feuk L

Sci Rep 8 (1) 16953 [2018-11-16; online 2018-11-16]

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Small-molecule inhibitor of OGG1 suppresses proinflammatory gene expression and inflammation.

Visnes T, Cázares-Körner A, Hao W, ..., Boldogh I, Helleday T

Science 362 (6416) 834-839 [2018-11-16; online 2018-11-18]

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Diet-dependent gene expression highlights the importance of Cytochrome P450 in detoxification of algal secondary metabolites in a marine isopod.

De Wit P, Yamada K, Panova M, André C, Johannesson K

Sci Rep 8 (1) 16824 [2018-11-14; online 2018-11-14]

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Disease-specific oligodendrocyte lineage cells arise in multiple sclerosis

Falcão AM, van Bruggen D, Marques S, ..., Guerreiro-Cacais AO, Castelo-Branco G

Nat Med - (-) - [2018-11-12; online 2018-11-12]

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Affinity to cellulose is a shared property among coiled-coil domains of intermediate filaments and prokaryotic intermediate filament-like proteins.

Söderholm N, Javadi A, Flores IS, Flärdh K, Sandblad L

Sci Rep 8 (1) 16524 [2018-11-08; online 2018-11-08]

Vandermonde Factorization of Hankel Matrix for Complex Exponential Signal Recovery—Application in Fast NMR Spectroscopy

Ying J, Cai JF, Guo D, ..., Chen Z, Qu X

IEEE Trans. Signal Process. 66 (21) 5520-5533 [2018-11-01; online 2018-11-01]

Detection of autoantibodies against cancer-testis antigens in non-small cell lung cancer.

Djureinovic D, Dodig-Crnković T, Hellström C, ..., Schwenk JM, Micke P

Lung Cancer 125 (-) 157-163 [2018-11-00; online 2018-09-17]

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VEGF receptor-2/neuropilin 1 trans-complex formation between endothelial and tumor cells is an independent predictor of pancreatic cancer survival

Morin E, Sjöberg E, Tjomsland V, ..., Sjöblom T, Claesson-Welsh L

J. Pathol 246 (3) 311-322 [2018-11-00; online 2018-09-04]

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Notch signaling promotes a HIF2α-driven hypoxic response in multiple tumor cell types.

Mutvei AP, Landor SK, Fox R, ..., Jin S, Lendahl U

Oncogene 37 (46) 6083-6095 [2018-11-00; online 2018-07-11]

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Fine-mapping type 2 diabetes loci to single-variant resolution using high-density imputation and islet-specific epigenome maps.

Mahajan A, Taliun D, Thurner M, ..., Boehnke M, McCarthy MI

Nat. Genet. 50 (11) 1505-1513 [2018-11-00; online 2018-10-08]

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Upregulated BMP-Smad signaling activity in the glucuronyl C5-epimerase knock out MEF cells

Batool T, Fang J, Jansson V, ..., Moustakas A, Li JP

Cellular Signalling - (-) - [2018-11-00; online 2018-11-00]

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Copper Chaperone Atox1 Interacts with Cell Cycle Proteins.

Matson Dzebo M, Blockhuys S, Valenzuela S, ..., Esbjörner EK, Wittung-Stafshede P

Computational and Structural Biotechnology Journal 16 (-) 443-449 [2018-10-31; online 2018-10-31]

Gene-level associations in suicide attempter families show overrepresentation of synaptic genes and genes differentially expressed in brain development

Sokolowski M, Wasserman J, Wasserman D

Am. J. Med. Genet. - (-) - [2018-10-31; online 2018-10-31]

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SMAD4 Is Essential for Human Cardiac Mesodermal Precursor Cell Formation.

Xu J, Gruber PJ, Chien KR

Stem Cells - (-) - [2018-10-30; online 2018-10-30]

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Targeting autophagy by small molecule inhibitors of vacuolar protein sorting 34 (Vps34) improves the sensitivity of breast cancer cells to Sunitinib.

Dyczynski M, Yu Y, Otrocka M, ..., De Milito A, Pokrovskaja Tamm K

Cancer Lett. 435 (-) 32-43 [2018-10-28; online 2018-07-25]

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Role of OmpA1 and OmpA2 in Aggregatibacter actinomycetemcomitans and Aggregatibacter aphrophilus serum resistance.

Lindholm M, Min Aung K, Nyunt Wai S, Oscarsson J

Journal of Oral Microbiology 11 (1) 1536192 [2018-10-26; online 2018-10-26]

Single-cell RNA-seq analysis reveals the platinum resistance gene COX7B and the surrogate marker CD63.

Tanaka N, Katayama S, Reddy A, ..., Oya M, Uhlén P

Cancer Med - (-) - [2018-10-26; online 2018-10-26]

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Role of Thiol Reactivity for Targeting Mutant p53.

Zhang Q, Bergman J, Wiman KG, Bykov VJN

Cell Chem Biol 25 (10) 1219-1230.e3 [2018-10-18; online 2018-07-26]

Single-Cell Transcriptomics of Traced Epidermal and Hair Follicle Stem Cells Reveals Rapid Adaptations during Wound Healing.

Joost S, Jacob T, Sun X, ..., Sur I, Kasper M

Cell Rep 25 (3) 585-597.e7 [2018-10-16; online 2018-10-18]

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Spatially Resolved Transcriptomics Enables Dissection of Genetic Heterogeneity in Stage III Cutaneous Malignant Melanoma

Thrane K, Eriksson H, Maaskola J, Hansson J, Lundeberg J

Cancer Res 78 (20) 5970-5979 [2018-10-15; online 2018-10-15]

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Enhanced validation of antibodies for research applications.

Edfors F, Hober A, Linderbäck K, ..., Forsström B, Uhlen M

Nat Commun 9 (1) 4130 [2018-10-08; online 2018-10-08]

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The Xerobranching Response Represses Lateral Root Formation When Roots Are Not in Contact with Water.

Orman-Ligeza B, Morris EC, Parizot B, ..., Beeckman T, Draye X

Curr. Biol. 28 (19) 3165-3173.e5 [2018-10-08; online 2018-09-27]

NormalyzerDE: Online tool for improved normalization of omics expression data and high-sensitivity differential expression analysis.

Willforss J, Chawade A, Levander F

J. Proteome Res. - (-) - [2018-10-02; online 2018-10-02]

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Mutation, methylation, and gene expression profiles in dup(1q)-positive pediatric B-cell precursor acute lymphoblastic leukemia.

Gunnarsson R, Dilorenzo S, Lundin-Ström KB, ..., Isaksson A, Johansson B

Leukemia 32 (10) 2117-2125 [2018-10-00; online 2018-03-12]

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Genome-wide binding of transcription factor ZEB1 in triple-negative breast cancer cells.

Maturi V, Enroth S, Heldin CH, Moustakas A

J. Cell. Physiol. 233 (10) 7113-7127 [2018-10-00; online 2018-05-10]

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Backbone 1H, 13C, and 15N resonance assignments of the ligand binding domain of the human wildtype glucocorticoid receptor and the F602S mutant variant

Köhler C, Carlström G, Tångefjord S, ..., Edman K, Akke M

Biomol NMR Assign 12 (2) 263-268 [2018-10-00; online 2018-04-17]

Exploring photoinactivation of microbial biofilms using laser scanning microscopy and confined 2-photon excitation.

Thomsen H, Graf FE, Farewell A, Ericson MB

J. Biophotonics 11 (10) e201800018 [2018-10-00; online 2018-06-19]

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Microbial Community and Metabolic Activity in Thiocyanate Degrading Low Temperature Microbial Fuel Cells.

Ni G, Canizales S, Broman E, ..., Sleutels T, Dopson M

Front Microbiol 9 (-) 2308 [2018-09-28; online 2018-09-28]

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Loss of zebrafish ctnnd2b results in disorganised forebrain neuron clusters

Hofmeister W, Vaz R, Edwards S, Dueñas Rey A, Lindstrand A

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Structural and Functional Characterization of the BcsG Subunit of the Cellulose Synthase in Salmonella typhimurium.

Sun L, Vella P, Schnell R, ..., Schneider G, Römling U

J. Mol. Biol. 430 (18 Pt B) 3170-3189 [2018-09-14; online 2018-07-12]

Continuous Immune Cell Differentiation Inferred From Single-Cell Measurements Following Allogeneic Stem Cell Transplantation.

Chen Y, Lakshmikanth T, Olin A, ..., Remberger M, Brodin P

Front Mol Biosci 5 (-) 81 [2018-09-12; online 2018-09-12]

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Attached stratified mucus separates bacteria from the epithelial cells in COPD lungs.

Fernández-Blanco JA, Fakih D, Arike L, ..., Ermund A, Hansson GC

JCI Insight 3 (17) - [2018-09-06; online 2018-09-06]

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Neuronal Expression of Opioid Gene is Controlled by Dual Epigenetic and Transcriptional Mechanism in Human Brain.

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

Cereb. Cortex 28 (9) 3129-3142 [2018-09-01; online 2017-10-03]

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Interactions between monomeric CCTδ and p150 Glued: A novel function for CCTδ at the cell periphery distinct from the protein folding activity of the molecular chaperone CCT.

Echbarthi M, Vallin J, Grantham J

Exp. Cell Res. 370 (1) 137-149 [2018-09-01; online 2018-06-18]

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

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

Xenobiotica 48 (9) 938-944 [2018-09-00; online 2017-10-13]

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Membrane Fluidity Is Regulated Cell Nonautonomously by Caenorhabditiselegans PAQR-2 and Its Mammalian Homolog AdipoR2.

Bodhicharla R, Devkota R, Ruiz M, Pilon M

Genetics 210 (1) 189-201 [2018-09-00; online 2018-07-11]

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The Protozoan Parasite Toxoplasma gondii Selectively Reprograms the Host Cell Translatome.

Leroux LP, Lorent J, Graber TE, ..., Larsson O, Jaramillo M

Infect. Immun. 86 (9) - [2018-09-00; online 2018-08-22]

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Sex-biased gene expression, sexual antagonism and levels of genetic diversity in the collared flycatcher (Ficedula albicollis) genome

Dutoit L, Mugal CF, Bolívar P, ..., Gustafsson L, Ellegren H

Mol Ecol 27 (18) 3572-3581 [2018-09-00; online 2018-09-04]

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Genome Sequence Resource for the Oomycete Taro Pathogen Phytophthora colocasiae.

Vetukuri RR, Kushwaha SK, Sen D, ..., Lamour KH, Grenville-Briggs LJ

Mol. Plant Microbe Interact. 31 (9) 903-905 [2018-09-00; online 2018-08-03]

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Sequentially acting SOX proteins orchestrate astrocyte‐ and oligodendrocyte‐specific gene expression

Klum S, Zaouter C, Alekseenko Z, ..., Muhr J, Bergsland M

EMBO Rep. - (-) e46635 [2018-08-30; online 2018-08-30]

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Metabolic reprogramming of acute lymphoblastic leukemia cells in response to glucocorticoid treatment.

Dyczynski M, Vesterlund M, Björklund AC, ..., Tamm KP, Nilsson R

Cell Death Dis 9 (9) 846 [2018-08-28; online 2018-08-28]

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Exploratory Profiling of Urine MicroRNAs in the dy Mouse Model of LAMA2-CMD: Relation to Disease Progression.2J/dy2J

Moreira Soares Oliveira B, Gawlik KI, Durbeej M, Holmberg J

PLoS Curr 10 (-) - [2018-08-27; online 2018-08-27]

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Reduced expression of PROX1 transitions glioblastoma cells into a mesenchymal gene expression subtype

Goudarzi KM, Espinoza JA, Guo M, ..., Lindström MS, Hägerstrand D

Cancer Res - (-) canres.0320.2018 [2018-08-22; online 2018-08-22]

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Single-cell RNA sequencing of mouse brain and lung vascular and vessel-associated cell types.

He L, Vanlandewijck M, Mäe MA, ..., Lendahl U, Betsholtz C

Sci Data 5 (1) 180160 [2018-08-21; online 2018-08-21]

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Diversity of Interneurons in the Dorsal Striatum Revealed by Single-Cell RNA Sequencing and PatchSeq.

Muñoz-Manchado AB, Bengtsson Gonzales C, Zeisel A, ..., Linnarsson S, Hjerling-Leffler J

Cell Rep 24 (8) 2179-2190.e7 [2018-08-21; online 2018-08-23]

Reduction in White Blood Cell, Neutrophil and Red Blood Cell counts Related to Gender, HLA and Islet Autoantibodies in Swedish TEDDY Children at Increased Risk for Type 1 Diabetes

Salami F, Lee HS, Freyhult E, ..., Lernmark Å, Törn C

Diabetes - (-) db180355 [2018-08-13; online 2018-08-13]

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Nutritional Metabolomics: Postprandial Response of Meals Relating to Vegan, Lacto-Ovo Vegetarian, and Omnivore Diets.

Rådjursöga M, Lindqvist HM, Pedersen A, ..., Ellegård L, Winkvist A

Nutrients 10 (8) 1063 [2018-08-10; online 2018-08-10]

Molecular Architecture of the Mouse Nervous System.

Zeisel A, Hochgerner H, Lönnerberg P, ..., Marklund U, Linnarsson S

Cell 174 (4) 999-1014.e22 [2018-08-09; online 2018-08-11]

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Huntingtin Aggregation Impairs Autophagy, Leading to Argonaute-2 Accumulation and Global MicroRNA Dysregulation.

Pircs K, Petri R, Madsen S, ..., Barker RA, Jakobsson J

Cell Rep 24 (6) 1397-1406 [2018-08-07; online 2018-08-09]

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Thermodynamics of Hg(II) Bonding to Thiol Groups in Suwannee River Natural Organic Matter Resolved by Competitive Ligand Exchange, Hg LIII-Edge EXAFS and 1H NMR Spectroscopy

Song Y, Jiang T, Liem-Nguyen V, ..., Björn E, Skyllberg U

Environ. Sci. Technol. 52 (15) 8292-8301 [2018-08-07; online 2018-07-07]

Substrate-Induced Response in Biogas Process Performance and Microbial Community Relates Back to Inoculum Source

Liu T, Sun L, Nordberg Å, Schnürer A

Microorganisms 6 (3) 80 [2018-08-05; online 2018-08-05]

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Prenatal arsenic exposure is associated with increased plasma IGFBP3 concentrations in 9-year-old children partly via changes in DNA methylation.

Gliga AR, Engström K, Kippler M, ..., Raqib R, Broberg K

Arch. Toxicol. 92 (8) 2487-2500 [2018-08-00; online 2018-06-08]

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Scanning electron microscopy as a tool for evaluating morphology of amyloid structures formed on surface plasmon resonance chips.

Bra Nnstro M K, Gharibyan AL, Islam T, ..., Pamren A, Olofsson A

Data Brief 19 (-) 1166-1170 [2018-08-00; online 2018-05-26]

Cryo-EM [Technology development]

Stereotypic Immune System Development in Newborn Children

Olin A, Henckel E, Chen Y, ..., Bohlin K, Brodin P

Cell 174 (5) 1277-1292.e14 [2018-08-00; online 2018-08-00]

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Acute sleep loss results in tissue-specific alterations in genome-wide DNA methylation state and metabolic fuel utilization in humans

Cedernaes J, Schönke M, Westholm JO, ..., Zierath JR, Benedict C

Sci Adv 4 (8) eaar8590 [2018-08-00; online 2018-08-22]

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Detailed analysis of the plasma extracellular vesicle proteome after separation from lipoproteins

Karimi N, Cvjetkovic A, Jang SC, ..., Lötvall J, Lässer C

Cell. Mol. Life Sci. 75 (15) 2873-2886 [2018-08-00; online 2018-02-13]

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RNA velocity of single cells.

La Manno G, Soldatov R, Zeisel A, ..., Linnarsson S, Kharchenko PV

Nature 560 (7719) 494-498 [2018-08-00; online 2018-08-08]

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Insights into Avian Incomplete Dosage Compensation: Sex-Biased Gene Expression Coevolves with Sex Chromosome Degeneration in the Common Whitethroat.

Sigeman H, Ponnikas S, Videvall E, ..., Naurin S, Hansson B

Genes 9 (8) 373 [2018-07-26; online 2018-07-26]

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Glyco-engineered cell line and computational docking studies reveals enterotoxigenic Escherichia coli CFA/I fimbriae bind to Lewis a glycans.

Mottram L, Liu J, Chavan S, ..., Svennerholm AM, Holgersson J

Sci Rep 8 (1) 11250 [2018-07-26; online 2018-07-26]

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Response of Microbial Communities to Changing Climate Conditions During Summer Cyanobacterial Blooms in the Baltic Sea.

Berner C, Bertos-Fortis M, Pinhassi J, Legrand C

Front Microbiol 9 (-) 1562 [2018-07-25; online 2018-07-25]

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A patient-derived xenograft pre-clinical trial reveals treatment responses and a resistance mechanism to karonudib in metastatic melanoma.

Einarsdottir BO, Karlsson J, Söderberg EMV, ..., Helleday T, Nilsson JA

Cell Death Dis 9 (8) 810 [2018-07-24; online 2018-07-24]

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Mebendazole stimulates CD14+ myeloid cells to enhance T-cell activation and tumour cell killing.

Rubin J, Mansoori S, Blom K, ..., Nygren P, Larsson R

Oncotarget 9 (56) 30805-30813 [2018-07-20; online 2018-07-20]

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Möller M, Lee YQ, Vidovic K, ..., Storry JR, Olsson ML

Blood 132 (3) 334-338 [2018-07-19; online 2018-05-10]

Structural Proteomics [Collaborative]

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

Mol. Cell. Endocrinol. 470 (-) 84-95 [2018-07-15; online 2017-10-03]

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Autoantibody profiling in intraocular fluid of patients with uveitis.

Ten Berge JC, Schreurs MW, van Rosmalen J, Rothova A

Exp. Eye Res. 176 (-) 141-146 [2018-07-10; online 2018-07-10]

Autoimmunity and Serology Profiling [Service]

Primary glioblastoma cells for precision medicine: a quantitative portrait of genomic (in)stability during the first 30 passages.

Baskaran S, Mayrhofer M, Kultima HG, ..., Isaksson A, Nelander S

Neuro-oncology 20 (8) 1080-1091 [2018-07-05; online 2018-02-21]

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Enteric Species F Human Adenoviruses use Laminin-Binding Integrins as Co-Receptors for Infection of Ht-29 Cells.

Rajan A, Persson BD, Frängsmyr L, ..., Gall J, Arnberg N

Sci Rep 8 (1) 10019 [2018-07-03; online 2018-07-03]

Human Immunodeficiency Virus-Infected Women Have High Numbers of CD103-CD8+ T Cells Residing Close to the Basal Membrane of the Ectocervical Epithelium.

Gibbs A, Buggert M, Edfeldt G, ..., Broliden K, Tjernlund A

J. Infect. Dis. 218 (3) 453-465 [2018-07-02; online 2017-12-23]

BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]

Calcium-activated Chloride Channel Regulator 1 (CLCA1) Controls Mucus Expansion in Colon by Proteolytic Activity.

Nyström EEL, Birchenough GMH, van der Post S, ..., Hansson GC, Johansson MEV

EBioMedicine 33 (-) 134-143 [2018-07-00; online 2018-06-07]

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The mycoparasitic fungus Clonostachys rosea responds with both common and specific gene expression during interspecific interactions with fungal prey

Nygren K, Dubey M, Zapparata A, ..., Jensen DF, Karlsson M

Evol Appl 11 (6) 931-949 [2018-07-00; online 2018-03-14]

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Multiplexed fluorescence microscopy reveals heterogeneity among stromal cells in mouse bone marrow sections

Holzwarth K, Köhler R, Philipsen L, ..., Niesner RA, Hauser AE

Cytometry 93 (9) 876-888 [2018-07-00; online 2018-08-14]

BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]

Assessment of titanium dioxide nanoparticle toxicity in the rainbow trout (Onchorynchus mykiss) liver and gill cell lines RTL-W1 and RTgill-W1 under particular consideration of nanoparticle stability and interference with fluorometric assays

Lammel T, Sturve J

NanoImpact 11 (-) 1-19 [2018-07-00; online 2018-07-00]

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OLMα2 Cells Bidirectionally Modulate Learning

Siwani S, França ASC, Mikulovic S, ..., Tort ABL, Kullander K

Neuron 99 (2) 404-412.e3 [2018-07-00; online 2018-07-00]

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The STAT4 SLE risk allele rs7574865[T] is associated with increased IL-12-induced IFN-γ production in T cells from patients with SLE.

Hagberg N, Joelsson M, Leonard D, ..., Bryceson YT, Rönnblom L

Ann. Rheum. Dis. 77 (7) 1070-1077 [2018-07-00; online 2018-02-23]

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CRISPR-Cas9 genome editing induces a p53-mediated DNA damage response.

Haapaniemi E, Botla S, Persson J, Schmierer B, Taipale J

Nat. Med. 24 (7) 927-930 [2018-07-00; online 2018-06-11]

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A heterogeneous response of liver and skeletal muscle fat to the combination of a Paleolithic diet and exercise in obese individuals with type 2 diabetes: a randomised controlled trial

Otten J, Stomby A, Waling M, ..., Hauksson J, Olsson T

Diabetologia 61 (7) 1548-1559 [2018-07-00; online 2018-04-26]

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Increased Neuronal Differentiation of Neural Progenitor Cells Derived from Phosphovimentin-Deficient Mice.

Chen M, Puschmann TB, Marasek P, ..., Wilhelmsson U, Pekny M

Mol Neurobiol 55 (7) 5478-5489 [2018-07-00; online 2017-09-27]

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A freshwater diatom challenged by Zn: Biochemical, physiological and metabolomic responses of Tabellaria flocculosa(Roth) Kützing.

Gonçalves S, Kahlert M, Almeida SFP, Figueira E

Environ Pollut 238 (-) 959-971 [2018-07-00; online 2018-04-28]

Confined photo-release of nitric oxide with simultaneous two-photon fluorescence tracking in a cellular system.

Thomsen H, Marino N, Conoci S, Sortino S, Ericson MB

Sci Rep 8 (1) 9753 [2018-06-27; online 2018-06-27]

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Gene expression profiling of periodontitis-affected gingival tissue by spatial transcriptomics.

Lundmark A, Gerasimcik N, Båge T, ..., Lundeberg J, Yucel-Lindberg T

Sci Rep 8 (1) 9370 [2018-06-19; online 2018-06-19]

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Poly(alkylidenimine) Dendrimers Functionalized with the Organometallic Moiety [Ru(η⁵-C₅H₅)(PPh₃)₂]⁺ as Promising Drugs Against Cisplatin-Resistant Cancer Cells and Human Mesenchymal Stem Cells.

Gouveia M, Figueira J, Jardim MG, ..., Rissanen K, Rodrigues J

Molecules 23 (6) 1471 [2018-06-17; online 2018-06-17]

Higher Concentrations of BCAAs and 3-HIB Are Associated with Insulin Resistance in the Transition from Gestational Diabetes to Type 2 Diabetes.

Andersson-Hall U, Gustavsson C, Pedersen A, ..., Joelsson L, Holmäng A

Journal of Diabetes Research 2018 (-) 4207067 [2018-06-05; online 2018-06-05]

Neuronal atlas of the dorsal horn defines its architecture and links sensory input to transcriptional cell types.

Häring M, Zeisel A, Hochgerner H, ..., Linnarsson S, Ernfors P

Nat. Neurosci. 21 (6) 869-880 [2018-06-00; online 2018-04-23]

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Assessing Cu impacts on freshwater diatoms: biochemical and metabolomic responses of Tabellaria flocculosa (Roth) Kützing

Gonçalves S, Kahlert M, Almeida SFP, Figueira E

Science of The Total Environment 625 (-) 1234-1246 [2018-06-00; online 2018-06-00]

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Genomewide binding of transcription factor Snail1 in triple-negative breast cancer cells

Maturi V, Morén A, Enroth S, Heldin CH, Moustakas A

Mol Oncol 12 (7) 1153-1174 [2018-06-00; online 2018-05-21]

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A novel ECEL1 mutation expands the phenotype of distal arthrogryposis multiplex congenita type 5D to include pretibial vertical skin creases.

Stattin EL, Johansson J, Gudmundsson S, ..., Bondeson ML, Wilbe M

Am. J. Med. Genet. A 176 (6) 1405-1410 [2018-06-00; online 2018-04-16]

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Paternally expressed imprinted genes associate with hybridization barriers in Capsella

Lafon-Placette C, Hatorangan MR, Steige KA, ..., Slotte T, Köhler C

NPLANTS 4 (6) 352-357 [2018-06-00; online 2018-05-28]

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Expression of ribosomal and actin network proteins and immunochemotherapy resistance in diffuse large B cell lymphoma patients

Bram Ednersson S, Stenson M, Stern M, ..., Hasselblom S, Andersson PO

Br J Haematol 181 (6) 770-781 [2018-06-00; online 2018-05-16]

Glycoproteomics and MS Proteomics [Service] Integrated Microscopy Technologies Gothenburg [Service]

Circadian clock components control daily growth activities by modulating cytokinin levels and cell division-associated gene expression in Populus trees.

Edwards KD, Takata N, Johansson M, ..., Ljung K, Eriksson ME

Plant Cell Environ. 41 (6) 1468-1482 [2018-06-00; online 2018-04-15]

Testis transcriptome alterations in zebrafish (Danio rerio) with reduced fertility due to developmental exposure to 17α-ethinyl estradiol

Porseryd T, Reyhanian Caspillo N, Volkova K, ..., Olsson PE, Porsch-Hällström I

General and Comparative Endocrinology 262 (-) 44-58 [2018-06-00; online 2018-06-00]

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Diminished CXCR5 expression in peripheral blood of patients with Sjögren's syndrome may relate to both genotype and salivary gland homing

Aqrawi LA, Ivanchenko M, Björk A, ..., Skarstein K, Wahren-Herlenius M

Clin Exp Immunol 192 (3) 259-270 [2018-05-25; online 2018-03-24]

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

Pseudouridylation of tRNA-Derived Fragments Steers Translational Control in Stem Cells.

Guzzi N, Cieśla M, Ngoc PCT, ..., Hsieh AC, Bellodi C

Cell 173 (5) 1204-1216.e26 [2018-05-17; online 2018-04-05]

Transcriptomic analysis of the harvested endothelial cells in a swine model of mechanical thrombectomy.

Jaff N, Grankvist R, Muhl L, ..., Eriksson U, Holmin S

Neuroradiology - (-) - [2018-05-14; online 2018-05-14]

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Impact of Dynamically Exposed Polarity on Permeability and Solubility of Chameleonic Drugs Beyond the Rule of 5

Rossi Sebastiano M, Doak BC, Backlund M, ..., Matsson P, Kihlberg J

J. Med. Chem. 61 (9) 4189-4202 [2018-05-10; online 2018-04-02]

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

Modulation of gene transcription and epigenetics of colon carcinoma cells by bacterial membrane vesicles.

Vdovikova S, Gilfillan S, Wang S, ..., Wai SN, Hurtado A

Sci Rep 8 (1) 7434 [2018-05-09; online 2018-05-09]

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Genome-wide association meta-analysis of circulating odd-numbered chain saturated fatty acids: Results from the CHARGE Consortium.

de Oliveira Otto MC, Lemaitre RN, Sun Q, ..., Siscovick DS, Mozaffarian D

PLoS ONE 13 (5) e0196951 [2018-05-08; online 2018-05-08]

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Time-resolved transcriptome and proteome landscape of human regulatory T cell (Treg) differentiation reveals novel regulators of FOXP3.

Schmidt A, Marabita F, Kiani NA, ..., Lahesmaa R, Tegnér J

BMC Biol. 16 (1) 47 [2018-05-07; online 2018-05-07]

Global Proteomics and Proteogenomics [Collaborative]

The structure of the N-terminal module of the cell wall hydrolase RipA and its role in regulating catalytic activity.

Steiner EM, Lyngsø J, Guy JE, ..., Schneider G, Schnell R

Proteins - (-) - [2018-05-02; online 2018-05-02]

BAP1 induces cell death via interaction with 14-3-3 in neuroblastoma.

Sime W, Niu Q, Abassi Y, ..., Fu H, Massoumi R

Cell Death Dis 9 (5) 458 [2018-05-01; online 2018-05-01]

Extended and Continuous Decline in Effective Population Size Results in Low Genomic Diversity in the World's Rarest Hyena Species, the Brown Hyena.

Westbury MV, Hartmann S, Barlow A, ..., Dalén L, Hofreiter M

Mol. Biol. Evol. 35 (5) 1225-1237 [2018-05-01; online 2018-03-13]

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Mitochondrial Translation Efficiency Controls Cytoplasmic Protein Homeostasis

Suhm T, Kaimal JM, Dawitz H, ..., Andréasson C, Ott M

Cell Metabolism - (-) - [2018-05-00; online 2018-05-00]

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Transcription profiling of peripheral B cells in antibody-positive primary Sjögren's syndrome reveals upregulated expression of CX3CR1 and a type I and type II interferon signature.

Imgenberg-Kreuz J, Sandling JK, Björk A, ..., Syvänen AC, Nordmark G

Scand. J. Immunol. 87 (5) e12662 [2018-05-00; online 2018-04-15]

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Quantification of endogenous and exogenous protein expressions of Na,K-ATPase with super-resolution PALM/STORM imaging.

Bernhem K, Blom H, Brismar H

PLoS ONE 13 (4) e0195825 [2018-04-25; online 2018-04-25]

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Experimental validation of predicted cancer genes using FRET

Guala D, Bernhem K, Blal HA, ..., Brismar H, Sonnhammer ELL

Methods Appl. Fluoresc. 6 (3) 035007 [2018-04-25; online 2018-04-25]

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Autophagic flux blockage by accumulation of weakly basic tenovins leads to elimination of B-Raf mutant tumour cells that survive vemurafenib

Ladds MJGW, Pastor-Fernández A, Popova G, ..., Bhatia R, Laín S

PLoS ONE 13 (4) e0195956 [2018-04-23; online 2018-04-23]

Expression of scavenger receptor MARCO defines a targetable tumor-associated macrophage subset in non-small cell lung cancer.

La Fleur L, Boura VF, Alexeyenko A, ..., Karlsson MCI, Botling J

Int. J. Cancer - (-) - [2018-04-18; online 2018-04-18]

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Transcriptome profiling of the interconnection of pathways involved in malignant transformation and response to hypoxia.

Danielsson F, Fasterius E, Sullivan D, ..., Williams C, Lundberg E

Oncotarget 9 (28) 19730-19744 [2018-04-13; online 2018-04-13]

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Rice auxin influx carrier OsAUX1 facilitates root hair elongation in response to low external phosphate.

Giri J, Bhosale R, Huang G, ..., Swarup R, Bennett MJ

Nat Commun 9 (1) 1408 [2018-04-12; online 2018-04-12]

Expression levels of long non-coding RNAs are prognostic for AML outcome.

Mer AS, Lindberg J, Nilsson C, ..., Lehmann S, Rantalainen M

J Hematol Oncol 11 (1) 52 [2018-04-07; online 2018-04-07]

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An Application-Directed, Versatile DNA FISH Platform for Research and Diagnostics.

Gelali E, Custodio J, Girelli G, ..., Crosetto N, Bienko M

Methods Mol. Biol. 1766 (-) 303-333 [2018-04-02; online 2018-04-02]

Advanced FISH Technologies [Technology development]

Identification of Potential MR-Derived Biomarkers for Tumor Tissue Response to 177Lu-Octreotate Therapy in an Animal Model of Small Intestine Neuroendocrine Tumor.

Montelius M, Spetz J, Jalnefjord O, ..., Ljungberg M, Forssell-Aronsson E

Transl Oncol 11 (2) 193-204 [2018-04-00; online 2018-01-11]

RNA Sequencing of Stentor Cell Fragments Reveals Transcriptional Changes during Cellular Regeneration

Onsbring H, Jamy M, Ettema TJG

Current Biology 28 (8) 1281-1288.e3 [2018-04-00; online 2018-04-00]

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GABA Regulates Release of Inflammatory Cytokines From Peripheral Blood Mononuclear Cells and CD4 + T Cells and Is Immunosuppressive in Type 1 Diabetes

Bhandage AK, Jin Z, Korol SV, ..., Kamali-Moghaddam M, Birnir B

EBioMedicine 30 (-) 283-294 [2018-04-00; online 2018-04-00]

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Confocal super-resolution imaging of the glomerular filtration barrier enabled by tissue expansion

Unnersjö-Jess D, Scott L, Sevilla SZ, ..., Blom H, Brismar H

Kidney International 93 (4) 1008-1013 [2018-04-00; online 2018-04-00]

Bioinformatics Support for Computational Resources [Service] Integrated Microscopy Technologies Stockholm [Technology development]

The neuroendocrine phenotype, genomic profile and therapeutic sensitivity of GEPNET cell lines. Correction

Hofving T, Arvidsson Y, Almobarak B, ..., Johanson V, Nilsson O

Endocr Relat Cancer 25 (4) X1-X2 [2018-04-00; online 2018-04-00]

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Protein Expression in Tonsillar and Base of Tongue Cancer and in Relation to Human Papillomavirus (HPV) and Clinical Outcome.

Ramqvist T, Näsman A, Franzén B, ..., Dalianis T, Munck-Wikland E

Int J Mol Sci 19 (4) 978 [2018-03-25; online 2018-03-25]

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Reducing Pericyte-Derived Scarring Promotes Recovery after Spinal Cord Injury.

Dias DO, Kim H, Holl D, ..., Göritz C, Frisén J

Cell 173 (1) 153-165.e22 [2018-03-22; online 2018-03-01]

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A DHODH inhibitor increases p53 synthesis and enhances tumor cell killing by p53 degradation blockage.

Ladds MJGW, van Leeuwen IMM, Drummond CJ, ..., McCormack E, Laín S

Nat Commun 9 (1) 1107 [2018-03-16; online 2018-03-16]

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Seyfferth C, Wessels B, Jokipii-Lukkari S, ..., Felten J, Tuominen H

Front Plant Sci 9 (-) 272 [2018-03-14; online 2018-03-14]

Increased thermal stability of nanocellulose composites by functionalization of the sulfate groups on cellulose nanocrystals with azetidinium ions

Börjesson M, Sahlin K, Bernin D, Westman G

J. Appl. Polym. Sci. 135 (10) 45963 [2018-03-10; online 2017-11-08]

CEP128 Localizes to the Subdistal Appendages of the Mother Centriole and Regulates TGF-β/BMP Signaling at the Primary Cilium.

Mönnich M, Borgeskov L, Breslin L, ..., Larsen LA, Pedersen LB

Cell Rep 22 (10) 2584-2592 [2018-03-06; online 2018-03-08]

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An Integrated Understanding of the Rapid Metabolic Benefits of a Carbohydrate-Restricted Diet on Hepatic Steatosis in Humans.

Mardinoglu A, Wu H, Bjornson E, ..., Taskinen MR, Borén J

Cell Metab. 27 (3) 559-571.e5 [2018-03-06; online 2018-02-15]

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Transcriptome analysis of embryonic domains in Norway spruce reveals potential regulators of suspensor cell death.

Reza SH, Delhomme N, Street NR, ..., Minina EA, Bozhkov PV

PLoS ONE 13 (3) e0192945 [2018-03-02; online 2018-03-02]

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Impact of genetic risk loci for multiple sclerosis on expression of proximal genes in patients.

James T, Lindén M, Morikawa H, ..., Gomez-Cabrero D, Kockum I

Hum. Mol. Genet. 27 (5) 912-928 [2018-03-01; online 2018-01-13]

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Lipids Shape the Electron Acceptor-Binding Site of the Peripheral Membrane Protein Dihydroorotate Dehydrogenase

Costeira-Paulo J, Gault J, Popova G, ..., Marklund EG, Landreh M

Cell Chem Biol 25 (3) 309-317.e4 [2018-03-00; online 2018-03-00]

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The neuroendocrine phenotype, genomic profile and therapeutic sensitivity of GEPNET cell lines.

Hofving T, Arvidsson Y, Almobarak B, ..., Johanson V, Nilsson O

Endocr. Relat. Cancer 25 (3) 367-380 [2018-03-00; online 2018-02-16]

Integrated Microscopy Technologies Gothenburg [Service]

A molecular atlas of cell types and zonation in the brain vasculature.

Vanlandewijck M, He L, Mäe MA, ..., Lendahl U, Betsholtz C

Nature 554 (7693) 475-480 [2018-02-22; online 2018-02-14]

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In Situ Target Engagement Studies in Adherent Cells

Axelsson H, Almqvist H, Otrocka M, ..., Lundbäck T, Seashore-Ludlow B

ACS Chem. Biol. - (-) - [2018-02-21; online 2018-02-21]

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Antibodies in children with malaria to PfEMP1, RIFIN and SURFIN expressed at the Plasmodium falciparum parasitized red blood cell surface.

Quintana MDP, Ch'ng JH, Moll K, ..., Qundos U, Wahlgren M

Sci Rep 8 (1) 3262 [2018-02-19; online 2018-02-19]

Autoimmunity and Serology Profiling [Service] Bioinformatics Support for Computational Resources [Service]

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

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

Cell Chem Biol 25 (2) 224-229.e2 [2018-02-15; online 2017-12-21]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Mesenchymal stem cell-derived exosomes have altered microRNA profiles and induce osteogenic differentiation depending on the stage of differentiation.

Wang X, Omar O, Vazirisani F, Thomsen P, Ekström K

PLoS ONE 13 (2) e0193059 [2018-02-15; online 2018-02-15]

Integrated Microscopy Technologies Gothenburg [Service]

Educated natural killer cells show dynamic movement of the activating receptor NKp46 and confinement of the inhibitory receptor Ly49A

Staaf E, Hedde PN, Bagawath Singh S, ..., Gratton E, Johansson S

Sci. Signal. 11 (517) eaai9200 [2018-02-13; online 2018-02-13]

Integrated Microscopy Technologies Stockholm [Service]

Kynurenic Acid and Gpr35 Regulate Adipose Tissue Energy Homeostasis and Inflammation.

Agudelo LZ, Ferreira DMS, Cervenka I, ..., Berggren PO, Ruas JL

Cell Metab. 27 (2) 378-392.e5 [2018-02-06; online 2018-02-08]

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Interferon γ treatment increases endocannabinoid and related N-acylethanolamine levels in T84 human colon carcinoma cells

Alhouayek M, Rankin L, Gouveia-Figueira S, Fowler CJ

British Journal of Pharmacology - (-) - [2018-02-05; online 2018-02-05]

Human Adenovirus Infection Causes Cellular E3 Ubiquitin Ligase MKRN1 Degradation Involving the Viral Core Protein pVII.

Inturi R, Mun K, Singethan K, Schreiner S, Punga T

J. Virol. 92 (3) - [2018-02-01; online 2018-01-17]

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

T cells are influenced by a long non-coding RNA in the autoimmune associated PTPN2 locus

Houtman M, Shchetynsky K, Chemin K, ..., Malmström V, Padyukov L

Journal of Autoimmunity 90 (-) 28-38 [2018-02-00; online 2018-02-00]

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Quantitative image analysis of protein expression and colocalisation in skin sections

Zhang H, Ericsson M, Virtanen M, ..., Vahlquist A, Törmä H

Exp Dermatol 27 (2) 196-199 [2018-02-00; online 2018-01-09]

BioImage Informatics [Service] Bioinformatics (NBIS) [Service]

Gene expression profiling across ontogenetic stages in the wood white (Leptidea sinapis) reveals pathways linked to butterfly diapause regulation.

Leal L, Talla V, Källman T, ..., Vila R, Backström N

Mol. Ecol. 27 (4) 935-948 [2018-02-00; online 2018-02-26]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Life after tree death: Does restored dead wood host different fungal communities to natural woody substrates?

Pasanen H, Junninen K, Boberg J, ..., Stenlid J, Kouki J

Forest Ecology and Management 409 (-) 863-871 [2018-02-00; online 2018-02-00]

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Small molecule PGC-1α1 protein stabilizers induce adipocyte Ucp1 expression and uncoupled mitochondrial respiration

Pettersson-Klein AT, Izadi M, Ferreira DMS, ..., Griffin PR, Ruas JL

Mol Metab - (-) - [2018-02-00; online 2018-02-00]

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Transposon-derived small RNAs triggered by miR845 mediate genome dosage response in Arabidopsis

Borges F, Parent JS, van Ex F, ..., Köhler C, Martienssen RA

Nat Genet 50 (2) 186-192 [2018-02-00; online 2018-01-15]

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

Pulmonary fibrosis in vivo displays increased p21 expression reduced by 5-HT2B receptor antagonists in vitro - a potential pathway affecting proliferation.

Löfdahl A, Rydell-Törmänen K, Larsson-Callerfelt A, Wenglén C, Westergren-Thorsson G

Sci Rep 8 (1) 1927 [2018-01-31; online 2018-01-31]

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In Situ Analyses Directly in Diarrheal Stool Reveal Large Variations in Bacterial Load and Active Toxin Expression of Enterotoxigenic Escherichia coli and Vibrio cholerae

Begum YA, Rydberg HA, Thorell K, ..., Qadri F, Sjöling Å

mSphere 3 (1) e00517-17 [2018-01-24; online 2018-01-24]

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Innate immune alterations are elicited in microglial cells before plaque deposition in the Alzheimer's disease mouse model 5xFAD.

Boza-Serrano A, Yang Y, Paulus A, Deierborg T

Sci Rep 8 (1) 1550 [2018-01-24; online 2018-01-24]

Targeted NUDT5 inhibitors block hormone signaling in breast cancer cells.

Page BDG, Valerie NCK, Wright RHG, ..., Beato M, Helleday T

Nat Commun 9 (1) 250 [2018-01-17; online 2018-01-17]

Bioinformatics Support for Computational Resources [Service] Drug Discovery and Development (DDD) [Service] Protein Science Facility (PSF) [Service]

Splicing of platelet resident pre-mRNAs upon activation by physiological stimuli results in functionally relevant proteome modifications.

Nassa G, Giurato G, Cimmino G, ..., Weisz A, Tarallo R

Sci Rep 8 (1) 498 [2018-01-11; online 2018-01-11]

Global Proteomics and Proteogenomics [Collaborative]

Bifidobacteria or Fiber Protects against Diet-Induced Microbiota-Mediated Colonic Mucus Deterioration.

Schroeder BO, Birchenough GMH, Ståhlman M, ..., Hansson GC, Bäckhed F

Cell Host Microbe 23 (1) 27-40.e7 [2018-01-10; online 2017-12-21]

Integrated Microscopy Technologies Gothenburg [Service]

The ATPase activity of Asna1/TRC40 is required for pancreatic progenitor cell survival.

Norlin S, Parekh V, Edlund H

Development 145 (1) dev154468 [2018-01-03; online 2018-01-03]

MicroRNA expression profiles in non‑epithelial ovarian tumors.

Chang RK, Li X, Mu N, ..., Larsson C, Lui WO

Int. J. Oncol. 52 (1) 55-66 [2018-01-00; online 2017-11-10]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Characterization of gamma-tubulin filaments in mammalian cells.

Lindström L, Alvarado-Kristensson M

Biochimica et Biophysica Acta (BBA) - Molecular Cell Research 1865 (1) 158-171 [2018-01-00; online 2017-10-16]

Integrated Microscopy Technologies Gothenburg [Service]

Protein-altering variants associated with body mass index implicate pathways that control energy intake and expenditure in obesity.

Turcot V, Lu Y, Highland HM, ..., MAGIC Investigators , Understanding Society Scientific Group

Nat. Genet. 50 (1) 26-41 [2018-01-00; online 2017-12-22]

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

Leucocyte recruitment and molecular fortification of keratinocytes triggered by streptococcal M1 protein.

Persson ST, Hauri S, Malmström J, Herwald H

Cell. Microbiol. 20 (1) - [2018-01-00; online 2017-10-19]

Surface treatment of cellulose nanocrystals (CNC): effects on dispersion rheology

Sahlin K, Forsgren L, Moberg T, ..., Rigdahl M, Westman G

Cellulose 25 (1) 331-345 [2018-01-00; online 2017-11-28]

Herpesvirus deconjugases inhibit the IFN response by promoting TRIM25 autoubiquitination and functional inactivation of the RIG-I signalosome.

Gupta S, Ylä-Anttila P, Callegari S, ..., Delecluse HJ, Masucci MG

PLoS Pathog. 14 (1) e1006852 [2018-01-00; online 2018-01-22]

Global Proteomics and Proteogenomics [Service]

Improved Reconstruction of Low Intensity Magnetic Resonance Spectroscopy With Weighted Low Rank Hankel Matrix Completion

Guo D, Qu X

IEEE Access 6 (-) 4933-4940 [2018-00-00; online 2018-00-00]

The CO2capturing ability of cellulose dissolved in NaOH(aq) at low temperature

Gunnarsson M, Bernin D, Östlund Å, Hasani M

Green Chem. 20 (14) 3279-3286 [2018-00-00; online 2018-00-00]

High purity and viability cell separation of a bacterivorous jakobid flagellate based on a steep velocity gradient induced soft inertial force

Deng P, Fu CJ, Wu Z

RSC Adv. 8 (62) 35512-35520 [2018-00-00; online 2018-00-00]

Microbial Single Cell Genomics [Service]

The CO2 capturing ability of cellulose dissolved in NaOH(aq) at low temperature

Gunnarsson M, Bernin D, Östlund Å, Hasani M

Green Chem. 20 (14) 3279-3286 [2018-00-00; online 2018-00-00]

Targeting tumor cells based on Phosphodiesterase 3A expression.

Nazir M, Senkowski W, Nyberg F, ..., Larsson R, Fryknäs M

Exp. Cell Res. 361 (2) 308-315 [2017-12-15; online 2017-10-26]

Discovery of the fourth mobile sulfonamide resistance gene.

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

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

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

Gene expression and risk of leukemic transformation in myelodysplasia.

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

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

Clinical Genomics [Service] Clinical Genomics Uppsala [Service]

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

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

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

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

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

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

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

Spatial Proteomics [Collaborative]

A Unique ISR Program Determines Cellular Responses to Chronic Stress.

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

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

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

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

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

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

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

Brassinosteroid signaling-dependent root responses to prolonged elevated ambient temperature

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

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

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

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

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

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

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

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

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

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

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

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

J. Intern. Med. 282 (6) 508-521 [2017-12-00; online 2017-09-21]

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

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

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

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

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Automated Training of Deep Convolutional Neural Networks for Cell Segmentation

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

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

BioImage Informatics [Technology development] Bioinformatics (NBIS) [Technology development]

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

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

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

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

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

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

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

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

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

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

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

Bliss and Loewe interaction analyses of clinically relevant drug combinations in human colon cancer cell lines reveal complex patterns of synergy and antagonism.

Kashif M, Andersson C, Mansoori S, ..., Nygren P, Gustafsson MG

Oncotarget 8 (61) 103952-103967 [2017-11-28; online 2017-10-19]

Evidence that circulating proteins are more promising than miRNAs for identification of patients with squamous cell carcinoma of the tongue.

Boldrup L, Troiano G, Gu X, ..., Wang L, Nylander K

Oncotarget 8 (61) 103437-103448 [2017-11-28; online 2017-09-30]

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

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

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

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

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

Female mice lacking Pald1 exhibit endothelial cell apoptosis and emphysema.

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

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

Clinical Proteomics Mass spectrometry [Service] Global Proteomics and Proteogenomics [Collaborative]

Integrative analysis of genome-wide gene copy number changes and gene expression in non-small cell lung cancer.

Jabs V, Edlund K, König H, ..., Hengstler JG, Micke P

PLoS ONE 12 (11) e0187246 [2017-11-07; online 2017-11-07]

Clinical Genomics [Collaborative] Clinical Genomics Uppsala [Collaborative]

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

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

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

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

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

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

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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

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

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

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

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

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

Int Union Crystallogr J IUCr J Int Union Cryst J IUCrJ 4 (6) 723-727 [2017-11-01; online 2017-09-22]

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

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

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

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

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

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

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

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

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

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

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] 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] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Service]

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

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

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

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

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

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

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

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

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

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

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

Orellanine specifically targets renal clear cell carcinoma.

Buvall L, Hedman H, Khramova A, ..., Haraldsson B, Nyström J

Oncotarget 8 (53) 91085-91098 [2017-10-31; online 2017-07-25]

Glycoproteomics and MS Proteomics [Collaborative]

Microbial mineralization of cellulose in frozen soils.

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

Nat Commun 8 (1) 1154 [2017-10-27; online 2017-10-27]

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

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

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

Spatial Proteomics [Collaborative]

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

Piltti J, Bygdell J, Qu C, Lammi MJ

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

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Glioblastoma and glioblastoma stem cells are dependent on functional MTH1.

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

Oncotarget 8 (49) 84671-84684 [2017-10-17; online 2017-07-20]

Integrated Microscopy Technologies Stockholm [Collaborative]

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

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

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

BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]

RANK rewires energy homeostasis in lung cancer cells and drives primary lung cancer.

Rao S, Sigl V, Wimmer RA, ..., Dougall W, Penninger JM

Genes Dev. 31 (20) 2099-2112 [2017-10-15; online 2017-11-08]

Clinical Genomics [Collaborative] Clinical Genomics Uppsala [Collaborative]

Delivery of cyclodextrin polymers to bacterial biofilms - An exploratory study using rhodamine labelled cyclodextrins and multiphoton microscopy.

Thomsen H, Benkovics G, Fenyvesi É, ..., Malanga M, Ericson MB

Int J Pharm 531 (2) 650-657 [2017-10-15; online 2017-06-06]

Integrated Microscopy Technologies Gothenburg [Service]

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

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

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

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

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

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

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

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

Hellgren JM, Lindberg S

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

Chemical Biology Consortium Sweden (CBCS) [Technology development]

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

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

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

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

Transcriptomic and Proteomic Profiling Provides Insight into Mesangial Cell Function in IgA Nephropathy.

Liu P, Lassén E, Nair V, ..., Ebefors K, Nyström J

J. Am. Soc. Nephrol. 28 (10) 2961-2972 [2017-10-00; online 2017-06-23]

Glycoproteomics and MS Proteomics [Collaborative]

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

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

Hum. Mutat. 38 (10) 1394-1401 [2017-10-00; online 2017-06-12]

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

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

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

Current Eye Research 42 (10) 1358-1367 [2017-10-00; online 2017-06-21]

Global Proteomics and Proteogenomics [Service]

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

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

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

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

Deep Convolutional Neural Networks for Detecting Cellular Changes Due to Malignancy

Forslid G, Wieslander H, Bengtsson E, ..., Stark CR, Sadanandan SK

The IEEE International Conference on Computer Vision (ICCV), 2017 - (-) - [2017-10-00; online 2017-10-00]

BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]

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

Rydin C, Wikström N, Bremer B

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

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

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

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

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

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

Tumor SHB gene expression affects disease characteristics in human acute myeloid leukemia.

Jamalpour M, Li X, Cavelier L, ..., Höglund M, Welsh M

Tumour Biol. 39 (10) 1010428317720643 [2017-10-00; online 2017-10-07]

Clinical Genomics [Collaborative] Clinical Genomics Uppsala [Collaborative]

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

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

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

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

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

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

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

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

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

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

Hilborn E, Stål O, Alexeyenko A, Jansson A

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

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

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

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

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

Clinical Proteomics Mass spectrometry [Service] Global Proteomics and Proteogenomics [Service]

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

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

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

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

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

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

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

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

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

Auxin minimum triggers the developmental switch from cell division to cell differentiation in the Arabidopsis root.

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

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

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

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

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

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Mayzel M, Ahlner A, Lundström P, Orekhov VY

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

The Abl-1 Kinase is Dispensable for NK Cell Inhibitory Signalling and is not Involved in Murine NK Cell Education.

Ganesan S, Luu TT, Chambers BJ, ..., Kadri N, Höglund P

Scand. J. Immunol. 86 (3) 135-142 [2017-09-00; online 2017-06-13]

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Drug Discovery and Development (DDD) [Collaborative]

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

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

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

Cerium oxide nanoparticles inhibit differentiation of neural stem cells.

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

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

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Clonal Evolution of Autoreactive Germinal Centers.

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

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

Autoimmunity and Serology Profiling [Service]

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

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

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

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

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

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

Clinical Genomics [Service] Clinical Genomics Uppsala [Service]

Circulating GDF-15 levels predict future secondary manifestations of cardiovascular disease explicitly in women but not men with atherosclerosis.

Gohar A, Gonçalves I, Vrijenhoek J, ..., Björkbacka H, de Jager SCA

Int. J. Cardiol. 241 (-) 430-436 [2017-08-15; online 2017-03-22]

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

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

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

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

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

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

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

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

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

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

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

Spang A, Caceres EF, Ettema TJG

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

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

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

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

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

Switchable ionic liquids enable efficient nanofibrillation of wood pulp

Berglund L, Anugwom I, Hedenström M, ..., Mikkola JP, Oksman K

Cellulose 24 (8) 3265-3279 [2017-08-00; online 2017-06-06]

Comprehensive Profiling of the Androgen Receptor in Liquid Biopsies from Castration-resistant Prostate Cancer Reveals Novel Intra-AR Structural Variation and Splice Variant Expression Patterns.

De Laere B, van Dam PJ, Whitington T, ..., Grönberg H, Lindberg J

Eur. Urol. 72 (2) 192-200 [2017-08-00; online 2017-01-16]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

Gene Expression Profiling of Large Cell Lung Cancer Links Transcriptional Phenotypes to the New Histological WHO 2015 Classification

Karlsson A, Brunnström H, Micke P, ..., Planck M, Staaf J

Journal of Thoracic Oncology 12 (8) 1257-1267 [2017-08-00; online 2017-08-00]

Clinical Genomics [Service] Clinical Genomics Lund [Service] Clinical Genomics Uppsala [Collaborative]

Aeromonas salmonicida Growth in Response to Atlantic Salmon Mucins Differs between Epithelial Sites, Is Governed by Sialylated and N-Acetylhexosamine-Containing O-Glycans, and Is Affected by Ca2.

Padra JT, Sundh H, Sundell K, ..., Karlsson NG, Lindén SK

Infect. Immun. 85 (8) - [2017-08-00; online 2017-07-19]

Site-specific gene expression analysis of implant-near cells in a soft tissue infection model - Application of laser microdissection to study biomaterial-associated infection.

Svensson S, Trobos M, Omar O, Thomsen P

J. Biomed. Mater. Res. 105 (8) 2210-2217 [2017-08-00; online 2017-05-10]

Integrated Microscopy Technologies Gothenburg [Service]

Dual action of bacteriocin PLNC8 αβ through inhibition of Porphyromonas gingivalis infection and promotion of cell proliferation.

Bengtsson T, Zhang B, Selegård R, ..., Aili D, Khalaf H

Pathog Dis 75 (5) - [2017-07-31; online 2017-06-13]

Solution NMR structure of the TRIM21 B-box2 and identification of residues involved in its interaction with the RING domain

Wallenhammar A, Anandapadamanaban M, Lemak A, ..., Wallner B, Sunnerhagen M

PLoS ONE 12 (7) e0181551 [2017-07-28; online 2017-07-28]

Prediction of intracellular exposure bridges the gap between target- and cell-based drug discovery

Mateus A, Gordon LJ, Wayne GJ, ..., Hann MM, Artursson P

Proc Natl Acad Sci USA 114 (30) E6231-E6239 [2017-07-25; online 2017-07-12]

Chemical Biology Consortium Sweden (CBCS) [Technology development]

Continuous immunotypes describe human immune variation and predict diverse responses.

Kaczorowski KJ, Shekhar K, Nkulikiyimfura D, ..., Chakraborty AK, Brodin P

Proc. Natl. Acad. Sci. U.S.A. 114 (30) E6097-E6106 [2017-07-25; online 2017-07-10]

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

Wain LV, Vaez A, Jansen R, ..., Caulfield MJ, Ehret GB

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

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

Loss of DIP2C in RKO cells stimulates changes in DNA methylation and epithelial-mesenchymal transition.

Larsson C, Ali MA, Pandzic T, ..., He L, Sjöblom T

BMC Cancer 17 (1) 487 [2017-07-17; online 2017-07-17]

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Transcriptional profiling of the rat nucleus accumbens after modest or high alcohol exposure.

Morud J, Ashouri A, Larsson E, Ericson M, Söderpalm B

PLoS ONE 12 (7) e0181084 [2017-07-17; online 2017-07-17]

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Analysis of aquaporins from the euryhaline barnacle Balanus improvisus reveals differential expression in response to changes in salinity.

Lind U, Järvå M, Alm Rosenblad M, ..., Hedfalk K, Blomberg A

PLoS ONE 12 (7) e0181192 [2017-07-17; online 2017-07-17]

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Moderate Expression of SEC16 Increases Protein Secretion by Saccharomyces cerevisiae.

Bao J, Huang M, Petranovic D, Nielsen J

Appl. Environ. Microbiol. 83 (14) - [2017-07-15; online 2017-06-30]

Integrated Microscopy Technologies Gothenburg [Service]

Does antifouling paint select for antibiotic resistance?

Flach CF, Pal C, Svensson CJ, ..., Tysklind M, Larsson DG

Sci. Total Environ. 590-591 (-) 461-468 [2017-07-15; online 2017-03-08]

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Multipotent peripheral glial cells generate neuroendocrine cells of the adrenal medulla.

Furlan A, Dyachuk V, Kastriti ME, ..., Ernfors P, Adameyko I

Science 357 (6346) - [2017-07-07; online 2017-07-08]

Niche-mediated depletion of the normal hematopoietic stem cell reservoir by Flt3-ITD-induced myeloproliferation.

Mead AJ, Neo WH, Barkas N, ..., Nerlov C, Jacobsen SEW

J. Exp. Med. 214 (7) 2005-2021 [2017-07-03; online 2017-06-21]

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Epitope mapping of a new anti-Tn antibody detecting gastric cancer cells.

Persson N, Stuhr-Hansen N, Risinger C, ..., Jansson B, Blixt O

Glycobiology 27 (7) 635-645 [2017-07-01; online 2017-04-19]

Reaching the limits of prognostication in non-small cell lung cancer: an optimized biomarker panel fails to outperform clinical parameters.

Grinberg M, Djureinovic D, Brunnström HR, ..., Rahnenführer J, Micke P

Mod. Pathol. 30 (7) 964-977 [2017-07-00; online 2017-03-10]

Clinical Genomics [Collaborative] Clinical Genomics Uppsala [Collaborative] Tissue Profiling [Collaborative]

Close Encounters – Probing Proximal Proteins in Live or Fixed Cells

Lönn P, Landegren U

Trends in Biochemical Sciences 42 (7) 504-515 [2017-07-00; online 2017-07-00]

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Integrative Genomics Identifies the Molecular Basis of Resistance to Azacitidine Therapy in Myelodysplastic Syndromes

Unnikrishnan A, Papaemmanuil E, Beck D, ..., Campbell PJ, Pimanda JE

Cell Rep 20 (3) 572-585 [2017-07-00; online 2017-07-00]

Clinical Genomics [Service] Clinical Genomics Uppsala [Service]

Wholegrain oat diet changes the expression of genes associated with intestinal bile acid transport.

Andersson KE, Chawade A, Thuresson N, ..., Olsson O, Hellstrand P

Mol Nutr Food Res 61 (7) - [2017-07-00; online 2017-03-30]

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Identification of a Sjögren's syndrome susceptibility locus at OAS1 that influences isoform switching, protein expression, and responsiveness to type I interferons

Li H, Reksten TR, Ice JA, ..., Sivils KL, None

PLoS Genet. 13 (6) e1006820 [2017-06-22; online 2017-06-22]

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

Protein expression in tension wood formation monitored at high tissue resolution in Populus

Bygdell J, Srivastava V, Obudulu O, ..., Mellerowicz EJ, Wingsle G

- 68 (13) 3405-3417 [2017-06-15; online 2017-06-13]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Four simple recommendations to encourage best practices in research software

Jiménez RC, Kuzak M, Alhamdoosh M, ..., Watson-Haigh NS, Crouch S

F1000Res 6 (-) 876 [2017-06-13; online 2017-06-13]

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Functional and Compositional Stability of Bacterial Metacommunities in Response to Salinity Changes

Berga M, Zha Y, Székely AJ, Langenheder S

Front Microbiol 8 (-) - [2017-06-08; online 2017-06-08]

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Mast Cell Infiltration in Human Brain Metastases Modulates the Microenvironment and Contributes to the Metastatic Potential.

Roy A, Libard S, Weishaupt H, ..., Alafuzoff I, Tchougounova E

Front Oncol 7 (-) 115 [2017-06-02; online 2017-06-02]

Injury Leads to the Appearance of Cells with Characteristics of Both Microglia and Astrocytes in Mouse and Human Brain.

Wilhelmsson U, Andersson D, de Pablo Y, ..., Pekny M, Pekna M

Cereb. Cortex 27 (6) 3360-3377 [2017-06-01; online 2017-04-12]

Fluorescence Tissue Profiling [Collaborative] Integrated Microscopy Technologies Gothenburg [Service]

Large-Scale Identification of Common Trait and Disease Variants Affecting Gene Expression.

Hauberg ME, Zhang W, Giambartolomei C, ..., Björkegren JLM, Roussos P

Am. J. Hum. Genet. 100 (6) 885-894 [2017-06-01; online 2017-05-25]

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

The transcriptome of the avian malaria parasite Plasmodium ashfordi displays host-specific gene expression.

Videvall E, Cornwallis CK, Ahrén D, ..., Valkiūnas G, Hellgren O

Mol. Ecol. 26 (11) 2939-2958 [2017-06-00; online 2017-04-08]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Affinity Proteomics Exploration of Melanoma Identifies Proteins in Serum with Associations to T-Stage and Recurrence.

Byström S, Fredolini C, Edqvist PH, ..., Pontén F, Schwenk JM

Transl Oncol 10 (3) 385-395 [2017-06-00; online 2017-04-20]

Affinity Proteomics Stockholm [Collaborative] Tissue Profiling [Collaborative]

Chemisorption of air CO2 on cellulose: an overlooked feature of the cellulose/NaOH(aq) dissolution system

Gunnarsson M, Theliander H, Hasani M

Cellulose 24 (6) 2427-2436 [2017-06-00; online 2017-04-12]

Levels of oxylipins, endocannabinoids and related lipids in plasma before and after low-level exposure to acrolein in healthy individuals and individuals with chemical intolerance

Claeson AS, Gouveia-Figueira S, Häggström J, Fowler CJ, Nording ML

Prostaglandins, Leukotrienes and Essential Fatty Acids (PLEFA) 121 (-) 60-67 [2017-06-00; online 2017-06-00]

A DNA methylation site within the KLF13 gene is associated with orexigenic processes based on neural responses and ghrelin levels.

Wiemerslage L, Islam R, van der Kamp C, ..., Benedict C, Schiöth HB

Int J Obes (Lond) 41 (6) 990-994 [2017-06-00; online 2017-02-14]

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

Expression of CD226 is associated to but not required for NK cell education.

Wagner AK, Kadri N, Snäll J, ..., Kärre K, Chambers BJ

Nat Commun 8 (-) 15627 [2017-05-31; online 2017-05-31]

Whole blood gene expression in adolescent chronic fatigue syndrome: an exploratory cross-sectional study suggesting altered B cell differentiation and survival.

Nguyen CB, Alsøe L, Lindvall JM, ..., Nilsen H, Wyller VB

J Transl Med 15 (1) 102 [2017-05-11; online 2017-05-11]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Spatially resolved transcriptome profiling in model plant species.

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

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

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] 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]

QTL mapping of stress related gene expression in a cross between domesticated chickens and ancestral red junglefowl.

Fallahsharoudi A, de Kock N, Johnsson M, ..., Wright D, Jensen P

Mol. Cell. Endocrinol. 446 (-) 52-58 [2017-05-05; online 2017-02-09]

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

Glioblastoma Cell Malignancy and Drug Sensitivity Are Affected by the Cell of Origin.

Jiang Y, Marinescu VD, Xie Y, ..., Nelander S, Uhrbom L

Cell Rep 19 (5) 1080-1081 [2017-05-02; online 2017-05-04]

PDE2A2 regulates mitochondria morphology and apoptotic cell death via local modulation of cAMP/PKA signalling.

Monterisi S, Lobo MJ, Livie C, ..., Micaroni M, Zaccolo M

Elife 6 (-) - [2017-05-02; online 2017-05-02]

Integrated Microscopy Technologies Gothenburg [Service]

Bayesian Inference of Allele-Specific Gene Expression Indicates Abundant Cis-Regulatory Variation in Natural Flycatcher Populations

Wang M, Uebbing S, Ellegren H

Genome Biol Evol 9 (5) 1266-1279 [2017-05-00; online 2017-05-01]

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

Absolute Quantification of Protein and mRNA Abundances Demonstrate Variability in Gene-Specific Translation Efficiency in Yeast

Lahtvee PJ, Sánchez BJ, Smialowska A, ..., Gatto F, Nielsen J

Cell Syst 4 (5) 495-504.e5 [2017-05-00; online 2017-05-00]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

A Preliminary Report: Radical Surgery and Stem Cell Transplantation for the Treatment of Patients With Pancreatic Cancer.

Omazic B, Ayoglu B, Löhr M, ..., Maeurer MJ, Ringden O

J. Immunother. 40 (4) 132-139 [2017-05-00; online 2017-03-25]

Affinity Proteomics Stockholm [Collaborative] Autoimmunity and Serology Profiling [Collaborative]

Loss of chromosome Y (LOY) in blood cells is associated with increased risk for disease and mortality in aging men

Forsberg LA

Hum Genet 136 (5) 657-663 [2017-05-00; online 2017-04-19]

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

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

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

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

Bioinformatics (NBIS) [Collaborative] 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) [Collaborative] National Genomics Infrastructure [Collaborative]

Comparative genomics and expression levels of hydrophobins from eight mycorrhizal genomes.

Rineau F, Lmalem H, Ahren D, ..., Martin F, Colpaert JV

Mycorrhiza 27 (4) 383-396 [2017-05-00; online 2017-01-09]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Corrigendum: MTH1 inhibition eradicates cancer by preventing sanitation of the dNTP pool.

Gad H, Koolmeister T, Jemth AS, ..., Scobie M, Ulrika Warpman Berglund &Thomas Helleday

Nature 544 (7651) 508 [2017-04-26; online 2017-04-28]

Correlation of histopathologic characteristics to protein expression and function in malignant melanoma.

Welinder C, Pawłowski K, Szasz AM, ..., Wieslander E, Marko-Varga G

PLoS ONE 12 (4) e0176167 [2017-04-26; online 2017-04-26]

Comprehensive mapping of the effects of azacitidine on DNA methylation, repressive/permissive histone marks and gene expression in primary cells from patients with MDS and MDS-related disease.

Tobiasson M, Abdulkadir H, Lennartsson A, ..., Hellström-Lindberg E, Ungerstedt J

Oncotarget 8 (17) 28812-28825 [2017-04-25; online 2017-04-22]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

The Influence of Hydroxyapatite Nanoparticle Morphology on Embryonic Development in a Zebrafish Exposure Model.

Pujari-Palmer S, Lu X, Karlsson Ott M

Nanomaterials (Basel) 7 (4) - [2017-04-22; online 2017-04-22]

Persistent Effects of Developmental Exposure to 17α-Ethinylestradiol on the Zebrafish (Danio rerio) Brain Transcriptome and Behavior

Porseryd T, Volkova K, Reyhanian Caspillo N, ..., Dinnetz P, Porsh Hällström I

Front. Behav. Neurosci. 11 (-) - [2017-04-20; online 2017-04-20]

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Adenovirus-mediated CD40L gene transfer increases Teffector/Tregulatory cell ratio and upregulates death receptors in metastatic melanoma patients.

Schiza A, Wenthe J, Mangsbo S, ..., Loskog A, Ullenhag G

J Transl Med 15 (1) 79 [2017-04-20; online 2017-04-20]

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Respiratory chain complex III deficiency due to mutated BCS1L: a novel phenotype with encephalomyopathy, partially phenocopied in a Bcs1l mutant mouse model.

Tegelberg S, Tomašić N, Kallijärvi J, ..., Eklund EA, Fellman V

Orphanet J Rare Dis 12 (1) 73 [2017-04-20; online 2017-04-20]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

Oriented clonal cell dynamics enables accurate growth and shaping of vertebrate cartilage

Kaucka M, Zikmund T, Tesarova M, ..., Fried K, Adameyko I

Elife 6 (-) - [2017-04-17; online 2017-04-17]

Integrated Microscopy Technologies Stockholm [Collaborative]

Adaptation to infectious disease exposure in indigenous Southern African populations.

Owers KA, Sjödin P, Schlebusch CM, ..., Soodyall H, Jakobsson M

Proc. Biol. Sci. 284 (1852) 20170226 [2017-04-12; online 2017-04-07]

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Serglycin as a potential biomarker for glioma: association of serglycin expression, extent of mast cell recruitment and glioblastoma progression.

Roy A, Attarha S, Weishaupt H, ..., Pontén F, Tchougounova E

Oncotarget 8 (15) 24815-24827 [2017-04-11; online 2017-04-28]

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

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

Sci Rep 7 (1) 623 [2017-04-04; online 2017-04-04]

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Membrane-Depolarizing Channel Blockers Induce Selective Glioma Cell Death by Impairing Nutrient Transport and Unfolded Protein/Amino Acid Responses.

Niklasson M, Maddalo G, Sramkova Z, ..., Enger PØ, Andäng M

Cancer Res. 77 (7) 1741-1752 [2017-04-01; online 2017-01-13]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Intranasal C3a treatment ameliorates cognitive impairment in a mouse model of neonatal hypoxic-ischemic brain injury.

Morán J, Stokowska A, Walker FR, ..., Hagberg H, Pekna M

Exp. Neurol. 290 (-) 74-84 [2017-04-00; online 2017-01-04]

Integrated Microscopy Technologies Gothenburg [Service]

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

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

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

The anti-inflammatory compound palmitoylethanolamide inhibits prostaglandin and hydroxyeicosatetraenoic acid production by a macrophage cell line

Gabrielsson L, Gouveia-Figueira S, Häggström J, Alhouayek M, Fowler CJ

Pharmacol Res Perspect 5 (2) e00300 [2017-04-00; online 2017-02-27]

The minimum information required for a glycomics experiment (MIRAGE) project: improving the standards for reporting glycan microarray-based data.

Liu Y, McBride R, Stoll M, ..., Feizi T, Smith DF

Glycobiology 27 (4) 280-284 [2017-04-00; online 2016-11-22]

Glycoproteomics and MS Proteomics [Collaborative]

FZD10-Gα13 signalling axis points to a role of FZD10 in CNS angiogenesis.

Hot B, Valnohova J, Arthofer E, ..., Mulder J, Schulte G

Cell. Signal. 32 (-) 93-103 [2017-04-00; online 2017-01-24]

Fluorescence Tissue Profiling [Collaborative]

Lipid response patterns in acute phase paediatric Plasmodium falciparum malaria

Orikiiriza J, Surowiec I, Lindquist E, ..., Trygg J, Normark J

Metabolomics 13 (4) - [2017-04-00; online 2017-02-23]

An assessment of the importance of exposure routes to the uptake and internal localisation of fluorescent nanoparticles in zebrafish (Danio rerio), using light sheet microscopy.

Skjolding LM, Ašmonaitė G, Jølck RI, ..., Baun A, Sturve J

Nanotoxicology 11 (3) 351-359 [2017-04-00; online 2017-03-29]

Integrated Microscopy Technologies Gothenburg [Service]

Genomic structure of the horse major histocompatibility complex class II region resolved using PacBio long-read sequencing technology

Viļuma A, Mikko S, Hahn D, ..., Andersson G, Bergström TF

Sci Rep 7 (-) 45518 [2017-03-31; online 2017-03-31]

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Altered expression of maize PLASTOCHRON1 enhances biomass and seed yield by extending cell division duration

Sun X, Cahill J, Van Hautegem T, ..., Inzé D, Nelissen H

Nat Commun 8 (-) 14752 [2017-03-16; online 2017-03-16]

Endocytic turnover of Rab8 controls cell polarization.

Vidal-Quadras M, Holst MR, Francis MK, ..., Martín-Belmonte F, Lundmark R

J. Cell. Sci. 130 (6) 1147-1157 [2017-03-15; online 2017-01-30]

Integrated Microscopy Technologies Gothenburg [Service]

Identification of Triazolothiadiazoles as Potent Inhibitors of the dCTP Pyrophosphatase 1.

Llona-Minguez S, Höglund A, Wiita E, ..., Scobie M, Helleday T

J. Med. Chem. 60 (5) 2148-2154 [2017-03-09; online 2017-02-15]

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

Life-Saving Degeneracy in the Human Immune System.

Brodin P

Cell Host Microbe 21 (3) 309-310 [2017-03-08; online 2017-03-11]

Peptide Functionalized Gold Nanoparticles as a Stimuli Responsive Contrast Medium in Multiphoton Microscopy.

Borglin J, Selegård R, Aili D, Ericson MB

Nano Lett. 17 (3) 2102-2108 [2017-03-08; online 2017-02-23]

Integrated Microscopy Technologies Gothenburg [Service]

Mating Changes Sexually Dimorphic Gene Expression in the Seed Beetle Callosobruchus maculatus.

Immonen E, Sayadi A, Bayram H, Arnqvist G

Genome Biol Evol 9 (3) 677-699 [2017-03-01; online 2017-04-10]

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

Overexpression of protein kinase STK25 in mice exacerbates ectopic lipid accumulation, mitochondrial dysfunction and insulin resistance in skeletal muscle.

Chursa U, Nuñez-Durán E, Cansby E, ..., Sihlbom C, Mahlapuu M

Diabetologia 60 (3) 553-567 [2017-03-00; online 2016-12-16]

Reducing VEGF-B Signaling Ameliorates Renal Lipotoxicity and Protects against Diabetic Kidney Disease

Falkevall A, Mehlem A, Palombo I, ..., Nash A, Eriksson U

Cell Metabolism 25 (3) 713-726 [2017-03-00; online 2017-03-00]

Tracing Cellular Origin of Human Exosomes Using Multiplex Proximity Extension Assays

Larssen P, Wik L, Czarnewski P, ..., Gabrielsson S, Kamali-Moghaddam M

Mol Cell Proteomics 16 (3) 502-511 [2017-03-00; online 2017-01-22]

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Signs of ongoing inflammation in female patients with chronic widespread pain: A multivariate, explorative, cross-sectional study of blood samples.

Gerdle B, Ghafouri B, Ghafouri N, Bäckryd E, Gordh T

Medicine 96 (9) e6130 [2017-03-00; online 2017-03-02]

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A genetic risk score is significantly associated with statin therapy response in the elderly population.

Ciuculete DM, Bandstein M, Benedict C, ..., Schiöth HB, Mwinyi J

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

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

Anaesthetic-induced cardioprotection in an experimental model of the Takotsubo syndrome - isoflurane vs. propofol.

Oras J, Redfors B, Ali A, ..., Omerovic E, Ricksten SE

Acta Anaesthesiol Scand 61 (3) 309-321 [2017-03-00; online 2017-01-22]

Measuring true localization accuracy in super resolution microscopy with DNA-origami nanostructures

Reuss M, Fördős F, Blom H, ..., Högberg B, Brismar H

New J. Phys. 19 (2) 025013 [2017-02-27; online 2017-02-27]

Integrated Microscopy Technologies Stockholm [Technology development]

Clonal reversal of ageing-associated stem cell lineage bias via a pluripotent intermediate.

Wahlestedt M, Erlandsson E, Kristiansen T, ..., Martin-Gonzalez J, Bryder D

Nat Commun 8 (-) 14533 [2017-02-22; online 2017-02-22]

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Defining the human copper proteome and analysis of its expression variation in cancers.

Blockhuys S, Celauro E, Hildesjö C, ..., Fierro-González JC, Wittung-Stafshede P

Metallomics 9 (2) 112-123 [2017-02-22; online 2016-12-13]

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Comparison of whole genome amplification techniques for human single cell exome sequencing.

Borgström E, Paterlini M, Mold JE, Frisen J, Lundeberg J

PLoS ONE 12 (2) e0171566 [2017-02-16; online 2017-02-16]

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

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

Cancer Res. 77 (4) 937-948 [2017-02-15; online 2016-11-29]

Drug Discovery and Development (DDD) [Collaborative]

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

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

Appl. Environ. Microbiol. 83 (4) e02533-16 [2017-02-15; online 2016-12-02]

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A novel RNA sequencing data analysis method for cell line authentication.

Fasterius E, Raso C, Kennedy S, ..., Uhlén M, Al-Khalili Szigyarto C

PLoS ONE 12 (2) e0171435 [2017-02-13; online 2017-02-13]

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IL-8 predicts early mortality in patients with acute hypercapnic respiratory failure treated with noninvasive positive pressure ventilation.

Jónsdóttir B, Jaworowski Å, San Miguel C, Melander O

BMC Pulm Med 17 (1) 35 [2017-02-08; online 2017-02-08]

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MASTL is essential for anaphase entry of proliferating primordial germ cells and establishment of female germ cells in mice.

Risal S, Zhang J, Adhikari D, ..., Kaldis P, Liu K

Cell Discov 3 (1) 16052 [2017-02-07; online 2017-02-07]

Integrated Microscopy Technologies Gothenburg [Service]

Posttranscriptional Regulation in Adenovirus Infected Cells.

Zhao H, Konzer A, Mi J, ..., Pettersson U, Lind SB

J. Proteome Res. 16 (2) 872-888 [2017-02-03; online 2016-12-13]

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

Defense Responses in Aspen with Altered Pectin Methylesterase Activity Reveal the Hormonal Inducers of Tyloses

Leśniewska J, Öhman D, Krzesłowska M, ..., Moritz T, Mellerowicz EJ

Plant Physiol. 173 (2) 1409-1419 [2017-02-00; online 2016-12-06]

Activation of myeloid and endothelial cells by CD40L gene therapy supports T-cell expansion and migration into the tumor microenvironment

Eriksson E, Moreno R, Milenova I, ..., Alemany R, Loskog A

Gene Ther 24 (2) 92-103 [2017-02-00; online 2016-12-01]

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

Genetic and Targeted eQTL Mapping Reveals Strong Candidate Genes Modulating the Stress Response During Chicken Domestication

Fallahsharoudi A, de Kock N, Johnsson M, ..., Wright D, Jensen P

G3 (Bethesda) 7 (2) 497-504 [2017-02-00; online 2016-12-14]

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

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

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

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

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

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

Biochimica et Biophysica Acta (BBA) - General Subjects 1861 (2) 246-255 [2017-02-00; online 2016-11-10]

Fluorescence Tissue Profiling [Collaborative]

Complement peptide C3a stimulates neural plasticity after experimental brain ischaemia.

Stokowska A, Atkins AL, Morán J, ..., Dragunow M, Pekna M

Brain 140 (2) 353-369 [2017-02-00; online 2016-12-12]

Integrated Microscopy Technologies Gothenburg [Service]

Copper chaperone Atox1 plays role in breast cancer cell migration.

Blockhuys S, Wittung-Stafshede P

Biochem. Biophys. Res. Commun. 483 (1) 301-304 [2017-01-29; online 2016-12-24]

Integrated Microscopy Technologies Gothenburg [Service]

Cell Cycle and Cell Size Dependent Gene Expression Reveals Distinct Subpopulations at Single-Cell Level.

Dolatabadi S, Candia J, Akrap N, ..., Åman P, Ståhlberg A

Front Genet 8 (-) 1 [2017-01-25; online 2017-01-25]

Integrated Microscopy Technologies Gothenburg [Service]

Early onset of inflammation during ontogeny of bipolar disorder: the NLRP2 inflammasome gene distinctly differentiates between patients and healthy controls in the transition between iPS cell and neural stem cell stages

Vizlin-Hodzic D, Zhai Q, Illes S, ..., Ågren H, Funa K

Transl Psychiatry 7 (1) e1010 [2017-01-24; online 2017-01-24]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Vimentin Levels and Serine 71 Phosphorylation in the Control of Cell-Matrix Adhesions, Migration Speed, and Shape of Transformed Human Fibroblasts

Terriac E, Coceano G, Mavajian Z, ..., Lautenschläger F, Gad A

Cells 6 (1) 2 [2017-01-22; online 2017-01-22]

Integrated Microscopy Technologies Stockholm [Service]

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

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

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

Tissue Profiling [Service]

Asgard archaea illuminate the origin of eukaryotic cellular complexity

Zaremba-Niedzwiedzka K, Caceres EF, Saw JH, ..., Spang A, Ettema TJG

Nature 541 (7637) 353-358 [2017-01-11; online 2017-01-11]

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

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

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

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

Spatial Proteomics [Technology development]

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

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

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

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

A systematic search strategy identifies cubilin as independent prognostic marker for renal cell carcinoma.

Gremel G, Djureinovic D, Niinivirta M, ..., Stewart GD, Pontén F

BMC Cancer 17 (1) 9 [2017-01-04; online 2017-01-04]

Association of Body Mass Index with DNA Methylation and Gene Expression in Blood Cells and Relations to Cardiometabolic Disease: A Mendelian Randomization Approach.

Mendelson MM, Marioni RE, Joehanes R, ..., Levy D, Deary IJ

PLoS Med. 14 (1) e1002215 [2017-01-00; online 2017-01-17]

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

Expression of Transient Receptor Potential Channels in the Purified Human Pancreatic β-Cells.

Marabita F, Islam MS

Pancreas 46 (1) 97-101 [2017-01-00; online 2016-07-29]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

VAV1 regulates experimental autoimmune arthritis and is associated with anti-CCP negative rheumatoid arthritis.

Guerreiro-Cacais AO, Norin U, Gyllenberg A, ..., Kockum I, Padyukov L

Genes Immun. 18 (1) 48-56 [2017-01-00; online 2017-01-05]

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

Epigenetic Patterns in Blood Associated With Lipid Traits Predict Incident Coronary Heart Disease Events and Are Enriched for Results From Genome-Wide Association Studies.

Hedman ÅK, Mendelson MM, Marioni RE, ..., Levy D, Ingelsson E

Circ Cardiovasc Genet 10 (1) - [2017-01-00; online 2017-02-19]

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

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

Comte J, Langenheder S, Berga M, Lindström ES

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

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

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

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

Eur. J. Haematol. 98 (1) 52-56 [2017-01-00; online 2016-07-12]

Identification of two distinct mesenchymal stromal cell populations in human malignant glioma.

Svensson A, Ramos-Moreno T, Eberstål S, Scheding S, Bengzon J

J. Neurooncol. 131 (2) 245-254 [2017-01-00; online 2016-10-18]

Clinical Genomics [Service] Clinical Genomics Lund [Service]

Low Rank Enhanced Matrix Recovery of Hybrid Time and Frequency Data in Fast Magnetic Resonance Spectroscopy

Lu H, Zhang X, Qiu T, ..., Chen Z, Qu X

IEEE Trans. Biomed. Eng. - (-) 1-1 [2017-00-00; online 2017-00-00]

Favored surface-limited oxidation of cellulose with Oxone® in water

Ruan CQ, Strømme M, Mihranyan A, Lindh J

RSC Adv. 7 (64) 40600-40607 [2017-00-00; online 2017-00-00]

Decoding Gene Expression in 2D and 3D

Bombrun M, Ranefall P, Lindblad J, ..., Nilsson M, Wählby C

Scandinavian Conference on Image Analysis 2017 - (-) 257-268 [2017-00-00; online 2017-05-19]

BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]

124 CHANGES IN GENE EXPRESSION FOLLOWING EXPOSURE OF BOVINE ENDOMETRIAL EPITHELIAL CELLS (bEEC) TO ESCHERICHIA COLI LPS; THEIR POSSIBLE EFFECT ON IMPLANTATION

Guo Y, Jahmat N, Van Shaik T, ..., Andersson G, Humblot P

Reprod. Fertil. Dev. 29 (1) 170 [2017-00-00; online 2017-00-00]

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

A Fast Low Rank Hankel Matrix Factorization Reconstruction Method for Non-Uniformly Sampled Magnetic Resonance Spectroscopy

Guo D, Lu H, Qu X

IEEE Access 5 (-) 16033-16039 [2017-00-00; online 2017-00-00]

Identification of a Differentially Expressed TIR-NBS-LRR Gene in a Major QTL Associated to Leaf Rust Resistance in Salix.

Martin T, Rönnberg-Wästljung AC, Stenlid J, Samils B

PLoS ONE 11 (12) e0168776 [2016-12-21; online 2016-12-21]

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

Aspen phenylpropanoid genes’ expression levels correlate with genets’ tannin richness and vary both in responses to soil nitrogen and associations with phenolic profiles

Decker VHG, Bandau F, Gundale MJ, Cole CT, Albrectsen BR

Tree Physiol - (-) - [2016-12-15; online 2016-12-15]

Genetic Variants in CHIA and CHI3L1 Are Associated with the IgE Response to the Ascaris Resistance Marker ABA-1 and the Birch Pollen Allergen Bet v 1.

Acevedo N, Bornacelly A, Mercado D, ..., Scheynius A, Caraballo L

PLoS ONE 11 (12) e0167453 [2016-12-15; online 2016-12-15]

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

Transposon Mutagenesis Reveals Fludarabine Resistance Mechanisms in Chronic Lymphocytic Leukemia.

Pandzic T, Larsson J, He L, ..., Sjöblom T, Hellström M

Clin. Cancer Res. 22 (24) 6217-6227 [2016-12-15; online 2016-03-10]

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

Ionization of Cellobiose in Aqueous Alkali and the Mechanism of Cellulose Dissolution.

Bialik E, Stenqvist B, Fang Y, ..., Lund M, Bernin D

J Phys Chem Lett 7 (24) 5044-5048 [2016-12-15; online 2016-11-29]

Clonal Variation in Drug and Radiation Response among Glioma-Initiating Cells Is Linked to Proneural-Mesenchymal Transition.

Segerman A, Niklasson M, Haglund C, ..., Segerman B, Westermark B

Cell Rep 17 (11) 2994-3009 [2016-12-13; online 2016-12-16]

Drug Discovery and Development (DDD) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

PDGFB, a new candidate plasma biomarker for venous thromboembolism: results from the VEREMA affinity proteomics study.

Bruzelius M, Iglesias MJ, Hong MG, ..., Trégouët DA, Odeberg J

Blood 128 (23) e59-e66 [2016-12-08; online 2016-10-14]

Affinity Proteomics Stockholm [Collaborative]

Iron chelators target both proliferating and quiescent cancer cells.

Fryknäs M, Zhang X, Bremberg U, ..., Linder S, Larsson R

Sci Rep 6 (-) 38343 [2016-12-07; online 2016-12-07]

A genetic risk score composed of rheumatoid arthritis risk alleles, HLA-DRB1 haplotypes, and response to TNFi therapy - results from a Swedish cohort study.

Jiang X, Askling J, Saevarsdottir S, ..., Viatte S, Frisell T

Arthritis Res. Ther. 18 (1) 288 [2016-12-03; online 2016-12-03]

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

Elucidating selection processes for antibiotic resistance in sewage treatment plants using metagenomics.

Bengtsson-Palme J, Hammarén R, Pal C, ..., Tysklind M, Larsson DG

Sci. Total Environ. 572 (-) 697-712 [2016-12-01; online 2016-08-21]

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

Quantitative and Selective Analysis of Feline Growth Related Proteins Using Parallel Reaction Monitoring High Resolution Mass Spectrometry.

Sundberg M, Strage EM, Bergquist J, Holst BS, Ramström M

PLoS ONE 11 (12) e0167138 [2016-12-01; online 2016-12-01]

Mass Spectrometry-based Proteomics, Uppsala [Technology development]

The PLETHORA Gene Regulatory Network Guides Growth and Cell Differentiation in Arabidopsis Roots.

Santuari L, Sanchez-Perez GF, Luijten M, ..., Scheres B, Heidstra R

Plant Cell 28 (12) 2937-2951 [2016-12-00; online 2016-12-05]

Structural and conformational determinants of macrocycle cell permeability

Over B, Matsson P, Tyrchan C, ..., Duvall JR, Kihlberg J

Nat Chem Biol 12 (12) 1065-1074 [2016-12-00; online 2016-10-17]

Chemical Biology Consortium Sweden (CBCS) [Technology development]

Distribution and expression of microbial rhodopsins in the Baltic Sea and adjacent waters.

Brindefalk B, Ekman M, Ininbergs K, ..., Pinhassi J, Bergman B

Environ. Microbiol. 18 (12) 4442-4455 [2016-12-00; online 2016-06-17]

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

Early Perspective: Microplate Applications of the Cellular Thermal Shift Assay (CETSA)

Seashore-Ludlow B, Lundbäck T

J Biomol Screen 21 (10) 1019-1033 [2016-12-00; online 2016-07-20]

Chemical Biology Consortium Sweden (CBCS) [Technology development]

Identification and Characterization of Novel Compounds Blocking Shiga Toxin Expression in Escherichia coli O157:H7.

Huerta-Uribe A, Marjenberg ZR, Yamaguchi N, ..., Gally DL, Roe AJ

Front Microbiol 7 (-) 1930 [2016-11-30; online 2016-11-30]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

A stromal cell population in the large intestine identified by tissue factor expression that is lost during colorectal cancer progression.

Eriksson O, Asplund A, Hegde G, ..., Pontén F, Siegbahn A

Thromb. Haemost. 116 (6) 1050-1059 [2016-11-30; online 2016-09-22]

A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism.

Hefzi H, Ang KS, Hanscho M, ..., Lee DY, Lewis NE

Cell Syst 3 (5) 434-443.e8 [2016-11-23; online 2016-11-25]

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

A microarray whole-genome gene expression dataset in a rat model of inflammatory corneal angiogenesis.

Mukwaya A, Lindvall JM, Xeroudaki M, ..., Jensen LD, Lagali N

Sci Data 3 (-) 160103 [2016-11-22; online 2016-11-22]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

ANLN is a prognostic biomarker independent of Ki-67 and essential for cell cycle progression in primary breast cancer.

Magnusson K, Gremel G, Rydén L, ..., Jirström K, Pontén F

BMC Cancer 16 (1) 904 [2016-11-18; online 2016-11-18]

Large-Scale Gene Expression Profiling Platform for Identification of Context-Dependent Drug Responses in Multicellular Tumor Spheroids.

Senkowski W, Jarvius M, Rubin J, ..., Larsson R, Fryknäs M

Cell Chem Biol 23 (11) 1428-1438 [2016-11-17; online 2016-10-27]

Drug Discovery and Development (DDD) [Service] Tissue Profiling [Service]

Nuclear Magnetic Resonance Structure and Mutational Analysis of the Lactococcin A Immunity Protein.

Kristiansen PE, Persson C, Fuochi V, ..., Nissen-Meyer J, Oppegård C

Biochemistry 55 (45) 6250-6257 [2016-11-15; online 2016-11-03]

Functional and Structural Characterization of a Novel HLA-DRB1*04:01-Restricted α-Enolase T Cell Epitope in Rheumatoid Arthritis.

Gerstner C, Dubnovitsky A, Sandin C, ..., Achour A, Malmström V

Front Immunol 7 (-) 494 [2016-11-14; online 2016-11-14]

Chemical Proteomics [Service]

Study on genetic stability in human urothelial cells in vitro.

Chamorro CI, Zeiai S, Reinfeldt Engberg G, ..., Nordenskjöld A, Fossum M

J Tissue Eng Regen Med - (-) - [2016-11-12; online 2016-11-12]

Bioinformatics and Expression Analysis (BEA) [Service]

Case-specific potentiation of glioblastoma drugs by pterostilbene.

Schmidt L, Baskaran S, Johansson P, ..., Krona C, Nelander S

Oncotarget 7 (45) 73200-73215 [2016-11-08; online 2016-10-01]

Drug Discovery and Development (DDD) [Collaborative]

PROX1 is a novel pathway-specific prognostic biomarker for high-grade astrocytomas; results from independent glioblastoma cohorts stratified by age and IDH mutation status.

Roodakker KR, Elsir T, Edqvist PD, ..., Malmström A, Smits A

Oncotarget 7 (45) 72431-72442 [2016-11-08; online 2016-09-15]

The Arabidopsis TOR Kinase Specifically Regulates the Expression of Nuclear Genes Coding for Plastidic Ribosomal Proteins and the Phosphorylation of the Cytosolic Ribosomal Protein S6.

Dobrenel T, Mancera-Martínez E, Forzani C, ..., Hanson J, Meyer C

Front Plant Sci 7 (-) 1611 [2016-11-07; online 2016-11-07]

Image analysis-derived metrics of histomorphological complexity predicts prognosis and treatment response in stage II-III colon cancer.

Mezheyeuski A, Hrynchyk I, Karlberg M, ..., Glimelius B, Östman A

Sci Rep 6 (-) 36149 [2016-11-02; online 2016-11-02]

Tissue Profiling [Service]

Central Metabolic Responses to Ozone and Herbivory Affect Photosynthesis and Stomatal Closure.

Papazian S, Khaling E, Bonnet C, ..., Blande JD, Albrectsen BR

Plant Physiol. 172 (3) 2057-2078 [2016-11-00; online 2016-10-21]

Extension of diffuse low-grade gliomas beyond radiological borders as shown by the coregistration of histopathological and magnetic resonance imaging data.

Zetterling M, Roodakker KR, Berntsson SG, ..., Larsson EM, Smits A

J. Neurosurg. 125 (5) 1155-1166 [2016-11-00; online 2016-02-26]

Acidithiobacillus ferrivorans SS3 presents little RNA transcript response related to cold stress during growth at 8 °C suggesting it is a eurypsychrophile.

Christel S, Fridlund J, Watkin EL, Dopson M

Extremophiles 20 (6) 903-913 [2016-11-00; online 2016-10-25]

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

Mesenchymal state of intimal cells may explain higher propensity to ascending aortic aneurysm in bicuspid aortic valves.

Maleki S, Kjellqvist S, Paloschi V, ..., Eriksson P, Björck HM

Sci Rep 6 (-) 35712 [2016-10-25; online 2016-10-25]

Clinical Proteomics Mass spectrometry [Collaborative] Global Proteomics and Proteogenomics [Collaborative]

Auxotrophy-based High Throughput Screening assay for the identification of Bacillus subtilis stringent response inhibitors.

Andresen L, Varik V, Tozawa Y, ..., Tenson T, Hauryliuk V

Sci Rep 6 (-) 35824 [2016-10-24; online 2016-10-24]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Identification of mutations, gene expression changes and fusion transcripts by whole transcriptome RNAseq in docetaxel resistant prostate cancer cells.

Ma Y, Miao Y, Peng Z, ..., Nilsson S, Li C

Springerplus 5 (1) 1861 [2016-10-24; online 2016-10-24]

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

Over Expression of NANOS3 and DAZL in Human Embryonic Stem Cells.

Panula S, Reda A, Stukenborg JB, ..., Reijo Pera RA, Hovatta O

PLoS ONE 11 (10) e0165268 [2016-10-21; online 2016-10-21]

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

Prokaryotic Responses to Ammonium and Organic Carbon Reveal Alternative CO2 Fixation Pathways and Importance of Alkaline Phosphatase in the Mesopelagic North Atlantic.

Baltar F, Lundin D, Palovaara J, ..., Herndl GJ, Pinhassi J

Front Microbiol 7 (-) 1670 [2016-10-21; online 2016-10-21]

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

(13)C NMR assignments of regenerated cellulose from solid-state 2D NMR spectroscopy.

Idström A, Schantz S, Sundberg J, ..., Gatenholm P, Nordstierna L

Carbohydr Polym 151 (-) 480-487 [2016-10-20; online 2016-05-31]

Gene-specific correlation of RNA and protein levels in human cells and tissues.

Edfors F, Danielsson F, Hallström BM, ..., Forsström B, Uhlén M

Mol. Syst. Biol. 12 (10) 883 [2016-10-20; online 2016-10-20]

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

The Transcriptome of Rhabdomyosarcoma Cells Infected with Cytolytic and Non-Cytolytic Variants of Coxsackievirus B2 Ohio-1.

Sävneby A, Luthman J, Nordenskjöld F, Andersson B, Lindberg AM

PLoS ONE 11 (10) e0164548 [2016-10-19; online 2016-10-19]

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

Analysis of the Distribution of CD103 on CD8 T Cells in Blood and Genital Mucosa of HIVinfected Female Sex Workers

Gibbs A, Buggert M, Ranefall P, ..., Broliden K, Tjernlund A

Conference on HIV Research for Prevention (HIV R4P), 2016, October 17–20, Chicago - (-) - [2016-10-17]

BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]

Massive and parallel expression profiling using microarrayed single-cell sequencing.

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

Nat Commun 7 (-) 13182 [2016-10-14; online 2016-10-14]

Advanced FISH Technologies Bioinformatics (NBIS) [Collaborative] 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) [Service] National Genomics Infrastructure [Service]

Analysis of the brain mural cell transcriptome.

He L, Vanlandewijck M, Raschperger E, ..., Keller A, Betsholtz C

Sci Rep 6 (-) 35108 [2016-10-11; online 2016-10-11]

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

Single-Cell Transcriptome Profiling of Human Pancreatic Islets in Health and Type 2 Diabetes.

Segerstolpe Å, Palasantza A, Eliasson P, ..., Ämmälä C, Sandberg R

Cell Metab. 24 (4) 593-607 [2016-10-11; online 2016-09-22]

The structure and diversity of human, animal and environmental resistomes.

Pal C, Bengtsson-Palme J, Kristiansson E, Larsson DG

Microbiome 4 (1) 54 [2016-10-07; online 2016-10-07]

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

Molecular Diversity of Midbrain Development in Mouse, Human, and Stem Cells.

La Manno G, Gyllborg D, Codeluppi S, ..., Arenas E, Linnarsson S

Cell 167 (2) 566-580.e19 [2016-10-06; online 2016-10-08]

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

MultiQC: summarize analysis results for multiple tools and samples in a single report.

Ewels P, Magnusson M, Lundin S, Käller M

Bioinformatics 32 (19) 3047-3048 [2016-10-01; online 2016-06-16]

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

DNA methylome analysis of acute lymphoblastic leukemia cells reveals stochastic de novo DNA methylation in CpG islands.

Wahlberg P, Lundmark A, Nordlund J, ..., Lönnerholm G, Syvänen AC

Epigenomics 8 (10) 1367-1387 [2016-10-00; online 2016-08-23]

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

Clonality of erythromycin resistance in Francisella tularensis.

Karlsson E, Golovliov I, Lärkeryd A, ..., Forsman M, Johansson A

J. Antimicrob. Chemother. 71 (10) 2815-2823 [2016-10-00; online 2016-06-24]

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

Expression of Interferon-Stimulated Genes in Insulitic Pancreatic Islets of Patients Recently Diagnosed With Type 1 Diabetes.

Lundberg M, Krogvold L, Kuric E, Dahl-Jørgensen K, Skog O

Diabetes 65 (10) 3104-3110 [2016-10-00; online 2016-07-17]

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

Genetic rescue in a severely inbred wolf population.

Åkesson M, Liberg O, Sand H, ..., Bensch S, Flagstad Ø

Mol. Ecol. 25 (19) 4745-4756 [2016-10-00; online 2016-08-09]

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

Serum thioredoxin reductase is highly increased in mice with hepatocellular carcinoma and its activity is restrained by several mechanisms.

Zhang L, Cheng Q, Zhang L, ..., Arnér ES, Zhang J

Free Radic. Biol. Med. 99 (-) 426-435 [2016-10-00; online 2016-08-28]

Mass Spectrometry-based Proteomics, Uppsala [Service]

Effect of Insulin Resistance on Monounsaturated Fatty Acid Levels: A Multi-cohort Non-targeted Metabolomics and Mendelian Randomization Study.

Nowak C, Salihovic S, Ganna A, ..., Ingelsson E, Fall T

PLoS Genet. 12 (10) e1006379 [2016-10-00; online 2016-10-21]

Affinity Proteomics Uppsala [Service] Bioinformatics Support for Computational Resources [Service] Clinical Biomarkers [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service] PLA and Single Cell Proteomics [Service]

Various Antibody Clones of Napsin A, Thyroid Transcription Factor 1, and p40 and Comparisons With Cytokeratin 5 and p63 in Histopathologic Diagnostics of Non-Small Cell Lung Carcinoma.

Tran L, Mattsson JS, Nodin B, ..., Micke P, Brunnström H

Appl. Immunohistochem. Mol. Morphol. 24 (9) 648-659 [2016-10-00; online 2016-10-18]

Abstracts of the HIV Research for Prevention Meeting, HIVR4P, 17-20 October, 2016, Chicago, USA

AIDS Research and Human Retroviruses 32 (S1) 1-409 [2016-10-00; online 2016-10-00]

BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]

Aberrant activation of the PI3K/mTOR pathway promotes resistance to sorafenib in AML.

Lindblad O, Cordero E, Puissant A, ..., Rönnstrand L, Kazi JU

Oncogene 35 (39) 5119-5131 [2016-09-29; online 2016-03-22]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Analysis of Body-wide Unfractionated Tissue Data to Identify a Core Human Endothelial Transcriptome.

Butler LM, Hallström BM, Fagerberg L, ..., Renné T, Odeberg J

Cell Syst 3 (3) 287-301.e3 [2016-09-28; online 2016-09-15]

Loss of ncm(5) and mcm(5) wobble uridine side chains results in an altered metabolic profile.

Karlsborn T, Mahmud AK, Tükenmez H, Byström AS

Metabolomics 12 (12) 177 [2016-09-27; online 2016-09-27]

Exploration of high-density protein microarrays for antibody validation and autoimmunity profiling.

Sjöberg R, Mattsson C, Andersson E, ..., Ayoglu B, Nilsson P

N Biotechnol 33 (5 Pt A) 582-592 [2016-09-25; online 2015-09-30]

Autoimmunity and Serology Profiling [Technology development]

Genetic Spectrum of Idiopathic Restrictive Cardiomyopathy Uncovered by Next-Generation Sequencing.

Kostareva A, Kiselev A, Gudkova A, ..., Sejersen T, Shlyakhto E

PLoS ONE 11 (9) e0163362 [2016-09-23; online 2016-09-23]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

Linkage between Fitness of Yeast Cells and Adenylate Kinase Catalysis

Tükenmez H, Magnussen HM, Kovermann M, Byström A, Wolf-Watz M

PLoS ONE 11 (9) e0163115 [2016-09-19; online 2016-09-19]

Immunoseq: the identification of functionally relevant variants through targeted capture and sequencing of active regulatory regions in human immune cells.

Morin A, Kwan T, Ge B, ..., Lathrop MG, Pastinen T

BMC Med Genomics 9 (1) 59 [2016-09-13; online 2016-09-13]

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

Limited clonal relatedness between gut IgA plasma cells and memory B cells after oral immunization.

Bemark M, Hazanov H, Strömberg A, ..., Mehr R, Lycke NY

Nat Commun 7 (-) 12698 [2016-09-06; online 2016-09-06]

Clinical Genomics [Collaborative] Clinical Genomics Gothenburg [Collaborative]

Electricity generation from an inorganic sulfur compound containing mining wastewater by acidophilic microorganisms.

Ni G, Christel S, Roman P, ..., Bijmans MF, Dopson M

Res. Microbiol. 167 (7) 568-575 [2016-09-00; online 2016-05-08]

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

The Impact of Endurance Training on Human Skeletal Muscle Memory, Global Isoform Expression and Novel Transcripts.

Lindholm ME, Giacomello S, Werne Solnestam B, ..., Kjellqvist S, Sundberg CJ

PLoS Genet. 12 (9) e1006294 [2016-09-00; online 2016-09-22]

Bioinformatics (NBIS) [Collaborative] 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 peroxisome proliferator-activated receptor α agonist, AZD4619, induces alanine aminotransferase-1 gene and protein expression in human, but not in rat hepatocytes: Correlation with serum ALT levels.

Thulin P, Bamberg K, Buler M, Dahl B, Glinghammar B

Int. J. Mol. Med. 38 (3) 961-968 [2016-09-00; online 2016-07-20]

Drug Discovery and Development (DDD) [Collaborative]

Mass spectrometry data from a quantitative analysis of protein expression in gills of immuno-challenged blue mussels (Mytilus edulis).

Hörnaeus K, Guillemant J, Mi J, ..., Bergquist J, Lind SB

Data Brief 8 (-) 470-473 [2016-09-00; online 2016-06-03]

Mass Spectrometry-based Proteomics, Uppsala [Collaborative]

Exploring structure and interactions of the bacterial adaptor protein YjbH by crosslinking mass spectrometry.

Al-Eryani Y, Ib Rasmussen M, Kjellström S, ..., Emanuelsson C, von Wachenfeldt C

Proteins 84 (9) 1234-1245 [2016-09-00; online 2016-06-15]

Data on the expression of cellular lncRNAs in human adenovirus infected cells.

Chen M, Zhao H, Lind SB, Pettersson U

Data Brief 8 (-) 1263-1279 [2016-09-00; online 2016-08-23]

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

Phenotypic Modulation of Smooth Muscle Cells in Atherosclerosis Is Associated With Downregulation of LMOD1, SYNPO2, PDLIM7, PLN, and SYNM.

Perisic Matic L, Rykaczewska U, Razuvaev A, ..., Hamsten A, Hedin U

Arterioscler. Thromb. Vasc. Biol. 36 (9) 1947-1961 [2016-09-00; online 2016-07-28]

Clinical Proteomics Mass spectrometry [Collaborative] Global Proteomics and Proteogenomics [Collaborative]

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 (NBIS) [Collaborative] 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]

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]

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]

Karolinska High Throughput Center (KHTC) [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]

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]

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]

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]

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 [Service] Clinical Genomics Uppsala [Service] Tissue Profiling [Collaborative]

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]

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 (NBIS) [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]

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]

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 (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

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]

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

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]

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]

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]

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 (NBIS) [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]

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]

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

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]

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

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]

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]

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 (NBIS) [Collaborative] 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]

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]

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]

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]

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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]

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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]

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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]

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]

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]

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]

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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]

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]

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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]

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]

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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]

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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]

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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]

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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]

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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]

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]

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]

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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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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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]

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

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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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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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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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]

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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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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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]

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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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]

Bioinformatics and Expression Analysis (BEA) [Service]

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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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]

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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]

Tissue Profiling [Service]

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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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]

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

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]

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]

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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]

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]

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]

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]

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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]

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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]

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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]

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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]

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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]

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]

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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]

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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]

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]

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]

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]

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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]

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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]

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]

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]

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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]

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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]

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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]

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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]

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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]

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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]

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]

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]

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]

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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]

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 (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

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]

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]

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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]

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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]

Karolinska High Throughput Center (KHTC) [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]

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]

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]

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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]

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]

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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]

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]

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]

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 [Collaborative] Clinical Genomics Stockholm [Collaborative] 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]

Bridging Histology and Bioinformatics—Computational Analysis of Spatially Resolved Transcriptomics

Mignardi M, Ishaq O, Qian X, Wahlby C

Proc. IEEE - (-) 1-12 [2016-00-00; online 2016-00-00]

BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]

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] Bioinformatics (NBIS) [Technology development]

Sequence and gene expression evolution of paralogous genes in willows.

Harikrishnan SL, Pucholt P, Berlin S

Sci Rep 5 (-) 18662 [2015-12-22; online 2015-12-22]

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

Exploring water as building bricks in enzyme engineering.

Hendil-Forssell P, Martinelle M, Syrén PO

Chem. Commun. (Camb.) 51 (97) 17221-17224 [2015-12-18; online 2015-10-02]

Powerful Populations Respond to Viruses and Vaccines.

Brodin P

Immunity 43 (6) 1035-1037 [2015-12-15; online 2015-12-20]

High levels of WNT-5A in human glioma correlate with increased presence of tumor-associated microglia/monocytes.

Dijksterhuis JP, Arthofer E, Marinescu VD, ..., Mulder J, Schulte G

Exp. Cell Res. 339 (2) 280-288 [2015-12-10; online 2015-10-25]

A Combination of Culture Conditions and Gene Expression Analysis Can Be Used to Investigate and Predict hES Cell Differentiation Potential towards Male Gonadal Cells.

Kjartansdóttir KR, Reda A, Panula S, ..., Hovatta O, Stukenborg JB

PLoS ONE 10 (12) e0144029 [2015-12-02; online 2015-12-02]

Metabolic Profiling of Chicken Embryos Exposed to Perfluorooctanoic Acid (PFOA) and Agonists to Peroxisome Proliferator-Activated Receptors.

Mattsson A, Kärrman A, Pinto R, Brunström B

PLoS ONE 10 (12) e0143780 [2015-12-01; online 2015-12-01]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Dietary Fiber-Induced Improvement in Glucose Metabolism Is Associated with Increased Abundance of Prevotella.

Kovatcheva-Datchary P, Nilsson A, Akrami R, ..., Björck I, Bäckhed F

Cell Metab. 22 (6) 971-982 [2015-12-01; online 2015-11-11]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Multi-level omics analysis in a murine model of dystrophin loss and therapeutic restoration.

Roberts TC, Johansson HJ, McClorey G, ..., El Andaloussi S, Wood MJ

Hum. Mol. Genet. 24 (23) 6756-6768 [2015-12-01; online 2015-09-20]

Nanocellulose from green algae modulates the in vitro inflammatory response of monocytes/macrophages

Hua K, Strømme M, Mihranyan A, Ferraz N

Cellulose 22 (6) 3673-3688 [2015-12-00; online 2015-10-03]

Phenotypic expansion of visceral myopathy associated with ACTG2 tandem base substitution.

Klar J, Raykova D, Gustafson E, ..., Wanders A, Dahl N

Eur. J. Hum. Genet. 23 (12) 1679-1683 [2015-12-00; online 2015-03-18]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Hormone Replacement Therapy Associated White Blood Cell DNA Methylation and Gene Expression are Associated With Within-Pair Differences of Body Adiposity and Bone Mass.

Bahl A, Pöllänen E, Ismail K, ..., Kovanen V, Ollikainen M

Twin Res Hum Genet 18 (6) 647-661 [2015-12-00; online 2015-12-19]

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

Emmprin Expression Predicts Response and Survival following Cisplatin Containing Chemotherapy for Bladder Cancer: A Validation Study.

Hemdan T, Malmström PU, Jahnson S, Segersten U

J. Urol. 194 (6) 1575-1581 [2015-12-00; online 2015-06-30]

Associations between circulating proteins and corresponding genes expressed in coronary thrombi in patients with acute myocardial infarction.

Helseth R, Weiss TW, Opstad TB, ..., Arnesen H, Seljeflot S

Thromb. Res. 136 (6) 1240-1244 [2015-12-00; online 2015-10-08]

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

Amelioration of the Fitness Costs of Antibiotic Resistance Due To Reduced Outer Membrane Permeability by Upregulation of Alternative Porins.

Knopp M, Andersson DI

Mol. Biol. Evol. 32 (12) 3252-3263 [2015-12-00; online 2015-09-12]

Mass Spectrometry-based Proteomics, Uppsala

The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome.

Hurst LD, Ghanbarian AT, Forrest AR, FANTOM consortium , Huminiecki L

PLoS Biol. 13 (12) e1002315 [2015-12-00; online 2015-12-18]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Experiences with workflows for automating data-intensive bioinformatics

Spjuth O, Bongcam-Rudloff E, Hernández GC, ..., Siretskiy A, Vassilev D

Biol. Direct 10 (1) - [2015-12-00; online 2015-08-19]

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

The Plant Genome Integrative Explorer Resource: PlantGenIE.org.

Sundell D, Mannapperuma C, Netotea S, ..., Hvidsten TR, Street NR

New Phytol. 208 (4) 1149-1156 [2015-12-00; online 2015-07-21]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Single cell analysis of cancer cells using an improved RT-MLPA method has potential for cancer diagnosis and monitoring.

Kvastad L, Werne Solnestam B, Johansson E, ..., Latta D, Lundeberg J

Sci Rep 5 (-) 16519 [2015-11-12; online 2015-11-12]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Normalization of Host Intestinal Mucus Layers Requires Long-Term Microbial Colonization.

Johansson ME, Jakobsson HE, Holmén-Larsson J, ..., Bäckhed F, Hansson GC

Cell Host Microbe 18 (5) 582-592 [2015-11-11; online 2015-11-04]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Elevated expression of the C-type lectin CD93 in the glioblastoma vasculature regulates cytoskeletal rearrangements that enhance vessel function and reduce host survival.

Langenkamp E, Zhang L, Lugano R, ..., Smits A, Dimberg A

Cancer Res. 75 (21) 4504-4516 [2015-11-01; online 2015-09-11]

Inactivation of the Deg protease family in the cyanobacterium Synechocystis sp. PCC 6803 has impact on the outer cell layers.

Cheregi O, Miranda H, Gröbner G, Funk C

Journal of Photochemistry and Photobiology B: Biology 152 (Pt B) 383-394 [2015-11-00; online 2015-05-22]

Rescue of primary ubiquinone deficiency due to a novel COQ7 defect using 2,4-dihydroxybensoic acid.

Freyer C, Stranneheim H, Naess K, ..., Wredenberg A, Wedell A

J. Med. Genet. 52 (11) 779-783 [2015-11-00; online 2015-06-19]

Clinical Genomics Clinical Genomics Stockholm NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

HaloPlex Targeted Resequencing for Mutation Detection in Clinical Formalin-Fixed, Paraffin-Embedded Tumor Samples.

Moens LN, Falk-Sörqvist E, Ljungström V, ..., Nilsson M, Botling J

J Mol Diagn 17 (6) 729-739 [2015-11-00; online 2015-09-03]

Clinical Genomics Clinical Genomics Uppsala NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Resolving Evolutionary Relationships in Closely Related Species with Whole-Genome Sequencing Data.

Nater A, Burri R, Kawakami T, Smeds L, Ellegren H

Syst. Biol. 64 (6) 1000-1017 [2015-11-00; online 2015-07-19]

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

Assessing the Barley Genome Zipper and Genomic Resources for Breeding Purposes.

Silvar C, Martis MM, Nussbaumer T, ..., Ordon F, Perovic D

Plant Genome 8 (3) eplantgenome2015.06.0045 [2015-11-00; online 2015-11-01]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Exploring the genetics of irritable bowel syndrome: a GWA study in the general population and replication in multinational case-control cohorts.

Ek WE, Reznichenko A, Ripke S, ..., Wouters MM, D'Amato M

Gut 64 (11) 1774-1782 [2015-11-00; online 2014-09-23]

Mutation Analysis Facility (MAF) NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Early Exposure to Dogs and Farm Animals and the Risk of Childhood Asthma.

Fall T, Lundholm C, Örtqvist AK, ..., Ingelsson E, Almqvist C

JAMA Pediatr 169 (11) e153219 [2015-11-00; online 2015-11-02]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Quinolone resistance mutations in the faecal microbiota of Swedish travellers to India.

Johnning A, Kristiansson E, Angelin M, ..., Johansson A, Larsson DG

BMC Microbiol. 15 (-) 235 [2015-10-24; online 2015-10-24]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Nurr1 and Retinoid X Receptor Ligands Stimulate Ret Signaling in Dopamine Neurons and Can Alleviate α-Synuclein Disrupted Gene Expression.

Volakakis N, Tiklova K, Decressac M, ..., Björklund A, Perlmann T

J. Neurosci. 35 (42) 14370-14385 [2015-10-21; online 2015-10-23]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

The folate-coupled enzyme MTHFD2 is a nuclear protein and promotes cell proliferation.

Gustafsson Sheppard N, Jarl L, Mahadessian D, ..., Jain M, Nilsson R

Sci Rep 5 (-) 15029 [2015-10-13; online 2015-10-13]

Genome-wide transcriptional and physiological responses to drought stress in leaves and roots of two willow genotypes.

Pucholt P, Sjödin P, Weih M, Rönnberg-Wästljung AC, Berlin S

BMC Plant Biol. 15 (-) 244 [2015-10-12; online 2015-10-12]

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

Growth of Chitinophaga pinensis on Plant Cell Wall Glycans and Characterisation of a Glycoside Hydrolase Family 27 β-l-Arabinopyranosidase Implicated in Arabinogalactan Utilisation.

McKee LS, Brumer H

PLoS ONE 10 (10) e0139932 [2015-10-08; online 2015-10-08]

Crosstalk between Gut Microbiota and Dietary Lipids Aggravates WAT Inflammation through TLR Signaling.

Caesar R, Tremaroli V, Kovatcheva-Datchary P, Cani PD, Bäckhed F

Cell Metab. 22 (4) 658-668 [2015-10-06; online 2015-09-01]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Standing genetic variation as a major contributor to adaptation in the Virginia chicken lines selection experiment.

Sheng Z, Pettersson ME, Honaker CF, Siegel PB, Carlborg Ö

Genome Biol. 16 (-) 219 [2015-10-01; online 2015-10-01]

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

The Human Gut Microbiome as a Transporter of Antibiotic Resistance Genes between Continents.

Bengtsson-Palme J, Angelin M, Huss M, ..., Larsson DGJ, Johansson A

Antimicrob. Agents Chemother. 59 (10) 6551-6560 [2015-10-00; online 2015-08-12]

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

Isolation of novel IncA/C and IncN fluoroquinolone resistance plasmids from an antibiotic-polluted lake.

Flach CF, Johnning A, Nilsson I, ..., Kristiansson E, Larsson DG

J. Antimicrob. Chemother. 70 (10) 2709-2717 [2015-10-00; online 2015-07-01]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Cytostatic Effect of Repeated Exposure to Simvastatin: A Mechanism for Chronic Myotoxicity Revealed by the Use of Mesodermal Progenitors Derived from Human Pluripotent Stem Cells.

Peric D, Barragan I, Giraud-Triboult K, ..., Laustriat D, Peschanski M

Stem Cells 33 (10) 2936-2948 [2015-10-00; online 2015-07-18]

Signatures of post-zygotic structural genetic aberrations in the cells of histologically normal breast tissue that can predispose to sporadic breast cancer.

Forsberg LA, Rasi C, Pekar G, ..., Tot T, Dumanski JP

Genome Res. 25 (10) 1521-1535 [2015-10-00; online 2015-10-03]

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

Transcriptome Profiling Reveals Degree of Variability in Induced Pluripotent Stem Cell Lines: Impact for Human Disease Modeling.

Schuster J, Halvardson J, Pilar Lorenzo L, ..., Feuk L, Dahl N

Cell Reprogram 17 (5) 327-337 [2015-10-00; online 2015-09-08]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

BCG Skin Infection Triggers IL-1R-MyD88-Dependent Migration of EpCAMlow CD11bhigh Skin Dendritic cells to Draining Lymph Node During CD4+ T-Cell Priming.

Bollampalli VP, Harumi Yamashiro L, Feng X, ..., Nylén S, Rothfuchs AG

PLoS Pathog. 11 (10) e1005206 [2015-10-00; online 2015-10-06]

Integrated Microscopy Technologies Stockholm [Service]

The Human Glioblastoma Cell Culture Resource: Validated Cell Models Representing All Molecular Subtypes.

Xie Y, Bergström T, Jiang Y, ..., Forsberg-Nilsson K, Uhrbom L

EBioMedicine 2 (10) 1351-1363 [2015-10-00; online 2015-08-15]

Exploring microbial dark matter to resolve the deep archaeal ancestry of eukaryotes.

Saw JH, Spang A, Zaremba-Niedzwiedzka K, ..., Guy L, Ettema TJG

Philos. Trans. R. Soc. Lond., B, Biol. Sci. 370 (1678) 20140328 [2015-09-26; online 2015-09-02]

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

Gene expression profiling of pre-eclamptic placentae by RNA sequencing.

Kaartokallio T, Cervera A, Kyllönen A, ..., Laivuori H, FINNPEC Core Investigator Group

Sci Rep 5 (-) 14107 [2015-09-21; online 2015-09-21]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Glioma-derived plasminogen activator inhibitor-1 (PAI-1) regulates the recruitment of LRP1 positive mast cells.

Roy A, Coum A, Marinescu VD, ..., Pontén F, Tchougounova E

Oncotarget 6 (27) 23647-23661 [2015-09-15; online 2015-07-15]

Comprehensive analysis of microRNA expression in regionalized human neural progenitor cells reveals microRNA-10 as a caudalizing factor.

Jönsson ME, Nelander Wahlestedt J, Åkerblom M, ..., Jakobsson J, Parmar M

Development 142 (18) 3166-3177 [2015-09-15; online 2015-09-24]

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

Surface Chemistry of Nanocellulose Fibers Directs Monocyte/Macrophage Response.

Hua K, Ålander E, Lindström T, ..., Strømme M, Ferraz N

Biomacromolecules 16 (9) 2787-2795 [2015-09-14; online 2015-08-08]

Determination of obesity associated gene variants related to TMEM18 through ultra-deep targeted re-sequencing in a case-control cohort for pediatric obesity.

Rask-Andersen M, Sällman Almén M, Jacobsson JA, ..., Fredriksson R, Schiöth HB

Genet Res (Camb) 97 (-) e16 [2015-09-14; online 2015-09-14]

NGI Uppsala (SNP&SEQ Technology Platform) NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

The epigenetic signature of subcutaneous fat cells is linked to altered expression of genes implicated in lipid metabolism in obese women.

Arner P, Sinha I, Thorell A, ..., Dahlman-Wright K, Dahlman I

Clin Epigenetics 7 (-) 93 [2015-09-08; online 2015-09-08]

Paternally expressed imprinted genes establish postzygotic hybridization barriers in Arabidopsis thaliana.

Wolff P, Jiang H, Wang G, Santos-González J, Köhler C

Elife 4 (-) - [2015-09-07; online 2015-09-07]

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

Transplanted Bone Marrow-Derived Cells Contribute to Human Adipogenesis.

Rydén M, Uzunel M, Hård JL, ..., Mattsson J, Arner P

Cell Metab. 22 (3) 408-417 [2015-09-01; online 2015-07-21]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Altered serotonin (5-HT) 1D and 2A receptor expression may contribute to defective insulin and glucagon secretion in human type 2 diabetes.

Bennet H, Balhuizen A, Medina A, ..., Wierup N, Fex M

Peptides 71 (-) 113-120 [2015-09-00; online 2015-07-25]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Analysis of the genetic architecture of susceptibility to cervical cancer indicates that common SNPs explain a large proportion of the heritability.

Chen D, Cui T, Ek WE, ..., Wang H, Gyllensten U

Carcinogenesis 36 (9) 992-998 [2015-09-00; online 2015-06-06]

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

Molecular profiling of prostate cancer derived exosomes may reveal a predictive signature for response to docetaxel.

Kharaziha P, Chioureas D, Rutishauser D, ..., Nilsson S, Panaretakis T

Oncotarget 6 (25) 21740-21754 [2015-08-28; online 2015-04-07]

Transcriptomic changes in the plant pathogenic fungus Rhizoctonia solani AG-3 in response to the antagonistic bacteria Serratia proteamaculans and Serratia plymuthica.

Gkarmiri K, Finlay RD, Alström S, ..., Cubeta MA, Högberg N

BMC Genomics 16 (-) 630 [2015-08-22; online 2015-08-22]

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

In Vitro and In Vivo Response to Low-Modulus PMMA-Based Bone Cement.

Carlsson E, Mestres G, Treerattrakoon K, ..., Larsson S, Persson C

Biomed Res Int 2015 (-) 594284 [2015-08-20; online 2015-08-20]

Adaptive mutations in sugar metabolism restore growth on glucose in a pyruvate decarboxylase negative yeast strain.

Zhang Y, Liu G, Engqvist MK, ..., Siewers V, Nielsen J

Microb. Cell Fact. 14 (-) 116 [2015-08-08; online 2015-08-08]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Comprehensive genomic profiles of small cell lung cancer

George J, Lim JS, Jang SJ, ..., Sage J, Thomas RK

Nature 524 (7563) 47-53 [2015-08-06; online 2015-07-13]

Clinical Genomics [Collaborative] Clinical Genomics Uppsala [Collaborative]

Roux-en-Y Gastric Bypass and Vertical Banded Gastroplasty Induce Long-Term Changes on the Human Gut Microbiome Contributing to Fat Mass Regulation.

Tremaroli V, Karlsson F, Werling M, ..., Nielsen J, Bäckhed F

Cell Metab. 22 (2) 228-238 [2015-08-04; online 2015-08-06]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Crystal structure, biochemical and cellular activities demonstrate separate functions of MTH1 and MTH2.

Carter M, Jemth AS, Hagenkort A, ..., Helleday T, Stenmark P

Nat Commun 6 (-) 7871 [2015-08-04; online 2015-08-04]

Genome-wide mapping of promoter-anchored interactions with close to single-enhancer resolution.

Sahlén P, Abdullayev I, Ramsköld D, ..., Lundeberg J, Sandberg R

Genome Biol. 16 (-) 156 [2015-08-03; online 2015-08-03]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Inbreeding Affects Gene Expression Differently in Two Self-Incompatible Arabidopsis lyrata Populations with Similar Levels of Inbreeding Depression.

Menzel M, Sletvold N, Ågren J, Hansson B

Mol. Biol. Evol. 32 (8) 2036-2047 [2015-08-00; online 2015-04-10]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Prevalence of polymorphisms with significant resistance to NS5A inhibitors in treatment-naive patients with hepatitis C virus genotypes 1a and 3a in Sweden.

Lindström I, Kjellin M, Palanisamy N, ..., Lannergard A, Lennerstrand J

Infect Dis (Lond) 47 (8) 555-562 [2015-08-00; online 2015-04-09]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Bioinformatic Challenges in Clinical Diagnostic Application of Targeted Next Generation Sequencing: Experience from Pheochromocytoma.

Crona J, Ljungström V, Welin S, ..., Hellman P, Björklund P

PLoS ONE 10 (7) e0133210 [2015-07-31; online 2015-07-31]

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

lobChIP: from cells to sequencing ready ChIP libraries in a single day.

Wallerman O, Nord H, Bysani M, Borghini L, Wadelius C

Epigenetics Chromatin 8 (-) 25 [2015-07-21; online 2015-07-21]

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

Evaluation of the protein biomarkers and the analgesic response to systemic methylene blue in patients with refractory neuropathic pain: a double-blind, controlled study.

Miclescu AA, Svahn M, Gordh TE

J Pain Res 8 (-) 387-397 [2015-07-15; online 2015-07-15]

Affinity Proteomics Uppsala [Technology development] Clinical Biomarkers PLA and Single Cell Proteomics [Service]

Two new loci and gene sets related to sex determination and cancer progression are associated with susceptibility to testicular germ cell tumor.

Kristiansen W, Karlsson R, Rounge TB, ..., Grotmol T, Wiklund F

Hum. Mol. Genet. 24 (14) 4138-4146 [2015-07-15; online 2015-04-17]

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

Distinguishing Mast Cell Progenitors from Mature Mast Cells in Mice.

Dahlin JS, Ding Z, Hallgren J

Stem Cells Dev. 24 (14) 1703-1711 [2015-07-15; online 2015-03-10]

Differential Expression Analysis by RNA-Seq Reveals Perturbations in the Platelet mRNA Transcriptome Triggered by Pathogen Reduction Systems.

Osman A, Hitzler WE, Ameur A, Provost P

PLoS ONE 10 (7) e0133070 [2015-07-14; online 2015-07-14]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Cell periphery-related proteins as major genomic targets behind the adaptive evolution of an industrial Saccharomyces cerevisiae strain to combined heat and hydrolysate stress.

Wallace-Salinas V, Brink DP, Ahrén D, Gorwa-Grauslund MF

BMC Genomics 16 (-) 514 [2015-07-09; online 2015-07-09]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Structural basis for cellobiose dehydrogenase action during oxidative cellulose degradation.

Tan TC, Kracher D, Gandini R, ..., Ludwig R, Divne C

Nat Commun 6 (-) 7542 [2015-07-07; online 2015-07-07]

Potential role of milk fat globule membrane in modulating plasma lipoproteins, gene expression, and cholesterol metabolism in humans: a randomized study.

Rosqvist F, Smedman A, Lindmark-Månsson H, ..., Dahlman I, Risérus U

Am. J. Clin. Nutr. 102 (1) 20-30 [2015-07-00; online 2015-05-29]

Genome-wide association study identifies new susceptibility loci for cutaneous lupus erythematosus.

Kunz M, König IR, Schillert A, ..., Kuhn A, Ibrahim SM

Exp. Dermatol. 24 (7) 510-515 [2015-07-00; online 2015-04-02]

Function of Isolated Pancreatic Islets From Patients at Onset of Type 1 Diabetes: Insulin Secretion Can Be Restored After Some Days in a Nondiabetogenic Environment In Vitro: Results From the DiViD Study.

Krogvold L, Skog O, Sundström G, ..., Korsgren O, Dahl-Jørgensen K

Diabetes 64 (7) 2506-2512 [2015-07-00; online 2015-02-14]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

UV irradiation responses in Giardia intestinalis.

Einarsson E, Svärd SG, Troell K

Exp. Parasitol. 154 (-) 25-32 [2015-07-00; online 2015-04-01]

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

Toward Rare Blood Cell Preservation for RNA Sequencing.

Vickovic S, Ahmadian A, Lewensohn R, Lundeberg J

J Mol Diagn 17 (4) 352-359 [2015-07-00; online 2015-05-16]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Ebf1 heterozygosity results in increased DNA damage in pro-B cells and their synergistic transformation by Pax5 haploinsufficiency.

Prasad MA, Ungerbäck J, Åhsberg J, ..., Hagman J, Sigvardsson M

Blood 125 (26) 4052-4059 [2015-06-25; online 2015-04-02]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Confrontation of fibroblasts with cancer cells in vitro: gene network analysis of transcriptome changes and differential capacity to inhibit tumor growth.

Alexeyenko A, Alkasalias T, Pavlova T, ..., Guven H, Klein G

J. Exp. Clin. Cancer Res. 34 (-) 62 [2015-06-18; online 2015-06-18]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Dynamics of Cell Generation and Turnover in the Human Heart.

Bergmann O, Zdunek S, Felker A, ..., Druid H, Frisén J

Cell 161 (7) 1566-1575 [2015-06-18; online 2015-06-16]

Integrated Microscopy Technologies Stockholm [Service]

IFN-α production by plasmacytoid dendritic cell associations with polymorphisms in gene loci related to autoimmune and inflammatory diseases.

Berggren O, Alexsson A, Morris DL, ..., Rönnblom L, Eloranta ML

Hum. Mol. Genet. 24 (12) 3571-3581 [2015-06-15; online 2015-03-18]

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

Functional Identification of Target by Expression Proteomics (FITExP) reveals protein targets and highlights mechanisms of action of small molecule drugs.

Chernobrovkin A, Marin-Vicente C, Visa N, Zubarev RA

Sci Rep 5 (-) 11176 [2015-06-08; online 2015-06-08]

Advanced Mass Spectrometry Proteomics Chemical Proteomics [Technology development]

PubMed

Differential Gene Regulation in Fibroblasts in Co-culture with Keratinocytes and Head and Neck SCC Cells.

Hakelius M, Saiepour D, Göransson H, ..., Gerdin B, Nowinski D

Anticancer Res. 35 (6) 3253-3265 [2015-06-00; online 2015-05-31]

Consequences of increased terrestrial dissolved organic matter and temperature on bacterioplankton community composition during a Baltic Sea mesocosm experiment.

Lindh MV, Lefébure R, Degerman R, ..., Andersson A, Pinhassi J

Ambio 44 Suppl 3 (-) 402-412 [2015-06-00; online 2015-05-30]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Tumor vessel up-regulation of INSR revealed by single-cell expression analysis of the tyrosine kinome and phosphatome in human cancers.

Kiflemariam S, Ljungström V, Pontén F, Sjöblom T

Am. J. Pathol. 185 (6) 1600-1609 [2015-06-00; online 2015-04-10]

Loss of ASRGL1 expression is an independent biomarker for disease-specific survival in endometrioid endometrial carcinoma.

Edqvist PH, Huvila J, Forsström B, ..., Pontén F, Auranen A

Gynecol. Oncol. 137 (3) 529-537 [2015-06-00; online 2015-04-07]

Three-Dimensional Cell Culture-Based Screening Identifies the Anthelmintic Drug Nitazoxanide as a Candidate for Treatment of Colorectal Cancer.

Senkowski W, Zhang X, Olofsson MH, ..., Larsson R, Fryknäs M

Mol Cancer Ther 14 (6) 1504-1516 [2015-06-00; online 2015-04-24]

Multiple Changes of Gene Expression and Function Reveal Genomic and Phenotypic Complexity in SLE-like Disease.

Wilbe M, Kozyrev SV, Farias FH, ..., Hansson-Hamlin H, Lindblad-Toh K

PLoS Genet. 11 (6) e1005248 [2015-06-00; online 2015-06-09]

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

PubMed

Circulating microRNA expression pattern separates patients with anti-neutrophil cytoplasmic antibody associated vasculitis from healthy controls.

Skoglund C, Carlsen AL, Weiner M, ..., Heegaard NH, Segelmark M

Clin. Exp. Rheumatol. 33 (2 Suppl 89) S-64-71 [2015-05-26; online 2015-05-26]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Complement inhibitor CD55 governs the integrity of membrane rafts in pancreatic beta cells, but plays no role in insulin secretion.

Nagaraj V, King B, Storm P, ..., Blom AM, Renström E

Biochem. Biophys. Res. Commun. 460 (3) 518-524 [2015-05-08; online 2015-03-24]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Mixed ancestry and admixture in Kauai's feral chickens: invasion of domestic genes into ancient Red Junglefowl reservoirs.

Gering E, Johnsson M, Willis P, Getty T, Wright D

Mol. Ecol. 24 (9) 2112-2124 [2015-05-00; online 2015-02-07]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Plant-mediated gene silencing restricts growth of the potato late blight pathogen Phytophthora infestans.

Jahan SN, Åsman AK, Corcoran P, ..., Vetukuri RR, Dixelius C

J. Exp. Bot. 66 (9) 2785-2794 [2015-05-00; online 2015-03-20]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Polymorphisms in chloroquine resistance-associated genes in Plasmodium vivax in Ethiopia.

Golassa L, Erko B, Baliraine FN, Aseffa A, Swedberg G

Malar. J. 14 (-) 164 [2015-04-16; online 2015-04-16]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Transplant experiments uncover Baltic Sea basin-specific responses in bacterioplankton community composition and metabolic activities.

Lindh MV, Figueroa D, Sjöstedt J, ..., Legrand C, Pinhassi J

Front Microbiol 6 (-) 223 [2015-04-01; online 2015-04-01]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Mixture effects of levonorgestrel and ethinylestradiol: estrogenic biomarkers and hormone receptor mRNA expression during sexual programming.

Säfholm M, Jansson E, Fick J, Berg C

Aquat. Toxicol. 161 (-) 146-153 [2015-04-00; online 2015-02-24]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Fluctuating expression of microRNAs in adenovirus infected cells.

Zhao H, Chen M, Tellgren-Roth C, Pettersson U

Virology 478 (-) 99-111 [2015-04-00; online 2015-03-07]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Discovery of molecular markers to discriminate corneal endothelial cells in the human body.

Yoshihara M, Ohmiya H, Hara S, ..., Tsujikawa M, Nishida K

PLoS ONE 10 (3) e0117581 [2015-03-25; online 2015-03-25]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Variations of gastric corpus microbiota are associated with early esophageal squamous cell carcinoma and squamous dysplasia.

Nasrollahzadeh D, Malekzadeh R, Ploner A, ..., Dawsey SM, Ye W

Sci Rep 5 (-) 8820 [2015-03-06; online 2015-03-06]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

A genomic duplication is associated with ectopic eomesodermin expression in the embryonic chicken comb and two duplex-comb phenotypes.

Dorshorst B, Harun-Or-Rashid M, Bagherpoor AJ, ..., Hallböök F, Andersson L

PLoS Genet. 11 (3) e1004947 [2015-03-00; online 2015-03-19]

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

Amplification-free sequencing of cell-free DNA for prenatal non-invasive diagnosis of chromosomal aberrations.

Karlsson K, Sahlin E, Iwarsson E, ..., Nordenskjöld M, Linnarsson S

Genomics 105 (3) 150-158 [2015-03-00; online 2014-12-30]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Detection of cell aggregation and altered cell viability by automated label-free video microscopy: a promising alternative to endpoint viability assays in high-throughput screening.

Aftab O, Fryknäs M, Hammerling U, Larsson R, Gustafsson MG

J Biomol Screen 20 (3) 372-381 [2015-03-00; online 2014-12-17]

Drug Discovery and Development (DDD)

The roles of SNF2/SWI2 nucleosome remodeling enzymes in blood cell differentiation and leukemia.

Prasad P, Lennartsson A, Ekwall K

Biomed Res Int 2015 (-) 347571 [2015-02-19; online 2015-02-19]

Transcriptional responses of the bacterial antagonist Serratia plymuthica to the fungal phytopathogen Rhizoctonia solani.

Neupane S, Finlay RD, Alström S, Elfstrand M, Högberg N

Environ Microbiol Rep 7 (1) 123-127 [2015-02-00; online 2014-08-21]

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

Expression of human skin-specific genes defined by transcriptomics and antibody-based profiling.

Edqvist PH, Fagerberg L, Hallström BM, ..., Uhlén M, Pontén F

J. Histochem. Cytochem. 63 (2) 129-141 [2015-02-00; online 2014-11-19]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Tissue Profiling [Technology development]

Prognostic impact of COX-2 in non-small cell lung cancer: a comprehensive compartment-specific evaluation of tumor and stromal cell expression.

Mattsson JS, Bergman B, Grinberg M, ..., Micke P, Gulyas M

Cancer Lett. 356 (2 Pt B) 837-845 [2015-01-28; online 2014-10-31]

Endonuclease specificity and sequence dependence of type IIS restriction enzymes.

Lundin S, Jemt A, Terje-Hegge F, ..., Lexow P, Lundeberg J

PLoS ONE 10 (1) e0117059 [2015-01-28; online 2015-01-28]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Next-generation sequencing reveals low-dose effects of cationic dendrimers in primary human bronchial epithelial cells.

Feliu N, Kohonen P, Ji J, ..., Nyström A, Fadeel B

ACS Nano 9 (1) 146-163 [2015-01-27; online 2014-12-23]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

TGF-β1-Induced Epithelial-Mesenchymal Transition Promotes Monocyte/Macrophage Properties in Breast Cancer Cells.

Johansson J, Tabor V, Wikell A, Jalkanen S, Fuxe J

Front Oncol 5 (-) 3 [2015-01-26; online 2015-01-26]

Variation in the human immune system is largely driven by non-heritable influences.

Brodin P, Jojic V, Gao T, ..., Maecker HT, Davis MM

Cell 160 (1-2) 37-47 [2015-01-15; online 2015-01-17]

The statistical geometry of transcriptome divergence in cell-type evolution and cancer.

Liang C, FANTOM Consortium , Forrest AR, Wagner GP

Nat Commun 6 (-) 6066 [2015-01-14; online 2015-01-14]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

The higher frequency of IgA deficiency among Swedish twins is not explained by HLA haplotypes.

Frankowiack M, Kovanen RM, Repasky GA, ..., Pedersen NL, Hammarström L

Genes Immun. 16 (3) 199-205 [2015-01-08; online 2015-01-08]

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

A Machine Learning Approach to Explain Drug Selectivity to Soluble and Membrane Protein Targets.

Freyhult E, Gustafsson MG, Strömbergsson H

Mol Inform 34 (1) 44-52 [2015-01-00; online 2015-01-08]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Combining an amyloid-beta (Aβ) cleaving enzyme inhibitor with a γ-secretase modulator results in an additive reduction of Aβ production.

Strömberg K, Eketjäll S, Georgievska B, ..., Cowburn RF, Dabrowski M

FEBS J. 282 (1) 65-73 [2015-01-00; online 2014-11-07]

Drug Discovery and Development (DDD) [Collaborative]

Expression of human leukocyte antigen class I in endocrine and exocrine pancreatic tissue at onset of type 1 diabetes.

Skog O, Korsgren S, Wiberg A, ..., Korsgren O, Dahl-Jørgensen K

Am. J. Pathol. 185 (1) 129-138 [2015-01-00; online 2014-12-20]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Healthy Nordic diet downregulates the expression of genes involved in inflammation in subcutaneous adipose tissue in individuals with features of the metabolic syndrome.

Kolehmainen M, Ulven SM, Paananen J, ..., Arner P, Dahlman I

Am. J. Clin. Nutr. 101 (1) 228-239 [2015-01-00; online 2014-12-21]

The Biobanking Analysis Resource Catalogue (BARCdb): a new research tool for the analysis of biobank samples.

Galli J, Oelrich J, Taussig MJ, ..., Ortega-Paino E, Landegren U

Nucleic Acids Res. 43 (Database issue) D1158-D1162 [2015-01-00; online 2014-10-23]

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

Exploration and pharmacokinetic profiling of phenylalanine based carbamates as novel substance p 1-7 analogues.

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

ACS Med Chem Lett 5 (12) 1272-1277 [2014-12-11; online 2014-10-29]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

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

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

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

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

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

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

Clin. Infect. Dis. 59 (11) 1546-1553 [2014-12-01; online 2014-08-05]

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

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

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

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

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

Gene expression associated with intersterility in Heterobasidion

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

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

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

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

Chen D, Enroth S, Ivansson E, Gyllensten U

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

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

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

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

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

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

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

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

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

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

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

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

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

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

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

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

Inter- and intratumoral heterogeneity of BCL2 correlates with IgH expression and prognosis in follicular lymphoma.

Barreca A, Martinengo C, Annaratone L, ..., van Oudenaarden A, Chiarle R

Blood Cancer J 4 (-) e249 [2014-10-10; online 2014-10-10]

Advanced FISH Technologies [Collaborative]

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

Tydén E, Tjälve H, Larsson P

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

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

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

Ameur A, Bunikis I, Enroth S, Gyllensten U

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

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

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

Swartling FJ, Bolin S, Phillips JJ, Persson AI

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

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

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

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

J. Pathol. 234 (2) 253-261 [2014-10-00; online 2014-08-04]

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

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

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

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

Lindberg BG, Oldenvi S, Steiner H

Dev. Comp. Immunol. 46 (2) 392-400 [2014-10-00; online 2014-06-04]

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

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

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

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

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

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

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

Integrated Microscopy Technologies Stockholm [Collaborative]

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Tydén E, Dahlberg J, Karlberg O, Höglund J

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

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

The Arthonialean challenge: Restructuring Arthoniaceae

Frisch A, Thor G, Ertz D, Grube M

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

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

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

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

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

Chemical Biology Consortium Sweden (CBCS) [Technology development]

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

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

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

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

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

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

J. Proteome Res. 13 (8) 3596-3606 [2014-08-01; online 2014-07-15]

Mechanisms of mRNA export.

Björk P, Wieslander L

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

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

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

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

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

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

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

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

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

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

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

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

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

Hepatic uptake of atorvastatin: influence of variability in transporter expression on uptake clearance and drug-drug interactions.

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

Drug Metab. Dispos. 42 (7) 1210-1218 [2014-07-00; online 2014-05-05]

Chemical Biology Consortium Sweden (CBCS) [Service]

Characterization of an experimental vaccine for bovine respiratory syncytial virus.

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

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

Mass Spectrometry-based Proteomics, Uppsala

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

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

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

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

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

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

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

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

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

Cancer Cell 25 (6) 794-808 [2014-06-16; online 2014-05-15]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

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

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

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

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Nucleosome regulatory dynamics in response to TGFβ.

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

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

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

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

Osman OA, Gudasz C, Bertilsson S

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

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

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

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

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

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Decreased decorin expression in the tumor microenvironment.

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

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

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

Aranda S, Rutishauser D, Ernfors P

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

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

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

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

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Responsibility and cooperativeness are constrained, not determined.

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

Front Psychol 5 (-) 308 [2014-05-07; online 2014-05-07]

The role of SATB2 as a diagnostic marker for tumors of colorectal origin: Results of a pathology-based clinical prospective study.

Dragomir A, de Wit M, Johansson C, Uhlen M, Pontén F

Am. J. Clin. Pathol. 141 (5) 630-638 [2014-05-00; online 2014-04-10]

Somatic cells with a heavy mitochondrial DNA mutational load render induced pluripotent stem cells with distinct differentiation defects.

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

Stem Cells 32 (5) 1173-1182 [2014-05-00; online 2014-01-22]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

The H1-receptor antagonist cetirizine protects partially against cytokine- and hydrogen peroxide-induced β-TC6 cell death in vitro.

Anvari E, Fred RG, Welsh N

Pancreas 43 (4) 624-629 [2014-05-00; online 2014-04-11]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

miR-20b regulates expression of proteinase-activated receptor-1 (PAR-1) thrombin receptor in melanoma cells.

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

Pigment Cell Melanoma Res 27 (3) 431-441 [2014-05-00; online 2014-02-06]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Single cell genomics of deep ocean bacteria

Zhao W, Andersson SGE

Trends Microbiol. 22 (5) 233-234 [2014-05-00; online 2014-05-00]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

PTPN6 expression is epigenetically regulated and influences survival and response to chemotherapy in high-grade gliomas.

Sooman L, Ekman S, Tsakonas G, ..., Gullbo J, Lennartsson J

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

A Drosophila immune response against Ras-induced overgrowth.

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

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

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

A high-throughput cell-based method to predict the unbound drug fraction in the brain.

Mateus A, Matsson P, Artursson P

J. Med. Chem. 57 (7) 3005-3010 [2014-04-10; online 2014-03-20]

Chemical Biology Consortium Sweden (CBCS) [Technology development]

Vulnerability of glioblastoma cells to catastrophic vacuolization and death induced by a small molecule.

Kitambi SS, Toledo EM, Usoskin D, ..., Hammarström LGJ, Ernfors P

Cell 157 (2) 313-328 [2014-04-10; online 2014-03-25]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

MTH1 inhibition eradicates cancer by preventing sanitation of the dNTP pool.

Gad H, Koolmeister T, Jemth A, ..., Berglund UW, Helleday T

Nature 508 (7495) 215-221 [2014-04-10; online 2014-04-02]

Chemical Biology Consortium Sweden (CBCS) [Collaborative] Drug Discovery and Development (DDD) [Collaborative] Protein Science Facility (PSF)

ZBED6 modulates the transcription of myogenic genes in mouse myoblast cells.

Jiang L, Wallerman O, Younis S, ..., Andersson G, Andersson L

PLoS ONE 9 (4) e94187 [2014-04-08; online 2014-04-08]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

NGI Uppsala (SNP&SEQ Technology Platform) NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Rask-Andersen M, Philippot G, Moschonis G, ..., Fredriksson R, Schiöth HB

PLoS ONE 9 (4) e93193 [2014-04-02; online 2014-04-02]

WNT5A-mediated β-catenin-independent signalling is a novel regulator of cancer cell metabolism.

Sherwood V, Chaurasiya SK, Ekström EJ, ..., James P, Andersson T

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

A novel SERPINE1-FOSB fusion gene results in transcriptional up-regulation of FOSB in pseudomyogenic haemangioendothelioma.

Walther C, Tayebwa J, Lilljebjörn H, ..., Fletcher CD, Mertens F

J. Pathol. 232 (5) 534-540 [2014-04-00; online 2014-01-29]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Impact of stereospecific intramolecular hydrogen bonding on cell permeability and physicochemical properties.

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

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

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge.

Brownstein CA, Beggs AH, Homer N, ..., Kohane IS, Margulies DM

Genome Biol. 15 (3) R53 [2014-03-25; online 2014-03-25]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Epitope-specific antibody response is controlled by immunoglobulin V(H) polymorphisms.

Raposo B, Dobritzsch D, Ge C, ..., Schneider G, Holmdahl R

J. Exp. Med. 211 (3) 405-411 [2014-03-10; online 2014-02-19]

ZapE is a novel cell division protein interacting with FtsZ and modulating the Z-ring dynamics.

Marteyn BS, Karimova G, Fenton AK, ..., Sansonetti PJ, Tang CM

MBio 5 (2) e00022-e00014 [2014-03-04; online 2014-03-04]

A study of embryonic stem cell-related proteins in human astrocytomas: identification of Nanog as a predictor of survival.

Elsir T, Edqvist PH, Carlson J, ..., Nistér M, Smits A

Int. J. Cancer 134 (5) 1123-1131 [2014-03-01; online 2013-09-17]

Detection of enterovirus in the islet cells of patients with type 1 diabetes: what do we learn from immunohistochemistry?

Hansson SF, Korsgren S, Pontén F, Korsgren O

Diabetologia 57 (3) 645-646 [2014-03-00; online 2013-12-20]

Robust isolation of malignant plasma cells in multiple myeloma

Frigyesi I, Adolfsson J, Ali M, ..., Hansson M, Nilsson B

Blood 123 (9) 1336-1340 [2014-02-27; online 2014-02-27]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Microevolution during an Anthrax outbreak leading to clonal heterogeneity and penicillin resistance.

Ågren J, Finn M, Bengtsson B, Segerman B

PLoS ONE 9 (2) e89112 [2014-02-13; online 2014-02-13]

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

Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics.

Fagerberg L, Hallström BM, Oksvold P, ..., Ponten F, Uhlén M

Mol. Cell Proteomics 13 (2) 397-406 [2014-02-00; online 2013-12-07]

Affinity Proteomics Stockholm [Technology development] Autoimmunity and Serology Profiling [Technology development] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Spatial Proteomics Tissue Profiling

Glioma-derived macrophage migration inhibitory factor (MIF) promotes mast cell recruitment in a STAT5-dependent manner.

Põlajeva J, Bergström T, Edqvist PH, ..., Forsberg Nilsson K, Tchougounova E

Mol Oncol 8 (1) 50-58 [2014-02-00; online 2013-10-05]

A prostate cancer susceptibility allele at 6q22 increases RFX6 expression by modulating HOXB13 chromatin binding.

Huang Q, Whitington T, Gao P, ..., Taipale J, Wei GH

Nat. Genet. 46 (2) 126-135 [2014-02-00; online 2014-01-07]

Mycobacteria bypass mucosal NF-kB signalling to induce an epithelial anti-inflammatory IL-22 and IL-10 response.

Lutay N, Håkansson G, Alaridah N, ..., Westergren-Thorsson G, Godaly G

PLoS ONE 9 (1) e86466 [2014-01-28; online 2014-01-28]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Metabolic enzyme expression highlights a key role for MTHFD2 and the mitochondrial folate pathway in cancer.

Nilsson R, Jain M, Madhusudhan N, ..., Asplund A, Mootha VK

Nat Commun 5 (-) 3128 [2014-01-24; online 2014-01-24]

FuseFISH: robust detection of transcribed gene fusions in single cells.

Semrau S, Crosetto N, Bienko M, ..., Chiarle R, van Oudenaarden A

Cell Rep 6 (1) 18-23 [2014-01-16; online 2013-12-27]

Advanced FISH Technologies [Technology development]

SNPs within the GH-signaling pathway are associated with the early IGF1 response to GH replacement therapy in GHD adults.

Glad CA, Barbosa EJ, Filipsson Nyström H, ..., Svensson PA, Johannsson G

Eur. J. Endocrinol. 170 (1) 101-107 [2014-01-00; online 2013-10-12]

Translational study between structure and biological response of nanocellulose from wood and green algae

Hua K, Carlsson DO, Ålander E, ..., Mihranyan A, Ferraz N

RSC Adv. 4 (6) 2892-2903 [2014-00-00; online 2014-00-00]

Structure-activity relationships of synthetic cordycepin analogues as experimental therapeutics for African trypanosomiasis.

Vodnala SK, Lundbäck T, Yeheskieli E, ..., Hammarström LG, Rottenberg ME

J. Med. Chem. 56 (24) 9861-9873 [2013-12-27; online 2013-12-10]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Combining genetic mapping with genome-wide expression in experimental autoimmune encephalomyelitis highlights a gene network enriched for T cell functions and candidate genes regulating autoimmunity.

Thessen Hedreul M, Möller S, Stridh P, ..., Olsson T, Jagodic M

Hum. Mol. Genet. 22 (24) 4952-4966 [2013-12-15; online 2013-07-29]

Urinary prognostic biomarkers and classification of IgA nephropathy by high resolution mass spectrometry coupled with liquid chromatography.

Kalantari S, Rutishauser D, Samavat S, ..., Rezaei-Tavirani M, Zubarev RA

PLoS ONE 8 (12) e80830 [2013-12-05; online 2013-12-05]

The resveratrol tetramer (-)-hopeaphenol inhibits type III secretion in the gram-negative pathogens Yersinia pseudotuberculosis and Pseudomonas aeruginosa.

Zetterström CE, Hasselgren J, Salin O, ..., Sundin C, Elofsson M

PLoS ONE 8 (12) e81969 [2013-12-04; online 2013-12-04]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Integrated molecular portrait of non-small cell lung cancers.

Lazar V, Suo C, Orear C, ..., Hansson J, Pawitan Y

BMC Med Genomics 6 (-) 53 [2013-12-03; online 2013-12-03]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Protein expansion is primarily due to indels in intrinsically disordered regions.

Light S, Sagit R, Sachenkova O, Ekman D, Elofsson A

Mol. Biol. Evol. 30 (12) 2645-2653 [2013-12-00; online 2013-09-17]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

High expression of glycolytic and pigment proteins is associated with worse clinical outcome in stage III melanoma.

Falkenius J, Lundeberg J, Johansson H, ..., Hansson J, Egyhazi Brage S

Melanoma Res. 23 (6) 452-460 [2013-12-00; online 2013-10-17]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Evaluation of real-time immunohistochemistry and interaction map as an alternative objective assessment of HER2 expression in human breast cancer tissue.

Gedda L, Björkelund H, Lebel L, ..., Malmqvist M, Andersson K

Appl. Immunohistochem. Mol. Morphol. 21 (6) 497-505 [2013-12-00; online 2013-03-05]

DNA damage leads to progressive replicative decline but extends the life span of long-lived mutant animals.

Lans H, Lindvall JM, Thijssen K, ..., Nilsen H, Vermeulen W

Cell Death Differ. 20 (12) 1709-1718 [2013-12-00; online 2013-09-10]

Early B-cell factor 1 regulates the expansion of B-cell progenitors in a dose-dependent manner.

Åhsberg J, Ungerbäck J, Strid T, ..., Qian H, Sigvardsson M

J. Biol. Chem. 288 (46) 33449-33461 [2013-11-15; online 2013-09-27]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

miR-128 regulates non-myocyte hyperplasia, deposition of extracellular matrix and Islet1 expression during newt cardiac regeneration.

Witman N, Heigwer J, Thaler B, Lui WO, Morrison JI

Dev. Biol. 383 (2) 253-263 [2013-11-15; online 2013-09-24]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Efficient cellular fractionation improves RNA sequencing analysis of mature and nascent transcripts from human tissues.

Zaghlool A, Ameur A, Nyberg L, ..., Cavelier L, Feuk L

BMC Biotechnol. 13 (-) 99 [2013-11-13; online 2013-11-13]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

7,8- and 5,8-Linoleate diol synthases support the heterolytic scission of oxygen-oxygen bonds by different amide residues.

Hoffmann I, Oliw EH

Arch. Biochem. Biophys. 539 (1) 87-91 [2013-11-01; online 2013-09-26]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Comparative drug pair screening across multiple glioblastoma cell lines reveals novel drug-drug interactions.

Schmidt L, Kling T, Monsefi N, ..., Gerlee P, Nelander S

Neuro-oncology 15 (11) 1469-1478 [2013-11-00; online 2013-10-06]

Drug Discovery and Development (DDD) [Collaborative]

Variants at multiple loci implicated in both innate and adaptive immune responses are associated with Sjögren's syndrome.

Lessard CJ, Li H, Adrianto I, ..., Harley JB, Sivils KL

Nat. Genet. 45 (11) 1284-1292 [2013-11-00; online 2013-10-08]

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

Molecular characterization of the α-subunit of Na⁺/K⁺ ATPase from the euryhaline barnacle Balanus improvisus reveals multiple genes and differential expression of alternative splice variants.

Lind U, Alm Rosenblad M, Wrange AL, ..., Havenhand J, Blomberg A

PLoS ONE 8 (10) e77069 [2013-10-09; online 2013-10-09]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Transcription factor ZBED6 affects gene expression, proliferation, and cell death in pancreatic beta cells.

Wang X, Jiang L, Wallerman O, ..., Andersson L, Welsh N

Proc. Natl. Acad. Sci. U.S.A. 110 (40) 15997-16002 [2013-10-01; online 2013-09-16]

NGI Uppsala (SNP&SEQ Technology Platform) NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Comprehensive genetic analysis identifies a pathognomonic NAB2/STAT6 fusion gene, nonrandom secondary genomic imbalances, and a characteristic gene expression profile in solitary fibrous tumor.

Mohajeri A, Tayebwa J, Collin A, ..., Nord KH, Mertens F

Genes Chromosomes Cancer 52 (10) 873-886 [2013-10-00; online 2013-06-14]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Recent advances in crayfish hematopoietic stem cell culture: a model for studies of hemocyte differentiation and immunity.

Söderhäll I

Cytotechnology 65 (5) 691-695 [2013-10-00; online 2013-05-21]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Heart research advances using database search engines, Human Protein Atlas and the Sydney Heart Bank.

Li A, Estigoy C, Raftery M, ..., Lal S, Dos Remedios CG

Heart Lung Circ 22 (10) 819-826 [2013-10-00; online 2013-07-17]

FHOD1, a formin upregulated in epithelial-mesenchymal transition, participates in cancer cell migration and invasion.

Gardberg M, Kaipio K, Lehtinen L, ..., Koivisto M, Carpén O

PLoS ONE 8 (9) e74923 [2013-09-26; online 2013-09-26]

Spinal deformity in aged zebrafish is accompanied by degenerative changes to their vertebrae that resemble osteoarthritis.

Hayes AJ, Reynolds S, Nowell MA, ..., Caterson B, Hammond CL

PLoS ONE 8 (9) e75787 [2013-09-24; online 2013-09-24]

Genome Engineering Zebrafish

Equine multiple congenital ocular anomalies and silver coat colour result from the pleiotropic effects of mutant PMEL.

Andersson LS, Wilbe M, Viluma A, ..., Ewart S, Lindgren G

PLoS ONE 8 (9) e75639 [2013-09-23; online 2013-09-23]

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

Deep resequencing of GWAS loci identifies rare variants in CARD9, IL23R and RNF186 that are associated with ulcerative colitis.

Beaudoin M, Goyette P, Boucher G, ..., Daly MJ, Rioux JD

PLoS Genet. 9 (9) e1003723 [2013-09-12; online 2013-09-12]

A tosyl-activated magnetic bead cellulose as solid support for sensitive protein detection.

Yan J, Horák D, Lenfeld J, Hammond M, Kamali-Moghaddam M

J. Biotechnol. 167 (3) 235-240 [2013-09-10; online 2013-07-03]

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

The Oct1 homolog Nubbin is a repressor of NF-κB-dependent immune gene expression that increases the tolerance to gut microbiota.

Dantoft W, Davis MM, Lindvall JM, ..., Beskow A, Engström Y

BMC Biol. 11 (-) 99 [2013-09-06; online 2013-09-06]

Transcription factor binding in human cells occurs in dense clusters formed around cohesin anchor sites.

Yan J, Enge M, Whitington T, ..., Taipale M, Taipale J

Cell 154 (4) 801-813 [2013-08-15; online 2013-08-21]

Bioinformatics and Expression Analysis (BEA) Karolinska High Throughput Center (KHTC)

Investigation of six testicular germ cell tumor susceptibility genes suggests a parent-of-origin effect in SPRY4.

Karlsson R, Andreassen KE, Kristiansen W, ..., Grotmol T, Wiklund F

Hum. Mol. Genet. 22 (16) 3373-3380 [2013-08-15; online 2013-05-04]

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

Chronic airway-induced allergy in mice modifies gene expression in the brain toward insulin resistance and inflammatory responses.

Sarlus H, Wang X, Cedazo-Minguez A, Schultzberg M, Oprica M

J Neuroinflammation 10 (-) 99 [2013-08-01; online 2013-08-01]

Proteome of the nematode-trapping cells of the fungus Monacrosporium haptotylum.

Andersson KM, Meerupati T, Levander F, ..., Ahrén D, Tunlid A

Appl. Environ. Microbiol. 79 (16) 4993-5004 [2013-08-00; online 2013-06-19]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Expression of chondroitin/dermatan sulfate glycosyltransferases during early zebrafish development.

Filipek-Górniok B, Holmborn K, Haitina T, ..., Kreuger J, Ledin J

Dev. Dyn. 242 (8) 964-975 [2013-08-00; online 2013-06-18]

Genome Engineering Zebrafish

Synergistic interactions between camptothecin and EGFR or RAC1 inhibitors and between imatinib and Notch signaling or RAC1 inhibitors in glioblastoma cell lines.

Sooman L, Ekman S, Andersson C, ..., Lennartsson J, Gullbo J

Cancer Chemother. Pharmacol. 72 (2) 329-340 [2013-08-00; online 2013-06-06]

In silico instrumental response correction improves precision of label-free proteomics and accuracy of proteomics-based predictive models.

Lyutvinskiy Y, Yang H, Rutishauser D, Zubarev RA

Mol. Cell Proteomics 12 (8) 2324-2331 [2013-08-00; online 2013-04-17]

Tumour expression of bladder cancer-associated urinary proteins.

Lindén M, Segersten U, Runeson M, ..., Lind SB, Malmström PU

BJU Int. 112 (3) 407-415 [2013-08-00; online 2013-03-09]

Retinoic acid receptor alpha is associated with tamoxifen resistance in breast cancer.

Johansson HJ, Sanchez BC, Mundt F, ..., Linderholm BK, Lehtiö J

Nat Commun 4 (-) 2175 [2013-07-23; online 2013-07-23]

Drug Discovery and Development (DDD) [Collaborative]

Estrogen receptor β expression induces changes in the microRNA pool in human colon cancer cells.

Edvardsson K, Nguyen-Vu T, Kalasekar SM, ..., Gustafsson JÅ, Williams C

Carcinogenesis 34 (7) 1431-1441 [2013-07-00; online 2013-02-26]

Response of Acidithiobacillus caldus toward suboptimal pH conditions.

Mangold S, Rao Jonna V, Dopson M

Extremophiles 17 (4) 689-696 [2013-07-00; online 2013-05-29]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Cenani-Lenz syndrome restricted to limb and kidney anomalies associated with a novel LRP4 missense mutation.

Khan TN, Klar J, Ali Z, ..., Baig SM, Dahl N

Eur J Med Genet 56 (7) 371-374 [2013-07-00; online 2013-05-15]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Implications of baseline polymorphisms for potential resistance to NS3 protease inhibitors in Hepatitis C virus genotypes 1a, 2b and 3a.

Palanisamy N, Danielsson A, Kokkula C, ..., Duberg AS, Lennerstrand J

Antiviral Res. 99 (1) 12-17 [2013-07-00; online 2013-05-08]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Constrained H-Phe-Phe-NH2 analogues with high affinity to the substance P 1-7 binding site and with improved metabolic stability and cell permeability.

Fransson R, Sköld C, Kratz JM, ..., Hallberg M, Sandström A

J. Med. Chem. 56 (12) 4953-4965 [2013-06-27; online 2013-06-06]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Vandetanib combined with a p38 MAPK inhibitor synergistically reduces glioblastoma cell survival.

Sooman L, Lennartsson J, Gullbo J, ..., Blomquist E, Ekman S

Med. Oncol. 30 (3) 638 [2013-06-20; online 2013-06-20]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training Tissue Profiling

Behavioural and Brain Gene Expression Profiling in Pigs during Tail Biting Outbreaks - Evidence of a Tail Biting Resistant Phenotype.

Brunberg E, Jensen P, Isaksson A, Keeling LJ

PLoS ONE 8 (6) e66513 [2013-06-18; online 2013-06-18]

The prognostic relevance of tumour-infiltrating plasma cells and immunoglobulin kappa C indicates an important role of the humoral immune response in non-small cell lung cancer.

Lohr M, Edlund K, Botling J, ..., Rahnenführer J, Micke P

Cancer Lett. 333 (2) 222-228 [2013-06-10; online 2013-02-02]

Parallel visualization of multiple protein complexes in individual cells in tumor tissue.

Leuchowius KJ, Clausson CM, Grannas K, ..., Landegren U, Söderberg O

Mol. Cell Proteomics 12 (6) 1563-1571 [2013-06-00; online 2013-02-26]

Affinity Proteomics Uppsala [Technology development] NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure PLA and Single Cell Proteomics

Gambogic acid is cytotoxic to cancer cells through inhibition of the ubiquitin-proteasome system.

Felth J, Lesiak-Mieczkowska K, D'Arcy P, ..., Fryknäs M, Rickardson L

Invest New Drugs 31 (3) 587-598 [2013-06-00; online 2012-11-28]

The value of selected in vitro and in silico methods to predict acute oral toxicity in a regulatory context: results from the European Project ACuteTox.

Prieto P, Kinsner-Ovaskainen A, Stanzel S, ..., Zurbano MJ, Kopp-Schneider A

Toxicol In Vitro 27 (4) 1357-1376 [2013-06-00; online 2012-08-28]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

A significant fraction of 21-nucleotide small RNA originates from phased degradation of resistance genes in several perennial species.

Källman T, Chen J, Gyllenstrand N, Lagercrantz U

Plant Physiol. 162 (2) 741-754 [2013-06-00; online 2013-04-13]

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

Stepping-stone expansion and habitat loss explain a peculiar genetic structure and distribution of a forest insect.

Cassel-Lundhagen A, Ronnås C, Battisti A, Wallén J, Larsson S

Mol. Ecol. 22 (12) 3362-3375 [2013-06-00; online 2013-05-31]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

A texture based pattern recognition approach to distinguish melanoma from non-melanoma cells in histopathological tissue microarray sections.

Rexhepaj E, Agnarsdóttir M, Bergman J, ..., Lundberg E, Ponten F

PLoS ONE 8 (5) e62070 [2013-05-17; online 2013-05-17]

Spatial Proteomics Tissue Profiling

Identification and expression of stressosomal proteins in Mycobacterium marinum under various growth and stress conditions.

Pettersson BMF, Nitharwal RG, Das S, ..., Bhattacharya A, Kirsebom LA

FEMS Microbiol. Lett. 342 (2) 98-105 [2013-05-00; online 2013-03-14]

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

The adenovirus VA RNA-derived miRNAs are not essential for lytic virus growth in tissue culture cells.

Kamel W, Segerman B, Öberg D, Punga T, Akusjärvi G

Nucleic Acids Res. 41 (9) 4802-4812 [2013-05-00; online 2013-03-26]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Genetic determinants of mortality. Can findings from genome-wide association studies explain variation in human mortality?

Ganna A, Rivadeneira F, Hofman A, ..., Ingelsson E, Tiemeier H

Hum. Genet. 132 (5) 553-561 [2013-05-00; online 2013-01-29]

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

The combined effects of single-nucleotide polymorphisms, tobacco products, and ethanol on normal resting blood mononuclear cells.

Cederblad L, Thunberg U, Engström M, ..., Rutqvist LE, Laytragoon-Lewin N

Nicotine Tob. Res. 15 (5) 890-895 [2013-05-00; online 2012-10-09]

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

Majority of differentially expressed genes are down-regulated during malignant transformation in a four-stage model.

Danielsson F, Skogs M, Huss M, ..., Uhlén M, Lundberg E

Proc. Natl. Acad. Sci. U.S.A. 110 (17) 6853-6858 [2013-04-23; online 2013-04-10]

Expression of fusion proteins of Aspergillus terreus reveals a novel allene oxide synthase.

Hoffmann I, Jernerén F, Oliw EH

J. Biol. Chem. 288 (16) 11459-11469 [2013-04-19; online 2013-03-13]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

European H16N3 gull influenza virus attaches to the human respiratory tract and eye.

Lindskog C, Ellström P, Olsen B, ..., Kuiken T, Jourdain E

PLoS ONE 8 (4) e60757 [2013-04-08; online 2013-04-08]

RNA-binding protein QKI regulates Glial fibrillary acidic protein expression in human astrocytes.

Radomska KJ, Halvardson J, Reinius B, ..., Feuk L, Jazin E

Hum. Mol. Genet. 22 (7) 1373-1382 [2013-04-01; online 2013-01-15]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Immunofluorescence and fluorescent-protein tagging show high correlation for protein localization in mammalian cells.

Stadler C, Rexhepaj E, Singan VR, ..., Simpson JC, Lundberg E

Nat. Methods 10 (4) 315-323 [2013-04-00; online 2013-02-26]

Degradation of Scots pine and beech wood exposed in four test fields used for testing of wood preservatives

Råberg U, Terziev N, Daniel G

International Biodeterioration & Biodegradation 79 (-) 20-27 [2013-04-00; online 2013-04-00]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Hierarchical molecular tagging to resolve long continuous sequences by massively parallel sequencing.

Lundin S, Gruselius J, Nystedt B, ..., Käller M, Lundeberg J

Sci Rep 3 (-) 1186 [2013-03-09; online 2013-03-09]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

A gene transfer agent and a dynamic repertoire of secretion systems hold the keys to the explosive radiation of the emerging pathogen Bartonella.

Guy L, Nystedt B, Toft C, ..., Eriksson AS, Andersson SG

PLoS Genet. 9 (3) e1003393 [2013-03-00; online 2013-03-28]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Fine-mapping of restless legs locus 4 (RLS4) identifies a haplotype over the SPATS2L and KCTD18 genes.

Pichler I, Schwienbacher C, Zanon A, ..., Hicks AA, Pramstaller PP

J. Mol. Neurosci. 49 (3) 600-605 [2013-03-00; online 2012-10-12]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Brain gene expression differences are associated with abnormal tail biting behavior in pigs.

Brunberg E, Jensen P, Isaksson A, Keeling LJ

Genes Brain Behav. 12 (2) 275-281 [2013-03-00; online 2012-11-14]

A modified Glenn shunt improves haemodynamics in acute right ventricular failure in an experimental model.

Vikholm P, Schiller P, Johansson J, Hellgren L

Eur J Cardiothorac Surg 43 (3) 612-618 [2013-03-00; online 2012-07-05]

Imatinib ameliorates neuroinflammation in a rat model of multiple sclerosis by enhancing blood-brain barrier integrity and by modulating the peripheral immune response.

Adzemovic MV, Adzemovic MZ, Zeitelhofer M, ..., Olsson T, Nilsson I

PLoS ONE 8 (2) e56586 [2013-02-20; online 2013-02-20]

STC1 expression by cancer-associated fibroblasts drives metastasis of colorectal cancer.

Peña C, Céspedes MV, Lindh MB, ..., Augsten M, Ostman A

Cancer Res. 73 (4) 1287-1297 [2013-02-15; online 2012-12-18]

Coastal bacterioplankton community dynamics in response to a natural disturbance.

Yeo SK, Huggett MJ, Eiler A, Rappé MS

PLoS ONE 8 (2) e56207 [2013-02-07; online 2013-02-07]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Early-phase GVHD gene expression profile in target versus non-target tissues: kidney, a possible target?

Sadeghi B, Al-Chaqmaqchi H, Al-Hashmi S, ..., Moshfegh A, Hassan M

Bone Marrow Transplant. 48 (2) 284-293 [2013-02-00; online 2012-07-25]

Adipose tissue resting energy expenditure and expression of genes involved in mitochondrial function are higher in women than in men.

Nookaew I, Svensson PA, Jacobson P, ..., Nielsen J, Carlsson LM

J. Clin. Endocrinol. Metab. 98 (2) E370-E378 [2013-02-00; online 2012-12-25]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

In vitro and in vivo activities of 2-aminopyrazines and 2-aminopyridines in experimental models of human African trypanosomiasis.

Vodnala SK, Lundbäck T, Sjöberg B, ..., Rottenberg ME, Hammarström LGJ

Antimicrob. Agents Chemother. 57 (2) 1012-1018 [2013-02-00; online 2012-12-21]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

DNA-binding specificities of human transcription factors.

Jolma A, Yan J, Whitington T, ..., Kivioja T, Taipale J

Cell 152 (1-2) 327-339 [2013-01-17; online 2013-01-22]

Gene expression deregulation in postnatal skeletal muscle of TK2 deficient mice reveals a lower pool of proliferating myogenic progenitor cells.

Paredes JA, Zhou X, Höglund S, Karlsson A

PLoS ONE 8 (1) e53698 [2013-01-14; online 2013-01-14]

RNA deep sequencing as a tool for selection of cell lines for systematic subcellular localization of all human proteins.

Danielsson F, Wiking M, Mahdessian D, ..., Uhlén M, Lundberg E

J. Proteome Res. 12 (1) 299-307 [2013-01-04; online 2012-12-12]

Biomarker discovery in non-small cell lung cancer: integrating gene expression profiling, meta-analysis, and tissue microarray validation.

Botling J, Edlund K, Lohr M, ..., Hengstler JG, Micke P

Clin. Cancer Res. 19 (1) 194-204 [2013-01-01; online 2012-10-02]

Array and Analysis Facility Tissue Profiling

450K-array analysis of chronic lymphocytic leukemia cells reveals global DNA methylation to be relatively stable over time and similar in resting and proliferative compartments.

Cahill N, Bergh AC, Kanduri M, ..., Rosén A, Rosenquist R

Leukemia 27 (1) 150-158 [2013-01-00; online 2012-08-28]

Array and Analysis Facility NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Powerful identification of cis-regulatory SNPs in human primary monocytes using allele-specific gene expression.

Almlöf JC, Lundmark P, Lundmark A, ..., Cambien F, Syvänen A

PLoS ONE 7 (12) e52260 [2012-12-26; online 2012-12-26]

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

Mice lacking a Myc enhancer that includes human SNP rs6983267 are resistant to intestinal tumors.

Sur IK, Hallikas O, Vähärautio A, ..., Aaltonen LA, Taipale J

Science 338 (6112) 1360-1363 [2012-12-07; online 2012-11-03]

PCR-based multiparametric assays in single cells.

Darmanis S, Gallant C, Landegren U

Clin. Chem. 58 (12) 1618-1619 [2012-12-00; online 2012-10-17]

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

Insights into p53 transcriptional function via genome-wide chromatin occupancy and gene expression analysis.

Nikulenkov F, Spinnler C, Li H, ..., Taipale J, Selivanova G

Cell Death Differ. 19 (12) 1992-2002 [2012-12-00; online 2012-07-14]

Estimating microtubule distributions from 2D immunofluorescence microscopy images reveals differences among human cultured cell lines.

Li J, Shariff A, Wiking M, ..., Rohde GK, Murphy RF

PLoS ONE 7 (11) e50292 [2012-11-28; online 2012-11-28]

Sequence based analysis of U-2973, a cell line established from a double-hit B-cell lymphoma with concurrent MYC and BCL2 rearrangements.

Hooper SD, Jiao X, Sundström E, ..., Sjöblom T, Cavelier L

BMC Res Notes 5 (-) 648 [2012-11-22; online 2012-11-22]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Comprehensive analysis of the genome transcriptome and proteome landscapes of three tumor cell lines.

Akan P, Alexeyenko A, Costea PI, ..., Uhlén M, Lundeberg J

Genome Med 4 (11) 86 [2012-11-18; online 2012-11-18]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Spatial Proteomics

CD99 is a novel prognostic stromal marker in non-small cell lung cancer.

Edlund K, Lindskog C, Saito A, ..., Ostman A, Micke P

Int. J. Cancer 131 (10) 2264-2273 [2012-11-15; online 2012-03-07]

Array and Analysis Facility Tissue Profiling

A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae.

Nookaew I, Papini M, Pornputtapong N, ..., Uhlén M, Nielsen J

Nucleic Acids Res. 40 (20) 10084-10097 [2012-11-01; online 2012-09-12]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Human cord blood derived immature basophils show dual characteristics, expressing both basophil and eosinophil associated proteins.

Grundström J, Reimer JM, Magnusson SE, ..., Wernersson S, Hellman L

PLoS ONE 7 (10) e48308 [2012-10-31; online 2012-10-31]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Secretagogin is expressed in sensory CGRP neurons and in spinal cord of mouse and complements other calcium-binding proteins, with a note on rat and human.

Shi TJ, Xiang Q, Zhang MD, ..., Harkany T, Hökfelt T

Mol Pain 8 (-) 80 [2012-10-29; online 2012-10-29]

Fluorescence Tissue Profiling

Strategy for minimizing between-study variation of large-scale phenotypic experiments using multivariate analysis.

Pinto RC, Gerber L, Eliasson M, Sundberg B, Trygg J

Anal. Chem. 84 (20) 8675-8681 [2012-10-16; online 2012-09-18]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

The Pseudomonas aeruginosa N-acylhomoserine lactone quorum sensing molecules target IQGAP1 and modulate epithelial cell migration.

Karlsson T, Turkina MV, Yakymenko O, Magnusson K, Vikström E

PLoS Pathog. 8 (10) e1002953 [2012-10-11; online 2012-10-11]

Integrated Microscopy Technologies Stockholm [Service]

Proteomic analysis reveals drug accessible cell surface N-glycoproteins of primary and established glioblastoma cell lines.

Bock T, Moest H, Omasits U, ..., Frei K, Wollscheid B

J. Proteome Res. 11 (10) 4885-4893 [2012-10-05; online 2012-08-23]

Gene expression profiles in paired gingival biopsies from periodontitis-affected and healthy tissues revealed by massively parallel sequencing.

Davanian H, Stranneheim H, Båge T, ..., Lundeberg J, Yucel-Lindberg T

PLoS ONE 7 (9) e46440 [2012-09-28; online 2012-09-28]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Comprehensive exploration of the effects of miRNA SNPs on monocyte gene expression.

Greliche N, Zeller T, Wild PS, ..., Blankenberg S, Trégouët DA

PLoS ONE 7 (9) e45863 [2012-09-21; online 2012-09-21]

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

Identification of candidate SNPs for drug induced toxicity from differentially expressed genes in associated tissues.

Hasmats J, Kupershmidt I, Rodríguez-Antona C, ..., Lundeberg J, Green H

Gene 506 (1) 62-68 [2012-09-10; online 2012-07-01]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Global transcriptional response to ISCOM-Matrix adjuvant at the site of administration and in the draining lymph node early after intramuscular injection in pigs.

Ahlberg V, Lövgren Bengtsson K, Wallgren P, Fossum C

Dev. Comp. Immunol. 38 (1) 17-26 [2012-09-00; online 2012-03-20]

MicroRNA-125b down-regulates matrix metallopeptidase 13 and inhibits cutaneous squamous cell carcinoma cell proliferation, migration, and invasion.

Xu N, Zhang L, Meisgen F, ..., Sonkoly E, Pivarcsi A

J. Biol. Chem. 287 (35) 29899-29908 [2012-08-24; online 2012-07-12]

Expression analysis in multiple muscle groups and serum reveals complexity in the microRNA transcriptome of the mdx mouse with implications for therapy.

Roberts TC, Blomberg KE, McClorey G, ..., Smith CI, Wood MJ

Mol Ther Nucleic Acids 1 (-) e39 [2012-08-14; online 2012-08-14]

Platelet-derived growth factor over-expression in retinal progenitors results in abnormal retinal vessel formation.

Edqvist PH, Niklasson M, Vidal-Sanz M, Hallböök F, Forsberg-Nilsson K

PLoS ONE 7 (8) e42488 [2012-08-03; online 2012-08-03]

Loss of cancer drug activity in colon cancer HCT-116 cells during spheroid formation in a new 3-D spheroid cell culture system.

Karlsson H, Fryknäs M, Larsson R, Nygren P

Exp. Cell Res. 318 (13) 1577-1585 [2012-08-01; online 2012-04-11]

Compensatory mutations in agrC partly restore fitness in vitro to peptide deformylase inhibitor-resistant Staphylococcus aureus.

Zorzet A, Andersen JM, Nilsson AI, Møller NF, Andersson DI

J. Antimicrob. Chemother. 67 (8) 1835-1842 [2012-08-00; online 2012-05-12]

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

The novel tyrosine kinase inhibitor AKN-028 has significant antileukemic activity in cell lines and primary cultures of acute myeloid leukemia

Eriksson A, Hermanson M, Wickström M, ..., Parrow V, Höglund M

Blood Cancer J 2 (8) e81 [2012-08-00; online 2012-08-00]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Differential DNA methylation in purified human blood cells: implications for cell lineage and studies on disease susceptibility.

Reinius LE, Acevedo N, Joerink M, ..., Scheynius A, Kere J

PLoS ONE 7 (7) e41361 [2012-07-25; online 2012-07-25]

Profiling cellular protein complexes by proximity ligation with dual tag microarray readout.

Hammond M, Nong RY, Ericsson O, Pardali K, Landegren U

PLoS ONE 7 (7) e40405 [2012-07-10; online 2012-07-10]

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

Antibodies for profiling the human proteome-The Human Protein Atlas as a resource for cancer research.

Asplund A, Edqvist PH, Schwenk JM, Pontén F

Proteomics 12 (13) 2067-2077 [2012-07-00; online 2012-05-25]

Affinity Proteomics Stockholm [Technology development] Tissue Profiling

1012 Synergistic Effects of PI3K or P38 MAPK Inhibition in Combination With Vandetanib Treatment in Glioblastoma Cells

Sooman L, Ekman S, Andersson C, ..., Lennartsson J, Gullbo J

European Journal of Cancer 48 (-) S244 [2012-07-00; online 2012-07-00]

Effects of redox modulation by inhibition of thioredoxin reductase on radiosensitivity and gene expression.

Selenius M, Hedman M, Brodin D, ..., Björnstedt M, Fernandes AP

J. Cell. Mol. Med. 16 (7) 1593-1605 [2012-07-00; online 2011-10-19]

Intercellular variation in signaling through the TGF-β pathway and its relation to cell density and cell cycle phase.

Zieba A, Pardali K, Söderberg O, ..., Heldin CH, Landegren U

Mol. Cell Proteomics 11 (7) M111.013482 [2012-07-00; online 2012-03-24]

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

Local contamination in relation to population genetic diversity and resilience of an arctic marine amphipod.

Bach L, Dahllöf I

Aquat. Toxicol. 114-115 (-) 58-66 [2012-06-15; online 2012-03-17]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Accelerated proliferation and differential global gene expression in pancreatic islets of five-week-old heterozygous Men1 mice: Men1 is a haploinsufficient suppressor.

Lejonklou MH, Barbu A, Stålberg P, Skogseid B

Endocrinology 153 (6) 2588-2598 [2012-06-00; online 2012-04-12]

Digital gene expression profiling of primary acute lymphoblastic leukemia cells.

Nordlund J, Kiialainen A, Karlberg O, ..., Lönnerholm G, Syvänen AC

Leukemia 26 (6) 1218-1227 [2012-06-00; online 2011-12-16]

Array and Analysis Facility NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Classification of Inhibitors of Hepatic Organic Anion Transporting Polypeptides (OATPs): Influence of Protein Expression on Drug–Drug Interactions

Karlgren M, Vildhede A, Norinder U, ..., Haglund U, Artursson P

J. Med. Chem. 55 (10) 4740-4763 [2012-05-24; online 2012-05-15]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Novel pancreatic beta cell-specific proteins: antibody-based proteomics for identification of new biomarker candidates.

Lindskog C, Korsgren O, Pontén F, ..., Johansson L, Danielsson A

J Proteomics 75 (9) 2611-2620 [2012-05-17; online 2012-04-03]

GABA-A channel subunit expression in human glioma correlates with tumor histology and clinical outcome.

Smits A, Jin Z, Elsir T, ..., Aronica E, Birnir B

PLoS ONE 7 (5) e37041 [2012-05-17; online 2012-05-17]

A genome-wide approach accounting for body mass index identifies genetic variants influencing fasting glycemic traits and insulin resistance.

Manning AK, Hivert MF, Scott RA, ..., Meigs JB, Langenberg C

Nat. Genet. 44 (6) 659-669 [2012-05-13; online 2012-05-13]

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

Multimodel pathway enrichment methods for functional evaluation of expression regulation.

Kirik U, Cifani P, Albrekt AS, ..., Heyden A, Levander F

J. Proteome Res. 11 (5) 2955-2967 [2012-05-04; online 2012-04-05]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

A comprehensive analysis of human gene expression profiles identifies stromal immunoglobulin κ C as a compatible prognostic marker in human solid tumors.

Schmidt M, Hellwig B, Hammad S, ..., Rahnenführer J, Hengstler JG

Clin. Cancer Res. 18 (9) 2695-2703 [2012-05-01; online 2012-02-22]

Transgenerational effects of early experience on behavioral, hormonal and gene expression responses to acute stress in the precocial chicken.

Goerlich VC, Nätt D, Elfwing M, Macdonald B, Jensen P

Horm Behav 61 (5) 711-718 [2012-05-00; online 2012-04-03]

Common SNPs explain some of the variation in the personality dimensions of neuroticism and extraversion.

Vinkhuyzen AA, Pedersen NL, Yang J, ..., Visscher PM, Wray NR

Transl Psychiatry 2 (-) e102 [2012-04-17; online 2012-04-17]

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

DNA methylation analysis of bone marrow cells at diagnosis of acute lymphoblastic leukemia and at remission.

Nordlund J, Milani L, Lundmark A, Lönnerholm G, Syvänen AC

PLoS ONE 7 (4) e34513 [2012-04-06; online 2012-04-06]

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

Proteinase production in Pseudomonas fluorescens ON2 is affected by carbon sources and allows surface-attached but not planktonic cells to utilize protein for growth in lake water.

Nicolaisen MH, Worm J, Jørgensen NOG, Middelboe M, Nybroe O

FEMS Microbiol. Ecol. 80 (1) 168-178 [2012-04-00; online 2012-01-10]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Tumor-mast cell interactions: induction of pro-tumorigenic genes and anti-tumorigenic 4-1BB in MCs in response to Lewis Lung Carcinoma.

Wensman H, Kamgari N, Johansson A, ..., Rönnberg E, Pejler G

Mol. Immunol. 50 (4) 210-219 [2012-04-00; online 2012-02-22]

Mantle cell lymphoma displays a homogenous methylation profile: a comparative analysis with chronic lymphocytic leukemia.

Halldórsdóttir AM, Kanduri M, Marincevic M, ..., Ehrencrona H, Rosenquist R

Am. J. Hematol. 87 (4) 361-367 [2012-04-00; online 2012-03-01]

Array and Analysis Facility NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

The transcriptome of the adenovirus infected cell.

Zhao H, Dahlö M, Isaksson A, Syvänen AC, Pettersson U

Virology 424 (2) 115-128 [2012-03-15; online 2012-01-13]

Array and Analysis Facility NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Can silencing of transposons contribute to variation in effector gene expression in Phytophthora infestans?

Whisson S, Vetukuri R, Avrova A, Dixelius C

Mob Genet Elements 2 (2) 110-114 [2012-03-01; online 2012-08-31]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

A Protein Epitope Signature Tag (PrEST) library allows SILAC-based absolute quantification and multiplexed determination of protein copy numbers in cell lines.

Zeiler M, Straube WL, Lundberg E, Uhlen M, Mann M

Mol. Cell Proteomics 11 (3) O111.009613 [2012-03-00; online 2011-10-04]

Signaling pathways involved in the regulation of TNFα-induced toll-like receptor 2 expression in human gingival fibroblasts.

Davanian H, Båge T, Lindberg J, ..., Sällberg Chen M, Yucel-Lindberg T

Cytokine 57 (3) 406-416 [2012-03-00; online 2012-01-10]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Oral contraceptive and progestin-only use correlates to tissue tumor marker expression in women with cervical intraepithelial neoplasia.

Samir R, Asplund A, Tot T, Pekar G, Hellberg D

Contraception 85 (3) 288-293 [2012-03-00; online 2011-11-10]

Combined chromatin and expression analysis reveals specific regulatory mechanisms within cytokine genes in the macrophage early immune response.

Iglesias MJ, Jesus Iglesias M, Reilly SJ, ..., Hamsten A, Odeberg J

PLoS ONE 7 (2) e32306 [2012-02-27; online 2012-02-27]

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

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

Forsberg LA, Rasi C, Razzaghian HR, ..., Absher D, Dumanski JP

Am. J. Hum. Genet. 90 (2) 217-228 [2012-02-10; online 2012-02-07]

Heritable genome-wide variation of gene expression and promoter methylation between wild and domesticated chickens.

Nätt D, Rubin CJ, Wright D, ..., Andersson L, Jensen P

BMC Genomics 13 (-) 59 [2012-02-04; online 2012-02-04]

Association of TMEM18 variants with BMI and waist circumference in children and correlation of mRNA expression in the PFC with body weight in rats.

Rask-Andersen M, Jacobsson JA, Moschonis G, ..., Fredriksson R, Schiöth HB

Eur. J. Hum. Genet. 20 (2) 192-197 [2012-02-00; online 2011-09-29]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Sequential closure of the cytoplasm and then the periplasm during cell division in Escherichia coli.

Skoog K, Söderström B, Widengren J, von Heijne G, Daley DO

J. Bacteriol. 194 (3) 584-586 [2012-02-00; online 2011-11-22]

Integrated Microscopy Technologies Stockholm [Collaborative]

BCL2L1 has a functional role in colorectal cancer and its protein expression is associated with chromosome 20q gain.

Sillars-Hardebol AH, Carvalho B, Beliën JA, ..., Fijneman RJ, Meijer GA

J. Pathol. 226 (3) 442-450 [2012-02-00; online 2011-10-20]

A strand specific high resolution normalization method for chip-sequencing data employing multiple experimental control measurements.

Enroth S, Andersson CR, Andersson R, ..., Gustafsson MG, Komorowski J

Algorithms Mol Biol 7 (1) 2 [2012-01-16; online 2012-01-16]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Long-range DNA looping and gene expression analyses identify DEXI as an autoimmune disease candidate gene.

Davison LJ, Wallace C, Cooper JD, ..., Syvannen AC, Tennstedt S

Hum. Mol. Genet. 21 (2) 322-333 [2012-01-15; online 2011-10-13]

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

Differential expression patterns of conserved miRNAs and isomiRs during Atlantic halibut development.

Bizuayehu TT, Lanes CFC, Furmanek T, ..., Johansen SD, Babiak I

BMC Genomics 13 (-) 11 [2012-01-10; online 2012-01-10]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

siRNA silencing of proteasome maturation protein (POMP) activates the unfolded protein response and constitutes a model for KLICK genodermatosis.

Dahlqvist J, Törmä H, Badhai J, Dahl N

PLoS ONE 7 (1) e29471 [2012-01-03; online 2012-01-03]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Lymphoblastoid cell line with B1 cell characteristics established from a chronic lymphocytic leukemia clone by in vitro EBV infection.

Rosén A, Bergh AC, Gogok P, ..., Rosenquist R, Klein E

Oncoimmunology 1 (1) 18-27 [2012-01-01; online 2012-06-22]

Mechanisms underlying the sparing of masticatory versus limb muscle function in an experimental critical illness model.

Aare S, Ochala J, Norman HS, ..., Hoffman EP, Larsson L

Physiol. Genomics 43 (24) 1334-1350 [2011-12-16; online 2011-10-20]

Muscle wasting and the temporal gene expression pattern in a novel rat intensive care unit model.

Llano-Diez M, Gustafson AM, Olsson C, Goransson H, Larsson L

BMC Genomics 12 (-) 602 [2011-12-13; online 2011-12-13]

High nuclear RBM3 expression is associated with an improved prognosis in colorectal cancer.

Hjelm B, Brennan DJ, Zendehrokh N, ..., Jirström K, Uhlen M

Proteomics Clin Appl 5 (11-12) 624-635 [2011-12-00; online 2011-10-01]

Salt-inducible kinase 1 influences Na(+),K(+)-ATPase activity in vascular smooth muscle cells and associates with variations in blood pressure.

Popov S, Silveira A, Wågsäter D, ..., Melander O, Bertorello AM

J. Hypertens. 29 (12) 2395-2403 [2011-12-00; online 2011-11-03]

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

Prognostic DNA methylation patterns in cytogenetically normal acute myeloid leukemia are predefined by stem cell chromatin marks.

Deneberg S, Guardiola P, Lennartsson A, ..., Döhner K, Lehmann S

Blood 118 (20) 5573-5582 [2011-11-17; online 2011-10-01]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Gene copy number aberrations are associated with survival in histologic subgroups of non-small cell lung cancer.

Micke P, Edlund K, Holmberg L, ..., Isaksson A, Botling J

J Thorac Oncol 6 (11) 1833-1840 [2011-11-00; online 2011-10-21]

The Human Protein Atlas as a proteomic resource for biomarker discovery.

Pontén F, Schwenk JM, Asplund A, Edqvist PH

J. Intern. Med. 270 (5) 428-446 [2011-11-00; online 2011-08-03]

Affinity Proteomics Stockholm [Technology development] Tissue Profiling

Deep resequencing of GWAS loci identifies independent rare variants associated with inflammatory bowel disease.

Rivas MA, Beaudoin M, Gardet A, ..., Xavier RJ, Daly MJ

Nat. Genet. 43 (11) 1066-1073 [2011-10-09; online 2011-10-09]

High-risk HPV infection and CIN grade correlates to the expression of c-myc, CD4+, FHIT, E-cadherin, Ki-67, and p16INK4a.

Samir R, Asplund A, Tot T, Pekar G, Hellberg D

J Low Genit Tract Dis 15 (4) 280-286 [2011-10-00; online 2011-05-12]

Early transcriptional regulation by C-peptide in freshly isolated rat proximal tubular cells.

Lindahl E, Nordquist L, Müller P, ..., Palm F, Jörnvall H

Diabetes Metab. Res. Rev. 27 (7) 697-704 [2011-10-00; online 2011-05-28]

The Lin28/let-7 axis regulates glucose metabolism.

Zhu H, Shyh-Chang N, Segrè AV, ..., Altshuler D, Daley GQ

Cell 147 (1) 81-94 [2011-09-30; online 2011-10-04]

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

High RBM3 expression in prostate cancer independently predicts a reduced risk of biochemical recurrence and disease progression.

Jonsson L, Gaber A, Ulmert D, ..., Bjartell A, Jirström K

Diagn Pathol 6 (-) 91 [2011-09-28; online 2011-09-28]

Engineering GST M2-2 for high activity with indene 1,2-oxide and indication of an H-site residue sustaining catalytic promiscuity.

Norrgård MA, Mannervik B

J. Mol. Biol. 412 (1) 111-120 [2011-09-09; online 2011-08-09]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Large-scale protein profiling in human cell lines using antibody-based proteomics.

Fagerberg L, Strömberg S, El-Obeid A, ..., Ponten F, Asplund A

J. Proteome Res. 10 (9) 4066-4075 [2011-09-02; online 2011-07-06]

Changes in the acetogenic population in a mesophilic anaerobic digester in response to increasing ammonia concentration.

Westerholm M, Müller B, Arthurson V, Schnürer A

Microbes Environ. 26 (4) 347-353 [2011-08-24; online 2011-08-24]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Identification of cis- and trans-acting genetic variants explaining up to half the variation in circulating vascular endothelial growth factor levels.

Debette S, Visvikis-Siest S, Chen MH, ..., Vasan RS, Seshadri S

Circ. Res. 109 (5) 554-563 [2011-08-19; online 2011-07-16]

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

Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis.

International Multiple Sclerosis Genetics Consortium N, Wellcome Trust Case Control Consortium 2 N, Sawcer S, ..., Donnelly P, Compston A

Nature 476 (7359) 214-219 [2011-08-10; online 2011-08-10]

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

Mapping the subcellular protein distribution in three human cell lines.

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

J. Proteome Res. 10 (8) 3766-3777 [2011-08-05; online 2011-06-17]

Correlation between LRIG1 and LRIG2 expressions and expression of 11 tumor markers, with special reference to tumor suppressors, in CIN and normal cervical epithelium.

Lindström AK, Asplund A, Hellberg D

Gynecol. Oncol. 122 (2) 372-376 [2011-08-00; online 2011-06-03]

Low RBM3 protein expression correlates with tumour progression and poor prognosis in malignant melanoma: an analysis of 215 cases from the Malmö Diet and Cancer Study.

Jonsson L, Bergman J, Nodin B, ..., Uhlén M, Jirström K

J Transl Med 9 (-) 114 [2011-07-21; online 2011-07-21]

The use of genome-wide eQTL associations in lymphoblastoid cell lines to identify novel genetic pathways involved in complex traits.

Min JL, Taylor JM, Richards JB, ..., Spector TD, Zondervan KT

PLoS ONE 6 (7) e22070 [2011-07-15; online 2011-07-15]

Replication and explorations of high-order epistasis using a large advanced intercross line pedigree.

Pettersson M, Besnier F, Siegel PB, Carlborg O

PLoS Genet. 7 (7) e1002180 [2011-07-00; online 2011-07-21]

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

Specific syndecan-1 domains regulate mesenchymal tumor cell adhesion, motility and migration.

Zong F, Fthenou E, Mundt F, ..., Hjerpe A, Dobra K

PLoS ONE 6 (6) e14816 [2011-06-23; online 2011-06-23]

(R,S)-dichlorprop herbicide in agricultural soil induces proliferation and expression of multiple dioxygenase-encoding genes in the indigenous microbial community.

Paulin MM, Nicolaisen MH, Sørensen J

Environ. Microbiol. 13 (6) 1513-1523 [2011-06-00; online 2011-03-23]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Genetic association and gene expression analysis identify FGFR1 as a new susceptibility gene for human obesity.

Jiao H, Arner P, Dickson SL, ..., Clement K, Dahlman I

J. Clin. Endocrinol. Metab. 96 (6) E962-E966 [2011-06-00; online 2011-03-25]

Bioinformatics and Expression Analysis (BEA) Mutation Analysis Facility (MAF) NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Feather pecking behavior in laying hens: hypothalamic gene expression in birds performing and receiving pecks.

Brunberg E, Jensen P, Isaksson A, Keeling L

Poult. Sci. 90 (6) 1145-1152 [2011-06-00; online 2011-05-21]

Cytochrome P450 1A, 1B, and 1C mRNA induction patterns in three-spined stickleback exposed to a transient and a persistent inducer.

Gao K, Brandt I, Goldstone JV, Jönsson ME

Comp. Biochem. Physiol. C Toxicol. Pharmacol. 154 (1) 42-55 [2011-06-00; online 2011-03-01]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Cys-X scanning for expansion of active-site residues and modulation of catalytic functions in a glutathione transferase.

Norrgård MA, Hellman U, Mannervik B

J. Biol. Chem. 286 (19) 16871-16878 [2011-05-13; online 2011-04-02]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Experimental evidence supports a sex-specific selective sieve in mitochondrial genome evolution.

Innocenti P, Morrow EH, Dowling DK

Science 332 (6031) 845-848 [2011-05-13; online 2011-05-14]

Melanoma cells produce multiple laminin isoforms and strongly migrate on α5 laminin(s) via several integrin receptors.

Oikawa Y, Hansson J, Sasaki T, ..., Tryggvason K, Patarroyo M

Exp. Cell Res. 317 (8) 1119-1133 [2011-05-01; online 2011-01-05]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Characterization of NPY Y2 receptor protein expression in the mouse brain. II. Coexistence with NPY, the Y1 receptor, and other neurotransmitter-related molecules.

Stanić D, Mulder J, Watanabe M, Hökfelt T

J. Comp. Neurol. 519 (7) 1219-1257 [2011-05-01; online 2011-04-01]

Fluorescence Tissue Profiling

Molecular characterization of acquired tolerance of tumor cells to picropodophyllin (PPP).

Hashemi J, Worrall C, Vasilcanu D, ..., Larsson O, Larsson C

PLoS ONE 6 (3) e14757 [2011-03-14; online 2011-03-14]

Bioinformatic tools for using whole genome sequencing as a rapid high resolution diagnostic typing tool when tracing bioterror organisms in the food and feed chain.

Segerman B, De Medici D, Ehling Schulz M, ..., Van Rotterdam B, Knutsson R

Int. J. Food Microbiol. 145 Suppl 1 (-) S167-S176 [2011-03-01; online 2010-09-10]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Expression of 5,8-LDS of Aspergillus fumigatus and its dioxygenase domain. A comparison with 7,8-LDS, 10-dioxygenase, and cyclooxygenase.

Hoffmann I, Jernerén F, Garscha U, Oliw EH

Arch. Biochem. Biophys. 506 (2) 216-222 [2011-02-15; online 2010-12-07]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

High-resolution genomic screening in mantle cell lymphoma--specific changes correlate with genomic complexity, the proliferation signature and survival.

Halldórsdóttir AM, Sander B, Göransson H, ..., Rosenquist R, Ehrencrona H

Genes Chromosomes Cancer 50 (2) 113-121 [2011-02-00; online 2010-12-01]

Array and Analysis Facility NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Tumor-specific HMG-CoA reductase expression in primary premenopausal breast cancer predicts response to tamoxifen.

Brennan DJ, Laursen H, O'Connor DP, ..., Rydén L, Jirström K

Breast Cancer Res. 13 (1) R12 [2011-01-31; online 2011-01-31]

Vitamin D receptor genotypes, ultraviolet radiation exposure, and risk of non-Hodgkin lymphoma.

Smedby KE, Eloranta S, Duvefelt K, ..., Hjalgrim H, Chang ET

Am. J. Epidemiol. 173 (1) 48-54 [2011-01-01; online 2010-11-16]

Meta-analysis of the association between variants in SORL1 and Alzheimer disease.

Reitz C, Cheng R, Rogaeva E, ..., Mayeux R, Genetic and Environmental Risk in Alzheimer Disease 1 Consortium

Arch. Neurol. 68 (1) 99-106 [2011-01-00; online 2011-01-12]

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

Targeted resequencing of candidate genes using selector probes.

Johansson H, Isaksson M, Sörqvist EF, ..., Ericsson O, Nilsson M

Nucleic Acids Res. 39 (2) e8 [2011-01-00; online 2010-11-08]

Array and Analysis Facility NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Mechanisms of blast induced brain injuries, experimental studies in rats.

Risling M, Plantman S, Angeria M, ..., Arborelius U, Davidsson J

Neuroimage 54 Suppl 1 (-) S89-S97 [2011-01-00; online 2010-05-25]

Defining the transcriptome and proteome in three functionally different human cell lines.

Lundberg E, Fagerberg L, Klevebring D, ..., Mann M, Uhlen M

Mol. Syst. Biol. 6 (-) 450 [2010-12-21; online 2010-12-24]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Spatial Proteomics

Analysis of transcript and protein overlap in a human osteosarcoma cell line.

Klevebring D, Fagerberg L, Lundberg E, ..., Uhlén M, Lundeberg J

BMC Genomics 11 (-) 684 [2010-12-02; online 2010-12-02]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure Spatial Proteomics

Distinct gene expression profiles in subsets of chronic lymphocytic leukemia expressing stereotyped IGHV4-34 B-cell receptors.

Marincevic M, Mansouri M, Kanduri M, ..., Stamatopoulos K, Rosenquist R

Haematologica 95 (12) 2072-2079 [2010-12-00; online 2010-08-31]

Array and Analysis Facility NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

SOX10 expression in superficial spreading and nodular malignant melanomas.

Agnarsdóttir M, Sooman L, Bolander A, ..., Uhlen M, Hedstrand H

Melanoma Res. 20 (6) 468-478 [2010-12-00; online 2010-10-05]

SNP detection and prediction of variability between chicken lines using genome resequencing of DNA pools.

Marklund S, Carlborg O

BMC Genomics 11 (-) 665 [2010-11-25; online 2010-11-25]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Gene expression profiling and chromatin immunoprecipitation identify DBN1, SETMAR and HIG2 as direct targets of SOX11 in mantle cell lymphoma.

Wang X, Björklund S, Wasik AM, ..., Christensson B, Sander B

PLoS ONE 5 (11) e14085 [2010-11-22; online 2010-11-22]

An exploratory model for G x E interaction on hippocampal volume in schizophrenia; obstetric complications and hypoxia-related genes.

Haukvik UK, Saetre P, McNeil T, ..., Jönsson EG, Agartz I

Prog. Neuropsychopharmacol. Biol. Psychiatry 34 (7) 1259-1265 [2010-10-01; online 2010-07-20]

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

Brain gene expression in relation to fearfulness in female red junglefowl (Gallus gallus).

Jöngren M, Westander J, Nätt D, Jensen P

Genes Brain Behav. 9 (7) 751-758 [2010-10-00; online 2010-07-06]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Somatic mosaicism for chromosome X and Y aneuploidies in monozygotic twins heterozygous for sickle cell disease mutation.

Razzaghian HR, Shahi MH, Forsberg LA, ..., Westerman MP, Dumanski JP

Am. J. Med. Genet. A 152A (10) 2595-2598 [2010-10-00; online 2010-08-25]

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

A trans-acting locus regulates an anti-viral expression network and type 1 diabetes risk.

Heinig M, Petretto E, Wallace C, ..., Hubner N, Cook SA

Nature 467 (7314) 460-464 [2010-09-23; online 2010-09-10]

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

Profiling protein expression and interactions: proximity ligation as a tool for personalized medicine.

Blokzijl A, Friedman M, Pontén F, Landegren U

J. Intern. Med. 268 (3) 232-245 [2010-09-00; online 2010-08-11]

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

Expression of the RNA-binding protein RBM3 is associated with a favourable prognosis and cisplatin sensitivity in epithelial ovarian cancer.

Ehlén A, Brennan DJ, Nodin B, ..., Pontén F, Jirström K

J Transl Med 8 (-) 78 [2010-08-20; online 2010-08-20]

The role of IL-1beta in reduced IL-7 production by stromal and epithelial cells: a model for impaired T-cell numbers in the gut during HIV-1 infection.

Thang PH, Ruffin N, Brodin D, ..., Vivar N, Chiodi F

J. Intern. Med. 268 (2) 181-193 [2010-08-00; online 2010-05-26]

Association of genetic risk variants with expression of proximal genes identifies novel susceptibility genes for cardiovascular disease.

Folkersen L, van't Hooft F, Chernogubova E, ..., Eriksson P, BiKE and ASAP study groups

Circ Cardiovasc Genet 3 (4) 365-373 [2010-08-00; online 2010-06-22]

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

Induction patterns of new CYP1 genes in environmentally exposed rainbow trout.

Jönsson ME, Gao K, Olsson JA, Goldstone JV, Brandt I

Aquat. Toxicol. 98 (4) 311-321 [2010-07-15; online 2010-04-08]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Topoisomerase I regulates open chromatin and controls gene expression in vivo.

Durand-Dubief M, Persson J, Norman U, Hartsuiker E, Ekwall K

EMBO J. 29 (13) 2126-2134 [2010-07-07; online 2010-06-08]

Subcellular distribution and expression of prenylated Rab acceptor 1 domain family, member 2 (PRAF2) in malignant glioma: Influence on cell survival and migration.

Borsics T, Lundberg E, Geerts D, ..., Wester K, Bachmann AS

Cancer Sci. 101 (7) 1624-1631 [2010-07-00; online 2010-03-19]

Gene expression analysis in hypoplastic lungs in the nitrofen model of congenital diaphragmatic hernia.

Burgos CM, Uggla AR, Fagerström-Billai F, ..., Frenckner B, Nord M

J. Pediatr. Surg. 45 (7) 1445-1454 [2010-07-00; online 2010-07-20]

Tissue factor pathway inhibitor-2 is induced by fluid shear stress in vascular smooth muscle cells and affects cell proliferation and survival.

Ekstrand J, Razuvaev A, Folkersen L, Roy J, Hedin U

J. Vasc. Surg. 52 (1) 167-175 [2010-07-00; online 2010-06-12]

HIV-1 exposed uninfected men who have sex with men have increased levels of salivary CC-chemokines associated with sexual behavior.

Hasselrot K, Bratt G, Duvefelt K, ..., Sandström E, Broliden K

AIDS 24 (10) 1569-1575 [2010-06-19; online 2010-06-16]

Analysis of oestrogen regulation of alpha-, beta- and gamma-secretase gene and protein expression in cultured human neuronal and glial cells.

Nord LC, Sundqvist J, Andersson E, Fried G

Neurodegener Dis 7 (6) 349-364 [2010-06-04; online 2010-06-04]

Antibody-based proteomics for discovery and exploration of proteins expressed in pancreatic islets.

PubMed

Lindskog C, Asplund A, Engkvist M, ..., Korsgren O, Ponten F

Discov Med 9 (49) 565-578 [2010-06-00; online 2010-07-01]

Tissue tumor marker expression in smokers, including serum cotinine concentrations, in women with cervical intraepithelial neoplasia or normal squamous cervical epithelium.

Samir R, Asplund A, Tot T, Pekar G, Hellberg D

Am. J. Obstet. Gynecol. 202 (6) 579.e1-579.e7 [2010-06-00; online 2010-01-12]

Chd1 remodelers maintain open chromatin and regulate the epigenetics of differentiation.

Persson J, Ekwall K

Exp. Cell Res. 316 (8) 1316-1323 [2010-05-01; online 2010-03-10]

Abundance and expression of enantioselective rdpA and sdpA dioxygenase genes during degradation of the racemic herbicide (R,S)-2-(2,4-dichlorophenoxy)propionate in soil.

Paulin MM, Nicolaisen MH, Sørensen J

Appl. Environ. Microbiol. 76 (9) 2873-2883 [2010-05-00; online 2010-03-23]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

The impact of RNA standardization and heterogeneous gene expression on the results of cDNA array of human breast carcinoma.

Khoshnoud R, He Q, Sylván M, ..., Rutqvist L, Skog S

Int. J. Mol. Med. 25 (5) 735-741 [2010-05-00; online 2010-04-08]

Increased serum progesterone and estradiol correlate to increased COX-2 tissue expression in cervical intraepithelial neoplasia.

PubMed

Samir R, Tot T, Asplund A, Pekar G, Hellberg D

Anticancer Res. 30 (4) 1217-1222 [2010-04-00; online 2010-06-10]

ELMOD2, a candidate gene for idiopathic pulmonary fibrosis, regulates antiviral responses.

Pulkkinen V, Bruce S, Rintahaka J, ..., Matikainen S, Kere J

FASEB J. 24 (4) 1167-1177 [2010-04-00; online 2009-12-08]

Novel associations of multiple genetic loci with plasma levels of factor VII, factor VIII, and von Willebrand factor: The CHARGE (Cohorts for Heart and Aging Research in Genome Epidemiology) Consortium.

Smith NL, Chen MH, Dehghan A, ..., Tang W, O'Donnell CJ

Circulation 121 (12) 1382-1392 [2010-03-30; online 2010-03-17]

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

Whole-genome resequencing reveals loci under selection during chicken domestication.

Rubin C, Zody MC, Eriksson J, ..., Lindblad-Toh K, Andersson L

Nature 464 (7288) 587-591 [2010-03-25; online 2010-03-12]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

In-depth transcriptome analysis reveals novel TARs and prevalent antisense transcription in human cell lines.

Klevebring D, Bjursell M, Emanuelsson O, Lundeberg J

PLoS ONE 5 (3) e9762 [2010-03-25; online 2010-03-25]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

The impact of tissue fixatives on morphology and antibody-based protein profiling in tissues and cells.

Paavilainen L, Edvinsson A, Asplund A, ..., Pontén F, Wester K

J. Histochem. Cytochem. 58 (3) 237-246 [2010-03-00; online 2009-11-11]

Appearance of Cxcl10-expressing cell clusters is common for traumatic brain injury and neurodegenerative disorders.

Israelsson C, Bengtsson H, Lobell A, ..., Hillered L, Ebendal T

Eur. J. Neurosci. 31 (5) 852-863 [2010-03-00; online 2010-04-09]

Infection of mast cells with live streptococci causes a toll-like receptor 2- and cell-cell contact-dependent cytokine and chemokine response.

Rönnberg E, Guss B, Pejler G

Infect. Immun. 78 (2) 854-864 [2010-02-00; online 2009-11-26]

Genetic variation in GIPR influences the glucose and insulin responses to an oral glucose challenge.

Saxena R, Hivert MF, Langenberg C, ..., Wareham NJ, Watanabe RM

Nat. Genet. 42 (2) 142-148 [2010-02-00; online 2010-01-19]

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

Global gene expression analysis of rodent motor neurons following spinal cord injury associates molecular mechanisms with development of postinjury spasticity.

Wienecke J, Westerdahl AC, Hultborn H, Kiehn O, Ryge J

J. Neurophysiol. 103 (2) 761-778 [2010-02-00; online 2009-11-27]

Connective tissue growth factor is expressed in malignant cells of Hodgkin lymphoma but not in other mature B-cell lymphomas.

Birgersdotter A, Baumforth KR, Wei W, ..., Porwit A, Ernberg I

Am. J. Clin. Pathol. 133 (2) 271-280 [2010-02-00; online 2010-01-23]

Genetic variants and disease-associated factors contribute to enhanced interferon regulatory factor 5 expression in blood cells of patients with systemic lupus erythematosus.

Feng D, Stone RC, Eloranta ML, ..., Rönnblom L, Barnes BJ

Arthritis Rheum. 62 (2) 562-573 [2010-02-00; online 2010-01-30]

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

Characterization of the cytotoxic properties of the benzimidazole fungicides, benomyl and carbendazim, in human tumour cell lines and primary cultures of patient tumour cells.

Laryea D, Gullbo J, Isaksson A, Larsson R, Nygren P

Anticancer Drugs 21 (1) 33-42 [2010-01-00; online 2009-09-30]

Tissue-Specific Protein Expression in Human Cells, Tissues and Organs

Marcus G, Oksvold P, Pontén F, Uhlén M

JPB 03 (10) - [2010-00-00; online 2010-00-00]

Relationship between antibiotic feeding in animals and emergence of bacterial resistance in man.

Pohl P

J. Antimicrob. Chemother. 3 Suppl C (-) 67-72 [1977-11-00; online 1977-11-01]