Sci Rep

ISSN	2045-2322
ISSN-L	2045-2322
IUID	e3ecf5f7f29840a1a64a01c388850719
Modified	2020-11-27T13:14:08.788Z
Created	2017-05-09T09:12:29.885Z

PubMed DOI Crossref

Sirtuin inhibitors reduce intracellular growth of M. tuberculosis in human macrophages via modulation of host cell immunity.

Kalsum S, Akber M, Loreti MG, ..., Lerm M, Brighenti S

Sci Rep 14 (1) 28150 [2024-11-15; online 2024-11-15]

Chemical Biology Consortium Sweden (CBCS) [Service]

PubMed DOI Crossref

Impact of thermal seed treatment on spermosphere microbiome, metabolome and viability of winter wheat.

Karlsson ME, Forsberg G, Rosberg AK, Thaning C, Alsanius B

Sci Rep 14 (1) 27197 [2024-11-08; online 2024-11-08]

Swedish Metabolomics Centre (SMC) [Service]

PubMed DOI Crossref

Autoantibodies to protein S may explain rare cases of coagulopathy following COVID-19 vaccination.

Yalcinkaya A, Cavalli M, Aranda-Guillén M, ..., Hallberg P, Landegren N

Sci Rep 14 (1) 24512 [2024-10-18; online 2024-10-18]

Autoimmunity and Serology Profiling [Service]

PubMed DOI Crossref

Estrogen-stimulated uropathogenic E. coli mediate enhanced neutrophil responses.

Pettersson C, Wu R, Demirel I

Sci Rep 14 (1) 23030 [2024-10-03; online 2024-10-03]

Affinity Proteomics Uppsala [Service]

PubMed DOI Crossref

Cancer associated variant enrichment CAVE, a gene agnostic approach to identify low burden variants in chronic lymphocytic leukemia.

Yaacov A, Lazarian G, Pandzic T, ..., Rosenberg S, Soussi T

Sci Rep 14 (1) 21962 [2024-09-20; online 2024-09-20]

Clinical Genomics Uppsala [Collaborative]

PubMed DOI Crossref

Monitoring SARS-CoV-2 IgA, IgM and IgG antibodies in dried blood and saliva samples using antibody proximity extension assays (AbPEA).

Wang M, Kamali-Moghaddam M, Löf L, ..., Landegren U, Zhao H

Sci Rep 14 (1) 21655 [2024-09-17; online 2024-09-17]

Affinity Proteomics Uppsala [Technology development]

PubMed DOI Crossref

Blood based metabolic markers of glioma from pre-diagnosis to surgery.

Löding S, Antti H, Sjöberg RL, Melin B, Björkblom B

Sci Rep 14 (1) 20680 [2024-09-05; online 2024-09-05]

Swedish Metabolomics Centre (SMC) [Service]

PubMed DOI Crossref

The involvement of cyclotides in the heavy metal tolerance of Viola spp.

Sychta K, Słomka A, Shariatgorji R, ..., Göransson U, Slazak B

Sci Rep 14 (1) 19306 [2024-08-20; online 2024-08-20]

Spatial Mass Spectrometry [Collaborative]

PubMed DOI Crossref

Decrease due to pollution in the rhizosphere microbial diversity can be amended by supplementation from adapted plants of another species.

Fetsiukh A, Pall T, Timmusk S

Sci Rep 14 (1) 18806 [2024-08-13; online 2024-08-13]

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

PubMed DOI Crossref

Systematic review and feasibility study on pre-analytical factors and genomic analyses on archival formalin-fixed paraffin-embedded breast cancer tissue.

Salgkamis D, Sifakis EG, Agartz S, ..., Matikas A, Zerdes I

Sci Rep 14 (1) 18275 [2024-08-06; online 2024-08-06]

Clinical Genomics Stockholm [Service]

PubMed DOI Crossref

Exploring the interplay between antiretroviral therapy and the gut-oral microbiome axis in people living with HIV.

Narayanan A, Kieri O, Vesterbacka J, ..., Ray S, Nowak P

Sci Rep 14 (1) 17820 [2024-08-01; online 2024-08-01]

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

PubMed DOI Crossref

The interaction of genetics and physical activity in the pathogenesis of metabolic dysfunction associated liver disease.

Frostdahl H, Ahmad N, Hammar U, ..., Brooke HL, Ahmad S

Sci Rep 14 (1) 17817 [2024-08-01; online 2024-08-01]

Bioinformatics Support for Computational Resources [Service]

PubMed DOI Crossref

The rate of W chromosome degeneration across multiple avian neo-sex chromosomes.

Sigeman H, Downing PA, Zhang H, Hansson B

Sci Rep 14 (1) 16548 [2024-07-17; online 2024-07-17]

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

PubMed DOI Crossref

Evaluating regression and probabilistic methods for ECG-based electrolyte prediction.

von Bachmann P, Gedon D, Gustafsson FK, ..., Sundström J, Schön TB

Sci Rep 14 (1) 15273 [2024-07-03; online 2024-07-03]

Bioinformatics Support for Computational Resources [Service]

PubMed DOI Crossref

Predicting type 2 diabetes via machine learning integration of multiple omics from human pancreatic islets.

Rönn T, Perfilyev A, Oskolkov N, Ling C

Sci Rep 14 (1) 14637 [2024-06-25; online 2024-06-25]

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

PubMed DOI Crossref

Structures of the Staphylococcus aureus ribosome inhibited by fusidic acid and fusidic acid cyclopentane.

González-López A, Larsson DSD, Koripella RK, ..., Sanyal S, Selmer M

Sci Rep 14 (1) 14253 [2024-06-20; online 2024-06-20]

Cryo-EM [Service]

PubMed DOI Crossref

Hearing loss and its association with the proteome of perilymph, cerebrospinal fluid, and tumor tissue in patients with vestibular schwannoma.

Edvardsson Rasmussen J, Li P, Laurell G, Bergquist J, Eriksson PO

Sci Rep 14 (1) 14118 [2024-06-19; online 2024-06-19]

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

PubMed DOI Crossref

Long-term impact of digital media on brain development in children.

Nivins S, Sauce B, Liebherr M, Judd N, Klingberg T

Sci Rep 14 (1) 13030 [2024-06-06; online 2024-06-06]

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

PubMed DOI Crossref

PIK3CA mutations in endocrine-resistant breast cancer.

Schagerholm C, Robertson S, Toosi H, Sifakis EG, Hartman J

Sci Rep 14 (1) 12542 [2024-05-31; online 2024-05-31]

Clinical Genomics Stockholm [Service]

PubMed DOI Crossref

Quantifying combined effects of colistin and ciprofloxacin against Escherichia coli in an in silico pharmacokinetic-pharmacodynamic model.

Zhao C, Kristoffersson AN, Khan DD, ..., Nielsen EI, Friberg LE

Sci Rep 14 (1) 11706 [2024-05-22; online 2024-05-22]

Bioinformatics Support for Computational Resources [Service]

PubMed DOI Crossref

The Gly82Ser polymorphism in the receptor for advanced glycation endproducts increases the risk for coronary events in the general population.

Grauen Larsen H, Sun J, Sjögren M, ..., Melander O, Schiopu A

Sci Rep 14 (1) 11567 [2024-05-21; online 2024-05-21]

Affinity Proteomics Uppsala [Service]

PubMed DOI Crossref

TMAO enhances TNF-α mediated fibrosis and release of inflammatory mediators from renal fibroblasts.

Stefania K, Ashok KK, Geena PV, Katarina P, Isak D

Sci Rep 14 (1) 9070 [2024-04-20; online 2024-04-20]

Affinity Proteomics Uppsala [Service]

PubMed DOI Crossref

Long-read sequencing and optical mapping generates near T2T assemblies that resolves a centromeric translocation.

Ten Berk de Boer E, Ameur A, Bunikis I, ..., Eisfeldt J, Lindstrand A

Sci Rep 14 (1) 9000 [2024-04-18; online 2024-04-18]

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

PubMed DOI Crossref

Cardiac biopsies reveal differences in transcriptomics between left and right ventricle in patients with or without diagnostic signs of heart failure.

Frisk C, Das S, Eriksson MJ, ..., Linde C, Persson B

Sci Rep 14 (1) 5811 [2024-03-09; online 2024-03-09]

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

PubMed DOI Crossref

Identification of microbial pathogens in Neolithic Scandinavian humans.

Bergfeldt N, Kırdök E, Oskolkov N, ..., Storå J, Götherström A

Sci Rep 14 (1) 5630 [2024-03-07; online 2024-03-07]

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

PubMed DOI Crossref

Population genomic analyses reveal that salinity and geographic isolation drive diversification in a free-living protist.

Rengefors K, Annenkova N, Wallenius J, ..., Kremp A, Ahrén D

Sci Rep 14 (1) 4986 [2024-02-29; online 2024-02-29]

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

PubMed DOI Crossref

Differential gene expression in two consecutive pregnancies between same sex siblings and implications on maternal constraint.

Kallak TK, Serapio S, Visser N, ..., Skalkidou A, Ahlsson F

Sci Rep 14 (1) 4210 [2024-02-20; online 2024-02-20]

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

PubMed DOI Crossref

Ancient reindeer mitogenomes reveal island-hopping colonisation of the Arctic archipelagos.

Hold K, Lord E, Brealey JC, ..., Martin MD, Dussex N

Sci Rep 14 (1) 4143 [2024-02-20; online 2024-02-20]

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

PubMed DOI Crossref

Genetic and environmental contributions to gaze lateralization across social and non-social stimuli in human infants.

Viktorsson C, Portugal AM, Falck-Ytter T

Sci Rep 14 (1) 3668 [2024-02-14; online 2024-02-14]

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

PubMed DOI Crossref

Batrachochytrium dendrobatidis strain affects transcriptomic response in liver but not skin in latitudinal populations of the common toad (Bufo bufo).

Chondrelli N, Kuehn E, Meurling S, ..., Laurila A, Höglund J

Sci Rep 14 (1) 2495 [2024-01-30; online 2024-01-30]

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

PubMed DOI Crossref

Dietary patterns, untargeted metabolite profiles and their association with colorectal cancer risk.

Bodén S, Zheng R, Ribbenstedt A, ..., Van Guelpen B, Brunius C

Sci Rep 14 (1) 2244 [2024-01-26; online 2024-01-26]

Bioinformatics Support for Computational Resources [Service] Chalmers Mass Spectrometry Infrastructure [Collaborative]

PubMed DOI Crossref

Metagenomic analysis of Mesolithic chewed pitch reveals poor oral health among stone age individuals.

Kırdök E, Kashuba N, Damlien H, ..., Aravena A, Götherström A

Sci Rep 13 (1) 22125 [2024-01-18; online 2024-01-18]

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

PubMed DOI Crossref

Elevated circulating adiponectin levels do not prevent anxiety-like behavior in a PCOS-like mouse model.

Samad M, Ek J, Börchers S, ..., Asterholm IW, Benrick A

Sci Rep 14 (1) 563 [2024-01-04; online 2024-01-04]

Glycoproteomics and MS Proteomics [Service]

PubMed DOI Crossref

The functional and molecular impact of triamcinolone acetonide on primary human bone marrow mesenchymal stem cells.

Kumlin M, Ungerstedt J, Cai H, ..., Felländer-Tsai L, Qian H

Sci Rep 13 (1) 21787 [2023-12-08; online 2023-12-08]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

Using trials of caloric restriction and bariatric surgery to explore the effects of body mass index on the circulating proteome.

Goudswaard LJ, Smith ML, Hughes DA, ..., Timpson NJ, Corbin LJ

Sci Rep 13 (1) 21077 [2023-11-29; online 2023-11-29]

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

PubMed DOI Crossref

Selection, characterization and in vivo evaluation of novel CD44v6-targeting antibodies for targeted molecular radiotherapy.

Mortensen ACL, Berglund H, Segerström L, ..., Frejd FY, Nestor M

Sci Rep 13 (1) 20648 [2023-11-24; online 2023-11-24] Open Access

Drug Discovery and Development (DDD) [Collaborative]

PubMed DOI Crossref

Dysregulations in hemostasis, metabolism, immune response, and angiogenesis in post-acute COVID-19 syndrome with and without postural orthostatic tachycardia syndrome: a multi-omic profiling study.

Mahdi A, Zhao A, Fredengren E, ..., Pernow J, Ståhlberg M

Sci Rep 13 (1) 20230 [2023-11-19; online 2023-11-19]

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

PubMed DOI Crossref

Single-cell transcriptomics delineates the immune cell landscape in equine lower airways and reveals upregulation of FKBP5 in horses with asthma.

Riihimäki M, Fegraeus K, Nordlund J, ..., Hellman L, Raine A

Sci Rep 13 (1) 16261 [2023-09-27; online 2023-09-27]

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

PubMed DOI Crossref

Genetic atlas of hygro-and thermosensory cells in the vinegar fly Drosophila melanogaster.

Corthals K, Andersson V, Churcher A, Reimegård J, Enjin A

Sci Rep 13 (1) 15202 [2023-09-14; online 2023-09-14]

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

PubMed DOI Crossref

The yeast guanine nucleotide exchange factor Sec7 is a bottleneck in spatial protein quality control and detoxifies neurological disease proteins.

Babazadeh R, Schneider KL, Fischbach A, ..., Liu B, Nystrom T

Sci Rep 13 (1) 14068 [2023-08-28; online 2023-08-28]

Integrated Microscopy Technologies Gothenburg [Service]

PubMed DOI Crossref

Insights into cellular behavior and micromolecular communication in urothelial micrografts.

Juul N, Willacy O, Mamand DR, ..., Chamorro CI, Fossum M

Sci Rep 13 (1) 13589 [2023-08-21; online 2023-08-21]

Global Proteomics and Proteogenomics [Service]

PubMed DOI Crossref

A novel quantitative targeted analysis of X-chromosome inactivation (XCI) using nanopore sequencing.

Johansson J, Lidéus S, Höijer I, ..., Bondeson ML, Wilbe M

Sci Rep 13 (1) 12856 [2023-08-08; online 2023-08-08]

NGI Long read [Collaborative] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

PubMed DOI Crossref

Multiyear analysis uncovers coordinated seasonality in stocks and composition of the planktonic food web in the Baltic Sea proper.

Fridolfsson E, Bunse C, Lindehoff E, ..., Legrand C, Hylander S

Sci Rep 13 (1) 11865 [2023-07-22; online 2023-07-22]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

Screening autism-associated environmental factors in differentiating human neural progenitors with fractional factorial design-based transcriptomics.

Arora A, Becker M, Marques C, ..., Lanekoff I, Tammimies K

Sci Rep 13 (1) 10519 [2023-06-29; online 2023-06-29]

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

PubMed DOI Crossref

Investigation of enzalutamide, docetaxel, and cabazitaxel resistance in the castration resistant prostate cancer cell line C4 using genome-wide CRISPR/Cas9 screening.

Haldrup J, Weiss S, Schmidt L, Sørensen KD

Sci Rep 13 (1) 9043 [2023-06-03; online 2023-06-03]

CRISPR Functional Genomics [Service]

PubMed DOI Crossref

DNA methylation variations and epigenetic aging in telomere biology disorders.

Carlund O, Norberg A, Osterman P, ..., Degerman S, Hultdin M

Sci Rep 13 (1) 7955 [2023-05-16; online 2023-05-16]

Clinical Genomics Umeå [Service]

PubMed DOI Crossref

Metagenomic sequencing of human cardiac tissue reveals Microbial RNA which correlates with Toll-like receptor-associated inflammation in patients with heart disease.

Sandstedt J, Vukusic K, Dellgren G, ..., Mattsson Hultén L, Rotter Sopasakis V

Sci Rep 13 (1) 7884 [2023-05-15; online 2023-05-15]

Clinical Genomics Gothenburg [Service]

PubMed DOI Crossref

A topical rectal douche product containing Q-Griffithsin does not disrupt the epithelial border or alter CD4+ cell distribution in the human rectal mucosa.

Franzén Boger M, Benhach N, Hasselrot T, ..., Broliden K, Tjernlund A

Sci Rep 13 (1) 7547 [2023-05-09; online 2023-05-09]

BioImage Informatics [Service]

PubMed DOI Crossref

Low-grade glioma risk SNP rs11706832 is associated with type I interferon response pathway genes in cell lines.

Rosenbaum A, Dahlin AM, Andersson U, ..., Wibom C, Melin B

Sci Rep 13 (1) 6777 [2023-04-25; online 2023-04-25]

Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service] Swedish Metabolomics Centre (SMC) [Service]

PubMed DOI Crossref

Transcriptomics unravels molecular changes associated with cilia and COVID-19 in chronic rhinosinusitis with nasal polyps.

Torinsson Naluai Å, Östensson M, Fowler PC, ..., Harandi AM, Bende M

Sci Rep 13 (1) 6592 [2023-04-21; online 2023-04-21]

Clinical Genomics Gothenburg [Collaborative]

PubMed DOI Crossref

Comparison of SARS-CoV-2 whole genome sequencing using tiled amplicon enrichment and bait hybridization.

Koskela von Sydow A, Lindqvist CM, Asghar N, ..., Mölling P, Stenmark B

Sci Rep 13 (1) 6461 [2023-04-20; online 2023-04-20]

Clinical Genomics Örebro [Technology development]

PubMed DOI Crossref

Genomic architecture of migration timing in a long-distance migratory songbird.

de Greef E, Suh A, Thorstensen MJ, Delmore KE, Fraser KC

Sci Rep 13 (1) 2437 [2023-02-10; online 2023-02-10]

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

PubMed DOI Crossref

PIK3CA is recurrently mutated in canine mammary tumors, similarly to in human mammary neoplasia.

Arendt ML, Sakthikumar S, Melin M, ..., Rönnberg H, Lindblad-Toh K

Sci Rep 13 (1) 632 [2023-01-12; online 2023-01-12]

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

PubMed DOI Crossref

An investigation of metabolome in blood in patients with chronic peripheral, posttraumatic/postsurgical neuropathic pain.

Ghafouri B, Thordeman K, Hadjikani R, ..., Gerdle B, Bäckryd E

Sci Rep 12 (1) 21714 [2022-12-15; online 2022-12-15]

Swedish NMR Centre (SNC) [Collaborative]

PubMed DOI Crossref

Hyaluronan nanoscale clustering and Hyaluronan synthase 2 expression are linked to the invasion of child fibroblasts and infantile fibrosarcoma in vitro and in vivo.

Tonge JJ, Notley SV, Dunning MJ, ..., Panoutsos G, Gad AKB

Sci Rep 12 (1) 19835 [2022-11-18; online 2022-11-18]

Integrated Microscopy Technologies Stockholm [Service]

PubMed DOI Crossref

Self-reported symptom severity, general health, and impairment in post-acute phases of COVID-19: retrospective cohort study of Swedish public employees.

Larsson SB, von Feilitzen GS, Andersson ME, ..., Nilsson S, Sigström R

Sci Rep 12 (1) 19818 [2022-11-17; online 2022-11-17]

Clinical Genomics Gothenburg [Collaborative]

PubMed DOI Crossref

Pax3 loss of function delays tumour progression in kRAS-induced zebrafish rhabdomyosarcoma models.

Kahsay A, Rodriguez-Marquez E, López-Pérez A, Hörnblad A, von Hofsten J

Sci Rep 12 (1) 17149 [2022-10-13; online 2022-10-13]

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

PubMed DOI Crossref

Absence of oxygen effect on microbial structure and methane production during drying and rewetting events.

Liu T, Li X, Yekta SS, ..., Schnürer A, Enrich-Prast A

Sci Rep 12 (1) 16570 [2022-10-04; online 2022-10-04]

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

PubMed DOI Crossref

Insight into the pulmonary molecular toxicity of heated tobacco products using human bronchial and alveolar mucosa models at air-liquid interface.

Rahman M, Irmler M, Introna M, ..., Upadhyay S, Ganguly K

Sci Rep 12 (1) 16396 [2022-09-30; online 2022-09-30]

Affinity Proteomics Uppsala [Service]

PubMed DOI Crossref

Seasonal dynamics in picocyanobacterial abundance and clade composition at coastal and offshore stations in the Baltic Sea.

Zufia JA, Legrand C, Farnelid H

Sci Rep 12 (1) 14330 [2022-08-22; online 2022-08-22]

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

PubMed DOI Crossref

Amplification of CDK4 and MDM2: a detailed study of a high-risk neuroblastoma subgroup.

Martinez-Monleon A, Kryh Öberg H, Gaarder J, ..., Fransson S, Martinsson T

Sci Rep 12 (1) 12420 [2022-07-20; online 2022-07-20]

Clinical Genomics Gothenburg [Service]

PubMed DOI Crossref

Single-cell transcriptional pharmacodynamics of trifluridine in a tumor-immune model.

Selvin T, Fasterius E, Jarvius M, ..., Larsson R, Andersson CR

Sci Rep 12 (1) 11960 [2022-07-13; online 2022-07-13]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Single cell [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

Integrated single cell and spatial transcriptomics reveal autoreactive differentiated B cells in joints of early rheumatoid arthritis.

Hardt U, Carlberg K, Af Klint E, ..., Ståhl PL, Malmström V

Sci Rep 12 (1) 11876 [2022-07-13; online 2022-07-13]

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

PubMed DOI Crossref

Niche partitioning between planktivorous fish in the pelagic Baltic Sea assessed by DNA metabarcoding, qPCR and microscopy.

Novotny A, Jan KMG, Dierking J, Winder M

Sci Rep 12 (1) 10952 [2022-06-29; online 2022-06-29]

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

PubMed DOI Crossref

Evaluation of within-host evolution of methicillin-resistant Staphylococcus aureus (MRSA) by comparing cgMLST and SNP analysis approaches.

Lagos AC, Sundqvist M, Dyrkell F, ..., Söderquist B, Mölling P

Sci Rep 12 (1) 10541 [2022-06-22; online 2022-06-22]

Clinical Genomics Örebro [Collaborative]

PubMed DOI Crossref

Development of gut microbiota during the first 2 years of life.

Wernroth ML, Peura S, Hedman AM, ..., Dicksved J, Fall T

Sci Rep 12 (1) 9080 [2022-05-31; online 2022-05-31]

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

PubMed DOI Crossref

Generalisation effects of predictive uncertainty estimation in deep learning for digital pathology.

Pocevičiūtė M, Eilertsen G, Jarkman S, Lundström C

Sci Rep 12 (1) 8329 [2022-05-18; online 2022-05-18]

AIDA Data Hub [Service]

PubMed DOI Crossref

Direct RNA targeted in situ sequencing for transcriptomic profiling in tissue.

Lee H, Marco Salas S, Gyllborg D, Nilsson M

Sci Rep 12 (1) 7976 [2022-05-13; online 2022-05-13]

In Situ Sequencing (ISS) [Technology development]

PubMed DOI Crossref

The impact of digital media on children's intelligence while controlling for genetic differences in cognition and socioeconomic background.

Sauce B, Liebherr M, Judd N, Klingberg T

Sci Rep 12 (1) 7720 [2022-05-11; online 2022-05-11]

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

PubMed DOI Crossref

A randomized controlled trial of the effects of whole grains versus refined grains diets on the microbiome in pregnancy.

Sun H, Yamada P, Paetow A, ..., Dominguez-Bello MG, Young BK

Sci Rep 12 (1) 7509 [2022-05-07; online 2022-05-07]

Chalmers Mass Spectrometry Infrastructure [Collaborative]

PubMed DOI Crossref

Age and sex effects across the blood proteome after ionizing radiation exposure can bias biomarker screening and risk assessment.

Langen B, Vorontsov E, Spetz J, ..., Helou K, Forssell-Aronsson E

Sci Rep 12 (1) 7000 [2022-04-29; online 2022-04-29]

Glycoproteomics and MS Proteomics [Collaborative]

PubMed DOI Crossref

Wastewater effluent affects behaviour and metabolomic endpoints in damselfly larvae.

Späth J, Fick J, McCallum E, ..., Nording ML, Brodin T

Sci Rep 12 (1) 6830 [2022-04-26; online 2022-04-26]

Swedish Metabolomics Centre (SMC) [Service]

PubMed DOI Crossref

scSPLAT, a scalable plate-based protocol for single cell WGBS library preparation.

Raine A, Lundmark A, Annett A, ..., Bergin C, Nordlund J

Sci Rep 12 (1) 5772 [2022-04-06; online 2022-04-06]

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

PubMed DOI Crossref

An inverse association between plasma benzoxazinoid metabolites and PSA after rye intake in men with prostate cancer revealed with a new method.

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Peters K, Herman S, Khoonsari PE, ..., Neumann S, Kultima K

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

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Strawbridge RJ, Johnston KJA, Bailey MES, ..., Sennblad B, Smith DJ

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Defining eligible patients for allele-selective chemotherapies targeting NAT2 in colorectal cancer.

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

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Clinical Genomics Gothenburg [Collaborative]

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

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Liao Z, Hodén KP, Singh RK, Dixelius C

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

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Petkov S, Bekele Y, Lakshmikanth T, ..., Brodin P, Chiodi F

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Inactivation of mediator complex protein 22 in podocytes results in intracellular vacuole formation, podocyte loss and premature death.

Rodriguez PQ, Unnersjö-Jess D, Zambrano SS, ..., Ebarasi L, Patrakka J

Sci Rep 10 (1) 20037 [2020-11-18; online 2020-11-18]

Integrated Microscopy Technologies Stockholm [Technology development]

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Sci Rep 10 (1) 19539 [2020-11-11; online 2020-11-11]

Clinical Genomics Lund [Service]

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

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

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Díez-Del-Molino D, von Seth J, Gyllenstrand N, ..., Sjögren-Gulve P, Dalén L

Sci Rep 10 (1) 18347 [2020-10-27; online 2020-10-27]

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

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Epigenetic alterations in skin homing CD4+CLA+ T cells of atopic dermatitis patients.

Acevedo N, Benfeitas R, Katayama S, ..., Söderhäll C, Scheynius A

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

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High-fat diet and estrogen impacts the colon and its transcriptome in a sex-dependent manner.

Hases L, Archer A, Indukuri R, ..., Korach-André M, Williams C

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

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Parvimonas micra as a putative non-invasive faecal biomarker for colorectal cancer.

Löwenmark T, Löfgren-Burström A, Zingmark C, ..., Edin S, Palmqvist R

Sci Rep 10 (1) 15250 [2020-09-17; online 2020-09-17]

Clinical Genomics Umeå [Collaborative]

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Compositional and functional differences of the mucosal microbiota along the intestine of healthy individuals.

Vaga S, Lee S, Ji B, ..., Engstrand L, Shoaie S

Sci Rep 10 (1) 14977 [2020-09-11; online 2020-09-11]

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

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Transcriptional mutagenesis dramatically alters genome-wide p53 transactivation landscape.

Liang S, Ezerskyte M, Wang J, Pelechano V, Dreij K

Sci Rep 10 (1) 13513 [2020-08-11; online 2020-08-11]

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

PubMed DOI Crossref

Mebendazole is unique among tubulin-active drugs in activating the MEK-ERK pathway.

Andersson CR, Selvin T, Blom K, ..., Nygren P, Larsson R

Sci Rep 10 (1) 13124 [2020-08-04; online 2020-08-04]

Drug Discovery and Development (DDD) [Service]

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Combining transcriptomics and genetic linkage based information to identify candidate genes associated with Heterobasidion-resistance in Norway spruce.

Chaudhary R, Lundén K, Dalman K, ..., Stenlid J, Elfstrand M

Sci Rep 10 (1) 12711 [2020-07-29; online 2020-07-29]

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

PubMed DOI Crossref

First evidence of microbial wood degradation in the coastal waters of the Antarctic.

Björdal CG, Dayton PK

Sci Rep 10 (1) 12774 [2020-07-29; online 2020-07-29]

Integrated Microscopy Technologies Gothenburg [Service]

PubMed DOI Crossref

Early Pleistocene origin and extensive intra-species diversity of the extinct cave lion.

Stanton DWG, Alberti F, Plotnikov V, ..., Skoglund P, Dalén L

Sci Rep 10 (1) 12621 [2020-07-28; online 2020-07-28]

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

PubMed DOI Crossref

Translating GWAS-identified loci for cardiac rhythm and rate using an in vivo image- and CRISPR/Cas9-based approach

von der Heyde B, Emmanouilidou A, Mazzaferro E, ..., Brooke HL, den Hoed M

Sci Rep 10 (1) 11831 [2020-07-16; online 2020-07-16]

BioImage Informatics [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] Genome Engineering Zebrafish [Service] 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]

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Disturbance history can increase functional stability in the face of both repeated disturbances of the same type and novel disturbances.

Renes SE, Sjöstedt J, Fetzer I, Langenheder S

Sci Rep 10 (1) 11333 [2020-07-09; online 2020-07-09]

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

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CAM-Delam: an in vivo approach to visualize and quantify the delamination and invasion capacity of human cancer cells.

Palaniappan TK, Šlekienė L, Jonasson AK, Gilthorpe J, Gunhaga L

Sci Rep 10 (1) 10472 [2020-06-26; online 2020-06-26]

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

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RNA-seq reveals altered gene expression levels in proximal tubular cell cultures compared to renal cortex but not during early glucotoxicity.

Nilsson LM, Castresana-Aguirre M, Scott L, Brismar H

Sci Rep 10 (1) 10390 [2020-06-25; online 2020-06-25]

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

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Amyloid precursor protein-b facilitates cell adhesion during early development in zebrafish.

Banote RK, Chebli J, Şatır TM, ..., Abramsson A, Zetterberg H

Sci Rep 10 (1) 10127 [2020-06-23; online 2020-06-23]

Genome Engineering Zebrafish [Collaborative] Integrated Microscopy Technologies Gothenburg [Service]

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Integration of whole-body [18F]FDG PET/MRI with non-targeted metabolomics can provide new insights on tissue-specific insulin resistance in type 2 diabetes.

Diamanti K, Visvanathar R, Pereira MJ, ..., Wadelius C, Ahlström H

Sci Rep 10 (1) 8343 [2020-05-20; online 2020-05-20]

Bioinformatics Support for Computational Resources [Service] Swedish Metabolomics Centre (SMC) [Service]

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Myocardial micro-biopsy procedure for molecular characterization with increased precision and reduced trauma.

Grankvist R, Chireh A, Sandell M, ..., Daub CO, Holmin S

Sci Rep 10 (1) 8029 [2020-05-15; online 2020-05-15]

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

PubMed DOI Crossref

Integrative genomics approach identifies molecular features associated with early-stage ovarian carcinoma histotypes.

Engqvist H, Parris TZ, Biermann J, ..., Karlsson P, Helou K

Sci Rep 10 (1) 7946 [2020-05-14; online 2020-05-14]

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

PubMed DOI Crossref

Genetic and environmental influences on human height from infancy through adulthood at different levels of parental education.

Jelenkovic A, Sund R, Yokoyama Y, ..., Kaprio J, Silventoinen K

Sci Rep 10 (1) 7974 [2020-05-14; online 2020-05-14]

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

PubMed DOI Crossref

The honeybee (Apis mellifera) developmental state shapes the genetic composition of the deformed wing virus-A quasispecies during serial transmission.

Yañez O, Chávez-Galarza J, Tellgren-Roth C, ..., Neumann P, de Miranda JR

Sci Rep 10 (1) 5956 [2020-04-06; online 2020-04-06]

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

PubMed DOI Crossref

Plant resistance does not compromise parasitoid-based biocontrol of a strawberry pest.

Weber D, Egan PA, Muola A, Ericson LE, Stenberg JA

Sci Rep 10 (1) 5899 [2020-04-03; online 2020-04-03]

Swedish Metabolomics Centre (SMC) [Service]

PubMed DOI Crossref

The conifer root rot pathogens Heterobasidion irregulare and Heterobasidion occidentale employ different strategies to infect Norway spruce.

Hu Y, Elfstrand M, Stenlid J, Durling MB, Olson Å

Sci Rep 10 (1) 5884 [2020-04-03; online 2020-04-03]

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

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Genomic characterization and outcome of prosthetic joint infections caused by Staphylococcus aureus.

Wildeman P, Tevell S, Eriksson C, ..., Söderquist B, Stenmark B

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Nordlund J, Marincevic-Zuniga Y, Cavelier L, ..., Lönnerholm G, Syvänen AC

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Vass M, Székely AJ, Lindström ES, Langenheder S

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

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Grönroos T, Mäkinen A, Laukkanen S, ..., Heinäniemi M, Lohi O

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Montoliu-Nerin M, Sánchez-García M, Bergin C, ..., Johannesson H, Rosling A

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CREBBP and WDR 24 Identified as Candidate Genes for Quantitative Variation in Red-Brown Plumage Colouration in the Chicken.

Fogelholm J, Henriksen R, Höglund A, ..., Jensen P, Wright D

Sci Rep 10 (1) 1161 [2020-01-24; online 2020-01-24]

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

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Etemadikhah M, Niazi A, Wetterberg L, Feuk L

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

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Ahi EP, Brunel M, Tsakoumis E, Schmitz M

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A Gene-Environment Interaction Between Smoking and Gene polymorphisms Provides a High Risk of Two Subgroups of Sarcoidosis.

Rivera NV, Patasova K, Kullberg S, ..., Grunewald J, Padyukov L

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Günaydın G, Edfeldt G, Garber DA, ..., Tjernlund A, Broliden K

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Redin D, Frick T, Aghelpasand H, ..., Olsen RA, Ahmadian A

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Transmission dynamics study of tuberculosis isolates with whole genome sequencing in southern Sweden

Alaridah N, Hallbäck ET, Tångrot J, ..., Kaijser B, Godaly G

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

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Metabolic phenotype of breast-fed infants, and infants fed standard formula or bovine MFGM supplemented formula: a randomized controlled trial

He X, Parenti M, Grip T, ..., Timby N, Slupsky CM

Sci Rep 9 (1) 339 [2019-12-00; online 2019-01-23]

Swedish Metabolomics Centre (SMC) [Service]

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Coro2b, a podocyte protein downregulated in human diabetic nephropathy, is involved in the development of protamine sulphate-induced foot process effacement

Schwarz A, Möller-Hackbarth K, Ebarasi L, ..., Lal M, Patrakka J

Sci Rep 9 (1) 8888 [2019-12-00; online 2019-06-20]

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Insight into the biology of Mycobacterium mucogenicum and Mycobacterium neoaurum clade members

Behra PRK, Pettersson BMF, Ramesh M, Dasgupta S, Kirsebom LA

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Intra- and inter-individual metabolic profiling highlights carnitine and lysophosphatidylcholine pathways as key molecular defects in type 2 diabetes

Diamanti K, Cavalli M, Pan G, ..., Komorowski J, Wadelius C

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ATAC-seq reveals alterations in open chromatin in pancreatic islets from subjects with type 2 diabetes

Bysani M, Agren R, Davegårdh C, ..., Bacos K, Ling C

Sci Rep 9 (1) - [2019-12-00; online 2019-05-23]

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] Systems Biology [Collaborative]

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Improved power and precision with whole genome sequencing data in genome-wide association studies of inflammatory biomarkers

Höglund J, Rafati N, Rask-Andersen M, ..., Ek WE, Johansson Å

Sci Rep 9 (1) - [2019-12-00; online 2019-11-14]

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

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The MTH1 inhibitor TH588 is a microtubule-modulating agent that eliminates cancer cells by activating the mitotic surveillance pathway

Gul N, Karlsson J, Tängemo C, ..., Bergö MO, Lindahl P

Sci Rep 9 (1) 14667 [2019-12-00; online 2019-10-11]

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Carnivores, competition and genetic connectivity in the Anthropocene.

Creel S, Spong G, Becker M, ..., Schiffthaler B, Chifunte C

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Näsström T, Andersson PO, Lejon C, Karlsson BCG

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

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Inhibition of translation termination by small molecules targeting ribosomal release factors.

Ge X, Oliveira A, Hjort K, ..., Sanyal S, Åqvist J

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Publisher Correction: Metabolic phenotype of breast-fed infants, and infants fed standard formula or bovine MFGM supplemented formula: a randomized controlled trial.

He X, Parenti M, Grip T, ..., Timby N, Slupsky CM

Sci Rep 9 (1) 12382 [2019-08-22; online 2019-08-22]

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

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Sci Rep 9 (1) 10730 [2019-07-24; online 2019-07-24]

BioImage Informatics [Collaborative] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Service] Clinical Genomics Uppsala [Collaborative] Genome Engineering Zebrafish [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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Genome and plasmid diversity of Extended-Spectrum β-Lactamase-producing Escherichia coli ST131 - tracking phylogenetic trajectories with Bayesian inference.

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

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Association between Copy Number Variation and Response to Social Skills Training in Autism Spectrum Disorder.

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

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Proteomic profiling of extracellular vesicles reveals additional diagnostic biomarkers for myocardial infarction compared to plasma alone.

Gidlöf O, Evander M, Rezeli M, ..., Laurell T, Erlinge D

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Systematic assessment of antibody selectivity in plasma based on a resource of enrichment profiles.

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Dysregulated autophagy in muscle precursor cells from humans with type 2 diabetes.

Henriksen TI, Wigge LV, Nielsen J, ..., Sandri M, Scheele C

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

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Backman S, Åkerström T, Maharjan R, ..., Hellman P, Björklund P

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Improved predictions of time-dependent drug-drug interactions by determination of cytosolic drug concentrations.

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Improved survival prognostication of node-positive malignant melanoma patients utilizing shotgun proteomics guided by histopathological characterization and genomic data.

Betancourt LH, Pawłowski K, Eriksson J, ..., Jönsson G, Marko-Varga G

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Thickness determines microbial community structure and function in nitrifying biofilms via deterministic assembly.

Suarez C, Piculell M, Modin O, ..., Persson F, Hermansson M

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Extended insight into the Mycobacterium chelonae-abscessus complex through whole genome sequencing of Mycobacterium salmoniphilum outbreak and Mycobacterium salmoniphilum-like strains.

Behra PRK, Das S, Pettersson BMF, ..., Ennis DG, Kirsebom LA

Sci Rep 9 (1) 4603 [2019-03-14; online 2019-03-14]

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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]

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A microfluidic platform towards automated multiplexed in situ sequencing.

Maïno N, Hauling T, Cappi G, ..., Dupouy DG, Nilsson M

Sci Rep 9 (1) 3542 [2019-03-05; online 2019-03-05]

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Transcriptomics of cardiac biopsies reveals differences in patients with or without diagnostic parameters for heart failure with preserved ejection fraction.

Das S, Frisk C, Eriksson MJ, ..., Linde C, Persson B

Sci Rep 9 (1) 3179 [2019-02-28; online 2019-02-28]

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

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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

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

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Genomic regions of speciation and adaptation among three species of grouse.

Kozma R, Rödin-Mörch P, Höglund J

Sci Rep 9 (1) 812 [2019-01-28; online 2019-01-28]

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

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Proline 411 biases the conformation of the intrinsically disordered plant UVR8 photoreceptor C27 domain altering the functional properties of the peptide.

Wu M, Farkas D, Eriksson LA, Strid Å

Sci Rep 9 (1) 818 [2019-01-28; online 2019-01-28]

Swedish NMR Centre (SNC) [Service]

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Carbonic Anhydrase 6 Gene Variation influences Oral Microbiota Composition and Caries Risk in Swedish adolescents.

Esberg A, Haworth S, Brunius C, Lif Holgerson P, Johansson I

Sci Rep 9 (1) 452 [2019-01-24; online 2019-01-24]

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

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Mercury methylating microbial communities of boreal forest soils.

Xu J, Buck M, Eklöf K, ..., Bertilsson S, Bravo AG

Sci Rep 9 (1) 518 [2019-01-24; online 2019-01-24]

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

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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]

Glycoproteomics and MS Proteomics [Service]

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Mycobacterium tuberculosis virulence inhibitors discovered by Mycobacterium marinum high-throughput screening.

Tükenmez H, Edström I, Ummanni R, ..., Elofsson M, Larsson C

Sci Rep 9 (1) 26 [2019-01-10; online 2019-01-10]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

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Comprehensive analysis of CTNNB1 in adrenocortical carcinomas: Identification of novel mutations and correlation to survival

Maharjan R, Backman S, Åkerström T, Hellman P, Björklund P

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

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Intramolecular 13C analysis of tree rings provides multiple plant ecophysiology signals covering decades

Wieloch T, Ehlers I, Yu J, ..., Gessler A, Schleucher J

Sci Rep 8 (1) - [2018-12-00; online 2018-03-22]

Swedish NMR Centre (SNC) [Service]

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Sharing of photobionts in sympatric populations of Thamnolia and Cetraria lichens: evidence from high-throughput sequencing

Onuț-Brännström I, Benjamin M, Scofield DG, ..., Lindström ES, Johannesson H

Sci Rep 8 (1) - [2018-12-00; online 2018-03-13]

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

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Anti-Rift Valley fever virus activity in vitro, pre-clinical pharmacokinetics and oral bioavailability of benzavir-2, a broad-acting antiviral compound

Islam MK, Strand M, Saleeb M, ..., Elofsson M, Evander M

Sci Rep 8 (1) - [2018-12-00; online 2018-01-31]

Bioinformatics Support for Computational Resources [Service] Chemical Biology Consortium Sweden (CBCS) [Service] Drug Discovery and Development (DDD) [Service]

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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]

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

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Whole Exome Sequencing of Patients from Multicase Families with Systemic Lupus Erythematosus Identifies Multiple Rare Variants

Delgado-Vega AM, Martínez-Bueno M, Oparina NY, ..., Kozyrev SV, Alarcón-Riquelme ME

Sci Rep 8 (1) - [2018-12-00; online 2018-06-08]

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

PubMed DOI Crossref

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

Johansson HJ, Vallhov H, Holm T, ..., Lehtiö J, Scheynius A

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

Bioinformatics Support for Computational Resources [Service] Cryo-EM [Service] Global Proteomics and Proteogenomics [Collaborative] Integrated Microscopy Technologies Stockholm [Collaborative]

PubMed DOI Crossref

A novel ulvan lyase family with broad-spectrum activity from the ulvan utilisation loci of Formosa agariphila KMM 3901

Konasani VR, Jin C, Karlsson NG, Albers E

Sci Rep 8 (1) - [2018-12-00; online 2018-10-02]

Glycoproteomics and MS Proteomics [Service] Swedish NMR Centre (SNC) [Service]

PubMed DOI Crossref

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]

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

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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]

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

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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]

Cryo-EM [Service]

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Single-Stranded Nucleic Acids Regulate TLR3/4/7 Activation through Interference with Clathrin-Mediated Endocytosis.

Järver P, Dondalska A, Poux C, ..., LeGrand R, Spetz AL

Sci Rep 8 (1) 15841 [2018-10-26; online 2018-10-26]

Global Proteomics and Proteogenomics [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

Amplification of the Melanocortin-1 Receptor in Nephrotic Syndrome Identifies a Target for Podocyte Cytoskeleton Stabilization.

Bergwall L, Wallentin H, Elvin J, ..., Nyström J, Buvall L

Sci Rep 8 (1) 15731 [2018-10-24; online 2018-10-24]

Glycoproteomics and MS Proteomics [Collaborative]

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A systems-approach reveals human nestin is an endothelial-enriched, angiogenesis-independent intermediate filament protein.

Dusart P, Fagerberg L, Perisic L, ..., Odeberg J, Butler LM

Sci Rep 8 (1) 14668 [2018-10-02; online 2018-10-02]

Spatial Proteomics [Service]

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Characterization of different fat depots in NAFLD using inflammation-associated proteome, lipidome and metabolome.

Lovric A, Granér M, Bjornson E, ..., Mardinoglu A, Boren J

Sci Rep 8 (1) 14200 [2018-09-21; online 2018-09-21]

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

PubMed DOI Crossref

Novel genome and genome-wide SNPs reveal early fragmentation effects in an edge-tolerant songbird population across an urbanized tropical metropolis.

Tan DJX, Chattopadhyay B, Garg KM, ..., Irestedt M, Rheindt FE

Sci Rep 8 (1) 12804 [2018-08-24; online 2018-08-24]

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

PubMed DOI Crossref

Extensive genomic diversity among Mycobacterium marinum strains revealed by whole genome sequencing

Das S, Pettersson F, Behra PRK, ..., Ennis DG, Kirsebom L

Sci. Rep. 8 (1) - [2018-08-13; online 2018-08-13]

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

PubMed DOI Crossref

Stationary and portable sequencing-based approaches for tracing wastewater contamination in urban stormwater systems.

Hu YOO, Ndegwa N, Alneberg J, ..., Fagerberg J, Andersson AF

Sci Rep 8 (1) 11907 [2018-08-09; online 2018-08-09]

Bioinformatics Long-term Support WABI [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]

PubMed DOI Crossref

Sample size effects on the assessment of eukaryotic diversity and community structure in aquatic sediments using high-throughput sequencing.

Nascimento FJA, Lallias D, Bik HM, Creer S

Sci Rep 8 (1) 11737 [2018-08-06; online 2018-08-06]

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

PubMed DOI Crossref

ClpB mutants of Francisella tularensis subspecies holarctica and tularensis are defective for type VI secretion and intracellular replication.

Alam A, Golovliov I, Javed E, Sjöstedt A

Sci Rep 8 (1) 11324 [2018-07-27; online 2018-07-27]

Cryo-EM [Service]

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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]

Integrated Microscopy Technologies Gothenburg [Service]

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Heterogeneity and interplay of the extracellular vesicle small RNA transcriptome and proteome.

Sork H, Corso G, Krjutskov K, ..., Mäger I, El Andaloussi S

Sci Rep 8 (1) 10813 [2018-07-17; online 2018-07-17]

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

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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]

Cryo-EM [Service]

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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]

Integrated Microscopy Technologies Gothenburg [Service]

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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]

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

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Investigating Holocene human population history in North Asia using ancient mitogenomes.

Kılınç GM, Kashuba N, Yaka R, ..., Storå J, Götherström A

Sci Rep 8 (1) 8969 [2018-06-12; online 2018-06-12]

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

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Common genetic variation in the autoimmune regulator (AIRE) locus is associated with autoimmune Addison's disease in Sweden.

Eriksson D, Bianchi M, Landegren N, ..., Rosengren Pielberg G, Kämpe O

Sci Rep 8 (1) 8395 [2018-05-30; online 2018-05-30]

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

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Habitual coffee consumption and cognitive function: a Mendelian randomization meta-analysis in up to 415,530 participants.

Zhou A, Taylor AE, Karhunen V, ..., Llewellyn DJ, Hyppönen E

Sci Rep 8 (1) 7526 [2018-05-14; online 2018-05-14]

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

PubMed DOI Crossref

Humanizing Miniature Hearts through 4-Flow Cannulation Perfusion Decellularization and Recellularization.

Nguyen DT, O'Hara M, Graneli C, ..., Althage M, Heydarkhan-Hagvall S

Sci Rep 8 (1) 7458 [2018-05-10; online 2018-05-10]

Integrated Microscopy Technologies Gothenburg [Service]

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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]

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

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Significant loss of mitochondrial diversity within the last century due to extinction of peripheral populations in eastern gorillas.

van der Valk T, Sandoval-Castellanos E, Caillaud D, ..., Dalén L, Guschanski K

Sci Rep 8 (1) 6551 [2018-04-25; online 2018-04-25]

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

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Abundant fish protein inhibits α-synuclein amyloid formation.

Werner T, Kumar R, Horvath I, Scheers N, Wittung-Stafshede P

Sci Rep 8 (1) 5465 [2018-04-03; online 2018-04-03]

Integrated Microscopy Technologies Gothenburg [Service]

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Improved efficiency of in situ protein analysis by proximity ligation using UnFold probes.

Klaesson A, Grannas K, Ebai T, ..., Söderberg O, Landegren U

Sci Rep 8 (1) 5400 [2018-03-29; online 2018-03-29]

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

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Peptide ion channel toxins from the bootlace worm, the longest animal on Earth.

Jacobsson E, Andersson HS, Strand M, ..., Tytgat J, Göransson U

Sci Rep 8 (1) 4596 [2018-03-22; online 2018-03-22]

Spatial Mass Spectrometry [Collaborative]

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ILF2 and ILF3 are autoantigens in canine systemic autoimmune disease.

Bremer HD, Landegren N, Sjöberg R, ..., Kämpe O, Hansson-Hamlin H

Sci Rep 8 (1) 4852 [2018-03-19; online 2018-03-19]

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

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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]

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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]

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

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A Single Bout of Electroacupuncture Remodels Epigenetic and Transcriptional Changes in Adipose Tissue in Polycystic Ovary Syndrome.

Kokosar M, Benrick A, Perfilyev A, ..., Ling C, Stener-Victorin E

Sci Rep 8 (1) 1878 [2018-01-30; online 2018-01-30]

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

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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]

Glycoproteomics and MS Proteomics [Service]

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Identification of shared genetic variants between schizophrenia and lung cancer.

Zuber V, Jönsson EG, Frei O, ..., Mills IG, Andreassen OA

Sci Rep 8 (1) 674 [2018-01-12; online 2018-01-12]

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

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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]

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Sample handling of gastric tissue and O-glycan alterations in paired gastric cancer and non-tumorigenic tissues.

Adamczyk B, Jin C, Polom K, ..., Roviello F, Karlsson NG

Sci Rep 8 (1) 242 [2018-01-10; online 2018-01-10]

Glycoproteomics and MS Proteomics [Technology development]

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Discovering viral genomes in human metagenomic data by predicting unknown protein families.

Barrientos-Somarribas M, Messina DN, Pou C, ..., Andersson B, Sonnhammer ELL

Sci Rep 8 (1) 28 [2018-01-08; online 2018-01-08]

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

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

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

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

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

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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]

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

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

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

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

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Increasing the permeability of Escherichia coli using MAC13243

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

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

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

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

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

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

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

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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]

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

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

Sci Rep 7 (1) 15821 [2017-11-17; online 2017-11-17]

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

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Novel KIAA0753 mutations extend the phenotype of skeletal ciliopathies.

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

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

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

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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]

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

Kumar R, Moche M, Winblad B, Pavlov PF

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

Protein Science Facility (PSF) [Collaborative]

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Proteolytic signatures define unique thrombin-derived peptides present in human wound fluid in vivo.

Saravanan R, Adav SS, Choong YK, ..., Sze SK, Schmidtchen A

Sci Rep 7 (1) 13136 [2017-10-13; online 2017-10-13]

Structural Proteomics [Service]

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

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

Sci Rep 7 (1) 13149 [2017-10-13; online 2017-10-13]

Affinity Proteomics Uppsala [Collaborative] Glycoproteomics and MS Proteomics [Collaborative] PLA and Single Cell Proteomics [Collaborative]

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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]

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Identification and characterization of the novel colonization factor CS30 based on whole genome sequencing in enterotoxigenic Escherichia coli (ETEC).

von Mentzer A, Tobias J, Wiklund G, ..., Sjöling Å, Svennerholm AM

Sci Rep 7 (1) 12514 [2017-10-02; online 2017-10-02]

Glycoproteomics and MS Proteomics [Service]

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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]

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]

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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]

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

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Fluorescent CRISPR Adaptation Reporter for rapid quantification of spacer acquisition.

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

Sci Rep 7 (1) 10392 [2017-09-04; online 2017-09-04]

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

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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]

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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]

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

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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]

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

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Quantitative proteomic characterization of lung-MSC and bone marrow-MSC using DIA-mass spectrometry.

Rolandsson Enes S, Åhrman E, Palani A, ..., Malmström J, Westergren-Thorsson G

Sci Rep 7 (1) 9316 [2017-08-24; online 2017-08-24]

Structural Proteomics [Service]

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Identification of NCAN as a candidate gene for developmental dyslexia.

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

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

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

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Identification of bacterial biofilm and the Staphylococcus aureus derived protease, staphopain, on the skin surface of patients with atopic dermatitis.

Sonesson A, Przybyszewska K, Eriksson S, ..., Potempa J, Schmidtchen A

Sci Rep 7 (1) 8689 [2017-08-18; online 2017-08-18]

Structural Proteomics [Service]

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Mass Spectrometry Imaging proves differential absorption profiles of well-characterised permeability markers along the crypt-villus axis.

Nilsson A, Peric A, Strimfors M, ..., Andrén PE, Hilgendorf C

Sci Rep 7 (1) 6352 [2017-07-25; online 2017-07-25]

Spatial Mass Spectrometry [Service]

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Recent increased identification and transmission of HIV-1 unique recombinant forms in Sweden.

Neogi U, Siddik AB, Kalaghatgi P, ..., Marrone G, Sönnerborg A

Sci Rep 7 (1) 6371 [2017-07-25; online 2017-07-25]

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

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Lipid Driven Nanodomains in Giant Lipid Vesicles are Fluid and Disordered.

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

Sci Rep 7 (1) 5460 [2017-07-14; online 2017-07-14]

Swedish NMR Centre (SNC) [Service]

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Isoelectric point-based fractionation by HiRIEF coupled to LC-MS allows for in-depth quantitative analysis of the phosphoproteome.

Panizza E, Branca RMM, Oliviusson P, Orre LM, Lehtiö J

Sci Rep 7 (1) 4513 [2017-07-03; online 2017-07-03]

Clinical Proteomics Mass spectrometry [Service] Global Proteomics and Proteogenomics [Service]

PubMed DOI Crossref

SNX10 gene mutation leading to osteopetrosis with dysfunctional osteoclasts.

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

Sci Rep 7 (1) 3012 [2017-06-07; online 2017-06-07]

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

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Mass spectrometry imaging identifies palmitoylcarnitine as an immunological mediator during Salmonella Typhimurium infection.

Hulme HE, Meikle LM, Wessel H, ..., Burchmore R, Wall DM

Sci Rep 7 (1) 2786 [2017-06-05; online 2017-06-05]

Spatial Mass Spectrometry [Service]

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SnoN Stabilizes the SMAD3/SMAD4 Protein Complex

Walldén K, Nyman T, Hällberg BM

Sci Rep 7 (-) 46370 [2017-04-11; online 2017-04-11]

Protein Science Facility (PSF) [Collaborative]

PubMed DOI Crossref

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]

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

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Genomic structure of the horse major histocompatibility complex class II region resolved using PacBio long-read sequencing technology

Viļuma A, Mikko S, Hahn D, ..., Andersson G, Bergström TF

Sci Rep 7 (-) 45518 [2017-03-31; online 2017-03-31]

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

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The evolutionary and phylogeographic history of woolly mammoths: a comprehensive mitogenomic analysis.

Chang D, Knapp M, Enk J, ..., Hofreiter M, Shapiro B

Sci Rep 7 (-) 44585 [2017-03-22; online 2017-03-22]

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

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Discovery of circulating proteins associated to knee radiographic osteoarthritis.

Lourido L, Ayoglu B, Fernández-Tajes J, ..., Nilsson P, Blanco FJ

Sci Rep 7 (1) 137 [2017-03-09; online 2017-03-09]

Affinity Proteomics Stockholm [Collaborative]

PubMed DOI Crossref

Diverse origin of mitochondrial lineages in Iron Age Black Sea Scythians.

Juras A, Krzewińska M, Nikitin AG, ..., Dabert M, Götherström A

Sci Rep 7 (-) 43950 [2017-03-07; online 2017-03-07]

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

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Postnatal development of the small intestinal mucosa drives age-dependent, regio-selective susceptibility to Escherichia coli K1 infection.

Birchenough GM, Dalgakiran F, Witcomb LA, ..., Hansson GC, Taylor PW

Sci Rep 7 (1) 83 [2017-03-06; online 2017-03-06]

Integrated Microscopy Technologies Gothenburg [Service]

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Epitopes of anti-RIFIN antibodies and characterization of rif-expressing Plasmodium falciparum parasites by RNA sequencing.

Ch'ng JH, Sirel M, Zandian A, ..., Qundos U, Wahlgren M

Sci Rep 7 (-) 43190 [2017-02-24; online 2017-02-24]

Autoimmunity and Serology Profiling [Service]

PubMed DOI Crossref

Evaluating Variant Calling Tools for Non-Matched Next-Generation Sequencing Data.

Sandmann S, de Graaf AO, Karimi M, ..., Jansen JH, Dugas M

Sci Rep 7 (-) 43169 [2017-02-24; online 2017-02-24]

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

PubMed DOI Crossref

Intracellular drug bioavailability: a new predictor of system dependent drug disposition.

Mateus A, Treyer A, Wegler C, ..., Matsson P, Artursson P

Sci Rep 7 (-) 43047 [2017-02-22; online 2017-02-22]

Drug Discovery and Development (DDD) [Service]

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SpotLight Proteomics: uncovering the hidden blood proteome improves diagnostic power of proteomics.

Lundström SL, Zhang B, Rutishauser D, Aarsland D, Zubarev RA

Sci Rep 7 (-) 41929 [2017-02-07; online 2017-02-07]

Chemical Proteomics [Technology development]

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Profile of upregulated inflammatory proteins in sera of Myasthenia Gravis patients.

Molin CJ, Westerberg E, Punga AR

Sci Rep 7 (1) 39716 [2017-01-03; online 2017-01-03]

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

PubMed DOI Crossref

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]

Drug Discovery and Development (DDD) [Service]

PubMed DOI Crossref

A novel process of viral vector barcoding and library preparation enables high-diversity library generation and recombination-free paired-end sequencing.

Davidsson M, Diaz-Fernandez P, Schwich OD, ..., Wang G, Björklund T

Sci Rep 6 (-) 37563 [2016-11-22; online 2016-11-22]

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

PubMed DOI Crossref

An automated approach to prepare tissue-derived spatially barcoded RNA-sequencing libraries.

Jemt A, Salmén F, Lundmark A, ..., Yucel-Lindberg T, Lundeberg J

Sci Rep 6 (-) 37137 [2016-11-16; online 2016-11-16]

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

PubMed DOI Crossref

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]

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Rawcopy: Improved copy number analysis with Affymetrix arrays.

Mayrhofer M, Viklund B, Isaksson A

Sci Rep 6 (-) 36158 [2016-10-31; online 2016-10-31]

Array and Analysis Facility [Technology development]

PubMed DOI Crossref

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]

PubMed DOI Crossref

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]

PubMed DOI Crossref

Penicillium arizonense, a new, genome sequenced fungal species, reveals a high chemical diversity in secreted metabolites.

Grijseels S, Nielsen JC, Randelovic M, ..., Workman M, Frisvad JC

Sci Rep 6 (-) 35112 [2016-10-14; online 2016-10-14]

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

PubMed DOI Crossref

No Association of Coronary Artery Disease with X-Chromosomal Variants in Comprehensive International Meta-Analysis.

Loley C, Alver M, Assimes TL, ..., Erdmann J, König IR

Sci Rep 6 (-) 35278 [2016-10-12; online 2016-10-12]

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

PubMed DOI Crossref

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]

PubMed DOI Crossref

ProQ3: Improved model quality assessments using Rosetta energy terms.

Uziela K, Shu N, Wallner B, Elofsson A

Sci Rep 6 (-) 33509 [2016-10-04; online 2016-10-04]

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

PubMed DOI Crossref

The domesticated brain: genetics of brain mass and brain structure in an avian species.

Henriksen R, Johnsson M, Andersson L, Jensen P, Wright D

Sci Rep 6 (1) 34031 [2016-09-30; online 2016-09-30]

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

PubMed DOI Crossref

Genomic Regions Associated With Interspecies Communication in Dogs Contain Genes Related to Human Social Disorders.

Persson ME, Wright D, Roth LS, Batakis P, Jensen P

Sci Rep 6 (-) 33439 [2016-09-29; online 2016-09-29]

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

PubMed DOI Crossref

Detecting individual extracellular vesicles using a multicolor in situ proximity ligation assay with flow cytometric readout.

Löf L, Ebai T, Dubois L, ..., Landegren U, Kamali-Moghaddam M

Sci Rep 6 (1) 34358 [2016-09-29; online 2016-09-29]

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

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