Comparative single-cell trajectory network enrichment identifies pseudo-temporal systems biology patterns in hematopoiesis and CD8 T-cell development

Autor: Kristiyan Kanev, Jan Baumbach, Zehn D, Grønning Agb, Jesper Lund, Richard Röttger, Mhaned Oubounyt, Tim Kacprowski

Single cell transcriptomics (scRNA-seq) technologies allow for investigating cellular processes on an unprecedented resolution. While software packages for scRNA-seq raw data analysis exist, no method for the extraction of systems biology signatures

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::37d0d031d38dc96fd59f64c50ac3c61e

Adipogenic and SWAT cells separate from a common progenitor in human brown and white adipose depots.

Autor: Palani NP; Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark., Horvath C; Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark., Timshel PN; Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark.; ZS Associates, Copenhagen, Denmark., Folkertsma P; Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark., Grønning AGB; Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark., Henriksen TI; The Center of Inflammation and Metabolism and the Center for Physical Activity Research, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark., Peijs L; Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark.; The Center of Inflammation and Metabolism and the Center for Physical Activity Research, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark., Jensen VH; Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark.; The Center of Inflammation and Metabolism and the Center for Physical Activity Research, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark., Sun W; Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland., Jespersen NZ; The Center of Inflammation and Metabolism and the Center for Physical Activity Research, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark., Wolfrum C; Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland., Pers TH; Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark.; The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA., Nielsen S; The Center of Inflammation and Metabolism and the Center for Physical Activity Research, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark. soeren.nielsen.01@regionh.dk.; The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA. soeren.nielsen.01@regionh.dk., Scheele C; Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark. cs@sund.ku.dk.; The Center of Inflammation and Metabolism and the Center for Physical Activity Research, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark. cs@sund.ku.dk.; The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA. cs@sund.ku.dk.

Publikováno v: Nature metabolism [Nat Metab] 2023 Jun; Vol. 5 (6), pp. 996-1013. Date of Electronic Publication: 2023 Jun 19.

MultiPep: a hierarchical deep learning approach for multi-label classification of peptide bioactivities.

Autor: Grønning AGB; Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark., Kacprowski T; Division Data Science in Biomedicine, Peter L. Reichertz Institute for Medical Informatics, TU Braunschweig and Hannover Medical School, 38106 Braunschweig, Germany.; Braunschweig Integrated Centre for Systems Biology (BRICS), 38106 Braunschweig, Germany., Schéele C; Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark.

Publikováno v: Biology methods & protocols [Biol Methods Protoc] 2021 Nov 23; Vol. 6 (1), pp. bpab021. Date of Electronic Publication: 2021 Nov 23 (Print Publication: 2021).

Network Medicine-Based Unbiased Disease Modules for Drug and Diagnostic Target Identification in ROSopathies.

Autor: Nogales C; Department of Pharmacology and Personalised Medicine, Maastricht University, Maastricht, The Netherlands. cnogales@ppmlab.net., Grønning AGB; Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark., Sadegh S; Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany., Baumbach J; Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark.; Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany., Schmidt HHHW; Department of Pharmacology and Personalised Medicine, Maastricht University, Maastricht, The Netherlands.

Publikováno v: Handbook of experimental pharmacology [Handb Exp Pharmacol] 2021; Vol. 264, pp. 49-68.

The Selection of a Hepatocyte Cell Line Susceptible to Plasmodium falciparum Sporozoite Invasion That Is Associated With Expression of Glypican-3.

Autor: Tweedell RE; Department of Infectious Diseases and Immunology, Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States.; W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States., Tao D; W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States., Hamerly T; Department of Infectious Diseases and Immunology, Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States.; W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States., Robinson TM; Malaria Vaccine Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States., Larsen S; Computational BioMedicine Lab, Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark., Grønning AGB; Computational BioMedicine Lab, Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark., Norris AM; Department of Infectious Diseases and Immunology, Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States., King JG; W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States.; Department of Biochemistry, Molecular Biology, Entomology & Plant Pathology, Mississippi State University, Starkville, MS, United States., Law HCH; Department of Infectious Diseases and Immunology, Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States., Baumbach J; Computational BioMedicine Lab, Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark.; Chair of Experimental Bioinformatics, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany., Bergmann-Leitner ES; Malaria Vaccine Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States., Dinglasan RR; Department of Infectious Diseases and Immunology, Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States.; W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States.

Publikováno v: Frontiers in microbiology [Front Microbiol] 2019 Feb 28; Vol. 10, pp. 127. Date of Electronic Publication: 2019 Feb 28 (Print Publication: 2019).