Drugst.One - a plug-and-play solution for online systems medicine and network-based drug repurposing.

Autor: Maier A; Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany., Hartung M; Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany., Abovsky M; Division of Orthopaedic Surgery, Schroeder Arthritis Institute, Toronto, Canada.; Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, Toronto, ON M5T 0S8, Canada., Adamowicz K; Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany., Bader GD; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.; The Donnelly Centre, University of Toronto, Toronto, ON, Canada.; Department of Computer Science, University of Toronto, Toronto, ON, Canada.; Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.; The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada., Baier S; Data Science in Systems Biology, TUM School of Life Sciences, Technical University of Munich, Munich, Germany., Blumenthal DB; Department Artificial Intelligence in Biomedical Engineering (AIBE), Friedrich-Alexander University Erlangen-Nürnberg (FAU), 91052 Erlangen, Germany., Chen J; Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA., Elkjaer ML; Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany.; Department of Neurology, Odense University Hospital, Odense, Denmark.; Institute of Clinical Research, University of Southern Denmark, Odense, Denmark.; Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark., Garcia-Hernandez C; Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain., Helmy M; Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Canada.; School of Public Health, University of Saskatchewan, Canada.; Department of Computer Science, University of Saskatchewan, Canada.; Department of Computer Science, Lakehead University, Canada.; Department of Computer Science, Idaho State University, USA.; Bioinformatics Institute (BII), A*STAR, Singapore., Hoffmann M; Data Science in Systems Biology, TUM School of Life Sciences, Technical University of Munich, Munich, Germany.; Institute for Advanced Study, Technical University of Munich, Germany.; National Institute of Diabetes, Digestive, and Kidney Diseases, Bethesda, MD 20892, USA., Jurisica I; Division of Orthopaedic Surgery, Schroeder Arthritis Institute, Toronto, Canada.; Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, Toronto, ON M5T 0S8, Canada.; Departments of Medical Biophysics and Computer Science, University of Toronto, Toronto, Canada.; Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia., Kotlyar M; Division of Orthopaedic Surgery, Schroeder Arthritis Institute, Toronto, Canada.; Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, Toronto, ON M5T 0S8, Canada., Lazareva O; Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.; Junior Clinical Cooperation Unit Multiparametric methods for early detection of prostate cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany.; European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany., Levi H; Blavatnik School of Computer Science, Tel-Aviv University, Tel-Aviv, Israel., List M; Data Science in Systems Biology, TUM School of Life Sciences, Technical University of Munich, Munich, Germany., Lobentanzer S; Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany., Loscalzo J; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA., Malod-Dognin N; Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain., Manz Q; Data Science in Systems Biology, TUM School of Life Sciences, Technical University of Munich, Munich, Germany., Matschinske J; Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany.; Data Science in Systems Biology, TUM School of Life Sciences, Technical University of Munich, Munich, Germany., Mee M; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.; The Donnelly Centre, University of Toronto, Toronto, ON, Canada.; Department of Computer Science, University of Toronto, Toronto, ON, Canada., Oubounyt M; Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany., Pastrello C; Division of Orthopaedic Surgery, Schroeder Arthritis Institute, Toronto, Canada.; Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, Toronto, ON M5T 0S8, Canada., Pico AR; Institute of Data Science and Biotechnology, Gladstone Institutes, 1650 Owens Street, San Francisco, 94158 California, USA., Pillich RT; Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA., Poschenrieder JM; Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany.; Data Science in Systems Biology, TUM School of Life Sciences, Technical University of Munich, Munich, Germany., Pratt D; Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA., Pržulj N; Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain.; Department of Computer Science, University College London, London WC1E 6BT, UK.; ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain., Sadegh S; Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany.; Data Science in Systems Biology, TUM School of Life Sciences, Technical University of Munich, Munich, Germany.; Department of Clinical Genetics, Odense University Hospital, Odense, Denmark.; Clinical Genome Center, Department of Clinical Research, University of Southern Denmark, Odense, Denmark., Saez-Rodriguez J; Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany., Sarkar S; Department Artificial Intelligence in Biomedical Engineering (AIBE), Friedrich-Alexander University Erlangen-Nürnberg (FAU), 91052 Erlangen, Germany., Shaked G; Blavatnik School of Computer Science, Tel-Aviv University, Tel-Aviv, Israel., Shamir R; Blavatnik School of Computer Science, Tel-Aviv University, Tel-Aviv, Israel., Trummer N; Data Science in Systems Biology, TUM School of Life Sciences, Technical University of Munich, Munich, Germany., Turhan U; Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany., Wang RS; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA., Zolotareva O; Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany.; Data Science in Systems Biology, TUM School of Life Sciences, Technical University of Munich, Munich, Germany., Baumbach J; Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany.; Computational Biomedicine Lab, Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark.

Publikováno v: Nucleic acids research [Nucleic Acids Res] 2024 Jul 05; Vol. 52 (W1), pp. W481-W488.

Drugst.One - A plug-and-play solution for online systems medicine and network-based drug repurposing.

Autor: Maier A; Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany., Hartung M; Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany., Abovsky M; Division of Orthopaedic Surgery, Schroeder Arthritis Institute, and Data Science Discovery Centre, Osteoarthritis Research Program, Krembil Research Institute, UHN, Toronto, Canada.; Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, 60 Leonard Avenue, 5KD-407, Toronto, ON, M5T 0S8, Canada., Adamowicz K; Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany., Bader GD; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.; The Donnelly Centre, University of Toronto, Toronto, ON, Canada.; Department of Computer Science, University of Toronto, Toronto, ON, Canada.; Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.; The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada., Baier S; Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany., Blumenthal DB; Department Artificial Intelligence in Biomedical Engineering (AIBE), Friedrich-Alexander University Erlangen-Nürnberg (FAU), 91052 Erlangen, Germany., Chen J; Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA., Elkjaer ML; Department of Neurology, Odense University Hospital, Odense, Denmark.; Institute of Clinical Research, University of Southern Denmark, Odense, Denmark.; Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark., Garcia-Hernandez C; Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain., Helmy M; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.; The Donnelly Centre, University of Toronto, Toronto, ON, Canada.; Department of Computer Science, University of Toronto, Toronto, ON, Canada., Hoffmann M; Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany.; Institute for Advanced Study (Lichtenbergstrasse 2a, D-85748 Garching, Germany), Technical University of Munich, Germany.; National Institute of Diabetes, Digestive, and Kidney Diseases, Bethesda, MD 20892, United States of America., Jurisica I; Division of Orthopaedic Surgery, Schroeder Arthritis Institute, and Data Science Discovery Centre, Osteoarthritis Research Program, Krembil Research Institute, UHN, Toronto, Canada.; Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, 60 Leonard Avenue, 5KD-407, Toronto, ON, M5T 0S8, Canada.; Departments of Medical Biophysics and Computer Science, University of Toronto, Toronto, Canada.; Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia., Kotlyar M; Division of Orthopaedic Surgery, Schroeder Arthritis Institute, and Data Science Discovery Centre, Osteoarthritis Research Program, Krembil Research Institute, UHN, Toronto, Canada.; Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, 60 Leonard Avenue, 5KD-407, Toronto, ON, M5T 0S8, Canada., Lazareva O; Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.; Junior Clinical Cooperation Unit Multiparametric methods for early detection of prostate cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany.; European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany., Levi H; Blavatnik School of Computer Science, Tel-Aviv University, Tel-Aviv, Israel., List M; Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany., Lobentanzer S; Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany., Loscalzo J; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA., Malod-Dognin N; Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain., Manz Q; Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany., Matschinske J; Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany.; Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany., Mee M; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.; The Donnelly Centre, University of Toronto, Toronto, ON, Canada.; Department of Computer Science, University of Toronto, Toronto, ON, Canada., Oubounyt M; Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany., Pico AR; Institute of Data Science and Biotechnology, Gladstone Institutes, 1650 Owens Street, San Francisco, 94158, California, USA., Pillich RT; Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA., Poschenrieder JM; Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany.; Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany., Pratt D; Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA., Pržulj N; Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain.; Department of Computer Science, University College London, London WC1E 6BT, UK.; ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain., Sadegh S; Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany.; Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany.; Department of Clinical Genetics, Odense University Hospital, Odense, Denmark., Saez-Rodriguez J; Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany., Sarkar S; Department Artificial Intelligence in Biomedical Engineering (AIBE), Friedrich-Alexander University Erlangen-Nürnberg (FAU), 91052 Erlangen, Germany., Shaked G; Blavatnik School of Computer Science, Tel-Aviv University, Tel-Aviv, Israel., Shamir R; Blavatnik School of Computer Science, Tel-Aviv University, Tel-Aviv, Israel., Trummer N; Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany., Turhan U; Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany., Wang R; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA., Zolotareva O; Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany.; Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany., Baumbach J; Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany.; Computational Biomedicine Lab, Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark.

Publikováno v: ArXiv [ArXiv] 2023 Jul 04. Date of Electronic Publication: 2023 Jul 04.

Osteoarthritis Data Integration Portal (OsteoDIP): A web-based gene and non-coding RNA expression database.

Autor: Pastrello C; Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, University Health Network, Toronto, Canada.; Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, Toronto Western Hospital, University Health Network, Toronto, Canada., Abovsky M; Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, University Health Network, Toronto, Canada.; Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, Toronto Western Hospital, University Health Network, Toronto, Canada., Lu R; Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, University Health Network, Toronto, Canada.; Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, Toronto Western Hospital, University Health Network, Toronto, Canada., Ahmed Z; Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, University Health Network, Toronto, Canada.; Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, Toronto Western Hospital, University Health Network, Toronto, Canada., Kotlyar M; Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, University Health Network, Toronto, Canada.; Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, Toronto Western Hospital, University Health Network, Toronto, Canada., Veillette C; Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, University Health Network, Toronto, Canada., Jurisica I; Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, University Health Network, Toronto, Canada.; Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, Toronto Western Hospital, University Health Network, Toronto, Canada.; Departments of Medical Biophysics and Computer Science, University of Toronto, Toronto, ON, Canada.; Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia.

Publikováno v: Osteoarthritis and cartilage open [Osteoarthr Cartil Open] 2022 Jan 27; Vol. 4 (1), pp. 100237. Date of Electronic Publication: 2022 Jan 27 (Print Publication: 2022).

Estrogen Receptor 1 Inhibition of Wnt/β-Catenin Signaling Contributes to Sex Differences in Hepatocarcinogenesis.

Autor: Bhat M; Ajmera Transplant Program, University Health Network, Toronto, ON, Canada.; Division of Gastroenterology & Hepatology, University of Toronto, Toronto, ON, Canada.; Institute of Medical Sciences, University of Toronto, Toronto, ON, Canada.; Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada., Pasini E; Ajmera Transplant Program, University Health Network, Toronto, ON, Canada., Pastrello C; Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, University Health Network, Toronto, ON, Canada.; Krembil Research Institute, University Health Network, Toronto, ON, Canada., Angeli M; Ajmera Transplant Program, University Health Network, Toronto, ON, Canada., Baciu C; Ajmera Transplant Program, University Health Network, Toronto, ON, Canada., Abovsky M; Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, University Health Network, Toronto, ON, Canada.; Krembil Research Institute, University Health Network, Toronto, ON, Canada., Coffee A; Department of Pathology and University of Minnesota Medical Center, University of Minnesota, Minneapolis, MN, United States., Adeyi O; Department of Pathology and University of Minnesota Medical Center, University of Minnesota, Minneapolis, MN, United States., Kotlyar M; Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, University Health Network, Toronto, ON, Canada.; Krembil Research Institute, University Health Network, Toronto, ON, Canada., Jurisica I; Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, University Health Network, Toronto, ON, Canada.; Krembil Research Institute, University Health Network, Toronto, ON, Canada.; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.; Department Computer Science, University of Toronto, Toronto, ON, Canada.; Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia.

Publikováno v: Frontiers in oncology [Front Oncol] 2021 Nov 22; Vol. 11, pp. 777834. Date of Electronic Publication: 2021 Nov 22 (Print Publication: 2021).

pathDIP 4: an extended pathway annotations and enrichment analysis resource for human, model organisms and domesticated species.

Autor: Rahmati S; Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada.; Department of Medicine, Toronto Western Hospital, University Health Network, Toronto, ON M5T 2S8, Canada.; Department of Medicine, Memorial University of Newfoundland, Saint John's, NL A1B 3V6, Canada., Abovsky M; Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada., Pastrello C; Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada., Kotlyar M; Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada., Lu R; Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada., Cumbaa CA; Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada., Rahman P; Department of Medicine, Memorial University of Newfoundland, Saint John's, NL A1B 3V6, Canada., Chandran V; Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada.; Department of Medicine, Toronto Western Hospital, University Health Network, Toronto, ON M5T 2S8, Canada.; Department of Medicine, Memorial University of Newfoundland, Saint John's, NL A1B 3V6, Canada.; Department of Medicine, Division of Rheumatology, University of Toronto, Toronto, ON M5G 2C4, Canada.; Department of Laboratory Medicine and Pathobiology (LMP), Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada.; Institute of Medical Science, University of Toronto, Toronto, ON M5S 1A8, Canada., Jurisica I; Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada.; Department of Medical Biophysics, University of Toronto, ON M 5G 1L7, Canada.; Department of Computer Science, University of Toronto, ON M5S 1A4, Canada.; Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia.

Publikováno v: Nucleic acids research [Nucleic Acids Res] 2020 Jan 08; Vol. 48 (D1), pp. D479-D488.