CODEX: COunterfactual Deep learning for the in silico EXploration of cancer cell line perturbations.

Autor: Schrod S; Department of Medical Bioinformatics, University Medical Center Göttingen, 37077 Niedersachsen, Germany., Zacharias HU; Peter L. Reichertz Institute for Medical Informatics of TU Braunschweig and Hannover Medical School, Hannover Medical School, 30625 Hannover, Germany., Beißbarth T; Department of Medical Bioinformatics, University Medical Center Göttingen, 37077 Niedersachsen, Germany., Hauschild AC; Department of Medical Informatics, University Medical Center Göttingen, 37075 Niedersachsen, Germany., Altenbuchinger M; Department of Medical Bioinformatics, University Medical Center Göttingen, 37077 Niedersachsen, Germany.

Publikováno v: Bioinformatics (Oxford, England) [Bioinformatics] 2024 Jun 28; Vol. 40 (Suppl 1), pp. i91-i99.

A primer on the use of machine learning to distil knowledge from data in biological psychiatry.

Autor: Quinn TP; Applied Artificial Intelligence Institute (A2I2), Burwood, VIC, 3125, Australia., Hess JL; Department of Psychiatry and Behavioral Sciences, Norton College of Medicine at SUNY Upstate Medical University, Syracuse, NY, 13210, USA., Marshe VS; Institute of Medical Science, University of Toronto, Toronto, ON, M5S 1A1, Canada.; Pharmacogenetics Research Clinic, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, M5S 1A1, Canada., Barnett MM; School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, 2308, Australia.; Precision Medicine Research Program, Hunter Medical Research Institute, Newcastle, NSW, 2308, Australia., Hauschild AC; Department of Medical Informatics, Medical University Center Göttingen, Göttingen, Lower Saxony, 37075, Germany., Maciukiewicz M; Hospital Zurich, University of Zurich, Zurich, 8091, Switzerland.; Department of Rheumatology and Immunology, University Hospital Bern, Bern, 3010, Switzerland.; Department for Biomedical Research (DBMR), University of Bern, Bern, 3010, Switzerland., Elsheikh SSM; Pharmacogenetics Research Clinic, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, M5S 1A1, Canada., Men X; Pharmacogenetics Research Clinic, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, M5S 1A1, Canada.; Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, M5S 1A1, Canada., Schwarz E; Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Mannheim, Baden-Württemberg, J5 68159, Germany., Trakadis YJ; Department Human Genetics, McGill University Health Centre, Montreal, QC, H4A 3J1, Canada., Breen MS; Psychiatry, Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA., Barnett EJ; Department of Neuroscience and Physiology, Norton College of Medicine at SUNY Upstate Medical University, Syracuse, NY, 13210, USA., Zhang-James Y; Department of Psychiatry and Behavioral Sciences, Norton College of Medicine at SUNY Upstate Medical University, Syracuse, NY, 13210, USA., Ahsen ME; Department of Business Administration, Gies College of Business, University of Illinois at Urbana-Champaign, Champaign, IL, 61820, USA.; Department of Biomedical and Translational Sciences, Carle-Illinois School of Medicine, University of Illinois at Urbana-Champaign, Champaign, IL, 61820, USA., Cao H; Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Mannheim, Baden-Württemberg, J5 68159, Germany., Chen J; Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Mannheim, Baden-Württemberg, J5 68159, Germany., Hou J; Department of Psychiatry and Behavioral Sciences, Norton College of Medicine at SUNY Upstate Medical University, Syracuse, NY, 13210, USA.; Department of Neuroscience and Physiology, Norton College of Medicine at SUNY Upstate Medical University, Syracuse, NY, 13210, USA., Salekin A; Electrical Engineering and Computer Science, Syracuse University, Syracuse, NY, 13244, USA., Lin PI; Discipline of Psychiatry and Mental Health, University of New South Wales, Sydney, NSW, 2052, Australia.; Mental Health Research Unit, South Western Sydney Local Health District, Liverpool, NSW, 2170, Australia., Nicodemus KK; Usher Institute, University of Edinburgh, Edinburgh, EH8 9YL, UK., Meyer-Lindenberg A; Clinical Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Mannheim, Baden-Württemberg, J5 68159, Germany., Bichindaritz I; Biomedical and Health Informatics/Computer Science Department, State University of New York at Oswego, Oswego, NY, 13126, USA.; Intelligent Bio Systems Lab, State University of New York at Oswego, Oswego, NY, 13126, USA., Faraone SV; Department of Psychiatry and Behavioral Sciences, Norton College of Medicine at SUNY Upstate Medical University, Syracuse, NY, 13210, USA.; Department of Neuroscience and Physiology, Norton College of Medicine at SUNY Upstate Medical University, Syracuse, NY, 13210, USA., Cairns MJ; School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, 2308, Australia.; Precision Medicine Research Program, Hunter Medical Research Institute, Newcastle, NSW, 2308, Australia., Pandey G; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA., Müller DJ; Pharmacogenetics Research Clinic, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, M5S 1A1, Canada.; Department of Psychiatry, University of Toronto, Toronto, ON, M5S 1A1, Canada.; Department of Psychiatry, Psychosomatics and Psychotherapy, Center of Mental Health, University Hospital of Würzburg, Würzburg, 97080, Germany., Glatt SJ; Department of Psychiatry and Behavioral Sciences, Norton College of Medicine at SUNY Upstate Medical University, Syracuse, NY, 13210, USA. stephen.glatt@psychgenelab.com.; Department of Neuroscience and Physiology, Norton College of Medicine at SUNY Upstate Medical University, Syracuse, NY, 13210, USA. stephen.glatt@psychgenelab.com.; Department of Public Health and Preventive Medicine, Norton College of Medicine at SUNY Upstate Medical University, Syracuse, NY, 13210, USA. stephen.glatt@psychgenelab.com.

Publikováno v: Molecular psychiatry [Mol Psychiatry] 2024 Feb; Vol. 29 (2), pp. 387-401. Date of Electronic Publication: 2024 Jan 04.

Species-agnostic transfer learning for cross-species transcriptomics data integration without gene orthology.

Autor: Park Y; Department of Medical Informatics, University Medical Center Göttingen, Göttingen, Germany.; International Max Planck Research Schools for Genome Science, Georg-August-Universität Göttingen Göttingen, Germany., Muttray NP; Applied Statistics, Georg-August-Universität Göttingen Göttingen, Germany., Hauschild AC; Department of Medical Informatics, University Medical Center Göttingen, Göttingen, Germany.; Campus-Institute Data Science (CIDAS), Georg-August-Universität Göttingen Göttingen, Germany.

Publikováno v: Briefings in bioinformatics [Brief Bioinform] 2024 Jan 22; Vol. 25 (2).

The FeatureCloud Platform for Federated Learning in Biomedicine: Unified Approach.

Autor: Matschinske J; University of Hamburg, Hamburg, Germany., Späth J; University of Hamburg, Hamburg, Germany., Bakhtiari M; University of Hamburg, Hamburg, Germany., Probul N; University of Hamburg, Hamburg, Germany., Kazemi Majdabadi MM; University of Hamburg, Hamburg, Germany., Nasirigerdeh R; Technical University Munich, Munich, Germany., Torkzadehmahani R; Technical University Munich, Munich, Germany., Hartebrodt A; University of Southern Denmark, Odense, Denmark., Orban BA; Gnome Design SRL, Sfântu Gheorghe, Romania., Fejér SJ; Gnome Design SRL, Sfântu Gheorghe, Romania., Zolotareva O; Technical University Munich, Munich, Germany., Das S; University of Hamburg, Hamburg, Germany., Baumbach L; University Medical Center Hamburg-Eppendorf, Hamburg, Germany., Pauling JK; Technical University Munich, Munich, Germany., Tomašević O; University of Novi Sad, Novi Sad, ., Bihari B; Gnome Design SRL, Sfântu Gheorghe, Romania., Bloice M; Medical University of Graz, Graz, Austria., Donner NC; Concentris Research Management gGmbH, Fürstenfeldbruck, Germany., Fdhila W; SBA Research gGmbH, Vienna, Austria., Frisch T; University of Southern Denmark, Odense, Denmark., Hauschild AC; University Medical Center Göttingen, Göttingen, Germany., Heider D; Philipps-University of Marburg, Marburg, Germany., Holzinger A; Medical University of Graz, Graz, Austria., Hötzendorfer W; Research Institute AG & Co KG, Vienna, Austria., Hospes J; Research Institute AG & Co KG, Vienna, Austria., Kacprowski T; Technical University Braunschweig and Hannover Medical School, Brunswick, Germany., Kastelitz M; Research Institute AG & Co KG, Vienna, Austria., List M; Technical University Munich, Munich, Germany., Mayer R; SBA Research gGmbH, Vienna, Austria., Moga M; Gnome Design SRL, Sfântu Gheorghe, Romania., Müller H; Medical University of Graz, Graz, Austria., Pustozerova A; SBA Research gGmbH, Vienna, Austria., Röttger R; University of Southern Denmark, Odense, Denmark., Saak CC; University of Hamburg, Hamburg, Germany., Saranti A; Medical University of Graz, Graz, Austria., Schmidt HHHW; Maastricht University, Maastricht, Netherlands., Tschohl C; Research Institute AG & Co KG, Vienna, Austria., Wenke NK; University of Hamburg, Hamburg, Germany., Baumbach J; University of Hamburg, Hamburg, Germany.

Publikováno v: Journal of medical Internet research [J Med Internet Res] 2023 Jul 12; Vol. 25, pp. e42621. Date of Electronic Publication: 2023 Jul 12.

MirDIP 5.2: tissue context annotation and novel microRNA curation.

Autor: Hauschild AC; Department of Medical Informatics, University Medical Center Göttingen, Georg-August University, Göttingen, Lower Saxony 37075, Germany., Pastrello C; Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto M5T 0S8, Canada., Ekaputeri GKA; Department of Medical Informatics, University Medical Center Göttingen, Georg-August University, Göttingen, Lower Saxony 37075, Germany., Bethune-Waddell D; Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto M5T 0S8, Canada., Abovsky M; Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto M5T 0S8, Canada., Ahmed Z; Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto M5T 0S8, Canada., Kotlyar M; Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto M5T 0S8, Canada., Lu R; Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto M5T 0S8, Canada., Jurisica I; Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto M5T 0S8, Canada.; Departments of Medical Biophysics and Computer Science, and Faculty of Dentistry, University of Toronto, Toronto, ON, Canada.; Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia.

Publikováno v: Nucleic acids research [Nucleic Acids Res] 2023 Jan 06; Vol. 51 (D1), pp. D217-D225.