On the identification of differentially-active transcription factors from ATAC-seq data.

Autor: Gerbaldo FE; Computational Neurogenomics, D-HEST Institute for Neurosciences, Zürich, Switzerland., Sonder E; Computational Neurogenomics, D-HEST Institute for Neurosciences, Zürich, Switzerland.; Systems Neuroscience, D-HEST Institute for Neurosciences, Zürich, Switzerland.; Department of Molecular Life Sciences, University of Zürich, Zürich, Switzerland.; SIB Swiss Institute of Bioinformatics, University of Zurich, Switzerland., Fischer V; Epigenetics and Neuroendocrinology, D-HEST Institute for Neurosciences, Zürich, Switzerland., Frei S; Epigenetics and Neuroendocrinology, D-HEST Institute for Neurosciences, Zürich, Switzerland., Wang J; Department of Molecular Life Sciences, University of Zürich, Zürich, Switzerland., Gapp K; Epigenetics and Neuroendocrinology, D-HEST Institute for Neurosciences, Zürich, Switzerland., Robinson MD; Department of Molecular Life Sciences, University of Zürich, Zürich, Switzerland.; SIB Swiss Institute of Bioinformatics, University of Zurich, Switzerland., Germain PL; Computational Neurogenomics, D-HEST Institute for Neurosciences, Zürich, Switzerland.; Department of Molecular Life Sciences, University of Zürich, Zürich, Switzerland.; SIB Swiss Institute of Bioinformatics, University of Zurich, Switzerland.

Publikováno v: PLoS computational biology [PLoS Comput Biol] 2024 Oct 23; Vol. 20 (10), pp. e1011971. Date of Electronic Publication: 2024 Oct 23 (Print Publication: 2024).

miRNA-mediated inhibition of an actomyosin network in hippocampal pyramidal neurons restricts sociability in adult male mice.

Autor: Narayanan R; Laboratory of Systems Neuroscience, Institute for Neuroscience, Department of Health Science and Technology, ETH-Zürich, Zürich, Switzerland., Levone BR; Laboratory of Systems Neuroscience, Institute for Neuroscience, Department of Health Science and Technology, ETH-Zürich, Zürich, Switzerland., Winterer J; Laboratory of Systems Neuroscience, Institute for Neuroscience, Department of Health Science and Technology, ETH-Zürich, Zürich, Switzerland., Nanda P; Laboratory of Systems Neuroscience, Institute for Neuroscience, Department of Health Science and Technology, ETH-Zürich, Zürich, Switzerland., Müller A; Laboratory of Systems Neuroscience, Institute for Neuroscience, Department of Health Science and Technology, ETH-Zürich, Zürich, Switzerland., Lobriglio T; Laboratory of Systems Neuroscience, Institute for Neuroscience, Department of Health Science and Technology, ETH-Zürich, Zürich, Switzerland., Fiore R; Laboratory of Systems Neuroscience, Institute for Neuroscience, Department of Health Science and Technology, ETH-Zürich, Zürich, Switzerland., Germain PL; Laboratory of Systems Neuroscience, Institute for Neuroscience, Department of Health Science and Technology, ETH-Zürich, Zürich, Switzerland; Laboratory of Molecular and Behavioural Neuroscience, Institute for Neuroscience, Department of Health Science and Technology, ETH-Zürich, Zürich, Switzerland; Laboratory of Statistical Bioinformatics, IMLS, University of Zürich, Zürich, Switzerland., Mihailovich M; European Institute of Oncology (IEO) IRCCS, Milan, Italy; Human Technopole, Milan, Italy., Testa G; European Institute of Oncology (IEO) IRCCS, Milan, Italy; Human Technopole, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy., Schratt G; Laboratory of Systems Neuroscience, Institute for Neuroscience, Department of Health Science and Technology, ETH-Zürich, Zürich, Switzerland. Electronic address: gerhard.schratt@hest.ethz.ch.

Publikováno v: Cell reports [Cell Rep] 2024 Jul 23; Vol. 43 (7), pp. 114429. Date of Electronic Publication: 2024 Jul 03.

Ten simple rules for computational biologists collaborating with wet lab researchers.

Autor: Robinson MD; Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.; SIB Swiss Institute of Bioinformatics, Zurich, Switzerland., Cai P; Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.; SIB Swiss Institute of Bioinformatics, Zurich, Switzerland., Emons M; Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.; SIB Swiss Institute of Bioinformatics, Zurich, Switzerland., Gerber R; Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.; SIB Swiss Institute of Bioinformatics, Zurich, Switzerland., Germain PL; Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.; SIB Swiss Institute of Bioinformatics, Zurich, Switzerland.; D-HEST Institute for Neuroscience, ETH Zurich, Zurich, Switzerland., Gunz S; Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.; SIB Swiss Institute of Bioinformatics, Zurich, Switzerland., Luo S; Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.; SIB Swiss Institute of Bioinformatics, Zurich, Switzerland., Moro G; Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland., Sonder E; Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.; SIB Swiss Institute of Bioinformatics, Zurich, Switzerland.; D-HEST Institute for Neuroscience, ETH Zurich, Zurich, Switzerland., Sonrel A; Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.; SIB Swiss Institute of Bioinformatics, Zurich, Switzerland., Wang J; Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.; SIB Swiss Institute of Bioinformatics, Zurich, Switzerland., Wissel D; Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.; SIB Swiss Institute of Bioinformatics, Zurich, Switzerland., Mallona I; Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.; SIB Swiss Institute of Bioinformatics, Zurich, Switzerland.

Publikováno v: PLoS computational biology [PLoS Comput Biol] 2024 Jun 20; Vol. 20 (6), pp. e1012174. Date of Electronic Publication: 2024 Jun 20 (Print Publication: 2024).

Harnessing PROTAC technology to combat stress hormone receptor activation.

Autor: Gazorpak M; Laboratory of Epigenetics and Neuroendocrinology, Institute for Neuroscience, Department of Health Science and Technology, ETH Zürich, 8057, Zürich, Switzerland.; Neuroscience Center Zürich, ETH Zürich and University of Zürich, 8057, Zürich, Switzerland., Hugentobler KM; Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093, Zürich, Switzerland., Paul D; Lab of Statistical Bioinformatics, University of Zürich, 8057, Zürich, Switzerland., Germain PL; Laboratory of Epigenetics and Neuroendocrinology, Institute for Neuroscience, Department of Health Science and Technology, ETH Zürich, 8057, Zürich, Switzerland.; Lab of Statistical Bioinformatics, University of Zürich, 8057, Zürich, Switzerland.; Computational Neurogenomics, Institute for Neuroscience, Department of Health Science and Technology, ETH Zürich, 8057, Zürich, Switzerland., Kretschmer M; Laboratory of Epigenetics and Neuroendocrinology, Institute for Neuroscience, Department of Health Science and Technology, ETH Zürich, 8057, Zürich, Switzerland.; Neuroscience Center Zürich, ETH Zürich and University of Zürich, 8057, Zürich, Switzerland., Ivanova I; Laboratory of Epigenetics and Neuroendocrinology, Institute for Neuroscience, Department of Health Science and Technology, ETH Zürich, 8057, Zürich, Switzerland., Frei S; Laboratory of Epigenetics and Neuroendocrinology, Institute for Neuroscience, Department of Health Science and Technology, ETH Zürich, 8057, Zürich, Switzerland., Mathis K; Laboratory of Epigenetics and Neuroendocrinology, Institute for Neuroscience, Department of Health Science and Technology, ETH Zürich, 8057, Zürich, Switzerland., Rudolf R; Laboratory of Epigenetics and Neuroendocrinology, Institute for Neuroscience, Department of Health Science and Technology, ETH Zürich, 8057, Zürich, Switzerland., Mompart Barrenechea S; Laboratory of Epigenetics and Neuroendocrinology, Institute for Neuroscience, Department of Health Science and Technology, ETH Zürich, 8057, Zürich, Switzerland., Fischer V; Laboratory of Epigenetics and Neuroendocrinology, Institute for Neuroscience, Department of Health Science and Technology, ETH Zürich, 8057, Zürich, Switzerland.; Neuroscience Center Zürich, ETH Zürich and University of Zürich, 8057, Zürich, Switzerland., Xue X; Bio Engineering Laboratory, Department of Biosystems Science and Engineering, ETH Zürich, 4056, Basel, Switzerland., Ptaszek AL; Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Max Perutz Laboratories, Department of Structural and Computational Biology, University of Vienna, Campus Vienna Biocenter 5, 1030, Vienna, Austria., Holzinger J; Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Max Perutz Laboratories, Department of Structural and Computational Biology, University of Vienna, Campus Vienna Biocenter 5, 1030, Vienna, Austria., Privitera M; Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Science and Technology, ETH Zürich, 8057, Zürich, Switzerland., Hierlemann A; Bio Engineering Laboratory, Department of Biosystems Science and Engineering, ETH Zürich, 4056, Basel, Switzerland., Meijer OC; Department of Medicine, Division of Endocrinology, Leiden University Medical Center, 2300, RA, Leiden, the Netherlands., Konrat R; Department of Structural and Computational Biology, University of Vienna, Campus Vienna Biocenter 5, 1030, Vienna, Austria., Carreira EM; Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093, Zürich, Switzerland., Bohacek J; Neuroscience Center Zürich, ETH Zürich and University of Zürich, 8057, Zürich, Switzerland.; Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Science and Technology, ETH Zürich, 8057, Zürich, Switzerland., Gapp K; Laboratory of Epigenetics and Neuroendocrinology, Institute for Neuroscience, Department of Health Science and Technology, ETH Zürich, 8057, Zürich, Switzerland. katharina.gapp@hest.ethz.ch.; Neuroscience Center Zürich, ETH Zürich and University of Zürich, 8057, Zürich, Switzerland. katharina.gapp@hest.ethz.ch.

Publikováno v: Nature communications [Nat Commun] 2023 Dec 09; Vol. 14 (1), pp. 8177. Date of Electronic Publication: 2023 Dec 09.

Reuniting philosophy and science to advance cancer research.

Autor: Pradeu T; CNRS UMR5164 ImmunoConcEpT, University of Bordeaux, 146 rue Leo Saignat, Bordeaux, 33076, France.; CNRS UMR8590, Institut d'Histoire et Philosophie des Sciences et des Technique, University Paris I Panthéon-Sorbonne, 13 rue du Four, Paris, 75006, France., Daignan-Fornier B; CNRS UMR 5095 Institut de Biochimie et Génétique Cellulaires, University of Bordeaux, 1 rue Camille St Saens, Bordeaux, 33077, France., Ewald A; Departments of Cell Biology and Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD, 21205, USA., Germain PL; Department of Health Sciences and Technology, Institute for Neurosciences, Eidgenössische Technische Hochschule (ETH) Zürich, Universitätstrasse 2, Zürich, 8092, Switzerland.; Department of Molecular Life Sciences, Laboratory of Statistical Bioinformatics, Universität Zürich, Winterthurerstrasse 190, Zurich, 8057, Switzerland., Okasha S; Department of Philosophy, University of Bristol, Cotham House, Bristol, BS6 6JL, UK., Plutynski A; Department of Philosophy, Washington University in St. Louis, and Associate with Division of Biology and Biomedical Sciences, St. Louis, MO, 63105, USA., Benzekry S; Computational Pharmacology and Clinical Oncology (COMPO) Unit, Inria Sophia Antipolis-Méditerranée, Cancer Research Center of Marseille, Inserm UMR1068, CNRS UMR7258, Aix Marseille University UM105, 27, bd Jean Moulin, Marseille, 13005, France., Bertolaso M; Research Unit of Philosophy of Science and Human Development, Università Campus Bio-Medico di Roma, Via Álvaro del Portillo, 21-00128, Rome, Italy.; Centre for Cancer Biomarkers, University of Bergen, Bergen, 5007, Norway., Bissell M; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA., Brown JS; Department of Integrated Mathematical Oncology, Moffitt Cancer Center, Tampa, FL, USA., Chin-Yee B; Division of Hematology, Department of Medicine, Schulich School of Medicine and Dentistry, Western University, 800 Commissioners Rd E, London, ON, Canada.; Rotman Institute of Philosophy, Western University, 1151 Richmond Street North, London, ON, Canada., Chin-Yee I; Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, 800 Commissioners Rd E, London, ON, Canada., Clevers H; Pharma, Research and Early Development (pRED) of F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, Basel, 4070, Switzerland.; Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands., Cognet L; CNRS UMR 5298, Laboratoire Photonique Numérique et Nanosciences, University of Bordeaux, Rue François Mitterrand, Talence, 33400, France., Darrason M; Department of Pneumology and Thoracic Oncology, University Hospital of Lyon, 165 Chem. du Grand Revoyet, 69310 Pierre Bénite, Lyon, France.; Lyon Institute of Philosophical Research, Lyon 3 Jean Moulin University, 1 Av. des Frères Lumière, Lyon, 69007, France., Farge E; Mechanics and Genetics of Embryonic and Tumor Development group, Institut Curie, CNRS, UMR168, Inserm, Centre Origines et conditions d'apparition de la vie (OCAV) Paris Sciences Lettres Research University, Sorbonne University, Institut Curie, 11 rue Pierre et Marie Curie, Paris, 75005, France., Feunteun J; INSERM U981, Gustave Roussy, 114 Rue Edouard Vaillant, Villejuif, 94800, France., Galon J; INSERM UMRS1138, Integrative Cancer Immunology, Cordelier Research Center, Sorbonne Université, Université Paris Cité, 15 rue de l'École de Médecine, Paris, 75006, France., Giroux E; Lyon Institute of Philosophical Research, Lyon 3 Jean Moulin University, 1 Av. des Frères Lumière, Lyon, 69007, France., Green S; Section for History and Philosophy of Science, Department of Science Education, University of Copenhagen, Rådmandsgade 64, Copenhagen, 2200, Denmark., Gross F; CNRS UMR5164 ImmunoConcEpT, University of Bordeaux, 146 rue Leo Saignat, Bordeaux, 33076, France., Jaulin F; INSERM U1279, Gustave Roussy, 114 Rue Edouard Vaillant, Villejuif, 94800, France., Knight R; Department of Bioengineering, University of California San Diego, 3223 Voigt Dr, La Jolla, CA, 92093, USA.; Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA.; Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, 92093, USA., Laconi E; Department of Biomedical Sciences, School of Medicine, University of Cagliari, Via Università 40, Cagliari, 09124, Italy., Larmonier N; CNRS UMR5164 ImmunoConcEpT, University of Bordeaux, 146 rue Leo Saignat, Bordeaux, 33076, France., Maley C; Arizona Cancer Evolution Center, Arizona State University, 427 East Tyler Mall, Tempe, AZ, 85287, USA.; School of Life Sciences, Arizona State University, 427 East Tyler Mall, Tempe, AZ, 85287, USA.; Biodesign Center for Biocomputing, Security and Society, Arizona State University, 1001 S McAllister Ave, Tempe, AZ, 85287, USA.; Biodesign Center for Mechanisms of Evolution, Arizona State University, 1001 S McAllister Ave, Tempe, AZ, 85287, USA.; Center for Evolution and Medicine, Arizona State University, 427 East Tyler Mall, Tempe, AZ, 85287, USA., Mantovani A; Department of Biomedical Sciences, Humanitas University, 4 Via Rita Levi Montalcini, 20090 Pieve Emanuele, Milan, Italy.; Department of Immunology and Inflammation, Istituto Clinico Humanitas Humanitas Cancer Center (IRCCS) Humanitas Research Hospital, Via Manzoni 56, Rozzano, Milan, 20089, Italy.; The William Harvey Research Institute, Queen Mary University of London, London, EC1M 6BQ, UK., Moreau V; INSERM UMR1312, Bordeaux Institute of Oncology (BRIC), University of Bordeaux, 146 Rue Léo Saignat, Bordeaux, 33076, France., Nassoy P; CNRS UMR 5298, Laboratoire Photonique Numérique et Nanosciences, University of Bordeaux, Rue François Mitterrand, Talence, 33400, France., Rondeau E; INSERM U1111, ENS Lyon and Centre International de Recherche en Infectionlogie (CIRI), 46 Allée d'Italie, Lyon, 69007, France., Santamaria D; Molecular Mechanisms of Cancer Program, Centro de Investigación del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, Salamanca, 37007, Spain., Sawai CM; INSERM UMR1312, Bordeaux Institute of Oncology (BRIC), University of Bordeaux, 146 Rue Léo Saignat, Bordeaux, 33076, France., Seluanov A; Department of Biology and Medicine, University of Rochester, Rochester, NY, 14627, USA., Sepich-Poore GD; Micronoma, 6342 Ferris Square, San Diego, CA, 92121, USA., Sisirak V; CNRS UMR5164 ImmunoConcEpT, University of Bordeaux, 146 rue Leo Saignat, Bordeaux, 33076, France., Solary E; INSERM U1287, Gustave Roussy, 114 Rue Edouard Vaillant, Villejuif, 94800, France.; Département d'hématologie, Gustave Roussy, 114 Rue Edouard Vaillant, Villejuif, 94800, France.; Université Paris-Saclay, Faculté de Médecine, 63 Rue Gabriel Péri, Le Kremlin-Bicêtre, 94270, France., Yvonnet S; Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Blegdamsvej 3B, Copenhagen, DK-2200, Denmark., Laplane L; CNRS UMR8590, Institut d'Histoire et Philosophie des Sciences et des Technique, University Paris I Panthéon-Sorbonne, 13 rue du Four, Paris, 75006, France.; INSERM U1287, Gustave Roussy, 114 Rue Edouard Vaillant, Villejuif, 94800, France.; Center for Biology and Society, College of Liberal Arts and Sciences, Arizona State University, 1100 S McAllister Ave, Tempe, AZ, 85281, USA.

Publikováno v: Biological reviews of the Cambridge Philosophical Society [Biol Rev Camb Philos Soc] 2023 Oct; Vol. 98 (5), pp. 1668-1686. Date of Electronic Publication: 2023 May 08.