Unveiling Forkhead-mediated regulation of yeast cell cycle and metabolic networks.

Autor: Barberis M; Systems Biology, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey GU2 7XH, UK.; Centre for Mathematical and Computational Biology, CMCB, University of Surrey, Guildford, Surrey GU2 7XH, UK.; Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam 1098 XH, The Netherlands., Mondeel TDGA; Systems Biology, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey GU2 7XH, UK.; Centre for Mathematical and Computational Biology, CMCB, University of Surrey, Guildford, Surrey GU2 7XH, UK.; Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam 1098 XH, The Netherlands.

Publikováno v: Computational and structural biotechnology journal [Comput Struct Biotechnol J] 2022 Apr 07; Vol. 20, pp. 1743-1751. Date of Electronic Publication: 2022 Apr 07 (Print Publication: 2022).

ROS networks: designs, aging, Parkinson's disease and precision therapies.

Autor: N Kolodkin A; Infrastructure for Systems Biology Europe (ISBE.NL), Amsterdam, The Netherlands. alexeykolodkin@gmail.com.; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg. alexeykolodkin@gmail.com.; Molecular Cell Physiology, VU University Amsterdam, Amsterdam, The Netherlands. alexeykolodkin@gmail.com.; Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands. alexeykolodkin@gmail.com., Sharma RP; Molecular Cell Physiology, VU University Amsterdam, Amsterdam, The Netherlands.; Environmental Engineering Laboratory, Departament d'Enginyeria Quimica, Universitat Rovira i Virgili, Tarragona, Spain., Colangelo AM; Infrastructure for Systems Biology Europe (ISBE.IT), Milan, Italy.; SysBio Centre of Systems Biology (ISBE.IT), University of Milano-Bicocca, Milan, Italy.; Laboratory of Neuroscience 'R Levi-Montalcini' Dept of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy., Ignatenko A; Luxembourg Institute of Science and Technology (LIST), Esch-sur-Alzette, Luxembourg., Martorana F; Infrastructure for Systems Biology Europe (ISBE.IT), Milan, Italy.; SysBio Centre of Systems Biology (ISBE.IT), University of Milano-Bicocca, Milan, Italy.; Laboratory of Neuroscience 'R Levi-Montalcini' Dept of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy., Jennen D; Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands., Briedé JJ; Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands., Brady N; Department of Molecular Microbiology & Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA., Barberis M; Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands.; Systems Biology, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Surrey, UK.; Centre for Mathematical and Computational Biology, CMCB, University of Surrey, Surrey, UK., Mondeel TDGA; Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands.; Systems Biology, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Surrey, UK.; Centre for Mathematical and Computational Biology, CMCB, University of Surrey, Surrey, UK., Papa M; SysBio Centre of Systems Biology (ISBE.IT), University of Milano-Bicocca, Milan, Italy.; Infrastructure for Systems Biology Europe (ISBE.IT), Naples, Italy.; Department of Mental and Physical Health, University of Campania-L. Vanvitelli, Napoli, Italia., Kumar V; Environmental Engineering Laboratory, Departament d'Enginyeria Quimica, Universitat Rovira i Virgili, Tarragona, Spain.; IISPV, Hospital Universitari Sant Joan de Reus, Universitat Rovira I Virgili, Reus, Spain., Peters B; Faculty of Science, Technology and Communication, University of Luxembourg, Esch-sur-Alzette, Luxembourg., Skupin A; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg., Alberghina L; Infrastructure for Systems Biology Europe (ISBE.IT), Milan, Italy.; SysBio Centre of Systems Biology (ISBE.IT), University of Milano-Bicocca, Milan, Italy., Balling R; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg., Westerhoff HV; Infrastructure for Systems Biology Europe (ISBE.NL), Amsterdam, The Netherlands. h.v.westerhoff@uva.nl.; Molecular Cell Physiology, VU University Amsterdam, Amsterdam, The Netherlands. h.v.westerhoff@uva.nl.; Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands. h.v.westerhoff@uva.nl.; Manchester Centre for Integrative Systems Biology, School for Chemical Engineering and Analytical Science, The University of Manchester, Manchester, UK. h.v.westerhoff@uva.nl.

Publikováno v: NPJ systems biology and applications [NPJ Syst Biol Appl] 2020 Oct 26; Vol. 6 (1), pp. 34. Date of Electronic Publication: 2020 Oct 26.

ChIP-exo analysis highlights Fkh1 and Fkh2 transcription factors as hubs that integrate multi-scale networks in budding yeast.

Autor: Mondeel TDGA; Systems Biology, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, GU2 7XH Guildford, Surrey, UK.; Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, 1098 XH, The Netherlands., Holland P; Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, SE412 96, Sweden., Nielsen J; Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, SE412 96, Sweden.; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, DK2800 Kgs., Denmark., Barberis M; Systems Biology, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, GU2 7XH Guildford, Surrey, UK.; Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, 1098 XH, The Netherlands.

Publikováno v: Nucleic acids research [Nucleic Acids Res] 2019 Sep 05; Vol. 47 (15), pp. 7825-7841.

Learning to read and write in evolution: from static pseudoenzymes and pseudosignalers to dynamic gear shifters.

Autor: Abudukelimu A; Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands.; Molecular Cell Physiology, VU University Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands., Mondeel TDGA; Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands., Barberis M; Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands., Westerhoff HV; Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands h.v.westerhoff@uva.nl.; Molecular Cell Physiology, VU University Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands.; Manchester Centre for Integrative Systems Biology, Manchester Interdisciplinary Biocentre, 131 Princess Street, Manchester M1 7DN, U.K.

Publikováno v: Biochemical Society transactions [Biochem Soc Trans] 2017 Jun 15; Vol. 45 (3), pp. 635-652.

Competitive, multi-objective, and compartmented Flux Balance Analysis for addressing tissue-specific inborn errors of metabolism.

Autor: Liu Y; Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands., Westerhoff HV; Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands.; Molecular Cell Biology, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.; School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.

Publikováno v: Journal of inherited metabolic disease [J Inherit Metab Dis] 2023 Jul; Vol. 46 (4), pp. 573-585. Date of Electronic Publication: 2023 Apr 07.