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Author Details

Claudine Chaouiya
Aix Marseille University CNRS
2003
45
24
Dexter Pratt (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
36350610YEASTRACT+: a portal for the exploitation of global transcription regulation and metabolic model data in yeast biotechnology and pathogenesis.Nucleic Acids Res2023
35671510Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology.Brief Bioinform2022
32313939Setting the basis of best practices and standards for curation and annotation of logical models in biology-highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop.Brief Bioinform2021
34179955SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems.Bioinformatics2021
34063110In Silico Logical Modelling to Uncover Cooperative Interactions in Cancer.Int J Mol Sci2021
32637990The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST).Bioinformatics2021
32217696Hybrid Epithelial-Mesenchymal Phenotypes Are Controlled by Microenvironmental Factors.Cancer Res2020
33082399Assessing regulatory features of the current transcriptional network of Saccharomyces cerevisiae.Sci Rep2020
32845085SBML Level 3: an extensible format for the exchange and reuse of biological models.Mol Syst Biol2020
31219795The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2.J Integr Bioinform2019
29792308Logical modelling uncovers developmental constraints for primary sex determination of chicken gonads.J R Soc Interface2018
29971009The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks.Front Physiol2018
29971008Logical Modeling and Analysis of Cellular Regulatory Networks With GINsim 3.0.Front Physiol2018
30117501Correction to: Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE).Stand Genomic Sci2018
30245634Estimating Attractor Reachability in Asynchronous Logical Models.Front Physiol2018
27229461Primary sex determination of placental mammals: a modelling study uncovers dynamical developmental constraints in the formation of Sertoli and granulosa cells.BMC Syst Biol2016
27303434Logical Modeling and Dynamical Analysis of Cellular Networks.Front Genet2016
25619997Cooperative development of logical modelling standards and tools with CoLoMoTo.Bioinformatics2015
26528568The Systems Biology Markup Language (SBML) Level 3 Package: Qualitative Models, Version 1, Release 1.J Integr Bioinform2015
26238783A Modeling Approach to Explain Mutually Exclusive and Co-Occurring Genetic Alterations in Bladder Tumorigenesis.Cancer Res2015
25674559Model checking to assess T-helper cell plasticity.Front Bioeng Biotechnol2015
24675973A discrete model of Drosophila eggshell patterning reveals cell-autonomous and juxtacrine effects.PLoS Comput Biol2014
25573782Modelling the onset of senescence at the G1/S cell cycle checkpoint.BMC Genomics2014
23341501Composition and abstraction of logical regulatory modules: application to multicellular systems.Bioinformatics2013
24324653Bringing dicynodonts back to life: paleobiology and anatomy of a new emydopoid genus from the Upper Permian of Mozambique.PLoS One2013
24321545SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools.BMC Syst Biol2013
24180668Path2Models: large-scale generation of computational models from biochemical pathway maps.BMC Syst Biol2013
23822512Dynamical modeling and analysis of large cellular regulatory networks.Chaos2013
23922761Majority rules with random tie-breaking in Boolean gene regulatory networks.PLoS One2013
23722297Logical modelling of regulatory networks, methods and applications.Bull Math Biol2013
22144167Logical modelling of gene regulatory networks with GINsim.Methods Mol Biol2012
20868697Mapping multivalued onto Boolean dynamics.J Theor Biol2011
20824124Diversity and plasticity of Th cell types predicted from regulatory network modelling.PLoS Comput Biol2010
19118495Modeling ERBB receptor-regulated G1/S transition to find novel targets for de novo trastuzumab resistance.BMC Syst Biol2009
19763337Modular logical modelling of the budding yeast cell cycle.Mol Biosyst2009
19426782Logical modelling of regulatory networks with GINsim 2.3.Biosystems2009
18689831Logical modelling of the role of the Hh pathway in the patterning of the Drosophila wing disc.Bioinformatics2008
18956339Segmenting the fly embryo: logical analysis of the role of the segment polarity cross-regulatory module.Int J Dev Biol2008
17626066Petri net modelling of biological networks.Brief Bioinform2007
16386357Dynamical modeling of biological regulatory networks.Biosystems2006
16873462Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle.Bioinformatics2006
16951066Dynamical analysis of the regulatory network defining the dorsal-ventral boundary of the Drosophila wing imaginal disc.Genetics2006
16434137GINsim: a software suite for the qualitative modelling, simulation and analysis of regulatory networks.Biosystems2006
16204102Qualitative modelling of regulated metabolic pathways: application to the tryptophan biosynthesis in E.coli.Bioinformatics2005
14534187A description of dynamical graphs associated to elementary regulatory circuits.Bioinformatics2003
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Collaborators

Denis Thieffry
Institut de Biologie de l'Ecole Normale Superieure, Inserm, CNRS, Universite PSL
Co-authored papers 24
Aur??lien Naldi
Institut de Biologie de l'Ecole Normale Superieure, Inserm, CNRS, Universite PSL
Co-authored papers 15
Julio Saez-Rodriguez
Institute of Computational Biomedicine, Heidelberg University
Co-authored papers 7
Laurence Calzone
Institut Curie, Universite PSL
Co-authored papers 5
Nicolas Le Nov??re
Babraham Institute
Co-authored papers 5
Henning Hermjakob
European Bioinformatics Institute (EMBL-EBI)
Co-authored papers 4
Ioannis Xenarios
University of Lausanne
Co-authored papers 3
Vasundra Tour??
Norwegian University of Science and Technology (NTNU)
Co-authored papers 2
Cristina Casals
Universidad Complutense
Co-authored papers 2
Martin Kuiper
Norwegian University of Science and Technology
Co-authored papers 2
Martin Golebiewski
Co-authored papers 2
Paul D Thomas
University of Southern California
Co-authored papers 2
Andrei Zinovyev
INSERM U, Institut Curie, PSL Research University
Co-authored papers 2
Neil Swainston
Institute of Systems, University of Liverpool
Co-authored papers 2
Stefan Wiemann
Co-authored papers 1
Steven Vercruysse
Norwegian University of Science and Technology (NTNU)
Co-authored papers 1
Tom C Freeman
The Roslin Institute, University of Edinburgh
Co-authored papers 1
Mar??a Rodr??guez Mart??nez
Herbert Irving Cancer Research Center, Columbia University Medical Center
Co-authored papers 1
Nick Juty
University of Manchester
Co-authored papers 1
Sandra Orchard
EMBL's European Bioinformatics Institute (EMBL-EBI)
Co-authored papers 1
Huaiyu Mi
University of Southern California
Co-authored papers 1
Bernhard O Palsson
University of California San Diego
Co-authored papers 1
Wolfgang M??ller
Heidelberg Institute for Theoretical Studies (HITS gGmbH)
Co-authored papers 1
Glyn Bradley
Co-authored papers 1
Kimberly Begley
California Institute of Technology
Co-authored papers 1
Noemi Del-Toro
European Bioinformatics Institute (EMBL-EBI)
Co-authored papers 1
Anne Niknejad
University of Lausanne
Co-authored papers 1
Marcio Luis Acencio
Norwegian University of Science and Technology
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Hiroaki Kitano
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Release 1.2