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2020 – today
- 2024
[i2]Marco Ruscone, Andrea Checcoli, Randy W. Heiland, Emmanuel Barillot, Paul Macklin, Laurence Calzone, Vincent Noël
:
Building multiscale models with PhysiBoSS, an agent-based modeling tool. CoRR abs/2406.18371 (2024)- 2022
- [j24]Anna Niarakis, Dagmar Waltemath, James A. Glazier, Falk Schreiber, Sarah M. Keating, David P. Nickerson, Claudine Chaouiya, Anne Siegel, Vincent Noël, Henning Hermjakob, Tomás Helikar, Sylvain Soliman, Laurence Calzone:
Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology. Briefings Bioinform. 23(4) (2022) - [j23]Anna Niarakis, Juilee Thakar, Matteo Barberis, María Rodríguez Martínez, Tomás Helikar, Marc R. Birtwistle, Claudine Chaouiya, Laurence Calzone, Andreas Dräger:
Computational modelling in health and disease: highlights of the 6th annual SysMod meeting. Bioinform. 38(21): 4990-4993 (2022) - [j22]Bilal Shaikh, Lucian P. Smith, Dan Vasilescu, Gnaneswara Marupilla, Michael Wilson, Eran Agmon, Henry Agnew, Steven S. Andrews, Azraf Anwar, Moritz E. Beber, Frank T. Bergmann, David Brooks, Lutz Brusch, Laurence Calzone, Kiri Choi, Joshua Cooper, John Detloff, Brian Drawert, Michel Dumontier, G. Bard Ermentrout, James R. Faeder, Andrew P. Freiburger, Fabian Fröhlich, Akira Funahashi, Alan Garny, John H. Gennari, Padraig Gleeson, Anne Goelzer, Zachary B. Haiman, Jan Hasenauer, Joseph L. Hellerstein, Henning Hermjakob, Stefan Hoops, Jon C. Ison, Diego Jahn, Henry V. Jakubowski, Ryann Jordan, Matús Kalas, Matthias König, Wolfram Liebermeister, Rahuman S. Malik-Sheriff, Synchon Mandal, Robert A. McDougal, J. Kyle Medley, Pedro Mendes, Robert Müller, Chris J. Myers, Aurélien Naldi, Tung V. N. Nguyen, David P. Nickerson, Brett G. Olivier, Drashti Patoliya, Loïc Paulevé, Linda R. Petzold, Ankita Priya, Anand K. Rampadarath, Johann M. Rohwer, Ali Sinan Saglam, Dilawar Singh, Ankur Sinha, Jacky L. Snoep, Hugh Sorby, Ryan K. Spangler, Jörn Starruß, Payton J. Thomas, David D. van Niekerk, Daniel Weindl, Fengkai Zhang, Anna Zhukova, Arthur P. Goldberg, James C. Schaff, Michael L. Blinov, Herbert M. Sauro, Ion I. Moraru, Jonathan R. Karr:
BioSimulators: a central registry of simulation engines and services for recommending specific tools. Nucleic Acids Res. 50(W1): 108-114 (2022) - [i1]Bilal Shaikh, Lucian P. Smith, Dan Vasilescu, Gnaneswara Marupilla, Michael Wilson, Eran Agmon, Henry Agnew, Steven S. Andrews, Azraf Anwar, Moritz E. Beber, Frank T. Bergmann, David Brooks, Lutz Brusch, Laurence Calzone, Kiri Choi, Joshua Cooper, John Detloff, Brian Drawert, Michel Dumontier, G. Bard Ermentrout, James R. Faeder, Andrew P. Freiburger, Fabian Fröhlich, Akira Funahashi, Alan Garny, John H. Gennari, Padraig Gleeson, Anne Goelzer, Zachary B. Haiman, Joseph L. Hellerstein, Stefan Hoops, Jon C. Ison, Diego Jahn, Henry V. Jakubowski, Ryann Jordan, Matús Kalas, Matthias König, Wolfram Liebermeister, Synchon Mandal, Robert A. McDougal, J. Kyle Medley, Pedro Mendes, Robert Müller, Chris J. Myers, Aurélien Naldi, Tung V. N. Nguyen, David P. Nickerson, Brett G. Olivier, Drashti Patoliya, Loïc Paulevé, Linda R. Petzold, Ankita Priya, Anand K. Rampadarath, Johann M. Rohwer, Ali Sinan Saglam, Dilawar Singh, Ankur Sinha, Jacky L. Snoep, Hugh Sorby, Ryan K. Spangler, Jörn Starruß, Payton J. Thomas, David D. van Niekerk, Daniel Weindl, Fengkai Zhang, Anna Zhukova, Arthur P. Goldberg, Michael L. Blinov, Herbert M. Sauro, Ion I. Moraru, Jonathan R. Karr:
BioSimulators: a central registry of simulation engines and services for recommending specific tools. CoRR abs/2203.06732 (2022) - 2021
- [j21]Anna Niarakis, Martin Kuiper, Marek Ostaszewski, Rahuman S. Malik-Sheriff, Cristina Casals-Casas, Denis Thieffry, Tom C. Freeman, Paul D. Thomas, Vasundra Touré, Vincent Noël, Gautier Stoll, Julio Saez-Rodriguez, Aurélien Naldi, Eugenia Oshurko, Ioannis Xenarios, Sylvain Soliman, Claudine Chaouiya, Tomás Helikar, Laurence Calzone:
Setting 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. Briefings Bioinform. 22(2): 1848-1859 (2021) - [j20]Andreas Dräger, Tomás Helikar, Matteo Barberis, Marc R. Birtwistle, Laurence Calzone, Claudine Chaouiya, Jan Hasenauer, Jonathan R. Karr, Anna Niarakis, María Rodríguez Martínez, Julio Saez-Rodriguez, Juilee Thakar:
SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems. Bioinform. 37(21): 3702-3706 (2021) - [j19]Jonas Béal, Lorenzo Pantolini, Vincent Noël, Emmanuel Barillot, Laurence Calzone:
Personalized logical models to investigate cancer response to BRAF treatments in melanomas and colorectal cancers. PLoS Comput. Biol. 17(1) (2021) - 2020
- [j18]Mihály Koltai, Vincent Noel, Andrei Yu. Zinovyev, Laurence Calzone, Emmanuel Barillot:
Exact solving and sensitivity analysis of stochastic continuous time Boolean models. BMC Bioinform. 21(1): 241 (2020) - [c1]Stéphanie Chevalier, Vincent Noël, Laurence Calzone, Andrei Yu. Zinovyev, Loïc Paulevé:
Synthesis and Simulation of Ensembles of Boolean Networks for Cell Fate Decision. CMSB 2020: 193-209
2010 – 2019
- 2019
- [j17]Arnau Montagud, Pauline Traynard, Loredana Martignetti, Eric Bonnet, Emmanuel Barillot, Andrei Yu. Zinovyev, Laurence Calzone:
Conceptual and computational framework for logical modelling of biological networks deregulated in diseases. Briefings Bioinform. 20(4): 1238-1249 (2019) - [j16]Gaëlle Letort, Arnau Montagud, Gautier Stoll, Randy W. Heiland, Emmanuel Barillot, Paul Macklin, Andrei Yu. Zinovyev, Laurence Calzone:
PhysiBoSS: a multi-scale agent-based modelling framework integrating physical dimension and cell signalling. Bioinform. 35(7): 1188-1196 (2019) - 2017
- [j15]Gautier Stoll, Barthélémy Caron, Eric Viara, Aurélien Dugourd, Andrei Yu. Zinovyev, Aurélien Naldi, Guido Kroemer, Emmanuel Barillot, Laurence Calzone:
MaBoSS 2.0: an environment for stochastic Boolean modeling. Bioinform. 33(14): 2226-2228 (2017) - 2016
- [j14]Adrien Rougny, Christine Froidevaux, Laurence Calzone, Loïc Paulevé:
Qualitative dynamics semantics for SBGN process description. BMC Syst. Biol. 10: 42 (2016) - 2015
- [j13]Urszula Czerwinska, Laurence Calzone, Emmanuel Barillot, Andrei Yu. Zinovyev:
DeDaL: Cytoscape 3 app for producing and morphing data-driven and structure-driven network layouts. BMC Syst. Biol. 9: 46 (2015) - [j12]Eric Bonnet, Eric Viara, Inna Kuperstein, Laurence Calzone, David P. A. Cohen, Emmanuel Barillot, Andrei Yu. Zinovyev:
NaviCell Web Service for network-based data visualization. Nucleic Acids Res. 43(Webserver-Issue): W560-W565 (2015) - [j11]Eric Bonnet, Laurence Calzone, Tom Michoel:
Integrative Multi-omics Module Network Inference with Lemon-Tree. PLoS Comput. Biol. 11(2) (2015) - [j10]David P. A. Cohen, Loredana Martignetti, Sylvie Robine, Emmanuel Barillot, Andrei Yu. Zinovyev, Laurence Calzone:
Mathematical Modelling of Molecular Pathways Enabling Tumour Cell Invasion and Migration. PLoS Comput. Biol. 11(11) (2015) - 2013
- [j9]Eric Bonnet, Laurence Calzone, Daniel Rovera, Gautier Stoll, Emmanuel Barillot, Andrei Yu. Zinovyev:
BiNoM 2.0, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats. BMC Syst. Biol. 7: 18 (2013) - [j8]Inna Kuperstein, David P. A. Cohen, Stuart Pook, Eric Viara, Laurence Calzone, Emmanuel Barillot, Andrei Yu. Zinovyev:
NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps. BMC Syst. Biol. 7: 100 (2013) - [j7]Luca Grieco, Laurence Calzone, Isabelle Bernard-Pierrot, François Radvanyi, Brigitte Kahn-Perlès, Denis Thieffry:
Integrative Modelling of the Influence of MAPK Network on Cancer Cell Fate Decision. PLoS Comput. Biol. 9(10) (2013) - 2012
- [j6]Gautier Stoll, Eric Viara, Emmanuel Barillot, Laurence Calzone:
Continuous time boolean modeling for biological signaling: application of Gillespie algorithm. BMC Syst. Biol. 6: 116 (2012) - 2010
- [j5]Laurence Calzone, Laurent Tournier, Simon Fourquet, Denis Thieffry, Boris Zhivotovsky, Emmanuel Barillot, Andrei Yu. Zinovyev:
Mathematical Modelling of Cell-Fate Decision in Response to Death Receptor Engagement. PLoS Comput. Biol. 6(3) (2010)
2000 – 2009
- 2008
- [j4]Andrei Yu. Zinovyev, Eric Viara, Laurence Calzone, Emmanuel Barillot:
BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks. Bioinform. 24(6): 876-877 (2008) - 2007
- [j3]Laurence Calzone, Nathalie Chabrier-Rivier, François Fages, L. Fosse, Sylvain Soliman:
Langages formels dans la machine abstraite biochimique BIOCHAM. Tech. Sci. Informatiques 26(1-2): 47-72 (2007) - 2006
- [j2]Laurence Calzone, François Fages, Sylvain Soliman:
BIOCHAM: an environment for modeling biological systems and formalizing experimental knowledge. Bioinform. 22(14): 1805-1807 (2006) - [j1]Laurence Calzone, Nathalie Chabrier-Rivier, François Fages, Sylvain Soliman:
Machine Learning Biochemical Networks from Temporal Logic Properties. Trans. Comp. Sys. Biology 6: 68-94 (2006)
Coauthor Index
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