Thomas Cokelaer

Publication Activity (10 Years)

Years Active: 2012-2023
Publications (10 Years): 6

Top Topics

Qualitative Models

Answer Set Programming

Biological Networks

Top Venues

J. Open Source Softw.

Publications

Thomas Cokelaer, Sarah Cohen-Boulakia, Frédéric Lemoine
Reprohackathons: promoting reproducibility in bioinformatics through training. Bioinform. 39 (Supplement-1) (2023)
Dimitri Desvillechabrol, Rachel Legendre, Claire Rioualen, Christiane Bouchier, Jacques van Helden, Sean Kennedy, Thomas Cokelaer
Sequanix: a dynamic graphical interface for Snakemake workflows. Bioinform. 34 (11) (2018)
Thomas Cokelaer, Elisabeth Chen, Francesco Iorio, Michael P. Menden, Howard Lightfoot, Julio Saez-Rodriguez, Mathew Garnett
GDSCTools for mining pharmacogenomic interactions in cancer. Bioinform. 34 (7) (2018)
Thomas Cokelaer, Jürgen Hasch
'Spectrum': Spectral Analysis in Python. J. Open Source Softw. 2 (18) (2017)
Thomas Cokelaer, Dimitri Desvillechabrol, Rachel Legendre, Mélissa Cardon
'Sequana': a Set of Snakemake NGS pipelines. J. Open Source Softw. 2 (16) (2017)
Francesco Iorio, Marti Bernardo-Faura, Andrea Gobbi, Thomas Cokelaer, Giuseppe Jurman, Julio Saez-Rodriguez
Efficient randomization of biological networks while preserving functional characterization of individual nodes. BMC Bioinform. 17 (2016)
Thomas Cokelaer, Mukesh Bansal, Christopher Bare, Erhan Bilal, Brian M. Bot, Elias Chaibub Neto, Federica Eduati, Mehmet Gönen, Steven M. Hill, Bruce R. Hoff, Jonathan R. Karr, Robert Küffner, Michael P. Menden, Pablo Meyer, Raquel Norel, Abhishek Pratap, Robert J. Prill, Matthew T. Weirauch, James C. Costello, Gustavo Stolovitzky, Julio Saez-Rodriguez
DREAMTools: a Python package for scoring collaborative challenges. F1000Research 4 (2015)
Pablo Meyer, Thomas Cokelaer, Deepak Chandran, Kyung Hyuk Kim, Po-Ru Loh, George Tucker, Mark Lipson, Bonnie Berger, Clemens Kreutz, Andreas Raue, Bernhard Steiert, Jens Timmer, Erhan Bilal, Herbert M. Sauro, Gustavo Stolovitzky, Julio Saez-Rodriguez
Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach. BMC Syst. Biol. 8 (2014)
Thomas Cokelaer, Julio Saez-Rodriguez
Using Python to Dive into Signalling Data with CellNOpt and BioServices. CoRR (2014)
Jose A. Egea, David Henriques, Thomas Cokelaer, Alejandro Fernández Villaverde, Aidan MacNamara, Diana-Patricia Danciu, Julio R. Banga, Julio Saez-Rodriguez
MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics. BMC Bioinform. 15 (2014)
Carito Guziolowski, Santiago Videla, Federica Eduati, Sven Thiele, Thomas Cokelaer, Anne Siegel, Julio Saez-Rodriguez
Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming. Bioinform. 30 (13) (2014)
Carito Guziolowski, Santiago Videla, Federica Eduati, Sven Thiele, Thomas Cokelaer, Anne Siegel, Julio Saez-Rodriguez
Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming. Bioinform. 29 (18) (2013)
Thomas Cokelaer, Dennis Pultz, Lea M. Harder, Jordi Serra-Musach, Julio Saez-Rodriguez
BioServices: a common Python package to access biological Web Services programmatically. Bioinform. 29 (24) (2013)
Claudine Chaouiya, Duncan Bérenguier, Sarah M. Keating, Aurélien Naldi, Martijn P. van Iersel, Nicolas Rodriguez, Andreas Dräger, Finja Büchel, Thomas Cokelaer, Bryan M. Kowal, Benjamin Wicks, Emanuel J. V. Gonçalves, Julien Dorier, Michel Page, Pedro T. Monteiro, Axel von Kamp, Ioannis Xenarios, Hidde de Jong, Michael Hucka, Steffen Klamt, Denis Thieffry, Nicolas Le Novère, Julio Saez-Rodriguez, Tomás Helikar
SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. BMC Syst. Biol. 7 (2013)
Jose A. Egea, David Henriques, Thomas Cokelaer, Alejandro Fernández Villaverde, Julio R. Banga, Julio Saez-Rodriguez
MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics. CoRR (2013)
Camille Terfve, Thomas Cokelaer, David Henriques, Aidan MacNamara, Emanuel J. V. Gonçalves, Melody K. Morris, Martijn P. van Iersel, Douglas A. Lauffenburger, Julio Saez-Rodriguez
CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms. BMC Syst. Biol. 6 (2012)