Thomas Cokelaer

16 papers Journal 16
YearRankTypeTitle / Venue / Authors
2023 J jnl
Reprohackathons: promoting reproducibility in bioinformatics through training.
Bioinform.
Thomas Cokelaer, Sarah Cohen-Boulakia, Frédéric Lemoine
2018 J jnl
GDSCTools for mining pharmacogenomic interactions in cancer.
Bioinform.
Thomas Cokelaer, Elisabeth Chen, Francesco Iorio, Michael P. Menden, Howard Lightfoot, Julio Saez-Rodriguez, Mathew Garnett
2018 J jnl
Sequanix: a dynamic graphical interface for Snakemake workflows.
Bioinform.
Dimitri Desvillechabrol, Rachel Legendre, Claire Rioualen, Christiane Bouchier, Jacques van Helden, Sean Kennedy, Thomas Cokelaer
2017 J jnl
'Sequana': a Set of Snakemake NGS pipelines.
J. Open Source Softw.
Thomas Cokelaer, Dimitri Desvillechabrol, Rachel Legendre, Mélissa Cardon
2017 J jnl
'Spectrum': Spectral Analysis in Python.
J. Open Source Softw.
Thomas Cokelaer, Jürgen Hasch
2016 J jnl
Efficient randomization of biological networks while preserving functional characterization of individual nodes.
BMC Bioinform.
Francesco Iorio, Marti Bernardo-Faura, Andrea Gobbi, Thomas Cokelaer, Giuseppe Jurman, Julio Saez-Rodriguez
2015 J jnl
DREAMTools: a Python package for scoring collaborative challenges.
F1000Research
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
2014 J jnl
Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming.
Bioinform.
Carito Guziolowski, Santiago Videla, Federica Eduati, Sven Thiele, Thomas Cokelaer, Anne Siegel, Julio Saez-Rodriguez
2014 J jnl
MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics.
BMC Bioinform.
Jose A. Egea, David Henriques, Thomas Cokelaer, Alejandro Fernández Villaverde, Aidan MacNamara, Diana-Patricia Danciu, Julio R. Banga, Julio Saez-Rodriguez
2014 J jnl
Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach.
BMC Syst. Biol.
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
2014 J jnl
Using Python to Dive into Signalling Data with CellNOpt and BioServices.
CoRR
Thomas Cokelaer, Julio Saez-Rodriguez
2013 J jnl
BioServices: a common Python package to access biological Web Services programmatically.
Bioinform.
Thomas Cokelaer, Dennis Pultz, Lea M. Harder, Jordi Serra-Musach, Julio Saez-Rodriguez
2013 J jnl
Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming.
Bioinform.
Carito Guziolowski, Santiago Videla, Federica Eduati, Sven Thiele, Thomas Cokelaer, Anne Siegel, Julio Saez-Rodriguez
2013 J jnl
MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics.
CoRR
Jose A. Egea, David Henriques, Thomas Cokelaer, Alejandro Fernández Villaverde, Julio R. Banga, Julio Saez-Rodriguez
2013 J jnl
SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools.
BMC Syst. Biol.
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
2012 J jnl
CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms.
BMC Syst. Biol.
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