Thomas Cokelaer

According to our database, Thomas Cokelaer authored at least 15 papers between 2012 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2023

Reprohackathons: promoting reproducibility in bioinformatics through training.

Thomas Cokelaer, Sarah Cohen-Boulakia, Frédéric Lemoine

Bioinform., 2023

2018

Sequanix: a dynamic graphical interface for Snakemake workflows.

Dimitri Desvillechabrol, Rachel Legendre, Claire Rioualen, Christiane Bouchier, Jacques van Helden, Sean Kennedy, Thomas Cokelaer

Bioinform., 2018

GDSCTools for mining pharmacogenomic interactions in cancer.

Thomas Cokelaer, Elisabeth Chen, Francesco Iorio, Michael P. Menden, Howard Lightfoot, Julio Saez-Rodriguez, Mathew Garnett

Bioinform., 2018

2017

'Spectrum': Spectral Analysis in Python.

Thomas Cokelaer, Jürgen Hasch

J. Open Source Softw., 2017

'Sequana': a Set of Snakemake NGS pipelines.

Thomas Cokelaer, Dimitri Desvillechabrol, Rachel Legendre, Mélissa Cardon

J. Open Source Softw., 2017

2016

Efficient randomization of biological networks while preserving functional characterization of individual nodes.

Francesco Iorio, Marti Bernardo-Faura, Andrea Gobbi, Thomas Cokelaer, Giuseppe Jurman, Julio Saez-Rodriguez

BMC Bioinform., 2016

2015

DREAMTools: a Python package for scoring collaborative challenges.

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

F1000Research, 2015

2014

Using Python to Dive into Signalling Data with CellNOpt and BioServices.

Thomas Cokelaer, Julio Saez-Rodriguez

CoRR, 2014

Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach.

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

BMC Syst. Biol., 2014

MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics.

Jose A. Egea, David Henriques, Thomas Cokelaer, Alejandro Fernández Villaverde, Aidan MacNamara, Diana-Patricia Danciu, Julio R. Banga, Julio Saez-Rodriguez

BMC Bioinform., 2014

2013

MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics.

Jose A. Egea, David Henriques, Thomas Cokelaer, Alejandro Fernández Villaverde, Julio R. Banga, Julio Saez-Rodriguez

CoRR, 2013

SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools.

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

BMC Syst. Biol., 2013

Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming.

Carito Guziolowski, Santiago Videla, Federica Eduati, Sven Thiele, Thomas Cokelaer, Anne Siegel, Julio Saez-Rodriguez

Bioinform., 2013

BioServices: a common Python package to access biological Web Services programmatically.

Thomas Cokelaer, Dennis Pultz, Lea M. Harder, Jordi Serra-Musach, Julio Saez-Rodriguez

Bioinform., 2013

2012

CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms.

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

BMC Syst. Biol., 2012