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2020 – today
- 2023
[j13]Thomas Cokelaer
, Sarah Cohen-Boulakia, Frédéric Lemoine:
Reprohackathons: promoting reproducibility in bioinformatics through training. Bioinform. 39(Supplement-1): 11-20 (2023)
2010 – 2019
- 2018
- [j12]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): 1226-1228 (2018) - [j11]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): 1934-1936 (2018) - 2017
- [j10]Thomas Cokelaer, Dimitri Desvillechabrol, Rachel Legendre, Mélissa Cardon:
'Sequana': a Set of Snakemake NGS pipelines. J. Open Source Softw. 2(16): 352 (2017) - [j9]Thomas Cokelaer, Jürgen Hasch:
'Spectrum': Spectral Analysis in Python. J. Open Source Softw. 2(18): 348 (2017) - 2016
- [j8]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: 542:1-542:14 (2016) - 2015
- [i3]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: 1030 (2015) - 2014
- [j7]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): 1942 (2014) - [j6]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: 136 (2014) - [j5]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: 13 (2014) - [i2]Thomas Cokelaer, Julio Saez-Rodriguez:
Using Python to Dive into Signalling Data with CellNOpt and BioServices. CoRR abs/1412.6386 (2014) - 2013
- [j4]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): 2320-2326 (2013) - [j3]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): 3241-3242 (2013) - [j2]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: 135 (2013) - [i1]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 abs/1311.5735 (2013) - 2012
- [j1]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: 133 (2012)
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