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Thomas Cokelaer
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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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