Cooperative development of logical modelling standards and tools with CoLoMoTo.
Bioinformatics (Oxford, England) 2015;31;7;1154-9
Phosphoproteomic analyses reveal novel cross-modulation mechanisms between two signaling pathways in yeast.
Molecular systems biology 2014;10;767
MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics.
BMC bioinformatics 2014;15;136
A community effort to assess and improve drug sensitivity prediction algorithms.
Nature biotechnology 2014;32;12;1202-12
Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach.
BMC systems biology 2014;8;13
SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools.
BMC systems biology 2013;7;135
BioServices: a common Python package to access biological Web Services programmatically.
Bioinformatics (Oxford, England) 2013;29;24;3241-2
Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming.
Bioinformatics (Oxford, England) 2013;29;18;2320-6
CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms.
BMC systems biology 2012;6;133
L-py: an L-system simulation framework for modeling plant architecture development based on a dynamic language.
Frontiers in plant science 2012;3;76