@TechReport{,
author = {Sylvain Soliman and Andrei Zinovyev},
title = {Reduction of differential models},
institution = {ANR CALAMAR (ANR-08-SYSC-003)},
year = {2011},
month = sep,
type = {deliverable},
number = {D1.2},
url = {http://tagc.univ-mrs.fr/welcome/IMG/pdf/Livrable-1-2.pdf},
}
@TechReport{,
author = {Sylvain Soliman},
title = {Preuves S{\'e}mantiques pour les Programmes Concurrents
avec Contraintes},
institution = {{INRIA}},
year = {1997},
type = {Rapport de stage de {DEA}},
}
@TechReport{,
author = {Sylvain Soliman},
title = {Constraint Programming for the Dynamical Analysis of
Biochemical Systems -- A Survey },
institution = {ANR CALAMAR (ANR-08-SYSC-003)},
year = {2011},
month = feb,
type = {deliverable},
number = {D1.6},
url = {http://tagc.univ-mrs.fr/welcome/IMG/pdf/Livrable-1-6.pdf},
}
@Misc{,
author = {Sylvain Soliman},
title = {Langages formels pour la biologie syst{\'e}mique dans la
machine abstraite biochimique {BIOCHAM}},
howpublished = {Avanc{\'e}es en Sciences de l'Information},
year = {2007},
month = oct,
address = {Acad{\'e}mie des sciences},
url = {http://contraintes.inria.fr/~soliman/publi/AcademieDesSciences071009.pdf}
}
@TechReport{,
author = {Sylvain Soliman},
title = {Pi-calculus and {LCC}, a Space Odyssey},
oai = {http://hal.inria.fr/inria-00071728/},
eprinttype = {HAL},
eprint = {inria-00071728},
institution = {{INRIA}},
number = {RR-4855},
year = {2003},
type = {Research Report},
month = jun,
}
@Misc{,
author = {Sylvain Soliman},
title = {{CLP} Implementation of a Phase Model Checker},
url = {http://contraintes.inria.fr/~soliman/publi/lics02.ps.gz},
year = {2002},
howpublished = {{LICS'02}: 17th Annual IEEE Symposium on Logic In Computer
Science, Short Session},
}
@PhDThesis{,
author = {Sylvain Soliman},
title = {Programmation concurrente avec con\-traintes et logique
lin{\'e}aire},
url = {http://contraintes.inria.fr/~soliman/publi/these.ps.gz},
school = {Universit{\'e} Paris 7, Denis Diderot},
month = apr,
year = {2001},
}
@Article{,
author = {Sylvain Soliman and Monika Heiner},
title = {A Unique Transformation from Ordinary Differential
Equations to Reaction Networks},
journal = {{PLoS} One},
publisher = {Public Library of Science},
volume = {5},
number = {12},
pages = {e14284},
doi = {10.1371/journal.pone.0014284},
year = {2010},
month = dec,
}
@TechReport{,
title = {Modelling molecular networks: relationships between
different formalisms and levels of details},
author = {Sylvain Soliman and Claudine Chaouiya and Gr{\'e}gory Batt
and Fran{\c{c}}ois Fages and {\'E}lisabeth Remy and Franck
Pommereau and Laurence Calzone},
institution = {{INRIA}},
type = {Research Report},
year = {2010},
number = {RR-7221},
oai = {http://hal.inria.fr/inria-00461084/},
eprinttype = {HAL},
eprint = {inria-00461084},
}
@TechReport{,
author = {Rolf Backofen and Liviu Badea and Pedro Barahona and
Mikael Berndtsson and Albert Burger and Gihan Dawelbait and
Andreas Doms and Fran{\c{c}}ois Fages and Anca Hotaran and
Vaida Jakoniene and Ludwig Krippahl and Patrick Lambrix and
Kenneth McLeod and Werner Nutt and Bjorn Olsson and Michael
Schroeder and Anna Schroiff and Loic Royer and Sylvain
Soliman and He Tan and Doina Tilivea and Sebastian Will},
title = {Requirements and specification of bioinformatics use
cases},
institution = {Dresden},
editor = {Michael Schroeder},
year = {2005},
month = aug,
type = {deliverable},
number = {A2-D3},
url = {http://www.rewerse.net/deliverables/m18/a2-d3.pdf},
}
@TechReport{,
author = {Rolf Backofen and Liviu Badea and Pedro Barahona and
Albert Burger and Gihan Dawelbait and Andreas Doms and
Fran{\c{c}}ois Fages and Anca Hotaran and Vaida Jakoniene
and Ludwig Krippahl and Patrick Lambrix and Kenneth McLeod
and Steffen M{\"o}ller and Werner Nutt and Bjorn Olsson and
Michael Schroeder and Sylvain Soliman and He Tan and Doina
Tilivea and Sebastian Will},
title = {Usage of Bioinformatics Tools and Identification of
Information Sources},
institution = {Lisbon},
editor = {Pedro Barahona},
year = {2005},
month = mar,
type = {deliverable},
number = {A2-D2},
url = {http://www.rewerse.net/deliverables/m12/a2-d2.pdf},
}
@TechReport{,
author = {Rolf Backofen and Mike Badea and Albert Burger and
Fran{\c{c}}ois Fages and Patrick Lambrix and Werner Nutt
and Michael Schroeder and Sylvain Soliman and Sebastian
Will},
title = {State-of-the-art in Bioinformatics},
institution = {Dresden},
editor = {Michael Schroeder},
year = {2004},
type = {deliverable},
number = {A2-D1},
url = {http://www.rewerse.net/deliverables/a2-d1.pdf},
}
@Article{,
author = {Aur{\'e}lien Rizk and Gr{\'e}gory Batt and Fran{\c{c}}ois
Fages and Sylvain Soliman},
title = {Continuous Valuations of Temporal Logic Specifications
with applications to Parameter Optimization and Robustness
Measures},
journal = {Theoretical Computer Science},
year = {2011},
volume = {412},
number = {26},
doi = {10.1016/j.tcs.2010.05.008},
pages = {2827--2839},
}
@Article{,
author = {Aur{\'e}lien Rizk and Gr{\'e}gory Batt and Fran{\c{c}}ois
Fages and Sylvain Soliman},
title = {A general computational method for robustness analysis
with applications to synthetic gene networks},
journal = {Bioinformatics},
year = {2009},
month = jun,
number = {25},
volume = {12},
pages = {il69--il78},
doi = {10.1093/bioinformatics/btp200},
}
@Book{,
editor = {Fran{\c{c}}ois Fages and Francesca Rossi and Sylvain
Soliman},
title = {Recent Advances in Constraints, post-proceedings of 12th
Annual ERCIM International Workshop on Constraint Solving
and Constraint Logic Programming CSCLP'07},
series = {Lecture Notes in Artificial Intelligence},
volume = {5129},
publisher = {Springer-Verlag},
year = {2008},
address = {Rocquencourt, France},
doi = {10.1007/978-3-540-89812-2},
}
@Misc{,
author = {{\'E}tienne Parizot and Sylvain Soliman and Fran{\c{c}}ois
Fages},
title = {La programmation par contraintes},
howpublished = {Dossier algorithmique du site web de vulgarisation
interstices.info},
year = {2004},
month = feb,
url = {http://interstices.info/jcms/c_5782/la-programmation-par-contraintes}
}
@Article{,
author = {Sriram Krishnamachari and Sylvain Soliman and
Fran{\c{c}}ois Fages},
title = {Dynamics of the interlocked positive feedback loops
explaining the robust epigenetic switching in Candida
albicans},
journal = {Journal of Theoretical Biology},
year = {2009},
volume = {258},
number = {1},
pages = {71--88},
doi = {10.1016/j.jtbi.2009.01.008},
}
@TechReport{,
author = {R{\'e}my Haemmerl{\'e} and Fran{\c{c}}ois Fages and
Sylvain Soliman},
title = {On Internalizing Modules as Agents in Concurrent
Constraint Programming},
institution = {{INRIA}},
year = {2006},
number = {RR-5981},
oai = {http://hal.inria.fr/inria-00096644/},
eprinttype = {HAL},
eprint = {inria-00096644},
}
@Article{,
author = {Steven Gay and Sylvain Soliman and Fran{\c{c}}ois Fages},
title = {A Graphical Method for Reducing and Relating Models in
Systems Biology},
journal = {Bioinformatics},
year = {2010},
volume = {26},
number = {18},
doi = {10.1093/bioinformatics/btq388},
pages = {i575--i581},
}
@Article{,
author = {Steven Gay and Fran{\c{c}}ois Fages and Thierry Martinez
and Sylvain Soliman and Christine Solnon },
title = {On the subgraph Epimorphism Problem},
journal = {Discrete Applied Mathematics},
year = {2011},
}
@Article{,
author = {Fran{\c{c}}ois Fages and Sylvain Soliman and Nathalie
Chabrier-Rivier},
title = {Modelling and Querying Interaction Networks in the
Biochemical Abstract Machine {BIOCHAM}},
journal = {Journal of Biological Physics and Chemistry},
volume = {4},
number = {2},
year = {2004},
pages = {64--73},
month = oct,
url = {http://contraintes.inria.fr/~soliman/publi/FSC04jbpc.ps.gz}
}
@Article{,
author = {Fran{\c{c}}ois Fages and Sylvain Soliman and R{\'e}mi
Coolen},
title = {{CLPGUI}: a Generic Graphical User Interface for
Constraint Logic Programming},
journal = {Journal of Constraints, Special Issue on User-Interaction
in Constraint Satisfaction},
volume = {9},
number = {4},
pages = {241--262},
month = oct,
year = {2004},
doi = {10.1023/B:CONS.0000049203.53383.c1},
publisher = {Kluwer Academic Publishers},
}
@Article{,
author = {Fran{\c{c}}ois Fages and Sylvain Soliman},
title = {Abstract Interpretation and Types for Systems Biology},
journal = {Theoretical Computer Science},
year = {2008},
volume = {403},
number = {1},
pages = {52--70},
doi = {10.1016/j.tcs.2008.04.024},
}
@Article{,
author = {Fran{\c{c}}ois Fages and Paul Ruet and Sylvain Soliman},
title = {Linear concurrent constraint programming: operational and
phase semantics},
year = {2001},
journal = {Information and Computation},
volume = {165},
number = {1},
month = feb,
pages = {14--41},
doi = {10.1006/inco.2000.3002}
}
@TechReport{,
author = {Fran{\c{c}}ois Fages and Philip Robin and Sylvain Soliman},
title = {Simulations hybrides},
institution = {{OSEO project BioIntelligence}},
year = {2011},
type = {deliverable},
number = {INR-04-L3-D14},
}
@Article{,
author = {Fran{\c{c}}ois Fages and Gr{\'e}gory Batt and Elisabetta
{{D}e Maria} and Dragana Jovanovska and Aur{\'e}lien Rizk
and Sylvain Soliman},
title = {Computational Systems Biology in BIOCHAM},
journal = {ERCIM News},
volume = {82},
month = jul,
year = {2010},
url = {http://ercim-news.ercim.eu/en82/special/computational-systems-biology-in-biocham}
}
@TechReport{,
author = {Elisabetta {{D}e Maria} and Fran{\c{c}}ois Fages and
Sylvain Soliman},
title = {Model-based Predictions of the Influence of Circadian
Clock Genes Knock-Outs on the Cell Cycle},
institution = {INRIA},
year = {2009},
month = jun,
type = {{INRIA} {Research} {Report}},
number = {RR-7064},
oai = {http://hal.inria.fr/inria-00424950/},
eprinttype = {HAL},
eprint = {inria-00424950},
}
@Article{,
author = {Elisabetta {{D}e Maria} and Fran{\c{c}}ois Fages and
Aur{\'e}lien Rizk and Sylvain Soliman},
title = {Design, Optimization, and Predictions of a Coupled Model
of the Cell Cycle, Circadian Clock, DNA Repair System,
Irinotecan Metabolism and Exposure Control under Temporal
Logic Constraints},
doi = {10.1016/j.tcs.2010.10.036},
journal = {Theoretical Computer Science},
year = {2011},
volume = {412},
number = {21},
pages = {2108--2127},
month = may,
}
@TechReport{,
author = {Laurence Calzone and Sylvain Soliman},
title = {Quantitative Modelling of the {RB/E2F} network},
institution = {ANR CALAMAR (ANR-08-SYSC-003)},
year = {2011},
month = sep,
type = {deliverable},
number = {D3.2},
url = {http://tagc.univ-mrs.fr/welcome/IMG/pdf/Livrable-3-2.pdf},
}
@TechReport{,
author = {Laurence Calzone and Sylvain Soliman},
title = {Coupling the Cell cycle and the Circadian Cycle},
institution = {{INRIA}},
type = {Research {R}eport},
number = {5835},
year = {2006},
month = feb,
oai = {http://hal.inria.fr/inria-00070191/},
eprinttype = {HAL},
eprint = {inria-00070191},
}
@Misc{,
author = {Laurence Calzone and Sylvain Soliman},
title = {{BIOCHAM}: une approche langage de la Biologie des
Syst{\`e}mes},
howpublished = {Conf{\'e}rence OUEST-genopole},
year = {2005},
month = sep,
address = {IRISA, Rennes},
url = {http://contraintes.inria.fr/~soliman/publi/GenopoleOuest050908.pdf}
}
@TechReport{,
author = {Nathalie Chabrier-Rivier and Fran{\c{c}}ois Fages and
Sylvain Soliman and Laurence Calzone},
title = {Learning transition rules from temporal logic properties},
institution = {{INRIA}},
type = {Research {R}eport},
number = {5543},
year = {2005},
month = apr,
oai = {http://hal.inria.fr/inria-00070464/},
eprinttype = {HAL},
eprint = {inria-00070464},
}
@Article{,
author = {Jean Clairambault and Fran{\c{c}}ois Fages and Sylvain
Soliman},
title = {Patient-tailored cancer therapeutics - The TEMPO Project},
journal = {ERCIM News},
volume = {69},
month = apr,
pages = {24--25},
year = {2007},
url = {http://ercim-news.ercim.eu/patient-tailored-cancer-therapeutics-the-tempo-project/}
}
@Article{,
author = {Laurence Calzone and Fran{\c{c}}ois Fages and Sylvain
Soliman},
title = {{BIOCHAM}: An Environment for Modeling Biological Systems
and Formalizing Experimental Knowledge},
journal = {Bioinformatics},
publisher = {Oxford Univ. Press},
year = {2006},
number = {14},
volume = {22},
pages = {1805--1807},
doi = {10.1093/bioinformatics/btl172},
}
@TechReport{,
author = {Laurence Calzone and Claudine Chaouiya and {\'E}lisabeth
Remy and Sylvain Soliman},
title = {Qualitative Modelling of the {RB/E2F} network},
institution = {ANR CALAMAR (ANR-08-SYSC-003)},
year = {2011},
month = feb,
type = {deliverable},
number = {D3.1},
url = {http://tagc.univ-mrs.fr/welcome/IMG/pdf/livrable-3-1.pdf},
}
@Article{,
author = {Laurence Calzone and Nathalie Chabrier-Rivier and
Fran{\c{c}}ois Fages and Sylvain Soliman},
title = {Langages formels dans la machine abstraite biochimique
{BIOCHAM}},
editor = {Herm{\`e}s},
journal = {Techniques et Sciences Informatiques},
volume = {26},
number = {1--2},
pages = {47--72},
year = {2007},
doi = {10.3166/tsi.26.47-72},
}
@Manual{,
title = {{BIOCHAM} v2.8 user's manual},
author = {Fran{\c{c}}ois Fages and Sylvain Soliman and Aur{\'e}lien
Rizk},
organization = {{INRIA}},
year = {2009},
url = {http://contraintes.inria.fr/BIOCHAM/DOC/biocham.html},
}
@Manual{,
title = {{BIOCHAM} user's manual},
author = {Nathalie Chabrier and Fran{\c{c}}ois Fages and Sylvain
Soliman},
organization = {{INRIA}},
year = {2004},
url = {http://contraintes.inria.fr/BIOCHAM/DOC/biocham.html},
}
@Manual{,
title = {{BIOCHAM} v3.3 Reference Manual},
author = {Fran{\c{c}}ois Fages and Dragana Jovanovska and
Aur{\'e}lien Rizk and Sylvain Soliman},
organization = {{INRIA}},
year = {2011},
url = {http://contraintes.inria.fr/BIOCHAM/DOC/manual.html},
}
@InProceedings{,
author = {Steven Gay and Thierry Martinez and Sylvain Soliman and
Fran{\c{c}}ois Fages},
title = {A Constraint Program For Subgraph Epimorphisms with
Application to Identifying Model Reductions in Systems
Biology},
booktitle = {Proceedings of the seventh Workshop on Constraint Based
Methods for Bioinformatics WCB'11, colocated with CP 2011},
month = sep,
url = {http://www.dmi.unipg.it/WCB11/wcb11proc.pdf},
year = {2011},
pages = {59--66},
}
@InProceedings{,
author = {Faten Nabli and Sylvain Soliman},
title = {Steady-state solution of biochemical systems, beyond
{S-Systems} via {T}-invariants},
booktitle = {{CMSB'10}: Proceedings of the 8th International Conference
on Computational Methods in Systems Biology},
year = {2010},
month = oct,
editor = {Paola Quaglia},
pages = {14--22},
location = {Trento, Italy},
organization = {CoSBi},
publisher = {ACM},
isbn = {978-1-4503-0068-1},
doi = {10.1145/1839764.1839768},
url = {http://portal.acm.org/citation.cfm?id=1839768},
}
@InProceedings{,
author = {Dragana Jovanovska and Fran{\c{c}}ois Fages and Sylvain
Soliman},
title = {{SBGN} support in {BIOCHAM}},
entrysubtype = {poster},
booktitle = {the COmputational Modeling in BIology NEtwork, (invited
talk)},
address = {University of Edinburgh, UK},
year = {2010},
month = oct,
doi = {10.1038/npre.2010.5189.1},
organization = {Nature Precedings},
}
@InProceedings{,
author = {Fran{\c{c}}ois Fages and Sylvain Soliman},
title = {New Computational Methods for Systems Biology (tutorial)},
booktitle = {{ICSB'10} 11th International Conference on Systems
Biology: abstract of tutorials},
year = {2010},
month = oct,
publisher = {University of Edinburgh, UK},
}
@Conference{,
author = {Dragana Jovanovska and Fran{\c{c}}ois Fages and Sylvain
Soliman},
title = {Modelling molecular networks with the Biocham Graphical
User Interface (poster)},
booktitle = {Evry Spring School on Modelling Complex Biological Systems
in the Context of Genomics},
address = {Evry, France},
year = {2010},
month = may,
}
@InProceedings{,
author = {Steven Gay and Fran{\c{c}}ois Fages and Sylvain Soliman},
title = {From models to metamodels},
booktitle = {{IPG'10} Integrative Post-Genomique},
year = {2010},
month = nov,
publisher = {University of Lyon, France},
}
@Conference{,
author = {Elisabetta {{D}e Maria} and Fran{\c{c}}ois Fages and
Aur{\'e}lien Rizk and Sylvain Soliman},
title = {Design, Optimization, and Predictions of a Coupled Model
of the Cell Cycle, Circadian Clock, DNA Repair System,
Irinotecan Metabolism and Exposure Control under Temporal
Logic Constraints (poster)},
booktitle = {European Conference on Computational Biology ECCB'10},
address = {Gent, Belgium},
year = {2010},
}
@Conference{,
author = {Faten Nabli and Sylvain Soliman and Fran{\c{c}}ois Fages},
title = {Bipartite Graph Properties and Systems Biology (poster)},
booktitle = {Evry Spring School on Modelling Complex Biological Systems
in the Context of Genomics},
address = {Evry, France},
year = {2010},
month = may,
}
@InProceedings{,
author = {Steven Gay and Sylvain Soliman and Fran{\c{c}}ois Fages},
title = {A Graphical Method for Reducing and Relating Models in
Systems Biology},
booktitle = {Graphical models for reasoning on biological systems:
computational challenges (Satellite workshop)},
address = {ISCTE Lisbon University Institute, Portugal},
year = {2010},
month = sep,
organization = {Complex Systems Society},
}
@InProceedings{,
author = {Elisabetta {{D}e Maria} and Fran{\c{c}}ois Fages and
Sylvain Soliman},
title = {A Coupled Model of Cell Cycle, Circadian Clock, DNA Repair
System, Irinotecan Metabolism, and Exposure Control},
booktitle = {42{\`e}me congr{\`e}s de la soci{\'e}t{\'e} Francophone de
Chronobiologie},
year = {2010},
}
@InProceedings{,
author = {Elisabetta {{D}e Maria} and Fran{\c{c}}ois Fages and
Sylvain Soliman},
title = {On Coupling Models using Model-Checking: Effects of
Irinotecan Injections on the Mammalian Cell Cycle},
booktitle = {{CMSB'09}: Proceedings of the seventh international
conference on Computational Methods in Systems Biology},
year = {2009},
series = {Lecture Notes in BioInformatics},
publisher = {Springer-Verlag},
volume = {5688},
pages = {142--157},
doi = {10.1007/978-3-642-03845-7_10},
}
@InProceedings{,
author = {Sylvain Soliman},
title = {Modelling Biochemical Reaction Networks with BIOCHAM
Extracting Qualitative and Quantitative Information from
the Structure},
booktitle = {Proceedings of the 6th Vienna Conference on Mathematical
Modelling {MATHMOD}'09},
month = feb,
year = {2009},
publisher = {{ARGESIM}},
volume = {35},
isbn = {978-3-901608-35-3},
pages = {2304--2312},
}
@InProceedings{,
author = {Attila Csik{\'a}sz-Nagy and Adrien Faure and Roberto
Larcher and Paola Lecca and Ivan Mura and Ferenc Jordan and
Alida Palmisano and Alessandro Romanel and Sean Sedwards
and Heike Siebert and Sylvain Soliman and Denis Thieffry
and Judit Z{\'a}mborszky and Tommaso Mazza and Paolo
Ballarini},
title = {Analyzing various models of Circadian Clock and Cell Cycle
coupling},
booktitle = {Formal Methods in Molecular Biology},
year = {2009},
month = may,
editor = {Rainer Breitling and David Roger Gilbert and Monika Heiner
and Corrado Priami},
number = {09091},
series = {Dagstuhl Seminar Proceedings},
issn = {1862-4405},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik,
Germany},
address = {Dagstuhl, Germany},
url = {http://drops.dagstuhl.de/opus/volltexte/2009/1994},
}
@InProceedings{,
author = {Aur{\'e}lien Rizk and Gr{\'e}gory Batt and Fran{\c{c}}ois
Fages and Sylvain Soliman},
title = {Towards a general computational method for robustness
analysis},
booktitle = {International Conference Frontiers in Synthetic Biology},
year = {2008},
address = {Boston},
}
@Conference{,
author = {Aur{\'e}lien Rizk and Gr{\'e}gory Batt and Fran{\c{c}}ois
Fages and Sylvain Soliman},
title = {Towards a general computational method for robustness
analysis (poster)},
booktitle = {International Conference Synthetic Biology 4.0},
year = {2008},
address = {Hong Kong},
}
@InProceedings{,
author = {Aur{\'e}lien Rizk and Gr{\'e}gory Batt and Fran{\c{c}}ois
Fages and Sylvain Soliman},
title = {On a Continuous Degree of Satisfaction of Temporal Logic
Formulae with Applications to Systems Biology},
editor = {Monika Heiner and Adeline Uhrmacher},
booktitle = {{CMSB'08}: Proceedings of the fourth international
conference on Computational Methods in Systems Biology},
year = {2008},
month = oct,
series = {Lecture Notes in Computer Science},
volume = {5307},
pages = {251--268},
publisher = {Springer-Verlag},
doi = {10.1007/978-3-540-88562-7_19},
}
@Conference{,
author = {Domitille Heitzler and Guillaume Durand and Laurence Dupuy
and Christophe Gauthier and Vincent Piketty and Pascale
Cr{\'e}pieux and Aur{\'e}lien Rizk and Sylvain Soliman and
Fran{\c{c}}ois Fages and Fr{\'e}d{\'e}rique Cl{\'e}ment and
Eric Reiter},
title = {Modelling of FSHR-induced Signalling Network},
entrysubtype = {poster},
booktitle = {Poster, International Conference on Gonadotropins and
Receptors IGCR'08},
address = {London, UK},
year = {2008},
}
@InCollection{,
author = {Fran{\c{c}}ois Fages and Sylvain Soliman},
title = {Model Revision from Temporal Logic Properties in Systems
Biology},
booktitle = {Probabilistic Inductive Logic Programming},
editor = {Luc de Raedt and Paolo Frasconi and Kristian Kersting and
Stephen Muggleton},
publisher = {Springer-Verlag},
series = {Lecture Notes in Computer Science},
volume = {4911},
year = {2008},
pages = {287--304},
doi = {10.1007/978-3-540-78652-8_11},
}
@InProceedings{,
author = {Fran{\c{c}}ois Fages and Sylvain Soliman},
title = {From reaction models to influence graphs and back: a
theorem},
booktitle = {Proceedings of Formal Methods in Systems Biology
{FMSB'08}},
year = {2008},
series = {Lecture Notes in Computer Science},
number = {5054},
publisher = {Springer-Verlag},
month = feb,
doi = {10.1007/978-3-540-68413-8_7},
}
@InProceedings{,
author = {Fran{\c{c}}ois Fages and Sylvain Soliman},
title = {Formal Cell Biology in {BIOCHAM}},
booktitle = {8th Int. School on Formal Methods for the Design of
Computer, Communication and Software Systems: Computational
Systems Biology {SFM'08}},
year = {2008},
editor = {M. Bernardo and P. Degano and G. Zavattaro},
series = {Lecture Notes in Computer Science},
address = {Bertinoro, Italy},
month = feb,
publisher = {Springer-Verlag},
volume = {5016},
pages = {54--80},
doi = {10.1007/978-3-540-68894-5_3},
}
@InProceedings{,
author = {Sylvain Soliman},
title = {Finding minimal {P/T}-invariants as a {CSP}},
booktitle = {Proceedings of the fourth Workshop on Constraint Based
Methods for Bioinformatics WCB'08, associated to
CPAIOR'08},
month = may,
year = {2008},
url = {http://wcb08.dimi.uniud.it/PAPERS/Soliman.pdf},
}
@InProceedings{,
author = {R{\'e}my Haemmerl{\'e} and Fran{\c{c}}ois Fages and
Sylvain Soliman},
title = {Closures and Modules within Linear Logic Concurrent
Constraint Programming},
booktitle = {Proceedings of {FSTTCS} 2007, IARCS Annual Conference on
Foundations of Software Technology and Theoretical Computer
Science},
year = {2007},
editor = {V. Arvind and Sanjiva Prasad},
pages = {544--556},
series = {Lecture Notes in Computer Science},
volume = {4855},
publisher = {Springer-Verlag},
doi = {10.1007/978-3-540-77050-3_45},
}
@Proceedings{,
editor = {Fran{\c{c}}ois Fages and Sylvain Soliman},
title = {Actes des 3i{\`e}mes Journ{\'e}es Francophones de
Programmation par Contraintes JFPC'07},
booktitle = {Actes des 3i{\`e}mes Journ{\'e}es Francophones de
Programmation par Contraintes JFPC'07},
publisher = {{INRIA}},
address = {Rocquencourt, France},
month = jun,
year = {2007},
url = {http://hal.inria.fr/JFPC07/},
}
@InProceedings{,
author = {Fran{\c{c}}ois Fages and Sylvain Soliman},
title = {Type Inference in Systems Biology},
editor = {Corrado Priami},
booktitle = {{CMSB'06}: Proceedings of the fourth international
conference on Computational Methods in Systems Biology},
year = {2006},
series = {Lecture Notes in Computer Science},
publisher = {Springer-Verlag},
volume = {4210},
doi = {10.1007/11885191_4},
}
@InCollection{,
author = {Laurence Calzone and Nathalie Chabrier-Rivier and
Fran{\c{c}}ois Fages and Sylvain Soliman},
title = {Machine learning biochemical networks from temporal logic
properties},
editor = {Gordon Plotkin},
booktitle = {Transactions on Computational Systems Biology VI},
series = {Lecture Notes in BioInformatics},
volume = {4220},
pages = {68--94},
year = {2006},
month = nov,
publisher = {Springer-Verlag},
doi = {10.1007/11880646_4},
}
@Proceedings{,
title = {Proceedings of {PPSWR}'05, Third International Workshop on
Principles and Practice of Sematic Web Reasoning},
booktitle = {Proceedings of {PPSWR}'05, Third International Workshop on
Principles and Practice of Sematic Web Reasoning},
year = {2005},
editor = {Fran{\c{c}}ois Fages and Sylvain Soliman},
address = {Dagstuhl Castle, Germany},
publisher = {Springer-Verlag},
series = {Lecture Notes in Computer Science},
volume = {3703},
doi = {10.1007/11552222},
}
@InProceedings{,
author = {Laurence Calzone and Nathalie Chabrier-Rivier and
Fran{\c{c}}ois Fages and Lucie Gentils and Sylvain Soliman},
title = {Machine learning bio-molecular interactions from temporal
logic properties},
editor = {Gordon Plotkin},
booktitle = {{CMSB'05}: Proceedings of the third international
conference on Computational Methods in Systems Biology},
year = {2005},
oai = {http://hal.inria.fr/inria-00000117/},
eprinttype = {HAL},
eprint = {inria-00000117},
}
@InProceedings{,
author = {Laurence Calzone and Nathalie Chabrier-Rivier and
Fran{\c{c}}ois Fages and Sylvain Soliman},
title = {Apprentissage de r{\`e}gles de r{\'e}actions biochimiques
{\`a} partir de propri{\'e}t{\'e}s en logique temporelle},
booktitle = {Actes de {JOBIM}'05},
editor = {Guy Perri{\`e}re and Alain Gu{\'e}noche and Christophe
Geourjon},
pages = {183--192},
address = {Lyon},
year = {2005},
month = jul,
oai = {http://hal.inria.fr/inria-00000813/},
eprinttype = {HAL},
eprint = {inria-00000813},
}
@InProceedings{,
author = {Laurence Calzone and Nathalie Chabrier-Rivier and
Fran{\c{c}}ois Fages and Sylvain Soliman},
title = {A Machine Learning approach to Biochemical Reaction Rules
Discovery},
booktitle = {Proceedings of Foundations of Systems Biology and
Engineering {FOSBE'05}},
year = {2005},
editor = {Francis J. Doyle III},
pages = {375--379},
address = {Santa Barbara},
oai = {http://hal.inria.fr/inria-00000812/},
eprinttype = {HAL},
eprint = {inria-00000812},
}
@InProceedings{,
author = {Nathalie Chabrier-Rivier and Fran{\c{c}}ois Fages and
Sylvain Soliman},
title = {The Biochemical Abstract Machine {BIOCHAM}},
editor = {Patrick Amar and Jean-Paul Cornet and Fran{\c{c}}ois
K{\'e}p{\`e}s and Victor Norris},
booktitle = {Proceedings of the Evry Spring School on Modelling and
Simulation of Biological Processes in the Context of
Genomics},
pages = {35--49},
year = {2004},
publisher = {Platypus Press},
url = {http://contraintes.inria.fr/~soliman/publi/CFS04evry.ps.gz}
}
@InProceedings{,
author = {Nathalie Chabrier-Rivier and Fran{\c{c}}ois Fages and
Sylvain Soliman},
title = {The Biochemical Abstract Machine {BIOCHAM}},
booktitle = {Proceedings of the 5th International Conference on Systems
Biology {ICSB}'04},
month = oct,
year = {2004},
}
@InProceedings{,
author = {Nathalie Chabrier-Rivier and Fran{\c{c}}ois Fages and
Sylvain Soliman},
title = {The Biochemical Abstract Machine {BIOCHAM}},
editor = {Vincent Danos and Vincent Sch{\"a}chter},
booktitle = {{CMSB'04}: Proceedings of the second international
workshop on Computational Methods in Systems Biology},
year = {2004},
series = {Lecture Notes in BioInformatics},
volume = {3082},
pages = {172--191},
publisher = {Springer-Verlag},
doi = {10.1007/978-3-540-25974-9_14},
}
@InProceedings{,
author = {Rolf Backofen and Mike Badea and Pedro Barahona and Liviu
Badea and Fran{\c{c}}ois Bry and G. Dawelbait and Andreas
Doms and Fran{\c{c}}ois Fages and C. Goble and A. Henschel
and A. Hotaran and B. Huang and L. Krippahl and Patrick
Lambrix and Werner Nutt and Michael Schroeder and Sylvain
Soliman and Sebastian Will},
title = {Poster: Towards a semantic web for bioinformatics},
booktitle = {Proceedings of Bioinformatics 2004},
year = {2004},
address = {Link{\"o}ping, Sweden},
month = jun,
organization = {{SocBIN} - Society for Bioinformatics in the Nordic
countries},
}
@InProceedings{,
author = {Sylvain Soliman},
title = {Pi-calcul et {LCC}, une odyss{\'e}e de l'espace},
url = {http://contraintes.inria.fr/~soliman/publi/pi.pdf},
booktitle = {Programmation en logique avec contraintes (Actes de JFPLC
2004)},
year = {2004},
editor = {Fred Mesnard},
address = {Angers (France)},
month = jun,
pages = {201--218},
publisher = {Herm{\`e}s},
}
@InProceedings{,
author = {Sylvain Soliman and Fran{\c{c}}ois Fages},
title = {{CMBS}lib: a Library for Comparing Formalisms and Models
of Biological Systems},
editor = {Vincent Danos and Vincent Sch{\"a}chter},
booktitle = {{CMSB'04}: Proceedings of the second international
workshop on Computational Methods in Systems Biology},
year = {2004},
series = {Lecture Notes in BioInformatics},
volume = {3082},
pages = {231--235},
publisher = {Springer-Verlag},
doi = {10.1007/978-3-540-25974-9_19},
}
@InProceedings{,
author = {Sylvain Soliman},
title = {Phase Model Checking for some Linear Logic Calculi},
booktitle = {Proceedings of the Second International Workshop of the
Implementation of Logics, Havana, Cuba},
url = {http://contraintes.inria.fr/~soliman/publi/iwil.ps.gz},
pages = {60--80},
year = {2001},
editor = {Hans de Nivelle and Stephan Schultz},
series = {MPI-I-2001-2-006},
month = dec,
publisher = {Max-Planck-Institut f{\"u}r Informatik},
}
@InProceedings{,
author = {Fran{\c{c}}ois Fages and Paul Ruet and Sylvain Soliman},
title = {Phase Semantics and Verification of Concurrent Constraint
Programs},
booktitle = {Proceedings of the 13thAnnual IEEE Symposium on Logic In
Computer Science},
publisher = {IEEE Computer Society},
address = {Indianapolis},
year = {1998},
pages = {141--152},
doi = {10.1109/LICS.1998.705651}
}
@InProceedings{,
author = {Fran{\c{c}}ois Fages and Paul Ruet and Sylvain Soliman},
title = {Linear concurrent constraint programming: operational and
phase semantics},
booktitle = {Proc. COMPULOG Workshop associated to Constraint
Programming Conf. CP'97},
address = {Linz, Austria},
month = oct,
year = {1997},
}