LRI : page d'accueil Équipe Bioinfo

LRI - BioInfo group

Adrien Rougny, Pauline Gloaguen, Nathalie Langonné, Eric Reiter, Pascale Crépieux, Anne Poupon & Christine Froidevaux
A logic-based method to build signaling networks and propose experimental plans
Scientific Reports, vol. 8: 7830, 2018.

Vincent Henry, Anne Goelzer, Arnaud Ferré, Stephan Fischer, Marc Dinh, Valentin Loux, Christine Froidevaux, Vincent Fromion
The bacterial interlocked process ONtology (BiPON): a systemic multi-scale unified representation of biological processes in prokaryotes
Journal of Biomedical Semantics, 8:53, 2017.

Sarah Cohen-Boulakia, Khalid Belhajjame, Olivier Collin, Jerome Chopard, Christine Froidevaux, et al.
Scientific workflows for computational reproducibility in the life sciences: Status challenges and opportunities
In Future Generation Computer Systems,, 2017.

Adrien Rougny, Christine Froidevaux, Laurence Calzone, Loïc Pauleve
Qualitative dynamics semantics for SBGN process description
In BMC Systems Biology, volume 10, 2016.

Adrien Rougny, Yoshitaka Yamamoto, Hidetomo Nabeshima, Gauvain Bourgne, Anne Poupon, Katsumi Inoue, Christine Froidevaux
Completing signaling networks by abductive reasoning with perturbation experiments
In 25th International Conference on Inductive Logic Programming, 2015.

Adrien Guilhot-Gaudeffroy, Christine Froidevaux, Jerome Aze, Julie Bernauer
Protein-RNA Complexes and Efficient Automatic Docking: Expanding RosettaDock Possibilities
In PLoS One, volume 9, e108928, 2014.

Adrien Rougny, Christine Froidevaux, Yoshitaka Yamamoto, Katsumi Inoue
Analyzing SBGN-AF Networks using Normal Logic Programs
In handbook "Logical Modeling of Biological Systems", Katsumi Inoue, Luis Farinas (eds.), ISTE-Ltd, 2014.

Jiuqiang Chen, Sarah Cohen-Boulakia, Christine Froidevaux, Carole Goble, Paolo Missier, Alan Williams
DistillFlow: Removing redundancy in Scientific Workflows
Proc. of the 22nd Int. Conf. in Scientific and Statistical Database Management (SSDBM), 2014.

Sarah Cohen-Boulakia, Jiuqiang Chen, Carole Goble, Paolo Missier, Alan Williams, Christine Froidevaux
Distilling Structure in Taverna Scientific Workflows: A refactoring approach
In BMC Bioinformatics, Vol. 15, Jan. 2014.

Sarah Cohen-Boulakia, Christine Froidevaux, Jiuqiang Chen
Scientific Workflow Rewriting while Preserving Provenance
Proc. of the 8th IEEE Int. Conference in eScience, Chicago, 2012.

Sarah Cohen-Boulakia, Christine Froidevaux, Carole Goble, Alan Williams, Jiuqiang Chen
Distilling scientific workflow structure
In EMBnet Journal, Proc. of the 12th International Workshop on Network Tools and Applications in Biology Nettab 2012 (poster), volume 18, 2012.

Zahira Aslaoui-Errafi, Sarah Cohen-Boulakia, Christine Froidevaux, Pauline Gloaguen, Anne Poupon, Adrien Rougny, Meriem Yahiaoui
Towards a logic-based method to infer provenance-aware molecular networks
ECML/PKDD Workshop on Learning and Discovery in Symbolic Systems Biology, Bristol, LDSSB'2012, Pre-proceedings, 103-110.

Marie Agier, Christine Froidevaux, Jean-Marc Petit, Yoan Renaud, Jef Wijsen
On Armstrong-compliant logical query languages
4th. Int. Workshop on Logic in Databases, LID 2011, Co-located with EDBT & ICDT 2011, Uppsala.

Bastien Rance, Jean-François Gibrat, Christine Froidevaux
An adaptive combination of matchers: application to the mapping of biological ontologies for genome annotation
Data Integration in the Life Sciences, 6th Int. Workshop DILS 2009, LNCS Vol. 5647, 113-126.

Jérôme Azé, Lucie Gentils, Claire Toffano-Nioche, Valentin Loux, Jean-François Gibrat, Philippe Bessières, Céline Rouveirol, Anne Poupon, Christine Froidevaux
Towards a semi-automatic functional annotation tool based on decision tree techniques
Extended version MLSB'07, BMC Proceedings, Vol.2 suppl.4, 2008.

Frédéric Lemoine, Bernard Labedan, Christine Froidevaux
GenoQuery: a new querying module for functional annotation in a genomic warehouse
Bioinformatics (ISMB 2008), Vol 24, n°13, i322-i329, 2008.
GenoQuery Site

Sarah Cohen-Boulakia, Olivier Biton, Susan Davidson, Christine Froidevaux
BioGuideSRS: Querying Multiple Sources with a user-centric perspective
Bioinformatics, 23(10), 1301-1303, 2007.

Christine Froidevaux, Frédérique Lisacek, Bastien Rance
Extracting Sequential Nuggets of Knowledge
In Proc. of Database and Expert Systems Applications, DEXA'07, LNCS, Vol. 4653, 740-750, September 2007.

Christine Froidevaux, Frédérique Lisacek, Bastien Rance
Discovering relevant sequential associations between heterogeneous features of proteins
Data Integration in the Life Sciences, DILS'07, Philadelphia, Demo, June 2007.

Sarah Cohen-Boulakia, Susan Davidson, Christine Froidevaux, Zoé Lacroix and Maria-Esther Vidal
Path-based systems to guide scientists in the maze of biological data sources
Journal of Bioinformatics and Computational Biology, 2006, Vol. 4, No. 5, 1069-1095.

Sarah Cohen Boulakia, Christine Froidevaux and Emmanuel Pietriga
Selecting biological data sources and tools with XPR, a path language for RDF
In Proc. of PSB'06 (Pacific Symposium on Biocomputing, Wailea).

Sarah Cohen Boulakia, Susan Davidson and Christine Froidevaux
A User-centric Framework for Accessing Biological Sources and Tools
In Proc. of DILS'05 (Data Integration in the Life Sciences), Springer-Verlag, Lecture Notes in BioInformatics (LNBI), Vol. 3615, 3-18.
BioGuide Site.

Sarah Cohen Boulakia, Séverine Lair, Nicolas Stransky, Stéphane Graziani, François Radvanyi, Emmanuel Barillot and Christine Froidevaux
Selecting biomedical data sources according to user preferences
In Proc. of the 12th International Conference on Intelligent Systems for Molecular Biology, ISMB/ECCB, Glasgow, Bioinformatics Vol 20 Suppl.1, i86-i93, 2004.

Géraldine Mercier, Nathalie Berthault, Jérémie Mary, Julie Peyre, A. Antoniadis, Jean-Paul Comet, Antoine Cornuéjols, Christine Froidevaux and Marie Dutreix
Biological detection of low radiation by combining results of two microarray analysis methods
Nucleic Acids Research, Vol 32 (1), e12, 2004.

Alain Bidault, Sarah Cohen Boulakia and Christine Froidevaux
Preferences for Queries in a Mediator Approach
In Proc. of the European Conference on Artificial Intelligence, ECAI-2004, Valencia.

Marie Dutreix, Jean-Paul Comet, Antoine Cornuéjols and Christine Froidevaux
Determination of cellular drug targets: searching for functional information in the jungle of microarrays data
In Proc. of the Conf. "Current trends in drug discovery research" (CTDDR-2004), India, Feb. 17-20, 2004.

Mickaël Bekaert, Laure Bidou, Alain Denise, Guillemette Duchateau-Nguyen, Jean-Paul Forest, Christine Froidevaux, Isabelle Hatin, Jean-Pierre Rousset and Michel Termier
Towards a computational model for -1 eukaryotic frameshifting sites
Bioinformatics, Vol 19, 327-335, 2003.

Mickaël Bekaert, Jean-Paul Forest, Laure Bidou, Alain Denise, Guillemette Duchateau-Nguyen, Céline Fabret, Christine Froidevaux, Isabelle Hatin, Jean-Pierre Rousset and Michel Termier
Searching the Saccharomyces cerevisiae genome for -1 frameshifting sites
In Proc. of ECCB'03, European Conference on Computational Biology, September 27-30, Paris, 4-6, 2003.
Also presented at the Yeast Meeting, Göteborg, July, 2003.

Jérémie Mary, Géraldine Mercier, Jean-Paul Comet, Antoine Cornuéjols, Christine Froidevaux and Marie Dutreix
An attribute estimation technique for the analysis of microarray data
In Proc. of the Dieppe Spring school on Modelling and simulation of biological processes in the context of genomics (eds. P. Amar, F. Képès, V. Norris and P. Tracqui), 2003, Publisher Frontier group, ISBN : 2 91 4601 09 3, 2003, 69-77.

Alain Bidault, Christine Froidevaux and Brigitte Safar
Similarity Between Queries in a Mediator
In Proc. of the 15th European Conference on Artificial Intelligence, ECAI-2002, Lyon, 235-239.

Alain Bidault, Christine Froidevaux and Brigitte Safar,
Finding Successful Queries in a Mediator Context
In Proc. of the 4th International Conference on Flexible Query Answering Systems FQAS-2000, 42-53.

Alain Bidault, Christine Froidevaux and Brigitte Safar,
Repairing Queries in a Mediator Approach,
In Proc. of the 14th European Conference on Artificial Intelligence, ECAI-2000, Berlin, 406-410.

Last update: September 2013.