Publications
2013
Revues avec comité de lecture
Non-redundant random generation algorithms for weighted context-free languages
Supersecondary structure prediction of transmembrane beta-barrel proteins.
OKVAR-Boost: a novel boosting algorithm to infer nonlinear dynamics and interactions in gene regulatory networks.
Characteristics of binding sites of intergenic, intronic and exonic miRNAs with mRNAs of oncogenes coding intronic miRNAs
SPARCS: a web server to analyze (un)structured regions in coding RNA sequences
Conférences avec comité de lecture et actes
Identification de complexes protéine-protéine par combinaison de classifieurs. Application à Escherichia coli
Proceedings of EGC 2013 - Extraction et Gestion des Connaissances, France, E.24419-430, 2013
A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotides distribution
Proceedings of ISMB/ECCB - 21st Annual international conference on Intelligent Systems for Molecular Biology/12th European Conference on Computational Biology - 2013, Allemagne, 2013 [pdf/hal]
A linear inside-outside algorithm for correcting sequencing errors in structured RNA sequences
Proceedings of RECOMB - 17th Annual International Conference on Research in Computational Molecular Biology - 2013, Chine, 2013 [pdf/hal]
Using the Fast Fourier Transform to accelerate the computational search for RNA conformational switches (extended abstract)
Proceedings of RECOMB - 17th Annual International Conference on Research in Computational Molecular Biology - 2013, Chine, 2013 [pdf/hal]
Thèses
Recherche d'associations séquentielles et alignement d'ontologies biologiques
Modèles combinatoires des structures d'ARN avec ou sans pseudonoeuds, application à la comparaison de structures.
Algorithmes pour l' étude de la structure secondaire des ARN et l'alignement de séquences
[Université Paris Sud - Paris XI][Université Paris Sud - Paris XI][Université Paris Sud - Paris XI], 2013 [pdf/hal]
Algorithmes de graphes pour la recherche de motifs récurrents dans les structures tertiaires d'ARN
Exploitation des algorithmes génétiques pour la prédiction de structure de complexe protéine-protéine
Miscellaneous
Flexible RNA design under structure and sequence constraints using formal languages
2012
Revues avec comité de lecture
Optimisation problems for pairwise RNA sequence and structure comparison: a brief survey
Transactions on Computational Collective Intelligence, to appear, 2012
Efficient Prediction of Co-Complexed Proteins Based on Coevolution
PLoS ONE, To appear 2012
A new dichotomic algorithm for the uniform random generation of words in regular languages (journal version)
Maximum expected accuracy structural neighbors of an RNA secondary structure.
Expected distance between terminal nucleotides of RNA secondary structures.
Evaluating mixture models for building RNA knowledge-based potentials.
Interactions of intergenic microRNAs with mRNAs of genes involved in carcinogenesis
A graph-theoretic approach for classification and structure prediction of transmembrane beta-barrel proteins
BMC Genomics, To appear 2012
An algorithmic game-theory approach for coarse-grain prediction of RNA 3D structure
IEEE/ACM Transactions on Computational Biology and Bioinformatics, to appear, 2012
Normal human melanocytes exposed to chronic insulin and glucose supplementation undergo oncogenic changes and methyl group metabolism cellular redistribution.
Using the Fast Fourier Transform to Accelerate the Computational Search for RNA Conformational Switches
Multiscale modeling of macromolecular biosystems.
Coverage-biased random exploration of large models and application to testing
Software Tools for Technology Transfer (STTT), 14(1):73-93, 2012
Automated prediction of three-way junction topological families in RNA secondary structures
A global sampling approach to designing and reengineering RNA secondary structures.
Tumor regression with a combination of drugs interfering with the tumor metabolism: efficacy of hydroxycitrate, lipoic acid and capsaicin.
BRASERO: A resource for benchmarking RNA secondary structure comparison algorithms
Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism.
Conférences avec comité de lecture et actes
HSIM: an hybrid stochastic simulation system for systems biology
Proceedings of The Third International Workshop on Static Analysis and Systems Biology (SASB 2012), France, 2012
(Re)Use in Public Scientific Workflow Repositories
Proceedings of Scientific and Statistical Database Management - 24th International Conference, SSDBM 2012, Grèce, 7338361-378, 2012
The weighted words collector
Impact Of The Energy Model On The Complexity Of RNA Folding With Pseudoknots
Scientific Workflow Rewriting while Preserving Provenance
Proceedings of Proc. of the 8th IEEE International Conference in eScience, États-Unis, 2012
Réécriture de workflows scientifiques et provenance
On the diversity of pattern distributions in combinatorial systems
Proceedings of ANALCO - 12th Meeting on Analytic Algorithmics and Combinatorics - 2012, Japon, 107--116, 2012 [pdf/hal]
Tree decomposition and parameterized algorithms for RNA structure-sequence alignment including tertiary interactions and pseudoknots
Optimisation of reconstruction for the registration of CT liver perfusion sequences
Distilling Structure in Scientific Workflows
Proceedings of Proc. of the 12th International Workshop on Network Tools and Applications in Biology, Nettab 2012 (Poster), Italie, 1810-102, 2012 [pdf/hal]
A-Brain: Using the Cloud to Understand the Impact of Genetic Variability on the Brain
Can Probabilistic Model Checking Explore Ribo-Nucleic Acid Folding Space?
Proceedings of IWBDA - 4th International Workshop on Bio-Design Automation - 2012, États-Unis, 2012
The Least Temporal Contradiction Measure: Application to Hydrological Data
Proceedings of AGILE'12: 15th International Conference on Geographic Information Science, France, 197-202, 2012
Towards a logic-based method to infer provenance-aware molecular networks
Proceedings of Proc. of the 1st ECML/PKDD International workshop on Learning and Discovery in Symbolic Systems Biology (LDSSB), Royaume-Uni, 103-110, 2012 [pdf/hal]
Graph Algorithms and Software Framework for Interactive RNA Structure Modelling
Proceedings of Journees Ouvertes de Biologie Informatique et Mathematiques - JOBIM'12, France, 475-476, 2012
Conférences avec comité de lecture
Large deviation properties for patterns
Thèses
Modeling and predicting super-secondary structures of transmembrane beta-barrel proteins
Rapports
A Dynamical Model for the Transmembrane Potential Regulation by pH
Miscellaneous
Prédiction d'Interactions et Amarrage Protéine-Protéine par combinaison de classifieurs
Miscellaneous
Rule-weighted and terminal-weighted context-free grammars have identical expressivity
Miscellaneous
Visualizing 2D & 3D Structures of RNA
Efficient Algorithms to Explore the RNA Mutational Landscape
Miscellaneous
Learning a Markov Logic Network for supervised gene regulatory network inference
2011
Revues avec comité de lecture
An unbiased adaptive sampling algorithm for the exploration of RNA mutational landscapes under evolutionary pressure.
Search, adapt, and reuse: the future of scientific workflows
Counting RNA pseudoknotted structures
Fully differentiable coarse-grained and all-atom knowledge-based potentials for RNA structure evaluation.
ACoM: A classification method for elementary flux modes based on motif finding
BioSystems, 103(3):410-419, 2011
A collaborative filtering approach for protein-protein docking scoring functions.
MULTI-SCALE MODELLING OF BIOSYSTEMS: FROM MOLECULAR TO MESOCALE - Session Introduction.
The construction of a library of synthetic promoters revealed some specific features of strong Streptomyces promoters.
Characteristics of Intronic and Intergenic Human miRNAs and Features of their Interaction with mRNA
Gene List significance at-a-glance with GeneValorization.
Toxicity of carbon dioxide: A review.
Computing with bacterial constituents, cells and populations: from bioputing to bactoputing
Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology.
Conférences avec comité de lecture et actes
Constant time estimation of ranking statistics by analytic combinatorics
Maximum expected accurate structural neighbors of an RNA secondary structure
Proceedings of Proceedings of 1st IEEE International Conference on Computational Advances in Bio and medical Sciences (ICCABS), États-Unis, 2011
An unbiased adaptive sampling algorithm for the exploration of RNA mutational landscapes under evolutionary pressure
Next Generation Data Integration for the Life Sciences
Proceedings of IEEE International Conference on Data Engineering (ICDE), Allemagne, 2011
A Combinatorial Framework for Designing (Pseudoknotted) RNA Algorithms
A new approach to suboptimal pairwise sequence alignment
Proceedings of CompBio 2011: IASTED International Conference on Computational Bioscience, Royaume-Uni, 2011
Using medians to generate consensus rankings for biological data
Proceedings of SSDBM 2011: Scientific and Statistical Database Management Conference, États-Unis, 2011
Protein-protein docking based on shape complementarity and Voronoi fingerprint
Energy-based Classification and Structure Prediction of Transmembrane Beta-Barrel Proteins
Proceedings of 1st IEEE International Conference on Computational Advances in Bio and medical Sciences (ICCABS), États-Unis, 2011
Uniform Monte-Carlo Model Checking
Proceedings of FASE 2011, Allemagne, 2011
Using Kendall-Tau Meta-Bagging to Improve Protein-Protein Docking Predictions
Proceedings of PRIB 2011, Pays-Bas, 284-295, 2011
On Armstrong-compliant Logical Query Languages
Proceedings of 4th International Workshop on Logic in Databases, (EDBT/ICDT '10 joint conference), Suède, 33-40, 2011
Conférences avec comité de lecture
Investigating the RFAM paradox: The pseudoknot explanation
Thèses
Un modèle mathématique de la biosynthèse des phospholipides
2010
Revues avec comité de lecture
Thermodynamics of RNA structures by Wang–Landau sampling
Controlled non uniform random generation of decomposable structures
Average complexity of the Jiang-Wang-Zhang pairwise tree alignment algorithm and of a RNA secondary structure alignment algorithm
ESBTL: efficient PDB parser and data structure for the structural and geometric analysis of biological macromolecules.
Automatic characterization of emergent phenomena in complex systems
Alignments of RNA structures.
Computing biological functions using BioPsi, a formal description of biological processes based on elementary bricks of actions.
MULTI-RESOLUTION MODELING OF BIOLOGICAL MACROMOLECULES - Session Introduction.
Paternity analysis in a litter of whale shark embryos
A Model of Phospholipid Biosynthesis in Tumor in Response to an Anticancer Agent in Vivo
Regulation of splicing enhancer activities by RNA secondary structures
BioNetCAD: design, simulation and experimental validation of synthetic biochemical networks.
Conférences avec comité de lecture et actes
Bounded Discrete Walks
Proceedings of AofA2010 - Conference on Analysis of Algorithms 2010, Autriche, 35-48, 2010 [pdf/hal]
Weighted random generation of context-free languages: Analysis of collisions in random urn occupancy models
Multi-dimensional Boltzmann Sampling of Languages
Uniform and non-uniform random generation of RNA secondary structures with pseudoknots
A new dichotomic algorithm for the uniform random generation of words in regular languages
Proceedings of GASCom 2010, Canada, 2010
2009
Revues avec comité de lecture
VARNA: Interactive drawing and editing of the RNA secondary structure.
Prediction of super-secondary structure in α-helical and β-barrel transmembrane proteins
Using profiles based on hydropathy properties to define essential regions for splicing
Profile of Tries
PDiffView: Viewing the Difference in Provenance of Workflow Results
PVLDB, Proc. of the 35th Int. Conf. on Very Large Data Bases, 2(2):1638-1641, 2009
Conférences avec comité de lecture et actes
BioBrowsing: Making the Most of the Data Available in Entrez
Proceedings of 21st Int. Conf. in Scientific and Statistical Database Management (SSDBM), LNCS 5566, Springer, États-Unis, 283-291, 2009
An Adaptive Combination of Matchers: Application to the Mapping of Biological Ontologies for Genome Annotation
Proceedings of DILS 2009-6th International Workshop on Data Integration in the Life Sciences, Royaume-Uni, 5647113-126, 2009 [doi]
PDiffView: Viewing the Difference in Provenance of Workflow Results
Proceedings of VLDB- Very Large DataBase systems-2009, France, 21638-1641, 2009
On User Views in Scientific Workflow Systems (Invited Paper)
Proceedings of Proc. of the the First Int. Workshop on the role of Semantic Web in Provenance Management (ISWC 2009 Workshop), États-Unis, 2009
Chapitres dans des ouvrages collectifs
Provenance in Scientific Databases
Encyclopedia of Database Systems, Springer US, 2202-2207, 2009
A Word Counting Graph
London Algorithmics 2008: Theory and Practice (Texts in Algorithmics), London College Publications, 31 p., 2009 [pdf/hal]
Biological Metadata Management
Encyclopedia of Database Systems, Springer US, 215-219, 2009
Biological Resource Discovery
Encyclopedia of Database Systems, Springer US, 220-223, 2009
2008
Revues avec comité de lecture
Efficient sampling of RNA secondary structures from the Boltzmann ensemble of low-energy: The boustrophedon method
Asymptotics of RNA shapes
LocalMove: computing on-lattice fits for biopolymers
A new method for 2D gel spot alignment: application to the analysis of large sample sets in clinical proteomics.
From Molecules to Organisms: Towards Multiscale Integrated Models of Biological Systems
Theoretical Biology Insights, 1:13--22, 2008
Conférences avec comité de lecture et actes
Non-redundant random generation from weighted context-free languages
2007
Revues avec comité de lecture
DIAL: A web server for the pairwise alignment of two RNA 3-dimensional structures using nucleotide, dihedral angle and base pairing similarities
2006
GenRGenS: Software for Generating Random Genomic Sequences and Structures
2000
Conférences avec comité de lecture et actes
Periods and quasiperiods characterization
Proceedings of 11th Conference on Combinatorial Pattern Matching, France, 388-396, 2000
