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Systematic evaluation of spliced alignment programs for RNA-seq data.

Non Renseigné , Tyler Alioto , Jonas Behr , Regina Bohnert , Davide Campagna , et al.
Nature Methods, 2013, epub ahead of print. ⟨10.1038/nmeth.2722⟩
Journal articles hal-00909047v1
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Computing Genomic Distances: An Algorihtmic Viewpoint

Guillaume Fertin , Irena Rusu
Wiley Science. Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications, Wiley Science, pp.773-798, 2011, ⟨10.1002/9780470892107.ch34⟩
Book sections hal-00606146v1

Complex update strategies for Probabilistic Boolean Networks

Théo Merle , Jérémie Bourdon
7th Workshop on Computational Systems Biology, Jun 2010, Luxembourg, France. pp.4
Conference papers hal-00480366v1
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Finding Common Structured Patterns in Linear Graphs

Guillaume Fertin , Danny Hermelin , Romeo Rizzi , Stéphane Vialette
Theoretical Computer Science, 2010, 411 (26-28), pp.2475-2486. ⟨10.1016/j.tcs.2010.02.017⟩
Journal articles hal-00482850v1

The topological fortress of termites

Andrea Perna , Pascale Kuntz , Sergi Valverde , Jacques Gautrais , Guy Theraulaz , et al.
Lecture Notes in Computer Science, 2008, 5151, pp.165-173
Journal articles hal-00318997v1
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Integrating heterogeneous knowledges for understanding biological behaviors: a probabilistic approach

Jérémie Bourdon , Damien Eveillard , Samuel Gabillard , Theo Merle
Preprints, Working Papers, ... hal-00199362v1
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A Pseudo-Boolean programming approach for computing the breakpoint distance between two genomes with duplicate genes

Sébastien Angibaud , Guillaume Fertin , Irena Rusu , Annelyse Thevenin , Stéphane Vialette
5th RECOMB Comparative Genomics Satellite Workshop (RECOMB-CG 2007), 2007, San Diego, United States. pp.16-29
Conference papers hal-00417902v1
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Comparison of Spectra in Unsequenced Species

Freddy Cliquet , Guillaume Fertin , Irena Rusu , Dominique Tessier
4th Brazilian Symposium on Bioinformatics (BSB 2009), 2009, Porto Alegre, Brazil. pp.24-35, ⟨10.1007/978-3-642-03223-3_3⟩
Conference papers hal-00416462v1
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How Pseudo-Boolean Programming can help Genome Rearrangement Distance Computation

Sébastien Angibaud , Guillaume Fertin , Irena Rusu , Stéphane Vialette
4th RECOMB Comparative Genomics Satellite Workshop (RECOMB-CG 2006), 2007, Montréal, Canada. pp.75-86
Conference papers hal-00418258v1

Semantics of Biological Regulatory Networks

Gilles Bernot , Franck Cassez , Jean-Paul Comet , Franck Delaplace , Céline Müller , et al.
Electronic Notes in Theoretical Computer Science, 2007, 180, pp.3--14. ⟨10.1016/j.entcs.2004.01.038⟩
Journal articles hal-00339588v1

Factor d-Domatic Colorings of Graphs

Noga Alon , Guillaume Fertin , Arthur L. Liestman , Thomas C. Shermer , Ladislav Stacho
Discrete Mathematics, 2003, 262 (1--3), pp.17--25
Journal articles hal-00442418v1

Compounding of Gossip Graphs

Guillaume Fertin , Roger Labahn
Networks, 2000, 36 (2), pp.126--137
Journal articles hal-00442427v1

POGG: Integrating qualitative and quantitative data of macromolecular networks. A probabilistic toolbox

Etienne Giraudet , Eric Docet , Jérémie Bourdon
Other publications hal-00445610v1
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Tractability and approximability of maximal strip recovery

Laurent Bulteau , Guillaume Fertin , Minghui Jiang , Irena Rusu
Theoretical Computer Science, 2012, 440-441, pp.14-28. ⟨10.1016/j.tcs.2012.04.034⟩
Journal articles hal-00700598v1
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Computational Discovery of Dynamic Cell Line Specific Boolean Networks from Multiplex Time-Course Data

Misbah Razzaq , Loïc Paulevé , Anne Siegel , Julio Saez-Rodriguez , Jérémie Bourdon , et al.
PLoS Computational Biology, 2018, 14, pp.1-23. ⟨10.1371/journal.pcbi.1006538⟩
Journal articles hal-01897020v1

Forests of latent tree models for the detection of genetic associations

Christine Sinoquet , Raphaël Mourad , Philippe Leray
International Conference on Bioinformatics Models, Methods and Algorithms (BIOINFORMATICS 2012), Feb 2012, Vilamoura, Portugal. pp.1-10, ⟨10.5220/0003703400050014⟩
Conference papers hal-00637500v1
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Refining Dynamics of Gene Regulatory Networks in a Stochastic π-Calculus Framework

Loïc Paulevé , Morgan Magnin , Olivier Roux
Transactions on Computational Systems Biology, 2011, XIII, pp.171-191. ⟨10.1007/978-3-642-19748-2_8⟩
Journal articles hal-00397235v2

On the Power of Uncertainties in Microbial System Modeling: No Need To Hide Them Anymore

Benoît Delahaye , Damien Eveillard , Nicholas Bouskill
mSystems, 2017, 2 (6), ⟨10.1128/mSystems.00169-17⟩
Journal articles hal-01658218v1
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Concretizing the Process Hitting into Biological Regulatory Networks

Maxime Folschette , Loïc Paulevé , Katsumi Inoue , Morgan Magnin , Olivier Roux
Computational Methods in Systems Biology, Oct 2012, London, United Kingdom. p. 166-186, ⟨10.1007/978-3-642-33636-2_11⟩
Conference papers hal-00704569v2
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Maximal Strip Recovery Problem with Gaps: Hardness and Approximation Algorithms

Laurent Bulteau , Guillaume Fertin , Irena Rusu
Journal of Discrete Algorithms, 2013, 19, pp.1-22
Journal articles hal-00826876v1
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Bacterial syntenies: an exact approach with gene quorum.

Yves-Pol Deniélou , Marie-France Sagot , Frédéric Boyer , Alain Viari
BMC Bioinformatics, 2011, 12, pp.193. ⟨10.1186/1471-2105-12-193⟩
Journal articles hal-00746864v1
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Mechanically induced development and maturation of human intestinal organoids in vivo

Holly Poling , David Wu , Nicole Brown , Michael Baker , Taylor Hausfeld , et al.
Nature Biomedical Engineering, 2018, 2 (6), pp.429 - 442. ⟨10.1038/s41551-018-0243-9⟩
Journal articles hal-01816387v1
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Combining graph and flux-based structures to decipher phenotypic essential metabolites within metabolic networks

Julie Laniau , Clémence Frioux , Jacques Nicolas , Caroline Baroukh , Maria-Paz Cortés , et al.
PeerJ, 2017, 5, pp.e3860. ⟨10.7717/peerj.3860⟩
Journal articles hal-01635688v1

Temporal constraints of a gene regulatory network: refining a qualitative simulation

Jamil Ahmad , Jérémie Bourdon , Damien Eveillard , Jonathan Fromentin , Olivier Roux , et al.
BioSystems, 2009, pp.10.1016/j.biosystems.2009.05.002. ⟨10.1016/j.biosystems.2009.05.002⟩
Journal articles istex hal-00423353v1

Hard problems in similarity searching

Christophe Moan , Irena Rusu
Discrete Applied Mathematics, 2004, 144 (1-2), pp.213-227. ⟨10.1016/j.dam.2004.06.003⟩
Journal articles istex hal-00455436v1

Targeting human Rad51 by specific DNA aptamers induces inhibition of homologous recombination.

Susan F Martinez , Axelle Renodon-Cornière , Julian Nomme , Damien Eveillard , Fabrice Fleury , et al.
Biochimie, 2010, 92 (12), pp.1832-8. ⟨10.1016/j.biochi.2010.08.006⟩
Journal articles istex hal-00626711v1

Building and analysing an integrative model of HIV-1 RNA alternative splicing

Alexander Bockmayr , Arnaud Courtois , Damien Eveillard , Myriam Vezain
International Conference on Computational Methods in Systems Biology - CMSB 2004, May 2004, Paris/France, pp.43--57, ⟨10.1007/b107287⟩
Conference papers inria-00000917v1

An expert-based approach for the identification of remote homologs

Nicolas Beaume , Gérard Ramstein , Yannick Jacques
WCSB, Nov 2008, Leipzig, Germany. pp.17-20
Conference papers hal-00421952v1

SNPShuttle: bi-directional scan of SNP arrays to gain accuracy in missing genotype inference

Christine Sinoquet
Proc. Seventh Asia-Pacific Bioinformatics Conference, APBC2009, ISBN 978-7-302-19048-6, Jan 2009, Beijing, China. pp.915-925
Conference papers hal-00423431v1

Modélisation des dépendances locales entre SNP à l'aide d'un réseau bayésien

Raphaël Mourad , Christine Sinoquet , Philippe Leray
Proc. SFC'09, XVIth Join Meeting of the French Society of Classification, actes des 16èmes rencontres de la Société Francophone de Classification, Sep 2009, Grenoble, France. pp.169-172
Conference papers hal-00423461v1