Major publications by the team in recent years
  • 1Z. Bao, S. Cohen-Boulakia, S. Davidson, P. Girard.

    PDiffView: Viewing the Difference in Provenance of Workflow Results, in: PVLDB, Proc. of the 35th Int. Conf. on Very Large Data Bases, 2009, vol. 2, no 2, pp. 1638-1641.
  • 2J. Bernauer, X. Huang, A. Y. L. Sim, M. Levitt.

    Fully differentiable coarse-grained and all-atom knowledge-based potentials for RNA structure evaluation, in: RNA, June 2011, vol. 17, no 6, pp. 1066-75. [ DOI : 10.1261/rna.2543711 ]

  • 3A. Denise, Y. Ponty, M. Termier.

    Controlled non uniform random generation of decomposable structures, in: Journal of Theoretical Computer Science (TCS), 2010, vol. 411, no 40-42, pp. 3527-3552. [ DOI : 10.1016/j.tcs.2010.05.010 ]
  • 4A. Lopes, S. Sacquin-Mora, V. Dimitrova, E. Laine, Y. Ponty, A. Carbone.

    Protein-protein interactions in a crowded environment: an analysis via cross-docking simulations and evolutionary information, in: PLoS Computational Biology, December 2013, vol. 9, no 12. [ DOI : 10.1371/journal.pcbi.1003369 ]

  • 5C. Saule, M. Regnier, J.-M. Steyaert, A. Denise.

    Counting RNA pseudoknotted structures, in: Journal of Computational Biology, October 2011, vol. 18, no 10, pp. 1339-1351. [ DOI : 10.1089/cmb.2010.0086 ]

Publications of the year

Articles in International Peer-Reviewed Journals

  • 6C. Barton, A. Heliou, L. Mouchard, S. P. Pissis.

    Linear-time computation of minimal absent words using suffix array, in: BMC Bioinformatics, 2014, vol. 15, 11 p. [ DOI : 10.1186/s12859-014-0388-9 ]

  • 7O. Berillo, M. Regnier, A. Ivashchenko.

    TmiRUSite and TmiROSite scripts: searching for mRNA fragments with miRNA binding sites with encoded amino acid residues, in: Bioinformation, July 2014, vol. 10, no 7, pp. 472-473.

  • 8S. Cohen-Boulakia, J. Chen, P. Missier, C. Goble, A. Williams, C. Froidevaux.

    Distilling structure in Taverna scientific workflows: a refactoring approach, in: BMC Bioinformatics, 2014, vol. 15, no Suppl 1, S12 p.

  • 9A. Denise, P. Rinaudo.

    Optimisation problems for pairwise RNA sequence and structure comparison: a brief survey, in: Transactions on Computational Collective Intelligence, January 2014, vol. 13, pp. 70-82. [ DOI : 10.1007/978-3-642-54455-2_3 ]

  • 10M. Folschette, L. Paulevé, K. Inoue, M. Magnin, O. Roux.

    Identification of Biological Regulatory Networks from Process Hitting models, in: Journal of Theoretical Computer Science (TCS), February 2015, vol. 568, 39 p. [ DOI : 10.1016/j.tcs.2014.12.002 ]

  • 11R. Fonseca, D. V. Pachov, J. Bernauer, H. Van Den Bedem.

    Characterizing RNA ensembles from NMR data with kinematic models, in: Nucleic Acids Research, August 2014, vol. 42, no 15, pp. 9562-72. [ DOI : 10.1093/nar/gku707 ]

  • 12A. Guilhot-Gaudeffroy, C. Froidevaux, J. Azé, J. Bernauer.

    Protein-RNA Complexes and Efficient Automatic Docking: Expanding RosettaDock Possibilities, in: PLoS ONE, 2014, vol. 9, no 9, e108928. [ DOI : 10.1371/journal.pone.0108928 ]

  • 13S. Laurent, B. Ludivine, I. Philippe, L. Hubert, J.-M. Steyaert.

    Metabolic Treatment of Cancer: Intermediate Results of a Prospective Case Series, in: Anticancer Research, January 2014.

  • 14C. Pereira, A. Denise, O. Lespinet.

    A meta-approach for improving the prediction and the functional annotation of ortholog groups, in: BMC Genomics, 2014, vol. 15(Suppl 6), S16 p. [ DOI : 10.1186/1471-2164-15-S6-S16 ]

  • 15E. Ranaei-Siadat, C. Mérigoux, B. Seijo, L. Ponchon, J.-M. Saliou, J. Bernauer, S. Sanglier-Cianférani, F. Dardel, P. Vachette, S. Nonin-Lecomte.

    In vivo tmRNA protection by SmpB and pre-ribosome binding conformation in solution, in: RNA, August 2014, vol. 20, no 10, pp. 1607-20. [ DOI : 10.1261/rna.045674.114 ]

  • 16C. Shao, B. Yang, T. Wu, J. Huang, P. Tang, Y. Zhou, J. Zhou, J. Qiu, L. Jiang, H. Li, G. Chen, H. Sun, Y. Zhang, A. Denise, D.-E. Zhang, X.-D. Fu.

    Mechanisms for U2AF to define 3' splice sites and regulate alternative splicing in the human genome, in: Nature Structural and Molecular Biology, 2014, vol. 21, pp. 997-1005. [ DOI : 10.1038/nsmb.2906 ]

  • 17J. Starlinger, B. Brancotte, S. Cohen-Boulakia, U. Leser.

    Similarity Search for Scientific Workflows, in: Proceedings of the VLDB Endowment (PVLDB), September 2014, 12 p.

  • 18T. V. D. Tran, P. Chassignet, J.-M. Steyaert.

    On permuted super-secondary structures of transmembrane β-barrel proteins, in: Theoretical Computer Science, 2014. [ DOI : 10.1016/j.tcs.2013.10.001 ]


Invited Conferences

  • 19P. Amar.

    Systèmes oscillants chaotiques en biologie, in: Ecole de Printemps 2014 de la Société Francophone de Biologie Théorique, St Flour, France, Société Francophone de Biologie Théorique, May 2014.


International Conferences with Proceedings

  • 20P. Amar, M. Baillieul, D. Barth, B. LeCun, F. Quessette, S. Vial.

    Parallel biological in silico simulation, in: 29th Intenational Symposium on Computer and Information Sciences, Krakow, Poland, October 2014, pp. 387-394. [ DOI : 10.1007/978-3-319-09465-6_40 ]

  • 21B. Brancotte, B. Rance, A. Denise, S. Cohen-Boulakia.

    ConQuR-Bio: Consensus Ranking with Query Reformulation for Biological Data, in: 10th International Conference, Data Integration in the Life Sciences, Lisbon, Portugal, July 2014, pp. 128 - 142. [ DOI : 10.1007/978-3-319-08590-6_13 ]

  • 22T. Chatain, S. Haar, L. Jezequel, L. Paulevé, S. Schwoon.

    Characterization of Reachable Attractors Using Petri Net Unfoldings, in: CMSB 2014, Manchester, United Kingdom, P. Mendes, J. Dada, K. Smallbone (editors), LNCS/LNBI, Springer Berlin Heidelberg, November 2014, forthcoming.

  • 23C. Chauve, Y. Ponty, J. P. P. Zanetti.

    Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach, in: BSB - Brazilian Symposium on Bioinformatics - 2014, Belo Horizonte, Brazil, October 2014, TBA.

  • 24J. Chen, S. Cohen-Boulakia, C. Froidevaux, C. Goble, P. Missier, A. Williams.

    DistillFlow: removing redundancy in scientific workflows, in: SSDBM '14 Proceedings of the 26th International Conference on Scientific and Statistical Database Management, Aalborg, Denmark, June 2014. [ DOI : 10.1145/2618243.2618287 ]

  • 25T. Opitz, J. Azé, S. Bringay, C. Joutard, C. Lavergne, C. Mollevi.

    Breast cancer and quality of life: medical information extraction from health forums, in: Medical Informatics Europe, Istanbul, Turkey, August 2014, pp. 1070-1074.

  • 26M. Regnier, B. Fang, D. Iakovishina.

    Clump Combinatorics, Automata, and Word Asymptotics, in: ANALCO'14, Portland, United States, M. Drmota, M. Ward (editors), SIAM, January 2014.

  • 27J. Starlinger, S. Cohen-Boulakia, S. Khanna, S. Davidson, U. Leser.

    Layer Decomposition: An Effective Structure-based Approach for Scientific Workflow Similarity, in: IEEE e-Science conference, Guarujá, Brazil, October 2014.


National Conferences with Proceedings

  • 28A. Guilhot-Gaudeffroy, J. Azé, J. Bernauer, C. Froidevaux.

    Apprentissage de fonctions de tri pour la prédiction d'interactions protéine-ARN, in: Extraction et Gestion des Connaissances, Rennes, France, January 2014.


Conferences without Proceedings

  • 29Y. Yamamoto, A. Rougny, H. Nabeshima, K. Inoue, H. Moriya, C. Froidevaux, K. Iwanuma.

    Completing SBGN-AF Networks by Logic-Based Hypothesis Finding, in: Formal Methods In Macro-Biology, Nouméa, New Caledonia, Formal Methods in Macro-Biology, Springer, September 2014, vol. 8738, pp. 165-179. [ DOI : 10.1007/978-3-319-10398-3_14 ]


Scientific Books (or Scientific Book chapters)

  • 30L. Paulevé, C. Chancellor, M. Folschette, M. Magnin, O. Roux.

    Analyzing Large Network Dynamics with Process Hitting, in: Logical Modeling of Biological Systems, L. F. del Cerro, K. Inoue (editors), Wiley, July 2014, pp. 125 - 166.

  • 31Y. Ponty, F. Leclerc.

    Drawing and Editing the Secondary Structure(s) of RNA, in: RNA Bioinformatics, E. Picardi (editor), Methods in Molecular Biology, Springer New York, 2015, vol. 1269, pp. 63-100. [ DOI : 10.1007/978-1-4939-2291-8_5 ]

  • 32A. Rougny, C. Froidevaux, Y. Yamamoto, K. Inoue.

    Analyzing SBGN-AF Networks Using Normal Logic Programs, in: Logical Modeling of Biological Systems, Wiley, July 2014. [ DOI : 10.1002/9781119005223.ch9 ]


Books or Proceedings Editing

  • 33F. Jossinet, Y. Ponty, J. Waldispühl (editors)

    Proceedings of the 1st workshop on Computational Methods for Structural RNAs, McGill University, France, September 2014, 76 p. [ DOI : 10.15455/CMSR.2014.0000 ]


Internal Reports

Scientific Popularization

  • 35Y. Ponty.

    Bio-algorithmique des ARN : petite promenade aux interfaces, in: 1024 - Bulletin de la société informatique de France, E. Sopena (editor), SIF, October 2014, vol. 4, pp. 23–53.


Other Publications

  • 36J. Haleš, J. Maňuch, Y. Ponty, L. Stacho.

    Combinatorial RNA Design: Designability and Structure-Approximating Algorithm, 2015, Submitted to CPM'15.

  • 37S. Kamgnia Wonkap.

    Extraction de motifs dans les graphes de workflows scientifiques, Laboratoire de Recherche en Informatique [LRI], UMR 8623, Bâtiments 650-660, Université Paris-Sud, 91405 Orsay Cedex, 2014, 38 p.

  • 38C. Pereira, A. Denise, O. Lespinet.

    A new method for improving the prediction and the functional annotation of ortholog groups, 2014, Proc. ECCB'14, the 13th European Conference on Computational Biology.

  • 39A. Rajaraman, C. Chauve, Y. Ponty.

    Assessing the robustness of parsimonious predictions for gene neighborhoods from reconciled phylogenies, 2015, Submitted to ECCB/ISMB 2015.

  • 40M. Régnier, E. Furletova, V. Yakovlev, M. Roytberg.

    Analysis of pattern overlaps and exact computation of P-values of pattern occurrences numbers: case of Hidden Markov Models, December 2014. [ DOI : 10.1186/s13015-014-0025-1 ]

References in notes
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    Comparative study of some methods for simulation of biochemical reactions, in: Ecole de Printemps 2012 de la Société Francophone de Biologie Théorique, Saint Flour, France, June 2012.

  • 42P. Amar, L. Paulevé.

    HSIM: an hybrid stochastic simulation system for systems biology, in: The Third International Workshop on Static Analysis and Systems Biology (SASB 2012), Deauville, France, September 2012.

  • 43Z. Aslaoui-Errafi, S. Cohen-Boulakia, C. Froidevaux, P. Gloaguen, A. Poupon, A. Rougny, M. Yahiaoui.

    Towards a logic-based method to infer provenance-aware molecular networks, in: Proc. of the 1st ECML/PKDD International workshop on Learning and Discovery in Symbolic Systems Biology (LDSSB), Bristol, Royaume-Uni, September 2012, pp. 103-110.

  • 44J. Azé, T. Bourquard, S. Hamel, A. Poupon, D. Ritchie.

    Using Kendall-Tau Meta-Bagging to Improve Protein-Protein Docking Predictions, in: PRIB 2011, DELFT, Pays-Bas, M. Loog, et al. (editors), Marcel Reinders and Dick de Ridder, 2011, pp. 284-295.

  • 45B. Beauvoit, S. Colombié, J.-P. Mazat, C. Nazaret, S. Pérès.

    Systematic study of a metabolic network, in: Advances in Systems and Synthetic Biology, Evry, France, EDP Sciences, March 2014.

  • 46J. Bernauer, R. P. Bahadur, F. Rodier, J. Janin, A. Poupon.

    DiMoVo: a Voronoi tessellation-based method for discriminating crystallographic and biological protein-protein interactions, in: Bioinformatics, March 2008, vol. 24, no 5, pp. 652-8. [ DOI : 10.1093/bioinformatics/btn022 ]

  • 47J. Bernauer, S. C. Flores, X. Huang, S. Shin, R. Zhou.

    Multi-Scale Modelling of Biosystems: from Molecular to Mesocale - Session Introduction, in: Pacific Symposium on Biocomputing, 2011, pp. 177-80. [ DOI : 10.1142/9789814335058_0019 ]

  • 48V. Boeva, T. Popova, K. Bleakley, P. Chiche, J. Cappo, G. Schleiermacher, I. Janoueix-Lerosey, O. Delattre, E. Barillot.

    Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data, in: Bioinformatics, 2012, vol. 28, no 3, pp. 423-425.

  • 49T. Bourquard, J. Bernauer, J. Azé, A. Poupon.

    Comparing Voronoi and Laguerre tessellations in the protein-protein docking context, in: Sixth annual International Symposium on Voronoi Diagrams, Copenhagen, Danemark, F. Anton and J. Andreas Bærentzen - Technical University of Denmark, June 2009.

  • 50T. Bourquard, J. Bernauer, J. Azé, A. Poupon.

    A collaborative filtering approach for protein-protein docking scoring functions, in: PLoS ONE, 2011, vol. 6, no 4. [ DOI : 10.1371/journal.pone.0018541 ]

  • 51E. A. Coutsias, C. Seok, M. P. Jacobson, K. A. Dill.

    A kinematic view of loop closure, in: J Comput Chem, Mar 2004, vol. 25, no 4, pp. 510–528.

  • 52K. Darty, A. Denise, Y. Ponty.

    VARNA: Interactive drawing and editing of the RNA secondary structure, in: Bioinformatics, August 2009, vol. 25, no 15, pp. 1974-5. [ DOI : 10.1093/bioinformatics/btp250 ]

  • 53A. Denise, M.-C. Gaudel, S.-D. Gouraud, R. Lassaigne, J. Oudinet, S. Peyronnet.

    Coverage-biased random exploration of large models and application to testing, in: Software Tools for Technology Transfer (STTT), 2012, vol. 14, no 1, pp. 73-93.

  • 54A. Denise, Y. Ponty, M. Termier.

    Controlled non uniform random generation of decomposable structures, in: Theoretical Computer Science, 2010, vol. 411, no 40-42, pp. 3527-3552. [ DOI : 10.1016/j.tcs.2010.05.010 ]

  • 55Y. Ding, C. Chan, C. Lawrence.

    RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble, in: RNA, 2005, vol. 11, pp. 1157–1166.
  • 56S. J. Fleishman, T. A. Whitehead, E.-M. Strauch, J. E. Corn, S. Qin, H.-X. Zhou, J. C. Mitchell, O. N. A. Demerdash, M. Takeda-Shitaka, G. Terashi, I. H. Moal, X. Li, P. A. Bates, M. Zacharias, H. Park, J.-S. Ko, H. Lee, C. Seok, T. Bourquard, J. Bernauer, A. Poupon, J. Azé, S. Soner, S. K. Ovalı, P. Ozbek, N. B. Tal, T. Haliloglu, H. Hwang, T. Vreven, B. G. Pierce, Z. Weng, L. Pérez-Cano, C. Pons, J. Fernández-Recio, F. Jiang, F. Yang, X. Gong, L. Cao, X. Xu, B. Liu, P. Wang, C. Li, C. Wang, C. H. Robert, M. Guharoy, S. Liu, Y. Huang, L. Li, D. Guo, Y. Chen, Y. Xiao, N. London, Z. Itzhaki, O. Schueler-Furman, Y. Inbar, V. Patapov, M. Cohen, G. Schreiber, Y. Tsuchiya, E. Kanamori, D. M. Standley, H. Nakamura, K. Kinoshita, C. M. Driggers, R. G. Hall, J. L. Morgan, V. L. Hsu, J. Zhan, Y. Yang, Y. Zhou, P. L. Kastritis, A. M. J. J. Bonvin, W. Zhang, C. J. Camacho, K. P. Kilambi, A. Sircar, J. J. Gray, M. Ohue, N. Uchikoga, Y. Matsuzaki, T. Ishida, Y. Akiyama, R. Khashan, S. Bush, D. Fouches, A. Tropsha, J. Esquivel-Rodríguez, D. Kihara, P. B. Stranges, R. Jacak, B. Kuhlman, S.-Y. Huang, X. Zou, S. J. Wodak, J. Janin, D. Baker.

    Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology, in: Journal of Molecular Biology, September 2011. [ DOI : 10.1016/j.jmb.2011.09.031 ]

  • 57S. C. Flores, J. Bernauer, S. Shin, R. Zhou, X. Huang.

    Multiscale modeling of macromolecular biosystems, in: Briefings in Bioinformatics, July 2012, vol. 13, no 4, pp. 395-405. [ DOI : 10.1093/bib/bbr077 ]

  • 58L. Jaroszewski, Z. Li, S. S. Krishna, C. Bakolitsa, J. Wooley, A. M. Deacon, I. A. Wilson, A. Godzik.

    Exploration of uncharted regions of the protein universe, in: PLoS Biol, Sep 2009, vol. 7, no 9.

  • 59A. Lamiable, D. Barth, A. Denise, F. Quessette, S. Vial, E. Westhof.

    Automated prediction of three-way junction topological families in RNA secondary structures, in: Computational Biology and Chemistry, January 2012, vol. 37, pp. 1-5. [ DOI : 10.1016 ]

  • 60A. Levin, M. Lis, Y. Ponty, C. W. O'Donnell, S. Devadas, B. Berger, J. Waldispühl.

    A global sampling approach to designing and reengineering RNA secondary structures, in: Nucleic Acids Research, November 2012, vol. 40, no 20, pp. 10041-52. [ DOI : 10.1093/nar/gks768 ]

  • 61S. Loriot, F. Cazals, J. Bernauer.

    ESBTL: efficient PDB parser and data structure for the structural and geometric analysis of biological macromolecules, in: Bioinformatics, April 2010, vol. 26, no 8, pp. 1127-8. [ DOI : 10.1093/bioinformatics/btq083 ]

  • 62D. J. Mandell, E. A. Coutsias, T. Kortemme.

    Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling, in: Nat Methods, Aug 2009, vol. 6, no 8, pp. 551–552.

  • 63D. Manocha, Y. Zhu.

    Kinematic manipulation of molecular chains subject to rigid constraints, in: Proc Int Conf Intell Syst Mol Biol, 1994, vol. 2, pp. 285–293.
  • 64D. Manocha, Y. Zhu, W. Wright.

    Conformational analysis of molecular chains using nano-kinematics, in: Comput Appl Biosci, Feb 1995, vol. 11, no 1, pp. 71–86.
  • 65J. Oudinet, A. Denise, M.-C. Gaudel.

    A new dichotomic algorithm for the uniform random generation of words in regular languages (journal version), in: Theoretical Computer Science, September 2013, vol. 502, pp. 165-176.

  • 66M. Parisien, F. Major.

    The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data, in: Nature, 2008, vol. 452, no 7183, pp. 51–55.
  • 67G. Park, H.-K. Hwang, P. Nicodème, W. Szpankowski.

    Profile of Tries, in: SIAM Journal on Computing, 2009, vol. 38, no 5, pp. 1821-1880. [ DOI : 10.1137/070685531 ]

  • 68Y. Ponty.

    Efficient sampling of RNA secondary structures from the Boltzmann ensemble of low-energy: The boustrophedon method, in: Journal of Mathematical Biology, Jan 2008, vol. 56, no 1-2, pp. 107–127.

  • 69Y. Ponty, M. Termier, A. Denise.

    GenRGenS: Software for Generating Random Genomic Sequences and Structures, in: Bioinformatics, 2006, vol. 22, no 12, pp. 1534–1535.

  • 70S. Pérès, M. Martin, L. Simon.

    SAT-Based Metabolics Pathways Analysis without Compilation , in: CMSB 2014, Manchester, United Kingdom, P. M. J. D. K. Smallbone (editor), LNCS/LNBI, Springer Berlin Heidelberg, November 2014.

  • 71V. Reinharz, Y. Ponty, J. Waldispühl.

    Using Structural and Evolutionary Information to Detect and Correct Pyrosequencing Errors in Noncoding RNAs, in: Journal of Computational Biology, November 2013, vol. 20, no 11, pp. 905-19, Extended version of RECOMB'13. [ DOI : 10.1089/cmb.2013.0085 ]

  • 72E. Senter, S. Sheikh, I. Dotu, Y. Ponty, P. Clote.

    Using the Fast Fourier Transform to Accelerate the Computational Search for RNA Conformational Switches, in: PLoS ONE, December 2012, vol. 7, no 12. [ DOI : 10.1371/journal.pone.0050506 ]

  • 73E. Senter, S. Sheikh, I. Dotu, Y. Ponty, P. Clote.

    Using the Fast Fourier Transform to accelerate the computational search for RNA conformational switches (extended abstract), in: RECOMB - 17th Annual International Conference on Research in Computational Molecular Biology - 2013, Beijing, Chine, 2013.

  • 74A. Y. L. Sim, O. Schwander, M. Levitt, J. Bernauer.

    Evaluating mixture models for building RNA knowledge-based potentials, in: Journal of Bioinformatics and Computational Biology, April 2012, vol. 10, no 2, 1241010. [ DOI : 10.1142/S0219720012410107 ]

  • 75T. V. D. Tran.

    Modeling and predicting super-secondary structures of transmembrane beta-barrel proteins, Ecole Polytechnique X, December 2011.

  • 76H. Van Den Bedem, I. Lotan, J. C. Latombe, A. M. Deacon.

    Real-space protein-model completion: an inverse-kinematics approach, in: Acta Crystallogr D Biol Crystallogr, Jan 2005, vol. 61, no Pt 1, pp. 2–13.

  • 77J. Waldispühl, Y. Ponty.

    An unbiased adaptive sampling algorithm for the exploration of RNA mutational landscapes under evolutionary pressure, in: Journal of Computational Biology, November 2011, vol. 18, no 11, pp. 1465-79. [ DOI : 10.1089/cmb.2011.0181 ]