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Bibliography

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, p. 1638-1641.
  • 2A. 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, p. 3527-3552. [ DOI : 10.1016/j.tcs.2010.05.010 ]

    http://hal.inria.fr/hal-00483581/en
  • 3Y. 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, p. 107–127.

    http://www.lri.fr/~ponty/docs/Ponty-07-JMB-Boustrophedon.pdf
Publications of the year

Doctoral Dissertations and Habilitation Theses

Articles in International Peer-Reviewed Journal

  • 6J. Allali, C. Saule, Y. D'Aubenton-Carafa, A. Denise, C. Drevet, P. Ferraro, D. Gautheret, C. Herrbach, F. Leclerc, A. De Monte, A. Ouangraoua, M.-F. Sagot, M. Termier, C. Thermes, H. Touzet.

    BRASERO: A resource for benchmarking RNA secondary structure comparison algorithms, in: Advanced in Bioinformatics, 2012, page : to appear.

    http://hal.inria.fr/hal-00647725/en
  • 7J. Bernauer, S. Flores, X. Huang, S. Shin, R. Zhou.

    MULTI-SCALE MODELLING OF BIOSYSTEMS: FROM MOLECULAR TO MESOCALE - Session Introduction., in: Pacific Symposium on Biocomputing, 2011, p. 177-80. [ DOI : 10.1142/9789814335058_0019 ]

    http://hal.inria.fr/inria-00542791/en
  • 8J. 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, p. 1066-75. [ DOI : 10.1261/rna.2543711 ]

    http://hal.inria.fr/inria-00624999/en
  • 9T. 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 ]

    http://hal.inria.fr/inria-00625000/en
  • 10B. Brancotte, A. Biton, I. Bernard-Pierrot, F. Radvanyi, F. Reyal, S. Cohen-Boulakia.

    Gene List significance at-a-glance with GeneValorization., in: Bioinformatics, April 2011, vol. 27, no 8, p. 1187-9. [ DOI : 10.1093/bioinformatics/btr073 ]

    http://hal.inria.fr/inria-00627865/en
  • 11P. Clote, Y. Ponty, J.-M. Steyaert.

    Expected distance between terminal nucleotides of RNA secondary structures, in: Journal of Mathematical Biology, 2011, 18 p.

    http://hal.inria.fr/inria-00619921/en
  • 12S. Cohen-Boulakia, U. Leser.

    Search, adapt, and reuse: the future of scientific workflows, in: Sigmod Record, 2011. [ DOI : 10.1145/2034863.2034865 ]

    http://hal.inria.fr/inria-00638043/en
  • 13A. 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), 2011.

    http://hal.inria.fr/inria-00560621/en
  • 14S. 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. Ovali, 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, in press. [ DOI : 10.1016/j.jmb.2011.09.031 ]

    http://hal.inria.fr/inria-00637848/en
  • 15A. Guais, G. Brand, L. Jacquot, M. Karrer, S. Dukan, G. Grévillot, T. J. Molina, J. Bonte, M. Regnier, L. Schwartz.

    Toxicity of Carbon Dioxide: A Review., in: Chemical Research in Toxicology, July 2011, epub ahead of print. [ DOI : 10.1021/tx200220r ]

    http://hal.inria.fr/hal-00641044/en
  • 16A. 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, November 2011.

    http://hal.inria.fr/hal-00641738/en
  • 17V. Norris, A. Zemirline, P. Amar, J. N. Audinot, P. Ballet, E. Ben-Jacob, G. Bernot, G. Beslon, A. Cabin, E. Fanchon, J.-L. Giavitto, N. Glade, P. Greussay, Y. Grondin, J. A. Foster, G. Hutzler, J. Jost, F. Kepes, O. Michel, F. Molina, J. Signorini, P. Stano, A. R. Thierry.

    Computing with bacterial constituents, cells and populations: from bioputing to bactoputing, in: Theorie in den Biowissenschaften / Theory in Biosciences, September 2011, vol. 130, no 3, p. 211-228. [ DOI : 10.1007/s12064-010-0118-4 ]

    http://hal.inria.fr/hal-00643738/en
  • 18S. Pérès, F. Vallée, M. Beurton-Aimar, J.-P. Mazat.

    ACoM: A classification method for elementary flux modes based on motif finding, in: BioSystems, 2011, vol. 103, no 3, p. 410-419.

    http://hal.inria.fr/hal-00642137/en
  • 19C. Saule, M. Regnier, J.-M. Steyaert, A. Denise.

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

    http://hal.inria.fr/inria-00537117/en
  • 20N. Seghezzi, P. Amar, B. Koebmann, P. R. Jensen, M.-J. Virolle.

    The construction of a library of synthetic promoters revealed some specific features of strong Streptomyces promoters., in: Applied Microbiology and Biotechnology, April 2011, vol. 90, no 2, p. 615-23. [ DOI : 10.1007/s00253-010-3018-0 ]

    http://hal.inria.fr/hal-00643741/en
  • 21S. Sheikh, P. Chassignet, J.-M. Steyaert, T. V. D. Tran.

    A graph-theoretic approach for classification and structure prediction of transmembrane beta-barrel proteins, in: BMC Genomics, 2012.

    http://hal.inria.fr/hal-00650429/en

International Conferences with Proceedings

  • 22M. Agier, C. Froidevaux, J.-M. Petit, Y. Renaud, J. Wijsen.

    On Armstrong-compliant Logical Query Languages, in: 4th International Workshop on Logic in Databases, (EDBT/ICDT '10 joint conference), Uppsala, Sweden, G. H. L. Fletcher, S. Staworko (editors), ACM, 2011, p. 33-40.

    http://hal.inria.fr/hal-00649604/en
  • 23J. Azé, T. Bourquard, S. Hamel, A. Poupon, D. Ritchie.

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

    http://hal.inria.fr/inria-00628038/en
  • 24C. Banderier, O. Bodini, Y. Ponty, H. Tafat.

    On the diversity of pattern distributions in combinatorial systems, in: ANALCO'12, Japan, 2012.

    http://hal.inria.fr/hal-00643598/en
  • 25C. Banderier, P. Nicodeme.

    Constant time estimation of ranking statistics by analytic combinatorics, in: Statistical Methods for Post-Genomic Data, Paris, France, January 2011.

    http://hal.inria.fr/hal-00567091/en
  • 26P. Clote, L. Feng, A. Denise.

    A new approach to suboptimal pairwise sequence alignment, in: CompBio 2011: IASTED International Conference on Computational Bioscience, Cambridge, United Kingdom, 2011.

    http://hal.inria.fr/inria-00594890/en
  • 27S. Cohen-Boulakia, A. Denise, S. Hamel.

    Using medians to generate consensus rankings for biological data, in: SSDBM 2011: Scientific and Statistical Database Management Conference, Portland, United States, 2011.

    http://hal.inria.fr/inria-00584690/en
  • 28S. Cohen-Boulakia, U. Leser.

    Next Generation Data Integration for the Life Sciences, in: IEEE International Conference on Data Engineering (ICDE), Hannover, Germany, April 2011.

    http://hal.inria.fr/inria-00542359/en
  • 29J. Oudinet, A. Denise, M.-C. Gaudel, R. Lassaigne, S. Peyronnet.

    Uniform Monte-Carlo Model Checking, in: FASE 2011, Saarbrücken, Germany, 2011.

    http://hal.inria.fr/hal-00644834/en
  • 30Y. Ponty, C. Saule.

    A Combinatorial Framework for Designing (Pseudoknotted) RNA Algorithms, in: 11th Workshop on Algorithms in Bioinformatics (WABI'11), Saarbrucken, Germany, 2011.

    http://hal.inria.fr/inria-00601060/en
  • 31T. V. D. Tran, P. Chassignet, S. Sheikh, J.-M. Steyaert.

    Energy-based Classification and Structure Prediction of Transmembrane Beta-Barrel Proteins, in: 1st IEEE International Conference on Computational Advances in Bio and medical Sciences (ICCABS), Orlando, FL, United States, February 2011.

    http://hal.inria.fr/inria-00562699/en
  • 32J. Waldispühl, Y. Ponty.

    An unbiased adaptive sampling algorithm for the exploration of RNA mutational landscapes under evolutionary pressure, in: RECOMB, Vancouver, Canada, V. Bafna, S. Sahinalp (editors), Lecture Notes in Computer Science, Springer Berlin / Heidelberg, 2011, vol. 6577, p. 501-515. [ DOI : 10.1007/978-3-642-20036-6_45 ]

    http://hal.inria.fr/hal-00546847/en

National Conferences with Proceeding

  • 33T. Bourquard, J. Azé, A. Poupon, D. Ritchie.

    Protein-protein docking based on shape complementarity and Voronoi fingerprint, in: Journées Ouvertes Biologie Informatique Mathématiques, Paris, France, E. Barillot, C. Froidevaux, Eduardo PC. Rocha (editors), Institut Pasteur, July 2011, p. 9-16.

    http://hal.inria.fr/inria-00613186/en

Other Publications

References in notes