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, n^o 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, n^o 6, pp. 1066-75. [ DOI : 10.1261/rna.2543711 ]
  http://hal.inria.fr/inria-00624999
• 3A. Denise, Y. Ponty, M. Termier.
  Controlled non uniform random generation of decomposable structures, in: Journal of Theoretical Computer Science (TCS), 2010, vol. 411, n^o 40-42, pp. 3527-3552. [ DOI : 10.1016/j.tcs.2010.05.010 ]
  http://hal.inria.fr/hal-00483581/en
• 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, n^o 12. [ DOI : 10.1371/journal.pcbi.1003369 ]
  http://hal.inria.fr/hal-00875116
• 5C. Saule, M. Regnier, J.-M. Steyaert, A. Denise.
  Counting RNA pseudoknotted structures, in: Journal of Computational Biology, October 2011, vol. 18, n^o 10, pp. 1339-1351. [ DOI : 10.1089/cmb.2010.0086 ]
  http://hal.inria.fr/inria-00537117

Publications of the year

Doctoral Dissertations and Habilitation Theses

• 6P. Amar.
  Contributions à l'étude de la dynamique des systèmes biologiques et aux systèmes de calcul en biologie synthétique, Université Paris Sud - Paris XI, December 2013, Habilitation à Diriger des Recherches.
  http://hal.inria.fr/tel-00929785
• 7J. Chen.
  Designing scientific workflows following a structure and provenance-aware strategy, Université Paris Sud - Paris XI, October 2013.
  http://hal.inria.fr/tel-00931122

Articles in International Peer-Reviewed Journals

• 8O. Berillo, A. Issabekova, M. Regnier, A. Ivashchenko.
  Characteristics of binding sites of intergenic, intronic and exonic miRNAs with mRNAs of oncogenes coding intronic miRNAs, in: African Journal of Biotechnology, March 2013, vol. 12, n^o 10, pp. 1016-1024. [ DOI : 10.5897/AJB12.2054 ]
  http://hal.inria.fr/hal-00825020
• 9O. Berillo, M. Regnier, A. Ivashchenko.
  Binding of intronic miRNAs to the mRNAs of host genes encoding intronic miRNAs and proteins that participate in tumourigenesis, in: Computers in Biology and Medicine, July 2013. [ DOI : 10.1016/j.compbiomed.2013.07.011 ]
  http://hal.inria.fr/hal-00850103
• 10S. 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, n^o Suppl 1, S12 p.
  http://hal.inria.fr/hal-00926827
• 11A. Denise, P. Rinaudo.
  Optimisation problems for pairwise RNA sequence and structure comparison: a brief survey, in: Transactions on Computational Collective Intelligence, 2013, to appear.
  http://hal.inria.fr/hal-00759573
• 12A. Lamiable, F. Quessette, S. Vial, D. Barth, A. Denise.
  An Algorithmic Game-Theory Approach for Coarse-Grain Prediction of RNA 3D Structure., in: IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2013, vol. 10, n^o 1, pp. 193-9. [ DOI : 10.1109/TCBB.2012.148 ]
  http://hal.inria.fr/hal-00832110
• 13A. Lamiable, F. Quessette, S. Vial, D. Barth, A. Denise.
  An algorithmic game-theory approach for coarse-grain prediction of RNA 3D structure, in: IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2013, vol. 10, n^o 1, pp. 193-199.
  http://hal.inria.fr/hal-00756340
• 14S. 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.
  http://hal.inria.fr/hal-00933725
• 15N. Lim, Y. Senbabaoglu, G. Michailidis, F. D'Alché-Buc.
  OKVAR-Boost: a novel boosting algorithm to infer nonlinear dynamics and interactions in gene regulatory networks., in: Bioinformatics, June 2013, vol. 29, n^o 11, pp. 1416–1423. [ DOI : 10.1093/bioinformatics/btt167 ]
  http://hal.inria.fr/hal-00819024
• 16A. 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, n^o 12. [ DOI : 10.1371/journal.pcbi.1003369 ]
  http://hal.inria.fr/hal-00875116
• 17A. Lorenz, Y. Ponty.
  Non-redundant random generation algorithms for weighted context-free languages, in: Theoretical Computer Science, September 2013, vol. 502, pp. 177-194. [ DOI : 10.1016/j.tcs.2013.01.006 ]
  http://hal.inria.fr/inria-00607745
• 18V. Norris, P. Amar, G. Legent, C. Ripoll, M. Thellier, J. Ovadi.
  Sensor potency of the moonlighting enzyme-decorated cytoskeleton, in: BMC Biochemistry, February 2013, vol. 14, n^o 3. [ DOI : 10.1186/1471-2091-14-3 ]
  http://hal.inria.fr/hal-00766058
• 19J. 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.
  http://hal.inria.fr/hal-00716558
• 20S. Pérès, L. Felicori, F. Molina.
  Elementary flux modes analysis of functional domain networks allows a better metabolic pathway interpretation, in: PLoS ONE, 2013.
  http://hal.inria.fr/hal-00861577
• 21M. Regnier, J. Bourdon.
  Large deviation properties for patterns, in: Journal of Discrete Algorithms, September 2013. [ DOI : 10.1016/j.jda.2013.09.004 ]
  http://hal.inria.fr/hal-00868462
• 22V. Reinharz, Y. Ponty, J. Waldispühl.
  A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotide distribution., in: Bioinformatics, July 2013, vol. 29, n^o 13, pp. i308-15, Extended version of ISMB/ECCB'13. [ DOI : 10.1093/bioinformatics/btt217 ]
  http://hal.inria.fr/hal-00840260
• 23V. 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, n^o 11, pp. 905-19, Extended version of RECOMB'13. [ DOI : 10.1089/cmb.2013.0085 ]
  http://hal.inria.fr/hal-00828062
• 24N. Seghezzi, M.-J. Virolle, P. Amar.
  Novel insights regarding the sigmoidal pattern of resistance to neomycin conferred by the aphII gene, in Streptomyces lividans., in: AMB Express, February 2013, vol. 3, n^o 1, 13 p. [ DOI : 10.1186/2191-0855-3-13 ]
  http://hal.inria.fr/hal-00794555
• 25V. D. T. Tran, P. Chassignet, J.-M. Steyaert.
  Supersecondary structure prediction of transmembrane beta-barrel proteins., in: Methods in Molecular Biology -Clifton then Totowa-, 2013, vol. 932, pp. 277-94. [ DOI : 10.1007/978-1-62703-065-6_17 ]
  http://hal.inria.fr/hal-00761759
• 26T. V. D. Tran, P. Chassignet, J.-M. Steyaert.
  On permuted super-secondary structures of transmembrane $\beta$-barrel proteins, in: Theoretical Computer Science, 2014. [ DOI : 10.1016/j.tcs.2013.10.001 ]
  http://hal.inria.fr/hal-00869141
• 27Y. Zhang, Y. Ponty, M. Blanchette, E. Lecuyer, J. Waldispühl.
  SPARCS: a web server to analyze (un)structured regions in coding RNA sequences., in: Nucleic Acids Research, July 2013, vol. 41, pp. W480-5. [ DOI : 10.1093/nar/gkt461 ]
  http://hal.inria.fr/hal-00819017

International Conferences with Proceedings

• 28M. 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.
  http://hal.inria.fr/hal-00864645
• 29V. Reinharz, Y. Ponty, J. Waldispühl.
  A linear inside-outside algorithm for correcting sequencing errors in structured RNA sequences, in: RECOMB - 17th Annual International Conference on Research in Computational Molecular Biology - 2013, Beijing, China, 2013.
  http://hal.inria.fr/hal-00766781
• 30V. Reinharz, Y. Ponty, J. Waldispühl.
  A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotides distribution, in: ISMB/ECCB - 21st Annual international conference on Intelligent Systems for Molecular Biology/12th European Conference on Computational Biology - 2013, Berlin, Germany, 2013.
  http://hal.inria.fr/hal-00811607
• 31A. Rougny, C. Froidevaux, Y. Yamamoto, K. Inoue.
  Translating the SBGN-AF language into logic to analyze signalling networks, in: LNMR - 1st International Workshop on Learning and Non Monotonic Reasoning, La Coruña, Spain, K. Inoue, C. Sakama (editors), CORR, November 2013, vol. arXiv:1311.4639, pp. 44-55.
  http://hal.inria.fr/hal-00924230
• 32E. 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, China, 2013.
  http://hal.inria.fr/hal-00766780
• 33Y. Zhou, Y. Ponty, S. Vialette, J. Waldispühl, Y. Zhang, A. Denise.
  Flexible RNA design under structure and sequence constraints using formal languages, in: ACM-BCB - ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics - 2013, Bethesda, Washigton DC, United States, 2013.
  http://hal.inria.fr/hal-00823279

National Conferences with Proceedings

• 34T. Bourquard, D. De Vienne, J. Azé.
  Identification de complexes protéine-protéine par combinaison de classifieurs. Application à Escherichia coli, in: EGC 2013 - 13eme conférence Francophone sur l'Extraction et la Gestion des Connaissances, Toulouse, France, D. A. Zighed, G. Venturini (editors), RNTI, Hermann, January 2013, vol. E.24, pp. 419-430.
  http://hal.inria.fr/hal-00785473
• 35C. Pereira, J. Azé, A. Denise, C. Drevet, C. Froidevaux, P. Silar, O. Lespinet.
  Comparative analysis of phylogenetic profiles for the enzymatic characterization of fungal group, in: JOBIM 2013, Toulouse, France, 2013, à paraître.
  http://hal.inria.fr/hal-00842021

Conferences without Proceedings

• 36A. Fouchet, J.-M. Delosme, F. D'Alché-Buc.
  Gene Regulatory Network Inference using ensembles of Local Multiple Kernel Models, in: Seventh international workshop on Machine Learning in Systems Biology, satellite meeting of ISMB'2013, Berlin, Germany, July 2013.
  http://hal.inria.fr/hal-00844494
• 37M. Heinonen, O. Guipaud, F. Milliat, V. Buard, B. Micheau, F. D'Alché-Buc.
  Time-dependent gaussian process regression and significance analysis for sparse time-series, in: Seventh international workshop on Machine Learning in Systems Biology, satellite meeting of ISMB'2013, Berlin, Germany, July 2013.
  http://hal.inria.fr/hal-00844474
• 38N. Lim, Y. Senbabaoglu, G. Michailidis, F. D'Alché-Buc.
  Boosting an operator-valued kernel-based model for gene regulatory network inference, in: Workshop on Dynamics of biological networks: from nodes' dynamics to network evolution, Edinburgh, United Kingdom, June 2013.
  http://hal.inria.fr/hal-00844424
• 39N. Lim, Y. Senbabaoglu, G. Michailidis, F. D'Alché-Buc.
  Nonparametric modeling for gene regulatory network inference using boosting and operator-valued kernels, in: Seventh International workshop on Machine Learning in Systems Biology, Satellite meeting of ISMB'2013, Berlin, Germany, July 2013.
  http://hal.inria.fr/hal-00844443

Scientific Books (or Scientific Book chapters)

• 40S. Schirmer, Y. Ponty, R. Giegerich.
  Introduction to RNA Secondary Structure Comparison, in: RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods, J. Gorodkin, W. L. Ruzzo (editors), Methods in molecular biology, Springer, 2014, vol. 1097.
  http://hal.inria.fr/hal-00846818

Books or Proceedings Editing

• 41P. Amar, F. Képès, V. Norris (editors)
  avances in Systems and Synthetic Biology, EDP Sciences, March 2013, 171 p.
  http://hal.inria.fr/hal-00930249

Other Publications

• 42M. Atoui, B. Blossier, V. Morénas, O. Pène, K. Petrov.
  Semileptonic $BtoD⌃**$ decays in Lattice QCD : a feasibility study and first results, 2013, 28 p.
  http://hal.inria.fr/hal-00917799
• 43E. Bigan, J.-M. Steyaert, S. Douady.
  Properties of Random Complex Chemical Reaction Networks and Their Relevance to Biological Toy Models, 2013.
  http://hal.inria.fr/hal-00859004
• 44M. Regnier, E. Furletova, M. Roytberg, V. Yakovlev.
  Pattern occurrences Pvalues, Hidden Markov Models and Overlap Graphs, 2014, to appear.
  http://hal.inria.fr/hal-00858701

References in notes

• 45P. Amar.
  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.
  http://hal.inria.fr/hal-00763571
• 46P. 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.
  http://hal.inria.fr/hal-00758168
• 47Z. 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.
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• 48J. 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.
  http://hal.inria.fr/inria-00628038
• 49J. 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, n^o 5, pp. 652-8. [ DOI : 10.1093/bioinformatics/btn022 ]
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• 50J. 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, pp. 177-80. [ DOI : 10.1142/9789814335058_0019 ]
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• 51V. 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, n^o 3, pp. 423-425. [ DOI : 10.1093/bioinformatics/btr670 ]
• 52T. 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.
  http://hal.inria.fr/inria-00429618
• 53T. Bourquard, J. Bernauer, J. Azé, A. Poupon.
  A collaborative filtering approach for protein-protein docking scoring functions, in: PLoS ONE, 2011, vol. 6, n^o 4. [ DOI : 10.1371/journal.pone.0018541 ]
  http://hal.inria.fr/inria-00625000
• 54E. A. Coutsias, C. Seok, M. P. Jacobson, K. A. Dill.
  A kinematic view of loop closure, in: J Comput Chem, Mar 2004, vol. 25, n^o 4, pp. 510–528.
  http://dx.doi.org/10.1002/jcc.10416
• 55K. Darty, A. Denise, Y. Ponty.
  VARNA: Interactive drawing and editing of the RNA secondary structure, in: Bioinformatics, August 2009, vol. 25, n^o 15, pp. 1974-5. [ DOI : 10.1093/bioinformatics/btp250 ]
  http://hal.inria.fr/hal-00432548
• 56A. 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, n^o 1, pp. 73-93.
  http://hal.inria.fr/inria-00560621
• 57A. Denise, Y. Ponty, M. Termier.
  Controlled non uniform random generation of decomposable structures, in: Theoretical Computer Science, 2010, vol. 411, n^o 40-42, pp. 3527-3552. [ DOI : 10.1016/j.tcs.2010.05.010 ]
  http://hal.inria.fr/hal-00483581
• 58Y. Ding, C. Chan, C. Lawrence.
  RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble, in: RNA, 2005, vol. 11, pp. 1157–1166.
• 59S. 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, in press. [ DOI : 10.1016/j.jmb.2011.09.031 ]
  http://hal.inria.fr/inria-00637848
• 60S. C. Flores, J. Bernauer, S. Shin, R. Zhou, X. Huang.
  Multiscale modeling of macromolecular biosystems, in: Briefings in Bioinformatics, July 2012, vol. 13, n^o 4, pp. 395-405. [ DOI : 10.1093/bib/bbr077 ]
  http://hal.inria.fr/hal-00684530
• 61A. Guilhot-Gaudreffroy, 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, 2014, vol. accepted.
• 62L. 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, n^o 9.
  http://dx.doi.org/10.1371/journal.pbio.1000205
• 63A. 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 ]
  http://hal.inria.fr/hal-00641738
• 64A. 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, n^o 20, pp. 10041-52. [ DOI : 10.1093/nar/gks768 ]
  http://hal.inria.fr/hal-00733924
• 65S. 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, n^o 8, pp. 1127-8. [ DOI : 10.1093/bioinformatics/btq083 ]
  http://hal.inria.fr/inria-00536404
• 66D. 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, n^o 8, pp. 551–552.
  http://dx.doi.org/10.1038/nmeth0809-551
• 67D. Manocha, Y. Zhu.
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• 68D. Manocha, Y. Zhu, W. Wright.
  Conformational analysis of molecular chains using nano-kinematics, in: Comput Appl Biosci, Feb 1995, vol. 11, n^o 1, pp. 71–86.
• 69M. Parisien, F. Major.
  The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data, in: Nature, 2008, vol. 452, n^o 7183, pp. 51–55.
• 70G. Park, H.-K. Hwang, P. Nicodème, W. Szpankowski.
  Profile of Tries, in: SIAM Journal on Computing, 2009, vol. 38, n^o 5, pp. 1821-1880. [ DOI : 10.1137/070685531 ]
  http://hal.inria.fr/hal-00781400
• 71Y. 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, n^o 1-2, pp. 107–127.
  http://www.lri.fr/~ponty/docs/Ponty-07-JMB-Boustrophedon.pdf
• 72Y. Ponty, M. Termier, A. Denise.
  GenRGenS: Software for Generating Random Genomic Sequences and Structures, in: Bioinformatics, 2006, vol. 22, n^o 12, pp. 1534–1535.
  http://hal.inria.fr/inria-00601060
• 73S. 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, n^o 3, pp. 410-419.
  http://hal.inria.fr/hal-00642137
• 74E. 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, n^o 12. [ DOI : 10.1371/journal.pone.0050506 ]
  http://hal.inria.fr/hal-00769740
• 75A. 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, n^o 2, 1241010 p. [ DOI : 10.1142/S0219720012410107 ]
  http://hal.inria.fr/hal-00757761
• 76T. V. D. Tran.
  Modeling and predicting super-secondary structures of transmembrane beta-barrel proteins, Ecole Polytechnique X, December 2011.
  http://hal.inria.fr/tel-00647947
• 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, n^o 11, pp. 1465-79. [ DOI : 10.1089/cmb.2011.0181 ]
  http://hal.inria.fr/hal-00681928
• 78H. 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, n^o Pt 1, pp. 2–13.
  http://dx.doi.org/10.1107/S0907444904025697