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 $β$ -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 $B t o D ⌃ * *$ 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.

http://hal.inria.fr/hal-00748041
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 ]

http://hal.inria.fr/inria-00431696
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 ]

http://hal.inria.fr/inria-00542791
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.

Kinematic manipulation of molecular chains subject to rigid constraints, in: Proc Int Conf Intell Syst Mol Biol, 1994, vol. 2, pp. 285–293.
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

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