Bibliography

Major publications by the team in recent years

• 1J. 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
• 2J. Haleš, J. Maňuch, Y. Ponty, L. Stacho.
  Combinatorial RNA Design: Designability and Structure-Approximating Algorithm, in: CPM - 26th Annual Symposium on Combinatorial Pattern Matching, Ischia Island, Italy, F. Cicalese, E. Porat (editors), June 2015, Accepted (To appear).
  https://hal.inria.fr/hal-01115349
• 3V. 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 ]
  https://hal.inria.fr/hal-00840260
• 4M. 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, in: Algorithms for Molecular Biology, December 2014, vol. 9, n^o 1. [ DOI : 10.1186/s13015-014-0025-1 ]
  https://hal.inria.fr/hal-00858701
• 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 ]
  https://hal.inria.fr/inria-00537117

Publications of the year

Doctoral Dissertations and Habilitation Theses

• 6J. Bernauer.
  Geometric and statistical methods for the analysis and prediction of structural interactions between biomolecules, Université Paris-Sud XI, January 2015, Habilitation à diriger des recherches.
  https://tel.archives-ouvertes.fr/tel-01136261

Articles in International Peer-Reviewed Journals

• 7M. Boudard, J. Bernauer, D. Barth, J. Cohen, A. Denise.
  GARN: Sampling RNA 3D Structure Space with Game Theory and Knowledge-Based Scoring Strategies, in: PLoS ONE, August 2015, vol. 10, n^o 8, e0136444.
  https://hal.archives-ouvertes.fr/hal-01201665
• 8T. Bourquard, F. Landomiel, E. Reiter, P. Crépieux, D. W. Ritchie, J. Azé, A. Poupon.
  Unraveling the molecular architecture of a G protein-coupled receptor/β-arrestin/Erk module complex, in: Scientific Reports, June 2015, 5:10760. [ DOI : 10.1038/srep10760 ]
  http://hal-lirmm.ccsd.cnrs.fr/lirmm-01162594
• 9C. Chauve, Y. Ponty, J. P. P. Zanetti.
  Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach, in: BMC Bioinformatics, December 2015, vol. 16, n^o Suppl 19, S6 p. [ DOI : 10.1186/1471-2105-16-S19-S6 ]
  https://hal.inria.fr/hal-01245495
• 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 ]
  https://hal.archives-ouvertes.fr/hal-01094249
• 11M. Heinonen, O. Guipaud, F. Milliat, V. Buard, B. Micheau, G. Tarlet, M. Benderitter, F. Zehraoui, F. D'Alché-Buc.
  Detecting time periods of differential gene expression using Gaussian processes: An application to endothelial cells exposed to radiotherapy dose fraction, in: Bioinformatics, March 2015, vol. 31, n^o 5, pp. 728–735. [ DOI : 10.1093/bioinformatics/btu699 ]
  https://hal.archives-ouvertes.fr/hal-01154010
• 12D. Iakovishina, I. Janoueix-Lerosey, E. Barillot, M. Regnier, V. Boeva.
  SV-Bay: structural variant detection in cancer genomes using a Bayesian approach with correction for GC-content and read map-pability, in: Bioinformatics (Oxford, England), January 2016.
  https://hal.inria.fr/hal-01253126
• 13H. Jiang, F. K. Sheong, L. Zhu, X. Gao, J. Bernauer, X. Huang.
  Markov State Models Reveal a Two-Step Mechanism of miRNA Loading into the Human Argonaute Protein: Selective Binding followed by Structural Re-arrangement, in: PLoS Computational Biology, June 2015, vol. 11, n^o 7, e1004404.
  https://hal.inria.fr/hal-01257437
• 14J. d. V. Moreira, S. Pérès, J.-M. Steyaert, E. Bigan, L. Paulevé, M. L. Nogeira, L. Schwartz.
  Cell cycle progression is regulated by intertwined redox oscillators, in: Theoretical Biology and Medical Modelling, May 2015, vol. 12, n^o 1, 10 p. [ DOI : 10.1186/s12976-015-0005-2 ]
  https://hal.archives-ouvertes.fr/hal-01158514

International Conferences with Proceedings

• 15J. Bernauer, R. Fonseca, H. Van Den Bedem.
  KGSrna: Efficient 3D Kinematics-Based Sampling for Nucleic Acids, in: RECOMB 2015, Warsaw, Poland, Research in Computational Molecular Biology, April 2015, vol. 9029. [ DOI : 10.1007/978-3-319-16706-0_11 ]
  https://hal.inria.fr/hal-01257755
• 16B. Brancotte, B. Yang, G. Blin, S. Cohen-Boulakia, A. Denise, S. Hamel.
  Rank aggregation with ties: Experiments and Analysis, in: The 41st International Conference on Very Large Data Bases, Kohala Coast, Hawaï, United States, August 2015, vol. 8, n^o 11.
  https://hal.archives-ouvertes.fr/hal-01152098
• 17J. Haleš, J. Maňuch, Y. Ponty, L. Stacho.
  Combinatorial RNA Design: Designability and Structure-Approximating Algorithm, in: CPM - 26th Annual Symposium on Combinatorial Pattern Matching, Ischia Island, Italy, F. Cicalese, E. Porat (editors), June 2015, forthcoming.
  https://hal.inria.fr/hal-01115349
• 18A. Rajaraman, C. Chauve, Y. Ponty.
  Assessing the robustness of parsimonious predictions for gene neighborhoods from reconciled phylogenies, in: ISBRA - 11th International Symposium on Bioinformatics Research and Applications - 2015, Norfolk, Virginia, United States, June 2015, forthcoming.
  https://hal.inria.fr/hal-01104587

Scientific Books (or Scientific Book chapters)

• 19F. Jossinet, Y. Ponty, J. Waldispühl.
  Preface, in: Computational methods for Structural RNAs (CMSR'14), Journal of Computational Biology, Mary Ann Liebert, February 2015, vol. 22, n^o 3, 189 p.
  https://hal.inria.fr/hal-01136745
• 20Y. 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 ]
  https://hal.inria.fr/hal-01079893

Other Publications

• 21C. Barton, A. Heliou, L. Mouchard, S. P. Pissis.
  Parallelising the Computation of Minimal Absent Words, January 2016, working paper or preprint.
  https://hal.archives-ouvertes.fr/hal-01255489
• 22C. Chauve, J. Courtiel, Y. Ponty.
  Counting, generating and sampling tree alignments, 2015, Submitted.
  https://hal.inria.fr/hal-01154030
• 23A. Heliou, M. Léonard, L. Mouchard, M. Salson.
  Efficient Dynamic Range Minimum Query, January 2016, working paper or preprint.
  https://hal.archives-ouvertes.fr/hal-01255499
• 24M. Regnier, P. Chassignet.
  Accurate prediction of the statistics of repetitions in random sequences : a case study in Archae genomes, 2015, working paper or preprint.
  https://hal.inria.fr/hal-01253628

References in notes

• 25C. 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 ]
  https://hal.inria.fr/hal-01110274
• 26J. 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 ]
  http://hal.inria.fr/inria-00542791
• 27V. 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.
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• 28S. Bérard, C. Gallien, B. Boussau, G. J. Szöllösi, V. Daubin, E. Tannier.
  Evolution of gene neighborhoods within reconciled phylogenies, in: Bioinformatics, 2012, vol. 28, n^o 18, pp. i382-i388. [ DOI : 10.1093/bioinformatics/bts374 ]
  http://bioinformatics.oxfordjournals.org/content/28/18/i382.abstract
• 29S. Chairungsee, M. Crochemore.
  Using minimal absent words to build phylogeny, in: Theoretical Computer Science, 2012, vol. 450, n^o 0, pp. 109-116.
• 30R. Chikhi, P. Medvedev.
  Informed and automated k-mer size selection for genome assembly., in: Bioinformatics, Jan 2014, vol. 30, n^o 1, pp. 31–37.
  http://dx.doi.org/10.1093/bioinformatics/btt310
• 31E. 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.
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• 32M. Crochemore, G. Fici, R. Mercas, S. Pissis.
  Linear-Time Sequence Comparison Using Minimal Absent Words, in: LATIN 2016: Theoretical Informatics - 12th Latin American Symposium, Lecture Notes in Computer Science, Springer Berlin Heidelberg, 2016.
  http://arxiv.org/abs/1506.04917
• 33A. 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
• 34H. Devillers, S. Schbath.
  Separating significant matches from spurious matches in DNA sequences, in: Journal of Computational Biology, 2012, vol. 19, n^o 1, pp. 1–12. [ DOI : 10.1089/cmb.2011.0070 ]
• 35Y. Ding, C. Chan, C. Lawrence.
  RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble, in: RNA, 2005, vol. 11, pp. 1157–1166.
• 36S. 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
• 37Z. Gu, H. Wang, A. Nekrutenko, W. H. Li.
  Densities, length proportions, and other distributional features of repetitive sequences in the human genome estimated from 430 megabases of genomic sequence., in: Gene, Dec 2000, vol. 259, n^o 1-2, pp. 81–88.
• 38L. 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
• 39A. 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
• 40S. 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
• 41D. 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
• 42D. 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.
• 43D. 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.
• 44M. 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.
• 45G. 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
• 46Y. 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
• 47M. Regnier, E. Furletova, M. Roytberg, V. Yakovlev.
  Pattern occurrences Pvalues, Hidden Markov Models and Overlap Graphs, 2013, submitted.
  http://hal.inria.fr/hal-00858701
• 48V. 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
• 49G. Rizk, D. Lavenier, R. Chikhi.
  DSK: k-mer counting with very low memory usage., in: Bioinformatics, Mar 2013, vol. 29, n^o 5, pp. 652–653. [ DOI : 10.1093/bioinformatics/btt020 ]
  http://bioinformatics.oxfordjournals.org/content/early/2013/02/01/bioinformatics.btt020.full
• 50E. 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
• 51E. 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.
  http://hal.inria.fr/hal-00766780
• 52R. M. Silva, D. Pratas, L. Castro, A. J. Pinho, P. J. S. G. Ferreira.
  Three minimal sequences found in Ebola virus genomes and absent from human DNA, in: Bioinformatics, 2015. [ DOI : 10.1093/bioinformatics/btv189 ]
• 53A. 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. [ DOI : 10.1142/S0219720012410107 ]
  http://hal.inria.fr/hal-00757761
• 54T. J. Treangen, S. L. Salzberg.
  Repetitive DNA and next-generation sequencing: computational challenges and solutions., in: Nat Rev Genet, Jan 2012, vol. 13, n^o 1, pp. 36–46.
  http://dx.doi.org/10.1038/nrg3117
• 55H. 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
• 56J. 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