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Bibliography

Publications of the year

Articles in International Peer-Reviewed Journals

  • 1E. Bigan, L. Paulevé, J.-M. Steyaert, S. S. Douady.
    Necessary and sufficient conditions for protocell growth, in: Journal of Mathematical Biology, April 2016. [ DOI : 10.1007/s00285-016-0998-0 ]
    https://hal.archives-ouvertes.fr/hal-01338156
  • 2A. Churkin, M. Drory Retwitzer, V. Reinharz, Y. Ponty, J. Waldispühl, D. Barash.
    Design of RNAs: Comparing Programs for inverse RNA folding, in: Briefings in Bioinformatics, 2017, forthcoming.
    https://hal.inria.fr/hal-01392958
  • 3M. Drory Retwitzer, V. Reinharz, Y. Ponty, J. Waldispühl, D. Barash.
    incaRNAfbinv : a web server for the fragment-based design of RNA sequences, in: Nucleic Acids Research, 2016, vol. 44, no W1, pp. W308 - W314. [ DOI : 10.1093/nar/gkw440 ]
    https://hal.inria.fr/hal-01319682
  • 4J. Haleš, A. Héliou, J. Maňuch, Y. Ponty, L. Stacho.
    Combinatorial RNA Design: Designability and Structure-Approximating Algorithm in Watson-Crick and Nussinov-Jacobson Energy Models, in: Algorithmica, 2016, forthcoming.
    https://hal.inria.fr/hal-01285499
  • 5A. Heliou, M. Léonard, L. Mouchard, M. Salson.
    Efficient dynamic range minimum query, in: Theoretical Computer Science, 2017. [ DOI : 10.1016/j.tcs.2016.07.002 ]
    https://hal.archives-ouvertes.fr/hal-01255499
  • 6D. 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
  • 7E. Jacox, C. Chauve, G. J. Szöllősi, Y. Ponty, C. Scornavacca.
    ecceTERA: comprehensive gene tree-species tree reconciliation using parsimony, in: Bioinformatics (Oxford, England), July 2016, pp. 2056-8, Accepted, forthcoming.
    https://hal.inria.fr/hal-01276903
  • 8B. Löwes, C. Chauve, Y. Ponty, R. Giegerich.
    The BRaliBase dent-a tale of benchmark design and interpretation. , in: Briefings in Bioinformatics, March 2016. [ DOI : 10.1093/bib/bbw022 ]
    https://hal.inria.fr/hal-01273406
  • 9M. Regnier, P. Chassignet.
    Accurate prediction of the statistics of repetitions in random sequences: a case study in Archaea genomes, in: Frontiers in Bioengineering and Biotechnology, May 2016.
    https://hal.inria.fr/hal-01304366
  • 10V. Reinharz, Y. Ponty, J. Waldispühl.
    Combining structure probing data on RNA mutants with evolutionary information reveals RNA-binding interfaces, in: Nucleic Acids Research, 2016, vol. 44, no 11, e104 - e104. [ DOI : 10.1093/nar/gkw217 ]
    https://hal.inria.fr/hal-01291754

International Conferences with Proceedings

  • 11C. Chauve, J. Courtiel, Y. Ponty.
    Counting, generating and sampling tree alignments, in: ALCOB - 3rd International Conference on Algorithms for Computational Biology - 2016, Trujillo, Spain, June 2016.
    https://hal.inria.fr/hal-01154030
  • 12J. Lumbroso, M. Mishna, Y. Ponty.
    Taming reluctant random walks in the positive quadrant, in: GASCOM - 10th conference on random generation of combinatorial structures - 2016, Bastia, France, Electronic Notes in Discrete Mathematics, June 2016, forthcoming.
    https://hal.inria.fr/hal-01291164

National Conferences with Proceedings

  • 13V. J. Henry, A. Ferré, C. Froidevaux, A. A. Goelzer, V. V. Fromion, S. Cohen-Boulakia, S. S. Derozier, M. Dinh, G. Fiévet, S. Fischer, J.-F. J.-F. Gibrat, V. L. Loux, S. Pérès.
    Représentation systémique multi-échelle des processus biologiques de la bactérie, in: IC2016: Ingénierie des Connaissances, Montpellier, France, June 2016.
    https://hal.archives-ouvertes.fr/hal-01442727
  • 14A. Saaidi, D. Allouche, B. Sargueil, Y. Ponty.
    Towards structural models for the Ebola UTR regions using experimental SHAPE probing data, in: JOBIM - Journées Ouvertes en Biologie, Informatique et Mathématiques - 2016, Lyon, France, June 2016.
    https://hal.inria.fr/hal-01332469
  • 15W. Wang​, M. Barba​, P. Rinaudo​, A. Denise, Y. Ponty.
    Homology ­modeling of complex structural RNAs, in: JOBIM - Journées Ouvertes en Biologie, Informatique et Mathématiques - 2016, Lyon, France, June 2016.
    https://hal.inria.fr/hal-01332642

Other Publications

References in notes
  • 18C. Barton, A. Heliou, L. Mouchard, S. 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
  • 19J. 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
  • 20V. 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.
    http://dx.doi.org/10.1093/bioinformatics/btr670
  • 21S. Chairungsee, M. Crochemore.
    Using minimal absent words to build phylogeny, in: Theoretical Computer Science, 2012, vol. 450, no 0, pp. 109-116.
  • 22R. Chikhi, P. Medvedev.
    Informed and automated k-mer size selection for genome assembly, in: Bioinformatics, Jan 2014, vol. 30, no 1, pp. 31–37.
    http://dx.doi.org/10.1093/bioinformatics/btt310
  • 23M. 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
  • 24A. 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 ]
    http://hal.inria.fr/hal-00483581
  • 25H. Devillers, S. Schbath.
    Separating significant matches from spurious matches in DNA sequences, in: Journal of Computational Biology, 2012, vol. 19, no 1, pp. 1–12.
    http://dx.doi.org/10.1089/cmb.2011.0070
  • 26Y. Ding, C. Chan, C. Lawrence.
    RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble, in: RNA, 2005, vol. 11, pp. 1157–1166.
  • 27S. 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 ]
    http://hal.inria.fr/hal-00684530
  • 28Z. 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, no 1-2, pp. 81–88.
  • 29J. Haleš, J. Maňuch, Y. Ponty, L. Stacho.
    Combinatorial RNA Design: Designability and Structure-Approximating Algorithm, in: Annual Symposium on Combinatorial Pattern Matching, Springer, 2015, pp. 231–246.
  • 30W. Kladwang, R. Das.
    A mutate-and-map strategy for inferring base pairs in structured nucleic acids: proof of concept on a DNA/RNA helix, in: Biochemistry, 2010, vol. 49, no 35, pp. 7414–7416.
  • 31A. 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 ]
    http://hal.inria.fr/hal-00733924
  • 32S. 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 ]
    http://hal.inria.fr/inria-00536404
  • 33M. 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.
  • 34Y. 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.
    http://www.lri.fr/~ponty/docs/Ponty-07-JMB-Boustrophedon.pdf
  • 35M. Regnier, E. Furletova, M. Roytberg, V. Yakovlev.
    Pattern occurrences Pvalues, Hidden Markov Models and Overlap Graphs, 2013, submitted.
    http://hal.inria.fr/hal-00858701
  • 36V. 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, Allemagne, 2013.
    http://hal.inria.fr/hal-00811607
  • 37V. 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 ]
    http://hal.inria.fr/hal-00828062
  • 38G. Rizk, D. Lavenier, R. Chikhi.
    DSK: k-mer counting with very low memory usage, in: Bioinformatics, Mar 2013, vol. 29, no 5, pp. 652–653. [ DOI : 10.1093/bioinformatics/btt020 ]
    http://bioinformatics.oxfordjournals.org/content/early/2013/02/01/bioinformatics.btt020.full
  • 39C. 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 ]
    http://hal.inria.fr/inria-00537117
  • 40E. 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 ]
    http://hal.inria.fr/hal-00769740
  • 41E. 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
  • 42R. 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 ]
  • 43T. J. Treangen, S. L. Salzberg.
    Repetitive DNA and next-generation sequencing: computational challenges and solutions, in: Nat Rev Genet, Jan 2012, vol. 13, no 1, pp. 36–46.
    http://dx.doi.org/10.1038/nrg3117
  • 44J. 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 ]
    http://hal.inria.fr/hal-00681928
  • 45L. Weinbrand, A. Avihoo, D. Barash.
    RNAfbinv: an interactive Java application for fragment-based design of RNA sequences, in: Bioinformatics, 2013, btt494.

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