Bibliography

Publications of the year

Articles in International Peer-Reviewed Journals

• 1H. F. Becker, A. Héliou, K. Djaout, R. Lestini, M. Regnier, H. Myllykallio.
  High-Throughput Sequencing Reveals Circular Substrates for an Archaeal RNA ligase, in: RNA Biology, March 2017.
  https://hal.archives-ouvertes.fr/hal-01491132
• 2M. Boudard, D. Barth, J. Bernauer, A. Denise, J. Cohen.
  GARN2: coarse-grained prediction of 3D structure of large RNA molecules by regret minimization, in: Bioinformatics, 2017, vol. 16, pp. 2479-2486. [ DOI : 10.1093/bioinformatics/btx175 ]
  https://hal.archives-ouvertes.fr/hal-01589347
• 3A. Churkin, M. D. Retwitzer, V. Reinharz, Y. Ponty, J. Waldispühl, D. Barash.
  Design of RNAs: comparing programs for inverse RNA folding, in: Briefings in Bioinformatics, January 2017. [ DOI : 10.1093/bib/bbw120 ]
  https://hal.inria.fr/hal-01392958
• 4J. Deforges, S. De Breyne, M. Ameur, N. Ulryck, N. Chamond, A. Saaidi, Y. Ponty, T. Ohlmann, B. Sargueil.
  Two ribosome recruitment sites direct multiple translation events within HIV1 Gag open reading frame, in: Nucleic Acids Research, July 2017, vol. 45, n^o 12, pp. 7382–7400. [ DOI : 10.1093/nar/gkx303 ]
  https://hal.archives-ouvertes.fr/hal-01505282
• 5W. Duchemin, Y. Anselmetti, M. Patterson, Y. Ponty, S. Bérard, C. Chauve, C. Scornavacca, V. Daubin, E. Tannier.
  DeCoSTAR: Reconstructing the ancestral organization of genes or genomes using reconciled phylogenies, in: Genome Biology and Evolution, 2017, vol. 9, n^o 5, pp. 1312-1319.
  https://hal.inria.fr/hal-01503766
• 6J. 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, November 2017, vol. 79, n^o 3, pp. 835–856, https://arxiv.org/abs/1603.03577. [ DOI : 10.1007/s00453-016-0196-x ]
  https://hal.inria.fr/hal-01285499
• 7A. Héliou, D. Budday, R. Fonseca, H. Van Den Bedem.
  Fast, clash-free RNA conformational morphing using molecular junctions, in: Bioinformatics, July 2017, vol. 33, n^o 14, pp. 2114 - 2122. [ DOI : 10.1093/bioinformatics/btx127 ]
  https://hal.archives-ouvertes.fr/hal-01569620
• 8A. Héliou, S. P. Pissis, S. J. Puglisi.
  emMAW: Computing Minimal Absent Words in External Memory, in: Bioinformatics, 2017. [ DOI : 10.1093/bioinformatics/btx209 ]
  https://hal.archives-ouvertes.fr/hal-01569271
• 9B. Löwes, C. Chauve, Y. Ponty, R. Giegerich.
  The BRaliBase dent - a tale of benchmark design and interpretation, in: Briefings in Bioinformatics, March 2017, vol. 18, n^o 2, pp. 306–311. [ DOI : 10.1093/bib/bbw022 ]
  https://hal.inria.fr/hal-01273406

Invited Conferences

• 10A. Saaidi, Y. Ponty, M. Blanchette, M. Regnier, B. Sargueil.
  An EM algorithm for mapping short reads in multiple RNA structure probing experiments, in: Matbio2017, London, United Kingdom, King's College London , September 2017.
  https://hal.inria.fr/hal-01590528

International Conferences with Proceedings

• 11J. Cohen, A. Héliou, P. Mertikopoulos.
  Hedging under uncertainty: regret minimization meets exponentially fast convergence, in: Symposium on Algorithmic Game Theory (SAGT) 2017, L'Aquila, Italy, Proceedings of the 10th International Symposium on Algorithmic Game Theory, September 2017, https://arxiv.org/abs/1607.08863. [ DOI : 10.1007/978-3-319-66700-3_20 ]
  https://hal.archives-ouvertes.fr/hal-01382290
• 12J. Cohen, A. Héliou, P. Mertikopoulos.
  Learning with bandit feedback in potential games, in: NIPS '17: Proceedings of the 31st International Conference on Neural Information Processing Systems, Long Beach, CA, United States, December 2017.
  https://hal.archives-ouvertes.fr/hal-01643352
• 13M. Crochemore, A. Héliou, G. Kucherov, L. Mouchard, S. P. Pissis, Y. Ramusat.
  Minimal absent words in a sliding window & applications to on-line pattern matching, in: FCT 2017, Bordeaux, France, Lecture Notes in Computer Science, Springer, September 2017, forthcoming.
  https://hal.archives-ouvertes.fr/hal-01569264
• 14S. Hammer, Y. Ponty, W. Wang, S. Will.
  Fixed-Parameter Tractable Sampling for RNA Design with Multiple Target Structures, in: RECOMB 2018 – 22nd Annual International Conference on Research in Computational Molecular Biology, Paris, France, April 2018.
  https://hal.inria.fr/hal-01631277
• 15J. Michálik, H. Touzet, Y. Ponty.
  Efficient approximations of RNA kinetics landscape using non-redundant sampling, in: ISMB/ECCB - 25th Annual international conference on Intelligent Systems for Molecular Biology/16th European Conference on Computational Biology - 2017, Prague, Czech Republic, July 2017, vol. 33, n^o 14, pp. i283 - i292. [ DOI : 10.1093/bioinformatics/btx269 ]
  https://hal.inria.fr/hal-01500115
• 16G. v. Zundert, D. Keedy, P. Suresh, A. Héliou, K. Borrelli, T. Day, J. Fraser, H. Van Den Bedem.
  Objectively and automatically building multi-conformer ligand models in electron densities, in: Conformational ensembles from experimental data and computer simulations, Berlin, Germany, August 2017.
  https://hal.inria.fr/hal-01569829

Conferences without Proceedings

• 17A. Saaidi, Y. Ponty, B. Sargueil.
  An integrative approach for predicting the RNA secondary structure for the HIV–1 Gag UTR using probing data, in: JOBIM 2017 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Lille, France, July 2017, 1 p.
  https://hal.archives-ouvertes.fr/hal-01534587

Other Publications

• 18C. Chauve, J. Courtiel, Y. Ponty.
  Counting, generating, analyzing and sampling tree alignments, 2017, Submitted to IJFCS.
  https://hal.inria.fr/hal-01500116
• 19D. Surujon, Y. Ponty, P. Clote.
  Small-world networks and RNA secondary structures, January 2017, working paper or preprint.
  https://hal.inria.fr/hal-01424452

References in notes

• 20C. 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
• 21J. 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
• 22S. Chairungsee, M. Crochemore.
  Using minimal absent words to build phylogeny, in: Theoretical Computer Science, 2012, vol. 450, n^o 0, pp. 109-116.
• 23R. 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
• 24M. 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
• 25A. 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
• 26H. 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.
  http://dx.doi.org/10.1089/cmb.2011.0070
• 27Y. Ding, C. Chan, C. Lawrence.
  RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble, in: RNA, 2005, vol. 11, pp. 1157–1166.
• 28S. 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
• 29Z. 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.
• 30J. 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.
• 31A. 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
• 32A. 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
• 33S. 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
• 34M. 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.
• 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 nucleotide distribution, in: Bioinformatics, July 2013, vol. 29, n^o 13, i308 p. [ DOI : 10.1093/bioinformatics/btt217 ]
  http://hal.inria.fr/hal-00840260
• 37V. 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
• 38V. 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
• 39P. Rinaudo, Y. Ponty, D. Barth, A. Denise.
  Tree decomposition and parameterized algorithms for RNA structure-sequence alignment including tertiary interactions and pseudoknots, in: WABI - 12th Workshop on Algorithms in Bioinformatics - 2012, Ljubljana, Slovénie, B. Raphael, J. Tang (editors), University of Ljubljana, 2012.
  http://hal.inria.fr/hal-00708580
• 40G. 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
• 41C. 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
• 42E. 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
• 43E. 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
• 44R. 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 ]
• 45T. 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
• 46J. 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
• 47K. A. Wilkinson, E. J. Merino, K. M. Weeks.
  Selective 2 [prime]-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolution, in: Nature protocols, 2006, vol. 1, n^o 3, pp. 1610–1616.