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Bibliography

Major publications by the team in recent years
  • 1A. Abdo, S. Caboche, V. Leclère, P. Jacques, M. Pupin.

    A new fingerprint to predict nonribosomal peptides activity, in: Journal of Computer-Aided Molecular Design, October 2012, vol. 26, no 10, pp. 1187-94. [ DOI : 10.1007/s10822-012-9608-4 ]

    http://hal.inria.fr/hal-00750002
  • 2A. Abdo, V. Leclère, P. Jacques, N. Salim, M. Pupin.

    Prediction of new bioactive molecules using a bayesian belief network, in: Journal of Chemical Information and Modeling, January 2014, vol. 54, no 1, pp. 30-36. [ DOI : 10.1021/ci4004909 ]

    https://hal.archives-ouvertes.fr/hal-01090611
  • 3R. Chikhi, A. Limasset, P. Medvedev.

    Compacting de Bruijn graphs from sequencing data quickly and in low memory, in: Bioinformatics, November 2016, vol. 32, no 12, pp. i201 - i208. [ DOI : 10.1093/bioinformatics/btw279 ]

    https://hal.archives-ouvertes.fr/hal-01395704
  • 4Y. Dufresne, L. Noé, V. Leclère, M. Pupin.

    Smiles2Monomers: a link between chemical and biological structures for polymers, in: Journal of Cheminformatics, December 2015. [ DOI : 10.1186/s13321-015-0111-5 ]

    https://hal.inria.fr/hal-01250619
  • 5Y. Ferret, A. Caillault, S. Sebda, M. Duez, N. Grardel, N. Duployez, C. Villenet, M. Figeac, C. Preudhomme, M. Salson, M. Giraud.

    Multi-loci diagnosis of acute lymphoblastic leukaemia with high-throughput sequencing and bioinformatics analysis, in: British Journal of Haematology, 2016, bjh.13981 p. [ DOI : 10.1111/bjh.13981 ]

    https://hal.archives-ouvertes.fr/hal-01279160
  • 6A. Flissi, Y. Dufresne, J. Michalik, L. Tonon, S. Janot, L. Noé, P. Jacques, V. Leclère, M. Pupin.

    Norine, the knowledgebase dedicated to non-ribosomal peptides, is now open to crowdsourcing, in: Nucleic Acids Research, 2015. [ DOI : 10.1093/nar/gkv1143 ]

    https://hal.archives-ouvertes.fr/hal-01235996
  • 7M. Frith, L. Noé.

    Improved search heuristics find 20 000 new alignments between human and mouse genomes, in: Nucleic Acids Research, February 2014, vol. 42, no 7, e59 p. [ DOI : 10.1093/nar/gku104 ]

    https://hal.inria.fr/hal-00958207
  • 8R. Giegerich, H. Touzet.

    Modeling dynamic programming problems over sequences and trees with inverse coupled rewrite systems, in: Algorithms, 2014, vol. 7, pp. 62 - 144. [ DOI : 10.3390/a7010062 ]

    https://hal.archives-ouvertes.fr/hal-01084318
  • 9M. Giraud, M. Salson, M. Duez, C. Villenet, S. Quief, A. Caillault, N. Grardel, C. Roumier, C. Preudhomme, M. Figeac.

    Fast multiclonal clusterization of V(D)J recombinations from high-throughput sequencing, in: BMC Genomics, 2014, vol. 15, no 1, 409 p. [ DOI : 10.1186/1471-2164-15-409 ]

    https://hal.archives-ouvertes.fr/hal-01009173
  • 10E. Kopylova, L. Noé, H. Touzet.

    SortMeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data, in: Bioinformatics, October 2012, pp. 1-10. [ DOI : 10.1093/bioinformatics/bts611 ]

    http://hal.inria.fr/hal-00748990
  • 11M. Léonard, L. Mouchard, M. Salson.

    On the number of elements to reorder when updating a suffix array, in: Journal of Discrete Algorithms, February 2012, vol. 11, pp. 87-99. [ DOI : 10.1016/j.jda.2011.01.002 ]

    http://hal.inria.fr/inria-00636066
  • 12D. E. K. Martin, L. Noé.

    Faster exact distributions of pattern statistics through sequential elimination of states, in: Annals of the Institute of Statistical Mathematics, September 2015. [ DOI : 10.1007/s10463-015-0540-y ]

    https://hal.inria.fr/hal-01237045
  • 13L. Noé, D. E. K. Martin.

    A coverage criterion for spaced seeds and its applications to support vector machine string kernels and k-mer distances, in: Journal of Computational Biology, November 2014, vol. 21, no 12, 28 p. [ DOI : 10.1089/cmb.2014.0173 ]

    https://hal.inria.fr/hal-01083204
  • 14A. Perrin, J.-S. Varré, S. Blanquart, A. Ouangraoua.

    ProCARs: progressive reconstruction of ancestral gene orders, in: BMC Genomics, 2015, vol. 16, no Suppl 5, S6 p. [ DOI : 10.1186/1471-2164-16-S5-S6 ]

    https://hal.inria.fr/hal-01217311
  • 15M. Pupin, Q. Esmaeel, A. Flissi, Y. Dufresne, P. Jacques, V. Leclère.

    Norine: a powerful resource for novel nonribosomal peptide discovery, in: Synthetic and Systems Biotechnology, December 2015. [ DOI : 10.1016/j.synbio.2015.11.001 ]

    https://hal.inria.fr/hal-01250614
  • 16A. Saffarian, M. Giraud, A. De Monte, H. Touzet.

    RNA locally optimal secondary structures, in: Journal of Computational Biology, 2012, vol. 19, no 10, pp. 1120-1133. [ DOI : 10.1089/cmb.2010.0178 ]

    http://hal.inria.fr/hal-00756249
  • 17A. Saffarian, M. Giraud, H. Touzet.

    Modeling alternate RNA structures in genomic sequences, in: Journal of Computational Biology, February 2015, vol. 22, no 3, pp. 190-204.

    https://hal.archives-ouvertes.fr/hal-01228130
Publications of the year

Articles in International Peer-Reviewed Journals

  • 18J. Audoux, M. Salson, C. F. Grosset, S. Beaumeunier, J.-M. Holder, T. Commes, N. Philippe.

    SimBA: A methodology and tools for evaluating the performance of RNA-Seq bioinformatic pipelines, in: BMC Bioinformatics, September 2017, vol. 18, no 1, 428 p. [ DOI : 10.1186/s12859-017-1831-5 ]

    http://www.hal.inserm.fr/inserm-01612738
  • 19Q. Esmaeel, M. Pupin, P. Jacques, V. Leclère.

    Nonribosomal peptides and polyketides of Burkholderia: new compounds potentially implicated in biocontrol and pharmaceuticals, in: Environmental Science and Pollution Research, May 2017. [ DOI : 10.1007/s11356-017-9166-3 ]

    https://hal.archives-ouvertes.fr/hal-01548616
  • 20A. W. Langerak, M. Brüggemann, F. Davi, N. Darzentas, J. J. M. Van Dongen, D. Gonzalez, G. Cazzaniga, V. Giudicelli, M.-P. Lefranc, M. Giraud, E. A. Macintyre, M. Hummel, C. Pott, P. J. T. A. Groenen, K. Stamatopoulos.

    High-Throughput Immunogenetics for Clinical and Research Applications in Immunohematology: Potential and Challenges, in: Journal of Immunology, April 2017, 1602050 p. [ DOI : 10.4049/jimmunol.1602050 ]

    https://hal.archives-ouvertes.fr/hal-01516289
  • 21D. E. K. Martin, L. Noé.

    Faster exact distributions of pattern statistics through sequential elimination of states, in: Annals of the Institute of Statistical Mathematics, February 2017, vol. 69, no 1, pp. 231–248. [ DOI : 10.1007/s10463-015-0540-y ]

    https://hal.inria.fr/hal-01237045
  • 22L. Noé.

    Best hits of 11110110111: model-free selection and parameter-free sensitivity calculation of spaced seeds, in: Algorithms for Molecular Biology, February 2017, vol. 12, no 1. [ DOI : 10.1186/s13015-017-0092-1 ]

    https://hal.inria.fr/hal-01467970
  • 23P. Pericard, Y. Dufresne, L. Couderc, S. Blanquart, H. Touzet.

    MATAM: reconstruction of phylogenetic marker genes from short sequencing reads in metagenomes, in: Bioinformatics, October 2017. [ DOI : 10.1093/bioinformatics/btx644 ]

    https://hal.inria.fr/hal-01646297
  • 24M. Salson, M. Giraud, A. Caillault, N. Grardel, N. Duployez, Y. Ferret, M. Duez, R. Herbert, T. Rocher, S. Sebda, S. Quief, C. Villenet, M. Figeac, C. Preudhomme.

    High-throughput sequencing in acute lymphoblastic leukemia: Follow-up of minimal residual disease and emergence of new clones, in: Leukemia Research, 2017, vol. 53, pp. 1-7. [ DOI : 10.1016/j.leukres.2016.11.009 ]

    https://hal.archives-ouvertes.fr/hal-01404817
  • 25A. Sczyrba, P. Hofmann, P. Belmann, D. Koslicki, S. Janssen, J. Dröge, I. Gregor, S. Majda, J. Fiedler, E. Dahms, A. Bremges, A. Fritz, R. Garrido-Oter, T. S. Jørgensen, N. Shapiro, P. D. Blood, A. Gurevich, Y. Bai, D. Turaev, M. Z. DeMaere, R. Chikhi, N. Nagarajan, C. Quince, L. H. Hansen, S. J. Sørensen, B. K. H. Chia, B. Denis, J. L. Froula, Z. Wang, R. Egan, D. Don Kang, J. J. Cook, C. Deltel, M. Beckstette, C. Lemaitre, P. Peterlongo, G. Rizk, D. Lavenier, Y.-W. Wu, S. W. Singer, C. Jain, M. Strous, H. Klingenberg, P. Meinicke, M. D. Barton, T. Lingner, H.-H. Lin, Y.-C. Liao, G. G. Z. Silva, D. A. Cuevas, R. A. Edwards, S. Saha, V. C. Piro, B. Y. Renard, M. Pop, H.-P. Klenk, M. Göker, N. C. Kyrpides, T. Woyke, J. A. Vorholt, P. Schulze-Lefert, E. M. Rubin, A. E. Darling, T. Rattei, A. C. McHardy.

    Critical Assessment of Metagenome Interpretation – a benchmark of computational metagenomics software, in: Nature Methods, October 2017, vol. 14, no 11, pp. 1063 - 1071. [ DOI : 10.1038/nmeth.4458 ]

    https://hal.archives-ouvertes.fr/hal-01633525

International Conferences with Proceedings

  • 26A. Limasset, G. Rizk, R. Chikhi, P. Peterlongo.

    Fast and scalable minimal perfect hashing for massive key sets, in: 16th International Symposium on Experimental Algorithms, London, United Kingdom, June 2017, vol. 11, pp. 1 - 11, https://arxiv.org/abs/1702.03154.

    https://hal.inria.fr/hal-01566246
  • 27J. 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, no 14, pp. i283 - i292. [ DOI : 10.1093/bioinformatics/btx269 ]

    https://hal.inria.fr/hal-01500115
  • 28C. Sun, R. S. Harris, R. Chikhi, P. Medvedev.

    AllSome Sequence Bloom Trees, in: RECOMB 2017 - 21st Annual International Conference on Research in Computational Molecular Biology, Hong Kong, China, May 2017. [ DOI : 10.1007/978-3-319-56970-3_17 ]

    https://hal.inria.fr/hal-01575350

National Conferences with Proceedings

    Scientific Popularization

    • 30M. Pupin, P. Marquet, Y. Secq.

      How to make teenage girls love coding using Python and the visual arts orienting language Processing ?, in: PyParis2017, Paris, La Défense, France, Systematic Paris Region, June 2017.

      https://hal.inria.fr/hal-01552487
    • 31T. Rocher, M. Pupin, P. Marquet, Y. Secq.

      How to make teenage girls love coding ?, in: womENcourage2017 - 4th ACM Europe Celebration of Women in Computing, Barcelona, Spain, ACM, September 2017.

      https://hal.inria.fr/hal-01552490

    Other Publications

    • 32P. Marijon, J.-S. Varré, R. Chikhi.

      Debugging long-read genome and metagenome assemblies using string graph analysis, July 2017, JOBIM 2017- Journées Ouvertes en Biologie, Informatique et Mathématiques, Poster.

      https://hal.inria.fr/hal-01574824
    • 33C. Saad, L. Noé, H. Richard, J. Leclerc, M.-P. Buisine, H. Touzet, M. Figeac.

      DiNAMO: Exact method for degenerate IUPAC motifs discovery, characterization of sequence-specific errors, July 2017, JOBIM 2017 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Poster.

      https://hal.inria.fr/hal-01574630


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