Bibliography

Major publications by the team in recent years

• 1G. Benoit, C. Lemaitre, D. Lavenier, E. Drezen, T. Dayris, R. Uricaru, G. Rizk.
  Reference-free compression of high throughput sequencing data with a probabilistic de Bruijn graph, in: BMC Bioinformatics, September 2015, vol. 16, n^o 1. [ DOI : 10.1186/s12859-015-0709-7 ]
  https://hal.inria.fr/hal-01214682
• 2G. Benoit, P. Peterlongo, M. Mariadassou, E. Drezen, S. Schbath, D. Lavenier, C. Lemaitre.
  Multiple comparative metagenomics using multiset k -mer counting, in: PeerJ Computer Science, November 2016, vol. 2. [ DOI : 10.7717/peerj-cs.94 ]
  https://hal.inria.fr/hal-01397150
• 3R. Chikhi, G. Rizk.
  Space-efficient and exact de Bruijn graph representation based on a Bloom filter, in: Algorithms for Molecular Biology, 2013, vol. 8, n^o 1, 22 p. [ DOI : 10.1186/1748-7188-8-22 ]
  http://hal.inria.fr/hal-00868805
• 4E. Drezen, G. Rizk, R. Chikhi, C. Deltel, C. Lemaitre, P. Peterlongo, D. Lavenier.
  GATB: Genome Assembly & Analysis Tool Box, in: Bioinformatics, 2014, vol. 30, pp. 2959 - 2961. [ DOI : 10.1093/bioinformatics/btu406 ]
  https://hal.archives-ouvertes.fr/hal-01088571
• 5A. 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://hal.inria.fr/hal-01566246
• 6G. Rizk, A. Gouin, R. Chikhi, C. Lemaitre.
  MindTheGap: integrated detection and assembly of short and long insertions, in: Bioinformatics, December 2014, vol. 30, n^o 24, pp. 3451 - 3457. [ DOI : 10.1093/bioinformatics/btu545 ]
  https://hal.inria.fr/hal-01081089
• 7R. Uricaru, G. Rizk, V. Lacroix, E. Quillery, O. Plantard, R. Chikhi, C. Lemaitre, P. Peterlongo.
  Reference-free detection of isolated SNPs, in: Nucleic Acids Research, November 2014, pp. 1 - 12. [ DOI : 10.1093/nar/gku1187 ]
  https://hal.inria.fr/hal-01083715

Publications of the year

Doctoral Dissertations and Habilitation Theses

• 8C. Guyomar.
  Bioinformatic tools and applications for metagenomics of microbial communities associated to insects, Université Rennes 1, December 2018.
  https://tel.archives-ouvertes.fr/tel-01955222
• 9C. Marchet.
  From reads to transcripts: de novo methods for the analysis of transcriptome second and third generation sequencing, Université de Rennes 1, September 2018.
  https://tel.archives-ouvertes.fr/tel-01939193

Articles in International Peer-Reviewed Journals

• 10H. BOULAIN, F. Legeai, E. Guy, S. Morliere, N. Douglas, J. Oh, M. Murugan, M. Smith, J. Jaquiéry, J. Peccoud, F. White, J. Carolan, J.-C. Simon, A. Sugio.
  Fast Evolution and Lineage-Specific Gene Family Expansions of Aphid Salivary Effectors Driven by Interactions with Host-Plants, in: Genome Biology and Evolution, 2018, vol. 10, n^o 6, pp. 1554-1572. [ DOI : 10.1093/gbe/evy097 ]
  https://hal.archives-ouvertes.fr/hal-01891942
• 11C. Benoit-Pilven, C. Marchet, E. Chautard, L. Lima, M.-P. Lambert, G. Sacomoto, A. Rey, A. Cologne, S. Terrone, L. Dulaurier, J.-B. Claude, C. Bourgeois, D. Auboeuf, V. Lacroix.
  Complementarity of assembly-first and mapping-first approaches for alternative splicing annotation and differential analysis from RNAseq data, in: Scientific Reports, December 2018, vol. 8, n^o 1. [ DOI : 10.1038/s41598-018-21770-7 ]
  https://hal.inria.fr/hal-01924204
• 12G. Chapuis, H. Djidjev, G. Hahn, G. Rizk.
  Finding Maximum Cliques on the D-Wave Quantum Annealer, in: Journal of Signal Processing Systems, May 2018. [ DOI : 10.1007/s11265-018-1357-8 ]
  https://hal.archives-ouvertes.fr/hal-01920397
• 13S. Gay, J. Bugeon, A. BOUCHAREB, L. Henry, C. DELAHAYE, F. Legeai, J. Montfort, A. Le Cam, A. Siegel, J. Bobe, V. Thermes.
  MiR-202 controls female fecundity by regulating medaka oogenesis, in: PLoS Genetics, September 2018, vol. 14, n^o 9, pp. 1-26. [ DOI : 10.1371/journal.pgen.1007593 ]
  https://hal.archives-ouvertes.fr/hal-01871468
• 14C. Guyomar, F. Legeai, E. Jousselin, C. C. Mougel, C. Lemaitre, J.-C. Simon.
  Multi-scale characterization of symbiont diversity in the pea aphid complex through metagenomic approaches, in: Microbiome, December 2018, vol. 6, n^o 1, pp. 1-21. [ DOI : 10.1186/s40168-018-0562-9 ]
  https://hal.archives-ouvertes.fr/hal-01926402
• 15J. Jaquiéry, J. Peccoud, T. Ouisse, F. Legeai, N. Prunier-Leterme, A. Gouin, P. Nouhaud, J. A. Brisson, R. Bickel, S. Purandare, J. Poulain, C. Battail, C. Lemaitre, L. Mieuzet, G. Le Trionnaire, J.-C. Simon, C. Rispe.
  Disentangling the Causes for Faster-X Evolution in Aphids, in: Genome Biology and Evolution, January 2018, vol. 10, n^o 2, pp. 507-520. [ DOI : 10.1093/gbe/evy015 ]
  https://hal.archives-ouvertes.fr/hal-01701165
• 16C. Marchet, L. Lecompte, C. Da Silva, C. Cruaud, J.-M. Aury, J. Nicolas, P. Peterlongo.
  De Novo Clustering of Long Reads by Gene from Transcriptomics Data, in: Nucleic Acids Research, 2018, pp. 1-12. [ DOI : 10.1093/nar/gky834 ]
  https://hal.archives-ouvertes.fr/hal-01643156
• 17C. Marchet, L. Lecompte, A. Limasset, L. Bittner, P. Peterlongo.
  A resource-frugal probabilistic dictionary and applications in bioinformatics, in: Discrete Applied Mathematics, April 2018, pp. 1-11. [ DOI : 10.1016/j.dam.2018.03.035 ]
  https://hal.archives-ouvertes.fr/hal-01873312
• 18T. Marschall, M. Marz, T. Abeel, L. Dijkstra, B. E. Dutilh, A. Ghaffaari, P. Kersey, W. P. Kloosterman, V. Makinen, A. M. Novak, B. Paten, D. Porubsky, E. Rivals, C. Alkan, J. A. Baaijens, P. I. W. De Bakker, V. Boeva, R. J. P. Bonnal, F. Chiaromonte, R. Chikhi, F. D. Ciccarelli, R. Cijvat, E. Datema, C. M. V. Duijn, E. E. Eichler, C. Ernst, E. Eskin, E. Garrison, M. El-Kebir, G. W. Klau, J. O. Korbel, E.-W. Lameijer, B. Langmead, M. Martin, P. Medvedev, J. C. Mu, P. Neerincx, K. Ouwens, P. Peterlongo, N. Pisanti, S. Rahmann, B. Raphael, K. Reinert, D. De Ridder, J. De Ridder, M. Schlesner, O. Schulz-Trieglaff, A. D. Sanders, S. Sheikhizadeh, C. Shneider, S. Smit, D. Valenzuela, J. Wang, L. Wessels, Y. Zhang, V. Guryev, F. Vandin, K. Ye, A. Schönhuth.
  Computational pan-genomics: status, promises and challenges, in: Briefings in Bioinformatics, 2018, vol. 19, n^o 1, pp. 118-135. [ DOI : 10.1093/bib/bbw089 ]
  https://hal.inria.fr/hal-01390478
• 19A. Meng, C. Marchet, E. Corre, P. Peterlongo, A. Alberti, C. Da Silva, P. Wincker, E. Pelletier, I. Probert, J. Decelle, S. Le Crom, F. Not, L. Bittner.
  A de novo approach to disentangle partner identity and function in holobiont systems, in: Microbiome, June 2018, pp. 1-35. [ DOI : 10.1101/221424 ]
  https://hal.archives-ouvertes.fr/hal-01643153
• 20Y. Moné, S. Nhim, S. Gimenez, F. Legeai, I. Séninet, H. Parrinello, N. NEGRE, E. D'Alençon.
  Characterization and expression profiling of microRNAs in response to plant feeding in two host-plant strains of the lepidopteran pest Spodoptera frugiperda, in: BMC Genomics, December 2018, vol. 19, n^o 1, pp. 1-15. [ DOI : 10.1186/s12864-018-5119-6 ]
  https://hal.inria.fr/hal-01926342
• 21P. Nouhaud, M. Gautier, A. Gouin, J. Jaquiéry, J. Peccoud, F. Legeai, L. Mieuzet, C. Smadja, C. Lemaitre, R. Vitalis, J.-C. Simon.
  Identifying genomic hotspots of differentiation and candidate genes involved in the adaptive divergence of pea aphid host races, in: Molecular Ecology, August 2018, vol. 27, n^o 16, pp. 3287 - 3300. [ DOI : 10.1111/mec.14799 ]
  https://hal.archives-ouvertes.fr/hal-01892027
• 22R. Robertson, R. Waterhouse, K. Walden, L. Ruzzante, M. Reijnders, B. Coates, F. Legeai, J. Gress, S. Biyiklioglu, D. Weaver, K. Wanner, H. H. Budak.
  Genome sequence of the wheat stem sawfly, Cephus cinctus, representing an early-branching lineage of the Hymenoptera, illuminates evolution of hymenopteran chemoreceptors, in: Genome Biology and Evolution, October 2018, vol. 10, n^o 11, pp. 2997–3011. [ DOI : 10.1093/gbe/evy232 ]
  https://hal.inria.fr/hal-01926352
• 23G. Yazbeck, R. S. Oliveira, J. M. Ribeiro, R. Graciano, R. Santos, F. Carmo, D. Lavenier.
  A broad genomic panel of microsatellite loci from Brycon orbignyanus (Characiformes: Bryconidae) an endangered migratory Neotropical fish, in: Scientific Reports, December 2018, vol. 8, n^o 1, pp. 1-5. [ DOI : 10.1038/s41598-018-26623-x ]
  https://hal.archives-ouvertes.fr/hal-01919836

International Conferences with Proceedings

• 24F. Coste, J. Nicolas.
  Learning local substitutable context-free languages from positive examples in polynomial time and data by reduction, in: ICGI 2018 - 14th International Conference on Grammatical Inference, Wrocław, Poland, September 2018, vol. 93, pp. 155 - 168.
  https://hal.inria.fr/hal-01872266
• 25S. Francois, R. Andonov, H. Djidjev, M. Traikov, N. Yanev.
  Mixed Integer Linear Programming Approach for a Distance-Constrained Elementary Path Problem, in: CTW 2018 - 16th Cologne-Twente Workshop on Graphs and Combinatorial Optimization, Paris, France, June 2018, pp. 1-4.
  https://hal.inria.fr/hal-01937008
• 27A. Limasset, J.-F. Flot, P. Peterlongo.
  Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs, in: Recomb, Paris, France, April 2018, https://arxiv.org/abs/1711.03336 - RECOMB 2018 Submission.
  https://hal.inria.fr/hal-01644163

Conferences without Proceedings

• 28C. Marchet, L. Lecompte, C. Da Silva, C. Cruaud, J.-M. Aury, J. Nicolas, P. Peterlongo.
  CARNAC-LR : Clustering coefficient-based Acquisition of RNA Communities in Long Reads, in: JOBIM 2018 - Journées Ouvertes Biologie, Informatique et Mathématiques, Marseille, France, July 2018, pp. 1-3.
  https://hal.archives-ouvertes.fr/hal-01930211

Internal Reports

• 29M. Bridoux.
  Séparation d'haplotypes à partir de données de séquençage de troisième génération, Inria Rennes - Bretagne Atlantique, August 2018.
  https://hal.archives-ouvertes.fr/hal-01933561

Other Publications

• 30A. Belcour, J. Girard, M. Aite, L. Delage, C. Trottier, C. Marteau, C. J.-J. Leroux, S. M. Dittami, P. Sauleau, E. Corre, J. Nicolas, C. Boyen, C. Leblanc, J. Collén, A. Siegel, G. V. Markov.
  Inferring biochemical reactions and metabolite structures to cope with metabolic pathway drift, December 2018, working paper or preprint.
  https://hal.inria.fr/hal-01943880
• 31C. Guyomar, W. Delage, F. Legeai, C. C. Mougel, J.-C. Simon, C. Lemaitre.
  Reference guided genome assembly in metagenomic samples, April 2018, 1 p, RECOMB 2018 - 22nd International Conference on Research in Computational Molecular Biology, Poster.
  https://hal.archives-ouvertes.fr/hal-01934823
• 32L. Lecompte, C. Marchet, P. Morisse, A. Limasset, P. Peterlongo, A. Lefebvre, T. Lecroq.
  ELECTOR: EvaLuation of Error Correction Tools for lOng Reads, July 2018, pp. 1-2, JOBIM 2018 - Journées Ouvertes Biologie, Informatique et Mathématiques, Poster.
  https://hal.archives-ouvertes.fr/hal-01929900
• 33C. Marchet, L. Lecompte, C. Da Silva, C. Cruaud, J.-M. Aury, J. Nicolas, P. Peterlongo.
  CARNAC-LR: De novo Clustering of Gene Expressed Variants in Transcriptomic Long Reads Data Sets, April 2018, pp. 1-2, RECOMB-seq 2018 - Eighth RECOMB Satellite Workshop on Massively Parallel Sequencing, Poster.
  https://hal.archives-ouvertes.fr/hal-01929963
• 34C. Marchet, L. Lima.
  Simulation of RNA sequencIng with Oxford Nanopore Technologies, July 2018, pp. 1-2, JOBIM 2018 - Journées Ouvertes Biologie, Informatique et Mathématiques, Poster.
  https://hal.archives-ouvertes.fr/hal-01929917
• 35J. Nicolas.
  Artificial Intelligence and Bioinformatics, July 2018, working paper or preprint.
  https://hal.inria.fr/hal-01850570

References in notes

• 36J. T. Simpson, K. Wong, S. D. Jackman, J. E. Schein, S. J. M. Jones, I. Birol.
  ABySS: a parallel assembler for short read sequence data, in: Genome Res, Jun 2009, vol. 19, n^o 6, pp. 1117–1123.