Team, Visitors, External Collaborators
Overall Objectives
Research Program
Application Domains
Highlights of the Year
New Software and Platforms
New Results
Bilateral Contracts and Grants with Industry
Partnerships and Cooperations
Dissemination
Bibliography
XML PDF e-pub
PDF e-Pub


Bibliography

Major publications by the team in recent years
[1]
G. 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, no 1. [ DOI : 10.1186/s12859-015-0709-7 ]
https://hal.inria.fr/hal-01214682
[2]
G. 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
[3]
R. Chikhi, G. Rizk.
Space-efficient and exact de Bruijn graph representation based on a Bloom filter, in: Algorithms for Molecular Biology, 2013, vol. 8, no 1, 22 p. [ DOI : 10.1186/1748-7188-8-22 ]
http://hal.inria.fr/hal-00868805
[4]
E. 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
[5]
S. François, R. Andonov, D. Lavenier, H. Djidjev.
Global optimization approach for circular and chloroplast genome assembly, in: BICoB 2018 - 10th International Conference on Bioinformatics and Computational Biology, Las Vegas, United States, March 2018, pp. 1-11. [ DOI : 10.1101/231324 ]
https://hal.inria.fr/hal-01666830
[6]
C. 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, no 1. [ DOI : 10.1186/s40168-018-0562-9 ]
https://hal.archives-ouvertes.fr/hal-01926402
[7]
A. 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
[8]
C. 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
[9]
G. Rizk, A. Gouin, R. Chikhi, C. Lemaitre.
MindTheGap: integrated detection and assembly of short and long insertions, in: Bioinformatics, December 2014, vol. 30, no 24, pp. 3451-3457. [ DOI : 10.1093/bioinformatics/btu545 ]
https://hal.inria.fr/hal-01081089
[10]
R. 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

Articles in International Peer-Reviewed Journals

[11]
R. Andonov, H. Djidjev, S. François, D. Lavenier.
Complete Assembly of Circular and Chloroplast Genomes Based on Global Optimization, in: Journal of Bioinformatics and Computational Biology, 2019, pp. 1-28, forthcoming. [ DOI : 10.1142/S0219720019500148 ]
https://hal.archives-ouvertes.fr/hal-02151798
[12]
G. Benoit, M. Mariadassou, S. Robin, S. Schbath, P. Peterlongo, C. Lemaitre.
SimkaMin: fast and resource frugal de novo comparative metagenomics, in: Bioinformatics, September 2019, pp. 1-2. [ DOI : 10.1093/bioinformatics/btz685 ]
https://hal.inria.fr/hal-02308101
[13]
H. Boulain, F. Legeai, J. Jaquiéry, E. Guy, S. Morliere, J.-C. Simon, A. Sugio.
Differential Expression of Candidate Salivary Effector Genes in Pea Aphid Biotypes With Distinct Host Plant Specificity, in: Frontiers in Plant Science, October 2019, vol. 10, pp. 1-12. [ DOI : 10.3389/fpls.2019.01301 ]
https://hal.inria.fr/hal-02378266
[14]
J. Ferreira De Carvalho, J. Lucas, G. Deniot, C. Falentin, O. Filangi, M. Gilet, F. Legeai, M. Lode, J. Morice, G. Trotoux, J.-M. Aury, V. Barbe, J. Keller, R. Snowdon, Z. He, F. Denoeud, P. Wincker, I. Bancroft, A.-M. Chèvre, M. Rousseau-Gueutin.
Cytonuclear interactions remain stable during allopolyploid evolution despite repeated whole-genome duplications in Brassica, in: Plant Journal, February 2019, vol. 98, no 3, pp. 434-447. [ DOI : 10.1111/tpj.14228 ]
https://hal-univ-rennes1.archives-ouvertes.fr/hal-02019346
[15]
L. Guillot, L. Delage, A. Viari, Y. Vandenbrouck, E. Com, A. A. Ritter, R. Lavigne, D. Marie, P. Peterlongo, P. Potin, C. Pineau.
Peptimapper: proteogenomics workflow for the expert annotation of eukaryotic genomes, in: BMC Genomics, January 2019, vol. 20, no 1, 56 p. [ DOI : 10.1186/s12864-019-5431-9 ]
https://hal.inria.fr/hal-01987197
[16]
A. Limasset, J.-F. Flot, P. Peterlongo.
Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs, in: Bioinformatics, February 2019. [ DOI : 10.1093/bioinformatics/btz102 ]
https://hal.inria.fr/hal-02407243
[17]
C. Marchet, P. Morisse, L. Lecompte, A. Lefebvre, T. Lecroq, P. Peterlongo, A. Limasset.
ELECTOR: evaluator for long reads correction methods, in: NAR Genomics and Bioinformatics, March 2020, vol. 2, no 1. [ DOI : 10.1093/nargab/lqz015 ]
https://hal.inria.fr/hal-02371117
[18]
S. Robin, M. Ravallec, M. Frayssinet, J. Whitfield, V. Jouan, F. Legeai, A.-N. Volkoff.
Evidence for an ichnovirus machinery in parasitoids of coleopteran larvae, in: Virus Research, 2019, vol. 263, pp. 189-206. [ DOI : 10.1016/j.virusres.2019.02.001 ]
https://hal.archives-ouvertes.fr/hal-02059774
[19]
M. Wery, O. Dameron, J. Nicolas, E. Rémy, A. Siegel.
Formalizing and enriching phenotype signatures using Boolean networks, in: Journal of Theoretical Biology, 2019, vol. 467, pp. 66-79. [ DOI : 10.1016/j.jtbi.2019.01.015 ]
https://hal.inria.fr/hal-02018724

International Conferences with Proceedings

[20]
J. N. Alanko, H. Bannai, B. Cazaux, P. Peterlongo, J. Stoye.
Finding all maximal perfect haplotype blocks in linear time, in: WABI 2019 - Workshop on Algorithms in Bioinformatics, Niagara Falls, United States, ACM, September 2019, pp. 1-9.
https://hal.inria.fr/hal-02187246
[21]
L. Bourneuf, J. Nicolas.
Concept Lattices as a Search Space for Graph Compression, in: ICFCA 2019 - 15th International Conference on Formal Concept Analysis, Francfort, Germany, D. C. L. B. Sertkaya (editor), ICFCA: International Conference on Formal Concept Analysis, Springer, May 2019, vol. 15th International Conference, no 15, pp. 274-289. [ DOI : 10.1007/978-3-030-21462-3_18 ]
https://hal.inria.fr/hal-02399578

National Conferences with Proceedings

[22]
C. Guyomar, W. Delage, F. Legeai, C. Mougel, J.-C. Simon, C. Lemaitre.
Reference-guided genome assembly in metagenomic samples, in: JOBIM 2019 - Journées Ouvertes Biologie, Informatique et Mathématiques, Nantes, France, July 2019, pp. 1-8.
https://hal.inria.fr/hal-02308257
[23]
L. Lecompte, P. Peterlongo, D. Lavenier, C. Lemaitre.
Genotyping Structural Variations using Long Read data, in: JOBIM 2019 - Journées Ouvertes Biologie, Informatique et Mathématiques, Nantes, France, July 2019, pp. 1-8.
https://hal.inria.fr/hal-02288091

Conferences without Proceedings

[24]
L. Lecompte, P. Peterlongo, D. Lavenier, C. Lemaitre.
Genotyping Structural Variations using Long Read Data, in: HiTSeq 2019 - Conference on High Throughput Sequencing, Basel, Switzerland, July 2019, pp. 1-3.
https://hal.inria.fr/hal-02289484
[25]
C. Marchet, M. Kerbiriou, A. Limasset.
Indexing De Bruijn graphs with minimizers, in: Recomb seq, Whashinton, United States, April 2019. [ DOI : 10.1101/546309 ]
https://hal.archives-ouvertes.fr/hal-02435086
[26]
P. Morisse, C. Marchet, A. Limasset, T. Lecroq, A. Lefebvre.
CONSENT: Scalable self-correction of long reads with multiple sequence alignment, in: Recomb Seq, Washinton, France, May 2019.
https://hal.archives-ouvertes.fr/hal-02435116
[27]
H. S. Pham, G. Virlet, D. Lavenier, A. Termier.
Statistically Significant Discriminative Patterns Searching, in: DaWaK 2019 - 21st International Conference on Big Data Analytics and Knowledge Discovery, Linz, Austria, Springer, August 2019, pp. 105-115. [ DOI : 10.1007/978-3-030-27520-4_8 ]
https://hal.archives-ouvertes.fr/hal-02190793

Other Publications

[28]
A. Badual.
Stockage d'information sur ADN, Université Rennes 1, June 2019.
https://hal.inria.fr/hal-02401641
[29]
L. Conde-Canencia, B. Hamoum, D. Lavenier, E. Roux.
Error Correction Schemes for DNA Storage with Nanopore Sequencing, July 2019, JOBIM 2019 - Journées Ouvertes Biologie, Informatique et Mathématiques, Poster.
https://hal.archives-ouvertes.fr/hal-02400744
[30]
K. Da Silva, N. Pons, M. Berland, F. Plaza Oñate, M. Almeida, P. Peterlongo.
From genomics to metagenomics: benchmark of variation graphs, July 2019, JOBIM 2019 - Journées Ouvertes Biologie, Informatique et Mathématiques, Poster.
https://hal.inria.fr/hal-02284559
[31]
V. Epain.
De novo long reads assembly using integer linear programing, Université de Rennes 1 [UR1], September 2019.
https://hal.inria.fr/hal-02413832
[32]
J. Gauthier, C. Mouden, T. Suchan, N. Alvarez, N. Arrigo, C. Riou, C. Lemaitre, P. Peterlongo.
DiscoSnp-RAD: de novo detection of small variants for population genomics, October 2019, working paper or preprint.
https://hal.inria.fr/hal-01634232
[33]
R. Laso-Jadart, K. Sugier, E. Petit, K. Labadie, P. Peterlongo, C. Ambroise, P. Wincker, J.-L. Jamet, M.-A. Madoui.
Linking Allele-Specific Expression And Natural Selection In Wild Populations, September 2019, working paper or preprint. [ DOI : 10.1101/599076 ]
https://hal.inria.fr/hal-02275928
[34]
D. Lavenier, E. Roux, L. Conde-Canencia, B. Hamoum.
Advanced Coding Schemes for DNA-Based Data Storage Using Nanopore Sequencing Technologies, November 2019, Journées CominLabs 2019, Poster.
https://hal.archives-ouvertes.fr/hal-02400656
[35]
L. Lecompte, P. Peterlongo, D. Lavenier, C. Lemaitre.
SVJedi : Structural variation genotyping using long reads, July 2019, HiTSeq 2019 - Conference on High Throughput Sequencing, Poster.
https://hal.inria.fr/hal-02290884
[36]
T. Lemane.
Search engine for genomic sequencing data, Université Rennes1, July 2019.
https://hal.inria.fr/hal-02410102
[37]
K. Thuillier.
Linear programming for metabolic network completion, Inria Rennes - Bretagne Atlantique and University of Rennes 1, France, December 2019.
https://hal.inria.fr/hal-02408003
References in notes
[38]
R. S. Harris, P. Medvedev.
Improved representation of sequence bloom trees, in: Bioinformatics, 08 2019, btz662.
https://doi.org/10.1093/bioinformatics/btz662