Bibliography

Major publications by the team in recent years

1R. Andonov, S. Balev, N. Yanev.

Protein Threading: From Mathematical Models to Parallel Implementations, in: INFORMS Journal on Computing, 2004, vol. 16, n^o 4, p. 393-405. [ DOI : 10.1287/ijoc.1040.0092 ]

http://joc.journal.informs.org/content/16/4/393.abstract
2R. Andonov, N. Malod-Dognin, N. Yanev.

Maximum Contact Map Overlap Revisited, in: Journal of Computational Biology, January 2011, vol. 18, n^o 1, p. 1-15. [ DOI : 10.1089/cmb.2009.0196 ]

http://hal.inria.fr/inria-00536624/en
3R. Chikhi, G. Rizk.

Space-efficient and exact de Bruijn graph representation based on a Bloom filter, in: WABI 2012, Ljubljana, Slovenia, September 2012, vol. 7534, p. 236-248. [ DOI : 10.1007/978-3-642-33122-0_19 ]

http://hal.inria.fr/hal-00753930
4F. Legeai, G. Rizk, T. Walsh, O. Edwards, K. Gordon, D. Lavenier, N. Leterme, A. Mereau, J. Nicolas, D. Tagu, S. Jaubert-Possamai.

Bioinformatic prediction, deep sequencing of microRNAs and expression analysis during phenotypic plasticity in the pea aphid, Acyrthosiphon pisum, in: BMC Genomics, 2010, vol. 11, n^o 1, 281 p. [ DOI : 10.1186/1471-2164-11-281 ]

http://www.hal.inserm.fr/inserm-00482283
5A. Mucherino, C. Lavor, L. Liberti, N. Maculan.

The Discretizable Molecular Distance Geometry Problem, in: Computational Optimization and Applications, 2012, vol. 52, p. 115-146.

http://hal.inria.fr/hal-00756940
6V. H. Nguyen, D. Lavenier.

PLAST: parallel local alignment search tool for database comparison, in: Bmc Bioinformatics, October 2009, vol. 10, 329 p.

http://hal.inria.fr/inria-00425301
7P. Peterlongo, R. Chikhi.

Mapsembler, targeted and micro assembly of large NGS datasets on a desktop computer, in: BMC Bioinformatics, March 2012, vol. 13, n^o 48. [ DOI : 10.1186/1471-2105-13-48 ]

http://hal.inria.fr/hal-00675974
8G. Rizk, D. Lavenier.

GASSST: Global Alignment Short Sequence Search Tool, in: Bioinformatics, August 2010, vol. 26, n^o 20, p. 2534-2540.

http://hal.archives-ouvertes.fr/hal-00531499
9G. A. T. Sacomoto, J. Kielbassa, R. Chikhi, R. Uricaru, P. Antoniou, M.-F. Sagot, P. Peterlongo, V. Lacroix.

KisSplice: de-novo calling alternative splicing events from RNA-seq data, in: BMC Bioinformatics, March 2012.

http://hal.inria.fr/hal-00681995

Publications of the year

Doctoral Dissertations and Habilitation Theses

10R. Chikhi.

Computational methods for de novo assembly of next-generation genome sequencing data, École normale supérieure de Cachan - ENS Cachan, July 2012.

http://hal.inria.fr/tel-00752033

Articles in International Peer-Reviewed Journals

11J. Jaquiéry, S. Stoeckel, P. Nouhaud, L. Mieuzet, F. Mahéo, F. Legeai, N. Bernard, A. Bonvoisin, R. Vitalis, J. C. Simon.

Genome scans reveal candidate regions involved in the adaptation to host plant in the pea aphid complex., in: Molecular Ecology, November 2012, vol. 21, n^o 21, p. 5251-64. [ DOI : 10.1111/mec.12048 ]

http://hal.inria.fr/hal-00753439
12G. Le Trionnaire, S. Jaubert-Possamai, J. Bonhomme, J.-P. Gauthier, G. Guernec, A. Le Cam, F. Legeai, J. Monfort, D. Tagu.

Transcriptomic profiling of the reproductive mode switch in the pea aphid in response to natural autumnal photoperiod., in: Journal of Insect Physiology, December 2012, vol. 58, n^o 12, p. 1517–1524. [ DOI : 10.1016/j.jinsphys.2012.07.009 ]

http://hal.inria.fr/hal-00753429
13P. Leroy, N. Guilhot, H. Sakai, A. Bernard, F. Choulet, S. Theil, S. Reboux, N. Amano, T. Flutre, C. Pelegrin, H. Ohyanagi, M. Seidel, F. Giacomoni, M. Reichstadt, M. Alaux, E. Gicquello, F. Legeai, L. Cerutti, H. Numa, T. Tanaka, K. Mayer, T. Itoh, H. Quesneville, C. Feuillet.

TriAnnot: A Versatile and High Performance Pipeline for the Automated Annotation of Plant Genomes., in: Front Plant Sci, 2012, vol. 3, 5 p. [ DOI : 10.3389/fpls.2012.00005 ]

http://hal.inria.fr/hal-00753407
14A. Mucherino, C. Lavor, L. Jon, J. Lee S., L. Liberti, M. Sviridenko.

Discretization Orders for Distance Geometry Problems, in: Optimization Letters, 2012, vol. 6, n^o 4, p. 783-796.

http://hal.inria.fr/hal-00756941
15A. Mucherino, C. Lavor, L. Liberti, N. Maculan.

Recent Advances on the Discretizable Molecular Distance Geometry Problem, in: European Journal of Operational Research, 2012, vol. 219, p. 698-706.

http://hal.inria.fr/hal-00756942
16A. Mucherino, C. Lavor, L. Liberti, N. Maculan.

The Discretizable Molecular Distance Geometry Problem, in: Computational Optimization and Applications, 2012, vol. 52, p. 115-146.

http://hal.inria.fr/hal-00756940
17A. Mucherino, C. Lavor, L. Liberti.

Exploiting Symmetry Properties of the Discretizable Molecular Distance Geometry Problem, in: Journal of Bioinformatics and Computational Biology, 2012, vol. 10, n^o 3, 1242009(1-15).

http://hal.inria.fr/hal-00756939
18A. Mucherino, C. Lavor, L. Liberti.

The Discretizable Distance Geometry Problem, in: Optimization Letters, 2012, vol. 6, n^o 8, p. 1671-1686.

http://hal.inria.fr/hal-00756943
19M. Ollivier, T. Gabaldón, J. Poulain, F. Gavory, N. Leterme, J.-P. Gauthier, F. Legeai, D. Tagu, J. C. Simon, C. Rispe.

Comparison of gene repertoires and patterns of evolutionary rates in eight aphid species that differ by reproductive mode., in: Genome Biol Evol, 2012, vol. 4, n^o 2, p. 155-67. [ DOI : 10.1093/gbe/evr140 ]

http://hal.inria.fr/hal-00753402
20P. Peterlongo, R. Chikhi.

Mapsembler, targeted and micro assembly of large NGS datasets on a desktop computer, in: BMC Bioinformatics, March 2012, vol. 13, n^o 48. [ DOI : 10.1186/1471-2105-13-48 ]

http://hal.inria.fr/hal-00675974
21G. A. T. Sacomoto, J. Kielbassa, R. Chikhi, R. Uricaru, P. Antoniou, M.-F. Sagot, P. Peterlongo, V. Lacroix.

KisSplice: de-novo calling alternative splicing events from RNA-seq data, in: BMC Bioinformatics, March 2012.

http://hal.inria.fr/hal-00681995
22I. Wohlers, R. Andonov, G. W. Klau.

Optimal DALI protein structure alignment, in: IEEE/ACM Transactions on Computational Biology and Bioinformatics, November 2012, 20 p.

http://hal.inria.fr/hal-00685824
23I. Wohlers, N. Malod-Dognin, R. Andonov, G. W. Klau.

CSA: Comprehensive comparison of pairwise protein structure alignments, in: Nucleic Acids Research, 2012, p. 303-309, Preprint, submitted to Nucleic Acids Research.

http://hal.inria.fr/hal-00667920

International Conferences with Proceedings

24R. Chikhi, G. Rizk.

Space-efficient and exact de Bruijn graph representation based on a Bloom filter, in: WABI 2012, Ljubljana, Slovenia, September 2012, vol. 7534, p. 236-248. [ DOI : 10.1007/978-3-642-33122-0_19 ]

http://hal.inria.fr/hal-00753930
25N. Maillet, C. Lemaitre, R. Chikhi, D. Lavenier, P. Peterlongo.

Compareads: comparing huge metagenomic experiments, in: RECOMB Comparative Genomics 2012, Niterói, Brazil, October 2012.

http://hal.inria.fr/hal-00720951
26A. Mucherino, C. Lavor, L. Liberti, N. Maculan.

Finding Low-Energy Homopolymer Conformations by a Discrete Approach, in: Global Optimization Workshop 2012 (GOW12), Natal, Brazil, 2012.

http://hal.inria.fr/hal-00756946
27A. Mucherino, C. Lavor, L. Liberti, N. Maculan.

On the Discretization of Distance Geometry Problems, in: Mathematics of Distances and Applications 2012 (MDA12), Varna, Bulgaria, 2012.

http://hal.inria.fr/hal-00756945
28A. Mucherino, C. Virginia, C. Luiz Mariano, C. Lavor, N. Maculan.

On Suitable Orders for Discretizing Molecular Distance Geometry Problems related to Protein Side Chains, in: IEEE Conference Proceedings, Federated Conference on Computer Science and Information Systems (FedCSIS12), Workshop on Computational Optimization (WCO12), Warsaw, Poland, 2012.

http://hal.inria.fr/hal-00756944
29A. Mucherino, G. Warley, C. Lavor, N. Maculan.

A Parallel BP Algorithm for the Discretizable Distance Geometry Problem, in: Workshop on Parallel Computing and Optimization (PCO12), 26th IEEE International Parallel & Distributed Processing Symposium (IPDPS12), Shanghai, China, 2012.

http://hal.inria.fr/hal-00756947

National Conferences with Proceeding

30M. Le Boudic-Jamin, A. Mucherino, R. Andonov.

Modeling protein flexibility by distance geometry, in: ROADEF 2012, Angers, France, Université d'Angers, 2012.

http://hal.inria.fr/hal-00757717

Conferences without Proceedings

31G. Holley, P. Peterlongo.

BlastGraph: intensive approximate pattern matching in string graphs and de-Bruijn graphs, in: PSC 2012, Prague, Czech Republic, August 2012.

http://hal.inria.fr/hal-00711911

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