Bibliography

Publications of the year

Doctoral Dissertations and Habilitation Theses

• 1B. Donati.
  Graph models and algorithms in (co-)evolutionary contexts, Universite Claude Bernard Lyon 1 ; Università degli studi di Firenze, November 2014.
  https://hal.inria.fr/tel-01095298
• 2S. Higashi.
  MiRNA and co: Methodologically exploring the world of small RNAs, Universite Claude Bernard Lyon 1, November 2014.
  https://hal.archives-ouvertes.fr/tel-01096833
• 3P.-A. Rollat-Farnier.
  Evolution of the genomes of the endosymbionts in phloem-sap feeding insects: the case of Hamiltonella defensa interacting with its various partners, Université Claude Bernard Lyon 1, November 2014.
  https://hal.inria.fr/tel-01102943
• 4G. Sacomoto.
  Efficient Algorithms for de novo Assembly of Alternative Splicing Events from RNA-seq Data, Universite Claude Bernard Lyon 1, March 2014.
  https://hal.inria.fr/tel-01095280

Articles in International Peer-Reviewed Journals

• 5A. C. Azevedo-Martins, A. C. L. Machado, C. C. Klein, L. Ciapina, L. Gonzaga, A. T. R. Vasconcelos, M. F. Sagot, W. De Souza, M. Einicker-Lamas, A. Galina, M. C. M. Motta.
  Mitochondrial respiration and genomic analysis provide insight into the influence of the symbiotic bacterium on host trypanosomatid oxygen consumption, in: Parasitology, August 2014, pp. 1-11. [ DOI : 10.1017/S0031182014001139 ]
  https://hal.inria.fr/hal-01073754
• 6M. Badawi, I. Giraud, F. Vavre, P. Grève, R. Cordaux.
  Signs of Neutralization in a Redundant Gene Involved in Homologous Recombination in Wolbachia Endosymbionts, in: Genome Biology and Evolution, 2014, vol. 10, n^o 6, pp. 2654-2664. [ DOI : 10.1093/gbe/evu207 ]
  https://hal.inria.fr/hal-01091858
• 7D. Basquin, A. Spierer, F. Begeot, D. E. Koryakov, A.-L. Todeschini, S. Ronsseray, C. Vieira, P. Spierer, M. Delattre.
  The Drosophila Su(var)3-7 gene is required for oogenesis and female fertility, genetically interacts with piwi and aubergine, but impacts only weakly transposon silencing, in: PLoS ONE, 2014, vol. 9, n^o 5, e96802.
  https://hal.inria.fr/hal-01092623
• 8C. Baudet, B. Donati, B. Sinaimeri, P. Crescenzi, C. Gautier, C. Matias, M.- F. Sagot.
  Cophylogeny Reconstruction via an Approximate Bayesian Computation, in: Systematic Biology, December 2014, 49 p. [ DOI : 10.1093/sysbio/syu129 ]
  https://hal.inria.fr/hal-01092972
• 9T. Boivin, H. Henri, F. Vavre, C. Gidoin, P. Veber, J.-N. Candau, E. Magnoux, A. Roques, M.-A. Auger-Rozenberg.
  Epidemiology of asexuality induced by the endosymbiotic Wolbachia across phytophagous wasp species: host plant specialization matters, in: Molecular Ecology Notes, April 2014, pp. 2362-2375.
  https://hal.inria.fr/hal-01092614
• 10C. M. A. Carareto, E. H. Hernandez, C. Vieira.
  Genomic regions harboring insecticide resistance-associated Cyp genes are enriched by transposable element fragments carrying putative transcription factor binding sites in two sibling Drosophila species, in: Gene, 2014, vol. 537, n^o 1, pp. 93-99. [ DOI : 10.1016/j.gene.2013.11.080 ]
  https://hal.inria.fr/hal-00922703
• 11E. A. G. Carnelossi, E. Lerat, H. Henri, S. Martinez, C. M. A. Carareto, C. Vieira.
  Specific activation of an I-like element in Drosophila interspecific hybrids, in: Genome Biology and Evolution, June 2014, pp. 1806-17.
  https://hal.inria.fr/hal-01079996
• 12B. Donati, C. Baudet, B. Sinaimeri, P. Crescenzi, M.-F. Sagot.
  EUCALYPT: efficient tree reconciliation enumerator, in: Algorithms for Molecular Biology, January 2015, vol. 10, n^o 1, 11 p. [ DOI : 10.1186/s13015-014-0031-3 ]
  https://hal.inria.fr/hal-01092977
• 13M. Fablet, A. Akkouche, V. Braman, C. Vieira.
  Variable expression levels detected in the Drosophila effectors of piRNA biogenesis, in: Gene, 2014, vol. 537, n^o 1, pp. 149-153. [ DOI : 10.1016/j.gene.2013.11.095 ]
  https://hal.inria.fr/hal-00922704
• 14M. Federico, P. Peterlongo, N. Pisanti, M.-F. Sagot.
  Rime: Repeat identification, in: Discrete Applied Mathematics, 2014, vol. 163, n^o 3, pp. 275–286. [ DOI : 10.1016/j.dam.2013.02.016 ]
  https://hal.inria.fr/hal-00802023
• 15N. Kremer, F. Vavre.
  Microbial impacts on insect evolutionary diversification: from patterns to mechanisms, in: Current Opinion in Insect Science, October 2014, vol. 4, pp. 29–34. [ DOI : 10.1016/j.cois.2014.08.003 ]
  https://hal.inria.fr/hal-01104106
• 16W.-J. Ma, F. Vavre, L. W. Beukeboom.
  Manipulation of arthropod sex determination by endosymbionts: diversity and molecular mechanisms, in: Sex. Dev., 2014, pp. 59-73.
  https://hal.inria.fr/hal-01092616
• 17P. Mallinjoud, J.-P. Villemin, H. Mortada, M. Polay Espinoza, F.-O. Desmet, S. Samaan, E. Chautard, L.-C. Tranchevent, D. Auboeuf.
  Endothelial, epithelial, and fibroblast cells exhibit specific splicing programs independently of their tissue of origin, in: Genome Research, 2014, vol. 24, n^o 3, pp. 511-521. [ DOI : 10.1101/gr.162933.113 ]
  https://hal.archives-ouvertes.fr/hal-01091290
• 18P. V. Milreu, C. C. Klein, L. Cottret, V. Acuña, E. Birmelé, M. Borassi, C. Junot, A. Marchetti-Spaccamela, A. Marino, L. Stougie, F. Jourdan, P. Crescenzi, V. Lacroix, M.-F. Sagot.
  Telling metabolic stories to explore metabolomics data: a case study on the yeast response to cadmium exposure, in: Bioinformatics, January 2014, vol. 30, n^o 1, pp. 61-70. [ DOI : 10.1093/bioinformatics/btt597 ]
  https://hal.inria.fr/hal-00922567
• 19L. Mouton, O. Gnankiné, H. Henri, G. Terraz, G. Ketoh, T. Martin, F. Fleury, F. Vavre.
  Detection of genetically isolated entities within the Mediterranean species of Bemisia tabaci: new insights into the systematics of this worldwide pest, in: Pest Management Science, May 2014, pp. 2654-2664.
  https://hal.inria.fr/hal-01092608
• 20D. Roquis, J. M. J. Lepesant, E. Villafan, J. Boissier, C. Vieira, C. Cosseau, C. Grunau.
  Exposure to hycanthone alters chromatin structure around specific gene functions and specific repeats in Schistosoma mansoni, in: Frontiers in Genetics, 2014, vol. 5, 207 p.
  https://hal.inria.fr/hal-01092618
• 21G. Sacomoto, B. Sinaimeri, C. Marchet, V. Miele, M.-F. Sagot, V. Lacroix.
  Navigating in a Sea of Repeats in RNA-seq without Drowning, in: Lecture Notes in Bioinformatics, 2014, vol. 8701, pp. 82-96. [ DOI : 10.1007/978-3-662-44753-6_7 ]
  https://hal.inria.fr/hal-01079947
• 22K. Salikhov, G. Sacomoto, G. Kucherov.
  Using cascading Bloom filters to improve the memory usage for de Brujin graphs, in: Algorithms for Molecular Biology, 2014, vol. 9, n^o 1, 2 p. [ DOI : 10.1186/1748-7188-9-2 ]
  https://hal.inria.fr/hal-00971576
• 23D. Santos-Garcia, P.-A. Rollat-Farnier, F. Beitia, E. Zchori-Fein, F. Vavre, L. Mouton, A. Moya, A. Latorre, F. J. Silva.
  The genome of Cardinium cBtQ1 provides insights into genome reduction, symbiont motility, and its settlement in Bemisia tabaci, in: Genome Biology and Evolution, March 2014, pp. 1013-1030.
  https://hal.inria.fr/hal-01092610
• 24P. Sapountzis, G. Duport, S. Balmand, K. Gaget, S. Jaubert-Possamai, G. Febvay, H. Charles, Y. Rahbé, S. Colella, F. Calevro.
  New insight into the RNA interference response against cathepsin-L gene in the pea aphid, Acyrthosiphon pisum: Molting or gut phenotypes specifically induced by injection or feeding treatments, in: Insect Biochemistry and Molecular Biology, May 2014, epub ahead of print, forthcoming. [ DOI : 10.1016/j.ibmb.2014.05.005 ]
  https://hal.archives-ouvertes.fr/hal-01002574
• 25R. 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
• 26D. Vela, A. Fontdevila, C. Vieira, M. P. García Guerreiro.
  A genome-wide survey of genetic instability by transposition in Drosophila hybrids, in: PLoS ONE, 2014, vol. 9, n^o 2, e88992.
  https://hal.inria.fr/hal-01092626

International Conferences with Proceedings

• 27C. Baudet, U. Dias, Z. Dias.
  Length and Symmetry on the Sorting by Weighted Inversions Problem, in: BSB - 9th Brazilian Symposium on Bioinformatics, Belo Horizonte, Brazil, S. Campos (editor), Advances in Bioinformatics and Computational Biology, October 2014, vol. 8826, pp. 99 - 106. [ DOI : 10.1007/978-3-319-12418-6_13 ]
  https://hal.inria.fr/hal-01092607
• 28R. Ferreira, R. Grossi, R. Rizzi, G. Sacomoto, M.-F. Sagot.
  Amortized Õ(|V|) -Delay Algorithm for Listing Chordless Cycles in Undirected Graphs, in: 22th Annual European Symposium on Algorithms, Wroclaw, Poland, Algorithms ESA 2014, Lecture Notes in Computer Science, September 2014, vol. 8737, pp. 418-429. [ DOI : 10.1007/978-3-662-44777-2_35 ]
  https://hal.inria.fr/hal-01081031
• 29R. Rizzi, G. Sacomoto, M.-F. Sagot.
  Efficiently listing bounded length st-paths, in: Twenty-Fifth International Workshop on Combinatorial Algorithms (IWOCA 2014), Duluth, Minnesota, France, September 2014, forthcoming.
  https://hal.inria.fr/hal-01091924