Bibliography

Publications of the year

Doctoral Dissertations and Habilitation Theses

• 1C. C. Klein.
  Une étude bioinformatique du dialogue métabolique entre un trypanosome non pathogène et son endosymbiote à des buts évolutifs et fonctionnels, Université Claude Bernard - Lyon I, November 2013.
  http://hal.inria.fr/tel-00923295

Articles in International Peer-Reviewed Journals

• 2A. Akkouche, T. Grentzinger, M. Fablet, C. Armenise, N. Burlet, V. Braman, S. Chambeyron, C. Vieira.
  Maternally deposited germline piRNAs silence the tirant retrotransposon in somatic cells, in: EMBO reports, May 2013, vol. 14, n^o 5, pp. 458-64. [ DOI : 10.1038/embor.2013.38 ]
  http://hal.inria.fr/hal-00850319
• 3R. Alikiiteaga Gutiérrez, A. Viari, B. Godelle, R. Frutos, P. Buchy.
  Biased mutational pattern and quasispecies hypothesis in H5N1 virus, in: Infection, Genetics and Evolution, 2013, vol. 15, pp. 69-76. [ DOI : 10.1016/j.meegid.2011.10.019 ]
  http://hal.inria.fr/pasteur-00853145
• 4J. Alves, C. Klein, F. da Silva, A. Costa-Martins, M. Serrano, G. Buck, A. T. Vasconcelos, M.-F. Sagot, M. Teixeira, M. C. Motta, E. Camargo.
  Endosymbiosis in trypanosomatids: the genomic cooperation between bacterium and host in the synthesis of essential amino acids is heavily influenced by multiple horizontal gene transfers, in: BMC Evolutionary Biology, 2013, vol. 13, n^o 1, 190 p. [ DOI : 10.1186/1471-2148-13-190 ]
  http://hal.inria.fr/hal-00868763
• 5S. Berthoumieux, M. Brilli, D. Kahn, H. De Jong, E. Cinquemani.
  On the identifiability of metabolic network models, in: Journal of Mathematical Biology, 2013, vol. 67, n^o 6-7, pp. 1795-1832. [ DOI : 10.1007/s00285-012-0614-x ]
  http://hal.inria.fr/hal-00762620
• 6M. Brilli, P. Liò, V. Lacroix, M.-F. Sagot.
  Short and long-term genome stability analysis of prokaryotic genomes, in: BMC Genomics, 2013, vol. 14, n^o 1, 309 p. [ DOI : 10.1186/1471-2164-14-309 ]
  http://hal.inria.fr/hal-00834426
• 7L. Brinza, F. Calevro, H. Charles.
  Genomic analysis of the regulatory elements and links with intrinsic DNA structural properties in the shrunken genome of Buchnera, in: BMC Genomics, 2013, vol. 14, n^o 1, 73 p. [ DOI : 10.1186/1471-2164-14-73 ]
  http://hal.inria.fr/hal-00788161
• 8C. 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, December 2013, pp. 93-99. [ DOI : 10.1016/j.gene.2013.11.080 ]
  http://hal.inria.fr/hal-00922703
• 9D. Costechareyre, J.-F. Chich, J.-M. Strub, Y. Rahbé, G. Condemine.
  Transcriptome of Dickeya dadantii infecting Acyrthosiphon pisum reveals a strong defense against antimicrobial peptides, in: PLoS ONE, 2013, vol. 8, n^o 1. [ DOI : 10.1371/journal.pone.0054118 ]
  http://hal.inria.fr/hal-00850312
• 10V. Eyraud, L. Karaki, I. Rahioui, C. Sivignon, P. Da Silva, Y. Rahbé, C. Royer, F. Gressent.
  Expression and Biological Activity of the Cystine Knot Bioinsecticide PA1b (Pea Albumin 1 Subunit b)., in: PLoS ONE, 2013, vol. 8, n^o 12. [ DOI : 10.1371/journal.pone.0081619 ]
  http://hal.inria.fr/hal-00921788
• 11M. Fablet, A. Akkouche, V. Braman, C. Vieira.
  Variable expression levels detected in the Drosophila effectors of piRNA biogenesis, in: Gene, December 2013, pp. 149-153. [ DOI : 10.1016/j.gene.2013.11.095 ]
  http://hal.inria.fr/hal-00922704
• 12M. Federico, P. Peterlongo, N. Pisanti, M.-F. Sagot.
  Rime: Repeat identification, in: Discrete Applied Mathematics, March 2013. [ DOI : 10.1016/j.dam.2013.02.016 ]
  http://hal.inria.fr/hal-00802023
• 13M. Giacofci, S. Lambert-Lacroix, G. Marot, F. Picard.
  Wavelet-based clustering for mixed-effects functional models in high dimension, in: Biometrics, March 2013, vol. 69, n^o 1, pp. 31-40. [ DOI : 10.1111/j.1541-0420.2012.01828.x ]
  http://hal.inria.fr/hal-00782458
• 14C. C. Klein, J. M. P. Alves, M. G. Serrano, G. A. Buck, A. T. Vasconcelos, M.-F. Sagot, M. Teixeira, E. P. Camargo, M. C. M. Motta.
  Biosynthesis of vitamins and cofactors in bacterium-harbouring trypanosomatids depends on the symbiotic association as revealed by genomic analyses, in: PLoS ONE, 2013, vol. 8, n^o 11. [ DOI : 10.1371/journal.pone.0079786 ]
  http://hal.inria.fr/hal-00922587
• 15A. Merville, S. Venner, H. Henri, A. Vallier, F. Menu, F. Vavre, A. Heddi, M.-C. Bel-Venner.
  Endosymbiont diversity among sibling weevil species competing for the same resource, in: BMC Evolutionary Biology, 2013, vol. 13, 28 p. [ DOI : 10.1186/1471-2148-13-28 ]
  http://hal.inria.fr/hal-00850306
• 16P. 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 ]
  http://hal.inria.fr/hal-00922567
• 17M. C. M. Motta, A. C. D. A. Martins, S. S. De Souza, C. M. C. Catta-Preta, R. Silva, C. C. Klein, L. G. P. De Almeida, O. De Lima Cunha, L. P. Ciapina, M. Brocchi, A. C. Colabardini, B. De Araujo Lima, C. R. Machado, C. M. De Almeida Soares, C. M. Probst, C. B. A. De Menezes, C. E. Thompson, D. C. Bartholomeu, D. F. Gradia, D. P. Pavoni, E. C. Grisard, F. Fantinatti-Garboggini, F. K. Marchini, G. F. Rodrigues-Luiz, G. Wagner, G. H. Goldman, J. L. R. Fietto, M. C. Elias, M. H. S. Goldman, M.-F. Sagot, M. Pereira, P. H. Stoco, R. P. De Mendonça-Neto, S. M. R. Teixeira, T. E. F. Maciel, T. A. De Oliveira Mendes, T. P. Ürményi, W. De Souza, S. Schenkman, A. T. R. De Vasconcelos.
  Predicting the proteins of Angomonas deanei, Strigomonas culicis and their respective endosymbionts reveals new aspects of the trypanosomatidae family, in: PLoS ONE, 2013, vol. 8, n^o 4. [ DOI : 10.1371/journal.pone.0060209 ]
  http://hal.inria.fr/hal-00846833
• 18I. Nor, J. Engelstädter, O. Duron, M. Reuter, M.-F. Sagot, S. Charlat.
  On the genetic architecture of cytoplasmic incompatibility: inference from phenotypic data, in: American Naturalist, July 2013, vol. 182, n^o 1, pp. 15-24. [ DOI : 10.1086/670612 ]
  http://hal.inria.fr/hal-00837003
• 19E. Prestat, S. R. De Morais, J. A. Vendrell, A. Thollet, C. Gautier, P. A. Cohen, A. Aussem.
  Learning the local Bayesian network structure around the ZNF217 oncogene in breast tumours, in: Computers in Biology and Medicine, May 2013, vol. 43, n^o 4, pp. 334-341. [ DOI : 10.1016/j.compbiomed.2012.12.002 ]
  http://hal.inria.fr/hal-00851231
• 20A. Rabatel, G. Febvay, K. Gaget, G. Duport, P. Baa-Puyoulet, P. Sapountzis, N. Bendridi, M. Rey, Y. Rahbé, H. Charles, F. Calevro, S. Colella.
  Tyrosine pathway regulation is host-mediated in the pea aphid symbiosis during late embryonic and early larval development, in: BMC Genomics, 2013, vol. 14, n^o 1, 235 p. [ DOI : 10.1186/1471-2164-14-235 ]
  http://hal.inria.fr/hal-00824527
• 21O. Rey, A. Estoup, B. Facon, A. Loiseau, A. Aebi, O. Duron, F. Vavre, J. Foucaud.
  Distribution of endosymbiotic reproductive manipulators reflects invasion process and not reproductive system polymorphism in the little fire ant Wasmannia auropunctata, in: PLoS ONE, 2013, vol. 8, n^o 3. [ DOI : 10.1371/journal.pone.0058467 ]
  http://hal.inria.fr/hal-00850303
• 22M. Valizadeh, C. Deraison, S. Kazemitabar, Y. Rahbé, M. A. Jongsma.
  Aphid Resistance in Florist's Chrysanthemum (Chrysanthemum morifolium Ramat.) Induced by Sea Anemone Equistatin Overexpression, in: African Journal of Biotechnology, December 2013, pp. 6922-6930. [ DOI : 10.5897/AJB2013.12956 ]
  http://hal.inria.fr/hal-00919389

International Conferences with Proceedings

• 23E. Birmelé, R. Ferreira, R. Grossi, A. Marino, N. Pisanti, R. Rizzi, G. Sacomoto.
  Optimal Listing of Cycles and st-Paths in Undirected Graphs, in: 24th Annual ACM-SIAM Symposium on Discrete Algorithms, New Orleans, United States, 2013.
  http://hal.inria.fr/hal-00751345
• 24M. Borassi, P. Crescenzi, V. Lacroix, A. Marino, M.-F. Sagot, P. Vieira Milreu.
  Telling Stories Fast, in: 12th International Symposium Experimental Algorithms (SEA), Rome, Italy, Lecture Notes in Computer Science, 2013, vol. 7933, pp. 200-211.
  http://hal.inria.fr/hal-00835201
• 25U. Dias, C. Baudet, Z. Dias.
  Greedy Randomized Search Procedure to Sort Genomes using Symmetric, Almost-Symmetric and Unitary Inversions, in: Proceedings of the 4th ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics (ACM BCB 2013), Maryland, United States, J. Gao (editor), ACM Special Interest Group on Bioinformatics, Computational Biology, and Biomedical Informatics, 2013, pp. 181–190. [ DOI : 10.1145/2506583.2506614 ]
  http://hal.inria.fr/hal-00922670
• 26G. A. T. Sacomoto, V. Lacroix, M.-F. Sagot.
  A polynomial delay algorithm for the enumeration of bubbles with length constraints in directed graphs and its application to the detection of alternative splicing in RNA-seq data, in: Workshop on Algorithms in Bioinformatics (WABI), Nice, France, Lecture Notes in Computer Science, Springer-Verlag, 2013.
  http://hal.inria.fr/hal-00842982
• 27K. Salikhov, G. Sacomoto, G. Kucherov.
  Using cascading Bloom filters to improve the memory usage for de Brujin graphs, in: Workshop on Algorithms in Bioinformatics, Sophia Antipolis, France, Lecture Notes in Computer Science, Springer, 2013, vol. 8126, 13 p, submitted.
  http://hal.inria.fr/hal-00824697

National Conferences with Proceedings

• 28A. Bretaudeau, O. Dameron, F. Legeai, Y. Rahbé.
  AphidAtlas : avancées récentes, in: Proceedings of BAPOA 2013 MOP. INRA, CIRAD Lavalette Campus Montpellier, France, Montpellier, France, M. Uzest (editor), 2013, [In French].
  http://hal.inria.fr/hal-00913155
• 29A. Studeny, F. Forbes, E. Coissac, A. Viari, C. Mercier, L. Zinger, A. Bonin, F. Boyer, P. Taberlet.
  Spatial modelling of plant diversity from high-throughput environmental dna sequence data, in: 45èmes Journées de Statistique, Toulouse, France, Société Française de Statistique, May 2013.
  http://hal.inria.fr/hal-00933699