PRABI
Rhone-Alpes Bioinformatics Center


2013

Bulacu, M., Goga, N., Zhao, W., Rossi, G., Monticelli, L., Periole, X., Tieleman, D.P., Marrink, S.J. (2013) Improved angle potentials for coarse-grained molecular dynamics simulations. J. Chem Theory Comput., 9, 3282-3292. [DOI]

Hayer, J., Jadeau, F., Deléage, G., Kay, A., Zoulim, F. and Combet, C. (2013) HBVdb : a knowledge database for Hepatitis B Virus. Nucleic Acids Res., 41, D566-570. [PubMed]

2013

de Chassey, B., Meyniel-Schicklin, L., Aublin-Gex, A., Navratil, V., Chantier, T., Andre, P. and Lotteau, V. (2013) Structure homology and interaction redundancy for discovering virus-host protein interactions. EMBO Rep., 14, 938-944. [PubMed]

Lehembre, F., Doillon, D., David, E., Perrotto, S., Baude, J., Foulon, J., Harfouche, L., Vallon, L., Poulain, J., Da Silva, C., Wincker, P., Oger-Desfeux, C., Richaud, P., Colpaert, J.V., Chalot, M., Fraissinet-Tachet, L., Blaudez, D. and Marmeisse, R. (2013) Soil metatranscriptomics for mining eukaryotic heavy metal resistance genes. Environ. Microbiol., 15, 2829-2840. [PubMed]

Navratil, V., Pontoizeau, C., Billoir, E. and Blaise, B.J. (2013) SRV : an open-source toolbox to accelerate the recovery of metabolic biomarkers and correlations from metabolic phenotyping datasets. Bioinformatics, 29, 1348-1349. [PubMed]

Baptist, G., Pinel, C., Ranquet, C., Izard, J., Ropers, D., de Jong, H. and Geiselmann, J. (2013) A genome-wide screen for identifying all regulators of a target gene. Nucleic Acids Res., 41, e164. [PubMed]

Chaouiya, C., Berenguier, D., Keating, S.M., Naldi, A., van Iersel, M.P., Rodriguez, N., Drager, A., Buchel, F., Cokelaer, T., Kowal, B., Wicks, B., Goncalves, E., Dorier, J., Page, M., Monteiro, P.T., von Kamp, A., Xenarios, I., de Jong, H., Hucka, M., Klamt, S., Thieffry, D., Le Novere, N., Saez-Rodriguez, J. and Helikar, T. (2013) SBML qualitative models : a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. BMC Syst. Biol., 7, 135. [PubMed]

Batut, B., Parsons, D.P., Fischer, S., Beslon, G. and Knibbe, C. (2013) In silico experimental evolution : a tool to test evolutionary scenarios. BMC Bioinformatics, 14 (Suppl 15), S11. [PubMed]

Berthoumieux, S., Brilli, M., Kahn, D., de Jong, H. and Cinquemani, E. (2013) On the identifiability of metabolic network models. J. Math. Biol., 67, 1795-1832. [PubMed]

Bigot, T., Daubin, V., Lassalle, F. and Perrière, G. (2013) TPMS : a set of utilities for querying collections of gene trees. BMC Bioinformatics, 14, 109. [PubMed]

Boussau, B., Szöllósi, G.J., Duret, L., Gouy, M., Tannier, E. and Daubin, V. (2013) Genome-scale coestimation of species and gene trees. Genome Res., 23, 323-330. [PubMed]

Brilli, M., Lio, P., Lacroix, V. and Sagot, M.F. (2013) Short and long-term genome stability analysis of prokaryotic genomes. BMC Genomics, 14, 309. [PubMed]

Cariou, M., Duret, L. and Charlat, S. (2013) Is RAD-seq suitable for phylogenetic inference ? An in silico assessment and optimization. Ecol. Evol., 3, 846-852. [PubMed]

Giacofci, M., Lambert-Lacroix, S., Marot, G. and Picard, F. (2013) Wavelet-based clustering for mixed-effects functional models in high dimension. Biometrics, 69, 31-40. [PubMed]

Gueguen, L., Gaillard, S., Boussau, B., Gouy, M., Groussin, M., Rochette, N.C., Bigot, T., Fournier, D., Pouyet, F., Cahais, V., Bernard, A., Scornavacca, C., Nabholz, B., Haudry, A., Dachary, L., Galtier, N., Belkhir, K. and Dutheil, J.Y. (2013) Bio++ : efficient extensible libraries and tools for computational molecular evolution. Mol. Biol. Evol., 30, 1745-1750. [PubMed]

Groussin, M., Boussau, B. and Gouy, M. (2013) A branch-heterogeneous model of protein evolution for efficient inference of ancestral sequences. Syst. Biol., 62, 523-538. [PubMed]

Lafond, M., Semeria, M., Swenson, K.M., Tannier, E. and El-Mabrouk, N. (2013) Gene tree correction guided by orthology. BMC Bioinformatics, 14 (Suppl 15), S5. [PubMed]

Lartillot, N., Rodrigue, N., Stubbs, D. and Richer, J. (2013) PhyloBayes MPI : phylogenetic reconstruction with infinite mixtures of profiles in a parallel environment. Syst. Biol., 62, 611-615. [PubMed]

Frenkel-Morgenstern, M., Gorohovski, A., Lacroix, V., Rogers, M., Ibanez, K., Boullosa, C., Andres Leon, E., Ben-Hur, A. and Valencia, A. (2013) ChiTaRS : a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data. Nucleic Acids Res., 41, D142-151. [PubMed]

Patterson, M., Szöllósi, G., Daubin, V. and Tannier, E. (2013) Lateral gene transfer, rearrangement, reconciliation. BMC Bioinformatics, 14 (Suppl 15), S4. [PubMed]

Rajaraman, A., Tannier, E. and Chauve, C. (2013) FPSAC : fast phylogenetic scaffolding of ancient contigs. Bioinformatics, 29, 2987-2994. [PubMed]

Szöllósi, G.J., Rosikiewicz, W., Boussau, B., Tannier, E. and Daubin, V. (2013) Efficient exploration of the space of reconciled gene trees. Syst. Biol., 62, 901-912. [PubMed]

Szöllósi, G.J., Tannier, E., Lartillot, N. and Daubin, V. (2013) Lateral gene transfer from the dead. Syst. Biol., 62, 386-397. [PubMed]