PRABI
Rhone-Alpes Bioinformatics Center


Publications

2016

Jiang X, Zghidi-Abouzid O, Oger-Desfeux C, Hommais F, Greliche N, Muskhelishvili G, Nasser W, Reverchon S. (2016) Global transcriptional response of Dickeya dadantii to environmental stimuli relevant to the plant infection. Environ Microbiol. 18(11), 3651-3672. [PubMed]

Dumas ME, Domange C, Calderari S, Martínez AR, Ayala R, Wilder SP, Suárez-Zamorano N, Collins SC, Wallis RH, Gu Q, Wang Y, Hue C, Otto GW, Argoud K, Navratil V , Mitchell SC, Lindon JC, Holmes E, Cazier JB, Nicholson JK, Gauguier D. (2016) Topological analysis of metabolic networks integrating co-segregating transcriptomes and metabolomes in type 2 diabetic rat congenic series. Genome Med. 8, 101. [PubMed]

Carrouel F, Viennot S, Santamaria J, Veber P, Bourgeois D. (2016) Quantitative Molecular Detection of 19 Major Pathogens in the Interdental Biofilm of Periodontally Healthy Young Adults. Front Microbiol. 7, 840. [PubMed]

Salvetti A, Couté Y, Epstein A, Arata L, Kraut A, Navratil V, Bouvet P, Greco A. (2016) Nuclear Functions of Nucleolin through Global Proteomics and Interactomic Approaches. J Proteome Res. 15(5), 1659-69. [PubMed]

Freyermuth F, Rau F, Kokunai Y, Linke T, Sellier C, Nakamori M, Kino Y, Arandel L, Jollet A, Thibault C, Philipps M, Vicaire S, Jost B, Udd B,,, Day JW, Duboc D, Wahbi K, Matsumura T, Fujimura H, Mochizuki H, Deryckere F, Kimura T, Nukina N, Ishiura S, Lacroix V, Campan-Fournier A, Navratil V, Chautard E, Auboeuf D, Horie M, Imoto K, Lee KY, Swanson MS, Lopez de Munain A, Inada S, Itoh H, Nakazawa K, Ashihara T, Wang E, Zimmer T, Furling D, Takahashi MP, Charlet-Berguerand N. (2016) Splicing misregulation of SCN5A contributes to cardiac-conduction delay and heart arrhythmia in myotonic dystrophy Nat Commun. 7, 11067. [PubMed]

2015

Billoir E., Navratil V., Blaise BJ. (2015) Sample size calculation in metabolic phenotyping studies. Brief Bioinform. 16(5), 813-819. [PubMed]

Faucon F., Dusfour I., Gaude T., Navratil V., Boyer F., Chandre F., Sirisopa P. , Thanispong K., Juntarajumnong W., Poupardin R., Chareonviriyaphap T., Girod R., Corbel V., Reynaud S., David JP.(2015) Identifying genomic changes associated with insecticide resistance in the dengue mosquito Aedes aegypti by deep targeted sequencing.Genome Res. 25(9), 1347–1359. [PubMed]

Galia W, Mariani-Kurkdjian P, Bastien S, Loukiadis E, Blanquet-Diot S, Leriche F, Brugère H, Shima A, Oswald E, Cournoyer B, Thevenot-Sergentet D.(2015) Correction for Galia et al., Genome Sequence and Annotation of a Human Infection Isolate of Escherichia coli O26:H11 Involved in a Raw Milk Cheese Outbreak. Genome Announc. 3(4), e00880-15. [PubMed]

Chatagnon A, Veber P , Morin V, Bedo J, Triqueneaux G, Sémon M, Laudet V, d’Alché-Buc F, Benoit G. (2015) RAR/RXR binding dynamics distinguish pluripotency from differentiation associated cis-regulatory elements. Nucleic Acids Res.43(10), 4833-54. [PubMed]

Blavet N, Blavet H, Muyle A, Käfer J, Cegan R, Deschamps C, Zemp N, Mousset S, Aubourg S, Bergero R, Charlesworth D, Hobza R, Widmer A, Marais GA.(2015) Identifying new sex-linked genes through BAC sequencing in the dioecious plant Silene latifolia. BMC Genomics. 16, 546. doi : 10.1186/s12864-015-1698-7. [PubMed]

Mitchell A, Chang HY, Daugherty L, Fraser M, Hunter S, Lopez R, McAnulla C, McMenamin C, Nuka G, Pesseat S, Sangrador-Vegas A, Scheremetjew M, Rato C, Yong SY, Bateman A, Punta M, Attwood TK, Sigrist CJ, Redaschi N, Rivoire C, Xenarios I, Kahn D, Guyot D, Bork P, Letunic I, Gough J, Oates M, Haft D, Huang H, Natale DA, Wu CH, Orengo C, Sillitoe I, Mi H, Thomas PD, Finn RD. (2015) The InterPro protein families database : the classification resource after 15 years. Nucleic Acids Res. 43, D213-21. [PubMed]

Guirimand T, Delmotte S, Navratil V. (2015) VirHostNet 2.0 : surfing on the web of virus/host molecular interactions data. Nucleic Acids Res. 43, D583-7. [PubMed]

2014

Després L., Stalinski R., Faucon F., Navratil V., Viari A., Paris M., Tetreau G., Poupardin R., Asam Riaz M., Bonin A., Reynaud S., David JP. (2014) Chemical and biological insecticides select distinct gene expression patterns in Aedes aegypti mosquito Biol Lett.10(12), 20140716. [PubMed]

David, J.P., Faucon, F., Chandor-Proust, A., Poupardin, R., Asam Riaz, M., Bonin, A., Navratil, V. and Reynaud, S. (2014) Comparative analysis of response to selection with three insecticides in the dengue mosquito Aedes aegypti using mRNA sequencing. BMC Genomics, 15, 174. [PubMed]

Regnault C., Worms I.A., Oger-Desfeux C., MelodeLima C., Veyrenc S., Bayle M.L., Combourieu B., Bonin A., Renaud J., Raveton M., Reynaud S. (2014) Impaired liver function in Xenopus tropicalis exposed to benzo[a]pyrene : transcriptomic and metabolic evidence. BMC Genomics, 15,666 [PubMed]

Després, L., Stalinski, R., Tetreau, G., Paris, M., Bonin, A., Navratil, N., Reynaud, S. and David, J.P. (2014) Gene expression patterns and sequence polymorphisms associated with mosquito resistance to Bacillus thuringiensis israelensis toxins. BMC Genomics, 15, 926 [PubMed]

Guirimand, T., Delmotte, S. and Navratil, V. (2014) VirHostNet 2.0 : surfing on the web of virus/host molecular interactions data. Nucleic Acids Res., in press. [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]

2012

Damon, C., Lehembre, F., Oger-Desfeux, C., Luis, P., Ranger, J., Fraissinet-Tachet, L. and Marmeisse, R. (2012) Metatranscriptomics reveals the diversity of genes expressed by eukaryotes in forest soils. PLoS One, 7, e28967. [PubMed]

Muyle, A., Zemp, N., Deschamps, C., Mousset, S., Widmer, A. and Marais, G.A. (2012) Rapid de novo evolution of X chromosome dosage compensation in Silene latifolia, a plant with young sex chromosomes. PLoS Biol., 10, e1001308. [PubMed]

Shintu, L., Baudoin, R., Navratil, V., Prot, J.M., Pontoizeau, C., Defernez, M., Blaise, B.J., Domange, C., Pery, A.R., Toulhoat, P., Legallais, C., Brochot, C., Leclerc, E. and Dumas, M.E. (2012) Metabolomics-on-a-chip and predictive systems toxicology in microfluidic bioartificial organs. Anal. Chem., 84, 1840-1848. [PubMed]

Simonis, N., Rual, J.F., Lemmens, I., Boxus, M., Hirozane-Kishikawa, T., Gatot, J.S., Dricot, A., Hao, T., Vertommen, D., Legros, S., Daakour, S., Klitgord, N., Martin, M., Willaert, J.F., Dequiedt, F., Navratil, V., Cusick, M.E., Burny, A., Van Lint, C., Hill, D.E., Tavernier, J., Kettmann, R., Vidal, M. and Twizere, J.C. (2012) Host-pathogen interactome mapping for HTLV-1 and -2 retroviruses. Retrovirology, 9, 26. [PubMed]

Teulier, L., Degletagne, C., Rey, B., Tornos, J., Keime, C., de Dinechin, M., Raccurt, M., Rouanet, J.L., Roussel, D. and Duchamp, C. (2012) Selective upregulation of lipid metabolism in skeletal muscle of foraging juvenile king penguins : an integrative study. Proc. R. Soc. B, 279, 2464-2472. [PubMed]

2011

Blaise, B.J., Navratil, V., Emsley, L. and Toulhoat, P. (2011) Orthogonal filtered recoupled-STOCSY to extract metabolic networks associated with minor perturbations from NMR spectroscopy. J. Proteome Res., 10, 4342-4348. [PubMed]

Blavet, N., Charif, D., Oger-Desfeux, C., Marais, G.A. and Widmer, A. (2011) Comparative high-throughput transcriptome sequencing and development of SiESTa, the Silene EST annotation database. BMC Genomics, 12, 376. [PubMed]

Davidovic, L., Navratil, V., Bonaccorso, C.M., Catania, M.V., Bardoni, B. and Dumas, M.E. (2011) A metabolomic and systems biology perspective on the brain of the fragile X syndrome mouse model. Genome Res., 21, 2190-2202. [PubMed]

Grégoire, I.P., Richetta, C., Meyniel-Schicklin, L., Borel, S., Pradezynski, F., Diaz, O., Deloire, A., Azocar, O., Baguet, J., Le Breton, M., Mangeot, P.E., Navratil, V., Joubert, P.E., Flacher, M., Vidalain, P.O., André, P., Lotteau, V., Biard-Piechaczyk, M., Rabourdin-Combe, C. and Faure, M. (2011) IRGM is a common target of RNA viruses that subvert the autophagy network. PLoS Pathog., 7, e1002422. [PubMed]

Hommais, F., Zghidi-Abouzid, O., Oger-Desfeux, C., Pineau-Chapelle, E., Van Gijsegem, F., Nasser, W. and Reverchon, S. (2011) lpxC and yafS are the most suitable internal controls to normalize real time RT-qPCR expression in the phytopathogenic bacteria Dickeya dadantii. PLoS One, 6, e20269. [PubMed]

Jordheim, L.P., Plesa, A., Dreano, M., Cros-Perrial, E., Keime, C., Herveau, S., Demangel, D., Vendrell, J.A. and Dumontet, C. (2011) Sensitivity and gene expression profile of fresh human acute myeloid leukemia cells exposed ex vivo to AS602868. Cancer Chemother. Pharmacol., 68, 97-105. [PubMed]

Lassalle, F., Campillo, T., Vial, L., Baude, J., Costechareyre, D., Chapulliot, D., Shams, M., Abrouk, D., Lavire, C., Oger-Desfeux, C., Hommais, F., Gueguen, L., Daubin, V., Muller, D. and Nesme, X. (2011) Genomic species are ecological species as revealed by comparative genomics in Agrobacterium tumefaciens. Genome Biol. Evol., 3, 762–781. [PubMed]

Navratil, V., de Chassey, B., Combe, C.R. and Lotteau, V. (2011) When the human viral infectome and diseasome networks collide : towards a systems biology platform for the aetiology of human diseases. BMC Syst. Biol., 5, 13. [PubMed]

Palmeira, L., Penel, S., Lotteau, V., Rabourdin-Combe, C. and Gautier, C. (2011) PhEVER : a database for the global exploration of virus-host evolutionary relationships. Nucleic Acids Res., 39, D569-575. [PubMed]

Pontoizeau, C., Fearnside, J.F., Navratil, V., Domange, C., Cazier, J.B., Fernandez-Santamaria, C., Kaisaki, P.J., Emsley, L., Toulhoat, P., Bihoreau, M.T., Nicholson, J.K., Gauguier, D. and Dumas, M.E. (2011) Broad-ranging natural metabotype variation drives physiological plasticity in healthy control inbred rat strains. J. Proteome Res., 10, 1675-1689. [PubMed]

2010

Blaise, B.J., Navratil, V., Domange, C., Shintu, L., Dumas, M.E., Elena-Herrmann, B., Emsley, L. and Toulhoat, P. (2010) Two-dimensional statistical recoupling for the identification of perturbed metabolic networks from NMR spectroscopy. J. Proteome Res., 9, 4513-4520. [PubMed]

Brinza, L., Calevro, F., Duport, G., Gaget, K., Gautier, C. and Charles, H. (2010) Structure and dynamics of the operon map of Buchnera aphidicola sp. strain APS. BMC Genomics, 11, 666. [PubMed]

Degletagne, C., Keime, C., Rey, B., de Dinechin, M., Forcheron, F., Chuchana, P., Jouventin, P., Gautier, C. and Duchamp, C. (2010) Transcriptome analysis in non-model species : a new method for the analysis of heterologous hybridization on microarrays. BMC Genomics, 11, 344. [PubMed]

Navratil, V., de Chassey, B., Meyniel, L., Pradezynski, F., André, P., Rabourdin-Combe, C. and Lotteau, V. (2010) System-level comparison of protein-protein interactions between viruses and the human type I interferon system network. J. Proteome Res., 9, 3527-3536. [PubMed]

Pellet, J., Tafforeau, L., Lucas-Hourani, M., Navratil, V., Meyniel, L., Achaz, G., Guironnet-Paquet, A., Aublin-Gex, A., Caignard, G., Cassonnet, P., Chaboud, A., Chantier, T., Deloire, A., Demeret, C., Le Breton, M., Neveu, G., Jacotot, L., Vaglio, P., Delmotte, S., Gautier, C., Combet, C., Deléage, G., Favre, M., Tangy, F., Jacob, Y., André, P., Lotteau, V., Rabourdin-Combe, C. and Vidalain, P.O. (2010) ViralORFeome : an integrated database to generate a versatile collection of viral ORFs. Nucleic Acids Res., 38, D371-378. [PubMed]

2009

Deniaud, E., Baguet, J., Chalard, R., Blanquier, B., Brinza, L., Meunier, J., Michallet, M.C., Laugraud, A., Ah-Soon, C., Wierinckx, A., Castellazzi, M., Lachuer, J., Gautier, C., Marvel, J. and Leverrier, Y. (2009) Overexpression of transcription factor Sp1 leads to gene expression perturbations and cell cycle inhibition. PLoS One, 4, e7035. [PubMed]

Horard, B., Eymery, A., Fourel, G., Vassetzky, N., Puechberty, J., Roizes, G., Lebrigand, K., Barbry, P., Laugraud, A., Gautier, C., Simon, E.B., Devaux, F., Magdinier, F., Vourc’h, C. and Gilson, E. (2009) Global analysis of DNA methylation and transcription of human repetitive sequences. Epigenetics, 4, 339-350. [PubMed]

Hunter, S., Apweiler, R., Attwood, T.K., Bairoch, A., Bateman, A., Binns, D., Bork, P., Das, U., Daugherty, L., Duquenne, L., Finn, R.D., Gough, J., Haft, D., Hulo, N., Kahn, D., Kelly, E., Laugraud, A., Letunic, I., Lonsdale, D., Lopez, R., Madera, M., Maslen, J., McAnulla, C., McDowall, J., Mistry, J., Mitchell, A., Mulder, N., Natale, D., Orengo, C., Quinn, A.F., Selengut, J.D., Sigrist, C.J., Thimma, M., Thomas, P.D., Valentin, F., Wilson, D., Wu, C.H. and Yeats, C. (2009) InterPro : the integrative protein signature database. Nucleic Acids Res., 37, D211-215. [PubMed]

Navratil, V., de Chassey, B., Meyniel, L., Delmotte, S., Gautier, C., André, P., Lotteau, V. and Rabourdin-Combe, C. (2009) VirHostNet : a knowledge base for the management and the analysis of proteome-wide virus-host interaction networks. Nucleic Acids Res., 37, D661-668. [PubMed]

Moccia, M.D., Oger-Desfeux, C., Marais, G.A. and Widmer, A. (2009) A white campion (Silene latifolia) floral expressed sequence tag (EST) library : annotation, EST-SSR characterization, transferability, and utility for comparative mapping. BMC Genomics, 10, 243. [PubMed]