Publications

Propres à la plate-forme

Obadia, T., Sallou, O., Ouedraogo, M., Guernec, G. & Lecerf, F. The GAG database: A new resource to gather genomic annotation cross-references. Gene, (2013).

CyanoLyase: a database of phycobilin lyase sequences, motifs and functions. A Bretaudeau, F Coste, F Humily, L Garczarek, G Le Corguille, C Six, M Ratin, O Collin, W. M Schluchter, F Partensky. Nucleic Acids Research (2013) vol. 41 (D1) pp. D396-D401

Seqcrawler: biological data indexing and browsing platform. Olivier Sallou, Anthony Bretaudeau, Aurelien Roult – BMC Bioinformatics (2012) vol. 13 (1) pp. 175-175

Collaboration avec le laboratoire d’accueil

Abdou-Arbi, O., Lemosquet, S., Van Milgen, J., Siegel, A. & Bourdon, J. Exploring metabolism flexibility in complex organisms through quantitative study of precursor sets for system outputs. BMC Syst. Biol. 8, 8 (2014).

Blavy, P., Gondret, F., Lagarrigue, S., van Milgen, J. & Siegel, A. Using a large-scale knowledge database on reactions and regulations to propose key upstream regulators of various sets of molecules participating in cell metabolism. BMC Syst. Biol. 8, 32 (2014).

Andrieux, G., Le Borgne, M. & Théret, N. An integrative modeling framework reveals plasticity of TGF-beta signaling. BMC Syst. Biol. 8, 30 (2014).

Chikhi, R. & Rizk, G. Space-efficient and exact de Bruijn graph representation based on a Bloom filter. Algorithms Mol. Biol. 8, 22 (2013).

Guziolowski, C. et al. Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming. Bioinformatics 29, 2320–2326 (2013).

Transcriptomic profiling of the reproductive mode switch in the pea aphid in response to natural autumnal photoperiod Le Trionnaire G, Jaubert-Possamai S, Bonhomme J, Gauthier JP, Guernec G, Le Cam A, Legeai F, Monfort J, Tagu D.. J Insect Physiol. 2012 Dec;58(12):1517-24.

Candidate chemosensory genes in female antennae of the noctuid moth Spodoptera littoralis Jacquin-Joly E, Legeai F, Montagné N, Monsempes C, François MC, Poulain J,Gavory F, Walker WB 3rd, Hansson BS, Larsson MC.. Int J Biol Sci.2012;8(7):1036-50.

Comparison of gene repertoires and patterns of evolutionary rates in eight aphid species that differ by reproductive mode. Ollivier M, Gabaldón T, Poulain J, Gavory F, Leterme N, Gauthier JP, Legeai F, Tagu D, Simon JC, Rispe C. Genome Biol Evol. 2012;4(2):155-67.

Accelerated evolution of sex chromosomes in aphids, an x0 system. Jaquiéry J, Stoeckel S, Rispe C, Mieuzet L, Legeai F, Simon JC. Mol Biol Evol. 2012 Feb;29(2):837-47.

Candidate Chemosensory Genes In The Stemborer Sesamia nonagrioides, Glaser N, Gallot A, Legeai F, Montagné N, Poivet E, Harry M, Calatayud P-A, Jacquin-Joly E. Int J Biol Sci 2013; 9(5):481-495

A Comparison of the Olfactory Gene Repertoires of Adults and Larvae in the Noctuid Moth Spodoptera littoralis. Poivet E, Gallot A, Montagné N, Glaser N, Legeai F, Jacquin-Joly E. PLoS One. 2013;8(4):e60263

Collaboration avec des équipes de recherche extérieures

The ReproGenomics Viewer: an integrative cross-species toolbox for the reproductive science community. Darde T., Sallou, O., Becker, E., Evrard, B., Monjeaud, C., Le Bras, Y., Jegou, B., Collin, O., Rolland, A. D., Chalmel, F., Nucleic Acids Res.2015 Apr 16. pii: gkv345.

The BioMart community portal: an innovative alternative to large, centralized data repositories. Smedley, D., et al. (2015) – Nucleic Acids Res.

SRD: a Staphylococcus regulatory RNA database. Sassi M., Augagneur Y., Mauro T., Ivain L., Chabelskaya S., Hallier M., Sallou O., Felden B. RNA. 2015 Mar 24.

The first complete chloroplast genome of the Genistoid legume Lupinus luteus: evidence for a novel major lineage-specific rearrangement and new insights regarding plastome evolution in the legume family. G. E. Martin, M. Rousseau-Gueutin, S. Cordonnier, O. Lima, S. Michon-Coudouel, D. Naquin, J. Ferreira De Carvalho, M. L. Anouche, A. Salmon, A. Anouche. Ann Bot 113(7): 1197-1210.

High-Resolution Profiling of Novel Transcribed Regions During Rat Spermatogenesis. Chalmel F, Lardenois A, Evrard B, Rolland AD, Sallou O, Dumargne MC, Coiffec I, Collin O, Primig M, Jégou B. Biol. Reprod. biolreprod.114.118166– (2014).

Masculinization of the x chromosome in the pea aphid. J. Jaquiéry, C. Rispe, D. Roze, F. Legeai, G. Le Trionnaire, S. Stoeckel, L. Mieuzet, C. Da Silva, J. Poulain, N. Prunier-Leterme, B. Ségurens, D. Tagu, J.-C. Simon, PLoS Genet. 9, e1003690 (2013).

LIMLE, a New Molecule Over-Expressed following Activation, Is Involved in the Stimulatory Properties of Dendritic Cells. L. Le Texier, J. Durand, A. Lavault, P. Hulin, O. Collin, Y. Le Bras, M.-C. Cuturi, E. Chiffoleau, PLoS One 9, e93894 (2014).

Development of genomic resources for the tick Ixodes ricinus: isolation and characterization of Single Nucleotide Polymorphisms

The duplicated genes database: identification and functional annotation of co-localised duplicated genes across genomes. Marion Ouedraogo, Charles Bettembourg, Anthony Bretaudeau, Olivier Sallou, Christian Diot, Olivier Demeure, Frédéric Lecerf – PLoS One (2012) vol. 7 (11) pp. e50653

GPSy: a cross-species gene prioritization system for conserved biological processes–application in male gamete development. Ramona Britto, Olivier Sallou, Olivier Collin, Grégoire Michaux, Michael Primig, Frédéric Chalmel – Nucleic Acids Research (2012) vol. 40 (Web Server issue) pp. W458-65

PHYMYCO-DB: a curated database for analyses of fungal diversity and evolution. Stéphane Mahé, Marie Duhamel, Thomas Le Calvez, Laetitia Guillot, Ludmila Sarbu, Anthony Bretaudeau, Olivier Collin, Alexis Dufresne, E Toby Kiers, Philippe Vandenkoornhuyse – PLoS ONE (2012) vol. 7 (9) pp. e43117

Fitness of Macrolide Resistant Campylobacter coli and Campylobacter jejuni. Salman Zeitouni, Olivier Collin, Mathieu Andraud, Gwennola Ermel, Isabelle Kempf.- Microbial drug resistance (Larchmont, NY) (2012) pp.

Transcriptome de novo assembly from next-generation sequencing and comparative analyses in the hexaploid salt marsh species Spartina maritima and Spartina alterniflora (Poaceae). Ferreira de Carvalho J, Poulain J, Da Silva C, Wincker P, Michon-Coudouel S, Dheilly A, Naquin D, Boutte J, Salmon A, Ainouche M Heredity (Edinb). 110, 181–93 (2013).

Remerciements

Loux, V., et al. (2015). “Mutations and genomic islands can explain the strain dependency of sugar utilization in 21 strains of Propionibacterium freudenreichii.” BMC Genomics 16(1): 296.

Chevignon, G., Cambier, S., Da Silva, C., Poulain, J., Drezen, J. M., Huguet, E., & Moreau, S. (2015). Transcriptomic response of Manduca sexta immune tissues to parasitization by the bracovirus associated wasp Cotesia congregata. Insect biochemistry and molecular biology.

Becker, E., Liu, Y., Lardenois, A., Walther, T., Horecka, J., Stuparevic, I., … & Primig, M. (2015). Integrated RNA-and protein profiling of fermentation and respiration in diploid budding yeast provides insight into nutrient control of cell growth and development. Journal of proteomics, 119, 30-44.

Liu, Y., Stuparevic, I., Xie, B., Becker, E., Law, M. J., & Primig, M. (2015). The conserved histone deacetylase Rpd3 and the DNA binding regulator Ume6 repress BOI1’s meiotic transcript isoform during vegetative growth in Saccharomyces cerevisiae. Molecular microbiology.

Silva, L. G., Genteluci, G. L., de Mattos, M. C., Glatthardt, T., Figueiredo, A. M. S., & Ferreira-Carvalho, B. T. (2015). Group C Streptococcus dysgalactiae subsp. equisimilis in south-east Brazil: Genetic diversity, resistance profile, and the first report of human and equine isolates belonging to the same MLST lineage. Journal of medical microbiology,

Lardenois, A., Stuparevic, I., Liu, Y., Law, M. J., Becker, E., Smagulova, F., … & Primig, M. (2015). The conserved histone deacetylase Rpd3 and its DNA binding subunit Ume6 control dynamic transcript architecture during mitotic growth and meiotic development. Nucleic acids research, 43(1), 115-128.

Gaboyer, F., Burgaud, G., & Alain, K. (2015). Physiological and evolutionary potential of microorganisms from the Canterbury 1 Basin subseafloor, a metagenomic approach 2. FEMS Microbiology Ecology, fiv029.

Stuparevic, I., Becker, E., Law, M. J., & Primig, M. (2015). The histone deacetylase Rpd3/Sin3/Ume6 complex represses an acetate-inducible isoform of VTH2 in fermenting budding yeast cells. FEBS letters, 589(8), 924-932.

Emily, M., Talvas, A. & Delamarche, C. MetAmyl: a METa-predictor for AMYLoid proteins. PLoS One 8, e79722 (2013).

Mathieu et al. Expression screening of cancer/testis genes in prostate cancer identifies nr6a1 as a novel marker of disease progression and aggressiveness. Prostate. 2013 Jul;73(10):1103-14

Chalmel et al. Genome-wide identification of Sox8-, and Sox9-dependent genes during early post-natal testis development in the mouse. Andrology. 2013 Mar;1(2):281-92.

Genomic analysis of the biocontrol strain Pseudomonas fluorescens Pf29Arp with evidence of T3SS and T6SS gene expression on plant roots

Genome scans reveal candidate regions involved in the adaptation to host plant in the pea aphid complex. J Jaquiéry, S Stoeckel, P Nouhaud, L Mieuzet, F Mahéo, F Legeai, N Bernard, A Bonvoisin, R Vitalis, J-C Simon – Mol Ecol (2012) vol. 21 (21) pp. 5251-64

Nicolas et al. Assessment of the structural and functional impact of in-frame mutations of the DMD gene, using the tools included in the eDystrophin online database. Orphanet J Rare Dis (2012) vol. 7 pp. 45

Bettembourg et al. GO2PUB: Querying PubMed with semantic expansion of gene ontology terms. J Biomed Semantics (2012) vol. 3 (1) pp. 7

Chalmel et al. Global human tissue profiling and protein network analysis reveals distinct levels of transcriptional germline-specificity and identifies target genes for male infertility. Hum Reprod (2012) vol. 27 (11) pp. 3233-48

Salmon et al. Targeted capture of homoeologous coding and noncoding sequence in polyploid cotton. G3 (Bethesda) (2012) vol. 2 (8) pp. 921-30

A new twist to coiled coil. Le Rumeur et al. FEBS Lett (2012) vol. 586 (17) pp. 2717-22

The bioinformatics tool box for reproductive biology. Primig M. Biochimica et biophysica acta (2012) pp. Global human tissue profiling and protein network analysis reveals distinct levels of transcriptional germline-specificity and identifies target genes for male infertility. Chalmel et al. Hum Reprod (2012) vol. 27 (11) pp. 3233-48