Publications

Poinsignon, T. et al. Visual Integration of Omics Data to Improve 3D Models of Fungal Chromosomes. http://biorxiv.org/lookup/doi/10.1101/2023.03.28.534549 (2023) doi:10.1101/2023.03.28.534549.

Hepp, B., Da Cunha, V., Lorieux, F. & Oberto, J. BAGET 2.0: an updated web tool for the effortless retrieval of prokaryotic gene context and sequence. Bioinformatics 37, 2750–2752 (2021).

Postic, G. et al. Proteo3Dnet: a web server for the integration of structural information with interactomics data. Nucleic Acids Research 49, W567–W572 (2021).

Quignot, C. et al. InterEvDock3: a combined template-based and free docking server with increased performance through explicit modeling of complex homologs and integration of covariation-based contact maps. Nucleic Acids Research 49, W277–W284 (2021).

Badel, C., Da Cunha, V., Catchpole, R., Forterre, P. & Oberto, J. WASPS: web-assisted symbolic plasmid synteny server. Bioinformatics 36, 1629–1631 (2020).

Arnaiz, O., Meyer, E. & Sperling, L. ParameciumDB 2019: integrating genomic data across the genus for functional and evolutionary biology. Nucleic Acids Research gkz948 (2019) http://doi.org/10.1093/nar/gkz948.

Couvin, D. et al. CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins. Nucleic Acids Research 46, W246–W251 (2018).

Bienvenut, W. V., Scarpelli, J.-P., Dumestier, J., Meinnel, T. & Giglione, C. EnCOUNTer: a parsing tool to uncover the mature N-terminus of organelle-targeted proteins in complex samples. BMC Bioinformatics 18, 182 (2017).

Yu, J., Picord, G., Tuffery, P. & Guerois, R. HHalign-Kbest: exploring sub-optimal alignments for remote homology comparative modeling. Bioinformatics 31, 3850–3852 (2015).

Innocenti, N. et al. Whole-genome mapping of 5′ RNA ends in bacteria by tagged sequencing: a comprehensive view in Enterococcus faecalis. RNA 21, 1018–1030 (2015).

Abby, S. S., Néron, B., Ménager, H., Touchon, M. & Rocha, E. P. C. MacSyFinder: A Program to Mine Genomes for Molecular Systems with an Application to CRISPR-Cas Systems. PLoS ONE 9, e110726 (2014).

Lopes, A., Tavares, P., Petit, M.-A., Guérois, R. & Zinn-Justin, S. Automated classification of tailed bacteriophages according to their neck organization. BMC Genomics 15, 1027 (2014).

Oberto, J. SyntTax: a web server linking synteny to prokaryotic taxonomy. BMC Bioinformatics 14, 4 (2013).

Toffano-Nioche, C. et al. Detection of non-coding RNA in bacteria and archaea using the DETR’PROK Galaxy pipeline. Methods 63, 60–65 (2013).

Ott, A., Idali, A., Marchais, A. & Gautheret, D. NAPP: the Nucleic Acid Phylogenetic Profile Database. Nucleic Acids Research 40, D205–D209 (2012).

Faure, G., Andreani, J. & Guerois, R. InterEvol database: exploring the structure and evolution of protein complex interfaces. Nucleic Acids Research 40, D847–D856 (2012).

Naville, M., Ghuillot-Gaudeffroy, A., Marchais, A. & Gautheret, D. ARNold: A web tool for the prediction of Rho-independent transcription terminators. RNA Biology 8, 11–13 (2011).

Grossetête, S., Labedan, B. & Lespinet, O. FUNGIpath: a tool to assess fungal metabolic pathways predicted by orthology. BMC Genomics 11, 81 (2010).

Oberto, J. FITBAR: a web tool for the robust prediction of prokaryotic regulons. BMC Bioinformatics 11, 554 (2010).

Lopes, A., Amarir-Bouhram, J., Faure, G., Petit, M.-A. & Guerois, R. Detection of novel recombinases in bacteriophage genomes unveils Rad52, Rad51 and Gp2.5 remote homologs. Nucleic Acids Research 38, 3952–3962 (2010).

Espagne, E. et al. The genome sequence of the model ascomycete fungus Podospora anserina. Genome Biol 9, R77 (2008).

Grissa, I., Vergnaud, G. & Pourcel, C. CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Research 35, W52–W57 (2007).

Gautheret, D. & Lambert, A. Direct RNA motif definition and identification from multiple sequence alignments using secondary structure profiles 1 1Edited by J. Doudna. Journal of Molecular Biology 313, 1003–1011 (2001).