Publications

A list of publications associated with the BIOI2 plateform and the tools developed at the I2BC:

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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.
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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).
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Postic, G. et al. Proteo3Dnet: a web server for the integration of structural information with interactomics data. Nucleic Acids Research 49, W567–W572 (2021).
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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).
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Badel, C., Da Cunha, V., Catchpole, R., Forterre, P. & Oberto, J. WASPS: web-assisted symbolic plasmid synteny server. Bioinformatics 36, 1629–1631 (2020).
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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.
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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).
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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).
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Yu, J., Picord, G., Tuffery, P. & Guerois, R. HHalign-Kbest: exploring sub-optimal alignments for remote homology comparative modeling. Bioinformatics 31, 3850–3852 (2015).
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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).
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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).
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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).
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Oberto, J. SyntTax: a web server linking synteny to prokaryotic taxonomy. BMC Bioinformatics 14, 4 (2013).
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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).
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Ott, A., Idali, A., Marchais, A. & Gautheret, D. NAPP: the Nucleic Acid Phylogenetic Profile Database. Nucleic Acids Research 40, D205–D209 (2012).
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Faure, G., Andreani, J. & Guerois, R. InterEvol database: exploring the structure and evolution of protein complex interfaces. Nucleic Acids Research 40, D847–D856 (2012).
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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).
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Grossetête, S., Labedan, B. & Lespinet, O. FUNGIpath: a tool to assess fungal metabolic pathways predicted by orthology. BMC Genomics 11, 81 (2010).
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Oberto, J. FITBAR: a web tool for the robust prediction of prokaryotic regulons. BMC Bioinformatics 11, 554 (2010).
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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).
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Espagne, E. et al. The genome sequence of the model ascomycete fungus Podospora anserina. Genome Biol 9, R77 (2008).
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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).
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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).
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