RUIZ, Manuel

Publications Manuel Ruiz

• Agritrop
• Google Scholar

 

Main publications since 2002

 

• Larmande P, Tagny Ngompe G, Venkatesan A, Ruiz M: AgroLD: A Knowledge Graph Database for Plant Functional Genomics. Methods Mol Biol 2022, 2443:527-540
• Agret C, Chateau A, Droc G, Sarah G, Ruiz M, Mancheron A: RedOak: a reference-free and alignment-free structure for indexing a collection of similar genomes. Journal of Open Source Software 2022, 7(80):4363.
• Jean-François Dufayard, Stéphanie Bocs, Valentin Guignon, Delphine Larivière, Alexandra Louis, Nicolas Oubda, Mathieu Rouard, Manuel Ruiz, Frédéric de Lamotte, RapGreen, an interactive software and web package to explore and analyze phylogenetic trees, NAR Genomics and Bioinformatics, Volume 3, Issue 3, September 2021, lqab088, https://doi.org/10.1093/nargab/lqab088
• Fleury C, Gracy J, Gautier M, Pons J, Dufayard J, Labesse G, Ruiz M, de Lamotte F. 2019. Comprehensive classification of the plant non-specific lipid transfer protein superfamily towards its sequence-structure-function analysis. PeerJ 7:e7504 https://doi.org/10.7717/peerj.7504
• Juanillas, V., A. Dereeper, N. Beaume, G. Droc, J. Dizon, J. R. Mendoza, J. P. Perdon, L. Mansueto, L. Triplett, J. Lang, G. Zhou, K. Ratharanjan, B. Plale, J. Haga, J. E. Leach, M. Ruiz, M. Thomson, N. Alexandrov, P. Larmande, T. Kretzschmar and R. P. Mauleon (2019). "Rice Galaxy: an open resource for plant science." Gigascience 8(5).
• Venkatesan Aravind, Tagny Ngompé Gildas, El Hassouni Nordine, Chentli Imene, Guignon Valentin, Jonquet Clément, Ruiz Manuel, Larmande Pierre. Agronomic linked data (AgroLD): A knowledge-based system to enable integrative biology in agronomy. 2018. PloS One, 13 (11) e0198270, 17 p.https://doi.org/10.1371/journal.pone.0198270
• Clement Y, Sarah G, Holtz Y, Homa F, Pointet S, Contreras S, et al. Evolutionary forces affecting synonymous variations in plant genomes. PLoS Genet. 2017;13(5):e1006799.
• Sauvage C, Rau A, Aichholz C, Chadoeuf J, Sarah G, Ruiz M, et al. Domestication rewired gene expression and nucleotide diversity patterns in tomato. Plant J. 2017.
• Ruiz M, Sempéré G, Hamelin C. Using TropGeneDB: A Database Containing Data on Molecular Markers, QTLs, Maps, Genotypes, and Phenotypes for Tropical Crops. In: van Dijk ADJ, editor. Plant Genomics Databases: Methods and Protocols. New York, NY: Springer New York; 2017. p. 161-72.
• South Green c. The South Green portal: a comprehensive resource for tropical and Mediterranean crop genomics. Current Plant Biology. 2016.
• Sarah G, Homa F, Pointet S, Contreras S, Sabot F, Nabholz B, et al. A large set of 26 new reference transcriptomes dedicated to comparative population genomics in crops and wild relatives. Molecular ecology resources. 2016.
• Sempere G, Philippe F, Dereeper A, Ruiz M, Sarah G, Larmande P. Gigwa--Genotype investigator for genome-wide analyses. GigaScience. 2016;5(1):25.
• Dereeper A, Homa F, Andres G, Sempere G, Sarah G, Hueber Y, Dufayard J-F, Ruiz M. SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations. 2015. Nucleic Acids Research.
• Wu GA, Prochnik S, Jenkins J, Salse J, Hellsten U, Murat F, et al. Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication. Nat Biotech. 2014;advance online publication.
• Nabholz B, Sarah G, Sabot F, Ruiz M, Adam H, Nidelet S, et al. Transcriptome population genomics reveals severe bottleneck and domestication cost in the African rice (O. glaberrima). Mol Ecol. 2014. Epub 2014/04/02.
• Droc G, Larivière D, Guignon V, Yahiaoui N, This D, Garsmeur O, Dereeper A, Hamelin C, Argout X, Dufayard J-F et al: The Banana Genome Hub. Database 2013, 2013.
• Wollbrett J, Larmande P, de Lamotte F, Ruiz M: Clever generation of rich SPARQL queries from annotated relational schema: application to Semantic Web Service creation for biological databases. BMC Bioinformatics 2013, 14(1):126.
• Hamelin C, Sempere G, Jouffe V, Ruiz M: TropGeneDB, the multi-tropical crop information system updated and extended. Nucleic Acids Res 2013, 41(Database issue):D1172-1175.
• Lacape J-M, Claverie M, Vidal RO, Carazzolle MF, Guimarães Pereira GA, et al. Deep Sequencing Reveals Differences in the Transcriptional Landscapes of Fibers from Two Cultivated Species of Cotton, PLoS ONE, 2012, 7(11): e48855.
• D'Hont A, Denoeud F, Aury JM, Baurens FC, Carreel F, Garsmeur O, Noel B, Bocs S, Droc G, Rouard M et al: The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature 2012, 488(7410):213-+.
• Courtois B, Frouin J, Greco R, Bruschi G, Droc G, Hamelin C, Ruiz M, Clément G, Evrard J-C, van Coppenole S et al: Genetic Diversity and Population Structure in a European Collection of Rice. Crop Sci 2012, 52(4):1663-1675
• Dereeper A, Nicolas S, Le Cunff L, Bacilieri R, Doligez A, Peros JP, Ruiz M, This P: SNiPlay: a web-based tool for detection, management and analysis of SNPs. Application to grapevine diversity projects. BMC Bioinformatics 2011, 12(1):134.
• Courtois B., Greco R., Bruschi G., Frouin J., Ahmadi N., Droc G., Hamelin C., Ruiz M., Evrard J.C., Katsantonis D., Oliveira M., Negrao S., Cavigiolo S., Lupotto E., Piffanelli P. Molecular characterization of the European rice collection in view of association mapping. Plant Genetic Resources, 2011, 9(02) : 233-235
• Argout X, Salse J, Aury JM, Guiltinan MJ, Droc G, Gouzy J, Allegre M, Chaparro C, Legavre T, Maximova SN et al: The genome of Theobroma cacao. Nat Genet 2010.
• Courtois B, Ahmadi N, Khowaja F, Price A, Rami J-F, Frouin J, Hamelin C, Ruiz M: Rice Root Genetic Architecture: Meta-analysis from a Drought QTL Database. Rice 2009, 2(2):115-128.
• Wanchana S, Thongjuea S, Ulat VJ, Anacleto M, Mauleon R, Conte M, Rouard M, Ruiz M, Krishnamurthy N, Sjolander K et al: The Generation Challenge Programme comparative plant stress-responsive gene catalogue. Nucleic Acids Res 2008, 36(Database issue):D943-946.
• Lescot M, Piffanelli P, Ciampi AY, Ruiz M, Blanc G, Leebens-Mack J, da Silva FR, Santos CM, D'Hont A, Garsmeur O et al: Insights into the Musa genome: syntenic relationships to rice and between Musa species. BMC Genomics 2008, 9:58.
• Larmande P, Gay C, Lorieux M, Perin C, Bouniol M, Droc G, Sallaud C, Perez P, Barnola I, Biderre-Petit C et al: Oryza Tag Line, a phenotypic mutant database for the Genoplante rice insertion line library. Nucleic Acids Res 2008, 36(Database issue):D1022-1027.
• Bruskiewich R, Senger M, Davenport G, Ruiz M, Rouard M, Hazekamp T, Takeya M, Doi K, Satoh K, Costa M et al: The generation challenge programme platform: semantic standards and workbench for crop science. Int J Plant Genomics 2008, 2008:369601.
• Argout X, Fouet O, Wincker P, Gramacho K, Legavre T, Sabau X, Risterucci AM, Da Silva C, Cascardo J, Allegre M et al: Towards the understanding of the cocoa transcriptome: Production and analysis of an exhaustive dataset of ESTs of Theobroma cacao L. generated from various tissues and under various conditions. BMC Genomics 2008, 9:512.
• Dereeper A, Argout X, Billot C, Rami JF, Ruiz M: SAT, a flexible and optimized Web application for SSR marker development. BMC Bioinformatics 2007, 8:465.
• Droc G, Ruiz M, Larmande P, Pereira A, Piffanelli P, Morel JB, Dievart A, Courtois B, Guiderdoni E, Perin C: OryGenesDB: a database for rice reverse genetics. Nucleic Acids Res 2006, 34(Database issue):D736-740.
• Bruskiewich R, Davenport G, Hazekamp T, Metz T, Ruiz M, Simon R, Takeya M, Lee J, Senger M, McLaren G et al: Generation Challenge Programme (GCP): standards for crop data. OMICS 2006, 10(2):215-219.
• Lefranc MP, Pommie C, Kaas Q, Duprat E, Bosc N, Guiraudou D, Jean C, Ruiz M, Da Piedade I, Rouard M et al: IMGT unique numbering for immunoglobulin and T cell receptor constant domains and Ig superfamily C-like domains. Dev Comp Immunol 2005, 29(3):185-203.
• Ruiz M, Rouard M, Raboin LM, Lartaud M, Lagoda P, Courtois B: TropGENE-DB, a multi-tropical crop information system. Nucleic Acids Res 2004, 32(Database issue):D364-367.
• Kaas Q, Ruiz M, Lefranc MP: IMGT/3Dstructure-DB and IMGT/StructuralQuery, a database and a tool for immunoglobulin, T cell receptor and MHC structural data. Nucleic Acids Res 2004, 32(Database issue):D208-210.
• Clement D, Lanaud C, Sabau X, Fouet O, Le Cunff L, Ruiz E, Risterucci AM, Glaszmann JC, Piffanelli P: Creation of BAC genomic resources for cocoa ( Theobroma cacao L.) for physical mapping of RGA containing BAC clones. Theor Appl Genet 2004, 108(8):1627-1634.
• Sarrauste de Menthiere C, Terriere S, Pugnere D, Ruiz M, Demaille J, Touitou I: INFEVERS: the Registry for FMF and hereditary inflammatory disorders mutations. Nucleic Acids Res 2003, 31(1):282-285.
• Pugnere D, Ruiz M, Sarrauste de Menthiere C, Masdoua B, Demaille J, Touitou I: The MetaFMF website: a high quality tool for meta-analysis of FMF. Nucleic Acids Res 2003, 31(1):286-290.
• Lefranc MP, Pommie C, Ruiz M, Giudicelli V, Foulquier E, Truong L, Thouvenin-Contet V, Lefranc G: IMGT unique numbering for immunoglobulin and T cell receptor variable domains and Ig superfamily V-like domains. Dev Comp Immunol 2003, 27(1):55-77.
• Ruiz M, Lefranc MP: IMGT gene identification and Colliers de Perles of human immunoglobulins with known 3D structures. Immunogenetics 2002, 53(10-11):857-883.