Manuel Ruiz
Institute:
CIRAD
Public e-mail:
manuel [dot] ruiz [at] cirad [dot] fr Research Interests:
Knowledge representation, management of data related to genetics and plant genomics, Mediation-based approaches and Semantic Web for information systems interoperability, Comparative genomics and automatic annotations of genomes
Custom message:
Since July 2007, Head of the CIRAD Bioinformatics team "Data Integration" of the Joint Research Unit Plant Development and Genetic Improvement
Scientific manager of the South Green Bioinformatics Platform
http://agents.cirad.fr/index.php/manuel.ruiz@cirad.fr/manuel_ruiz_en
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Ngompé GT, Venkatesan A, El Hassouni N, Ruiz M, Larmande P.
Submitted. {AgroLD} {API}. An {API}-centric approach towards knowledge extraction in the agronomic linked data knowledge base,{AgroLD} {API}. Une architecture orientée services pour l?extraction de connaissances dans la base de données liées {AgroLD} 21:133–157.
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Sarah G, Homa F, Pointet S, Contreras S, Sabot F, Nabholz B, Santoni S, Sauné L, Ardisson M, Chantret N et al..
2016. A large set of 26 new reference transcriptomes dedicated to comparative population genomics in crops and wild relatives.. Molecular ecology resources. Abstract
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Sempéré G, Philippe F, Dereeper A, Ruiz M, Sarah G, Larmande P.
2016. Gigwa—Genotype investigator for genome-wide analyses. Gigascience. 5:25.
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Ngompé GT, Venkatesan A, El Hassouni N, Ruiz M, Larmande P.
2016. AgroLD API. An API-centric approach towards knowledge extraction in the agronomic linked data knowledge base,AgroLD API. Une architecture orientée services pour l?extraction de connaissances dans la base de données liées AgroLD Ingenierie des Systemes d{'}Information. 21:133-157.
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Zevio S, El Hassouni N, Ruiz M, Larmande P.
2016. AgroLD indexing tools with ontological annotations. CEUR Workshop Proceedings. 1795
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Dereeper A, Homa F, Andres G, Sempéré G, Sarah G, Hueber Y, Dufayard JF, Ruiz M.
2015. SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations. Nucleic Acids Research.
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Venkatesan A, El Hassouni N, Phillipe F, Pommier C, Quesneville H, Ruiz M, Larmande P.
2015. Exposing French agronomic resources as Linked Open Data. CEUR Workshop Proceedings. 1546:205-207.
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Wu AG, Prochnik S, Jenkins J, Salse J, Hellsten U, Murat F, Perrier X, Ruiz M, Scalabrin S, Terol J et al..
2014. Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication. Nature Biotechnology.
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Droc G, Larivière D, Guignon V, Yahiaoui N, This D, Garsmeur O, Dereeper A, Hamelin C, Argout X, Dufayard JF et al..
2013. The Banana Genome Hub. Database. 2013 Abstract
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Courtois B, Frouin J, Greco R, Bruschi G, Droc G, Hamelin C, Ruiz M, Clément G, Evrard J-C, Van Coppenole S et al..
2012. Genetic Diversity and Population Structure in a European Collection of Rice. Crop Sci.. 52(4):1663-1675. Abstract
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Lacape J-M, Claverie M, Vidal RO, Carazzolle MF, Guimarães Pereira GA, Ruiz M, Pré M, Llewellyn D, Al-Ghazi Y, Jacobs J et al..
2012. Deep sequencing reveals differences in the transcriptional landscapes of fibers from two cultivated species of cotton.. PloS one. 7(11):e48855. Abstract
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D’Hont A, Denoeud F, Aury J-M, Baurens F-C, Carreel F, Garsmeur O, Noel B, Bocs S, Droc G, Rouard M et al..
2012. The banana (Musa acuminata) genome and the evolution of monocotyledonous plants.. Nature. 488(7410):213-7. Abstract
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Maillol V, Bacilieri R, Bocs S, Boursiquot J-M, Carrier G, Dereeper A, Droc G, Fleury C, Larmande P, Lecunff L et al..
2012. Role of Galaxy in a bioinformatic plant breeding platform. Galaxy Community Conference.
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Wollbrett J, Larmande P, Ruiz M.
2012. Semi-automatic generation of Semantic Web Services for relational biological databases. CEUR Workshop Proceedings. 952
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Courtois B, Greco R, Bruschi G, Frouin J, Ahmadi N, Droc G, Hamelin C, Ruiz M, Evrard J-C, Katsantonis D et al..
2011. Molecular characterization of the European rice collection in view of association mapping. Plant Genetic Resources. 9:233–235.
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Argout X, Salse J, Aury J-M, Guiltinan MJ, Droc G, Gouzy J, Allegre M, Chaparro C, Legavre T, Maximova SN et al..
2011. The genome of Theobroma cacao. Nature Genetics. 43(2):101-108.
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Courtois B, Ahmadi N, Khowaja F, Price AH, Rami JF, Frouin J, Hamelin C, Ruiz M.
2009. Rice Root Genetic Architecture: Meta-analysis from a Drought QTL Database. Rice. 2(2-3):115-128.
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Risterucci AM, Nansot G, Grangeon R, Lepitre V, Dereeper A, Argout X, Ruiz M, Billotte N.
2008. Development of microsatellite (SSR) markers using the SAT software. 2nd International Symposium on Guava and Other Myrtaceae.
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Argout X, Fouet O, Wincker P, Gramacho K, Legavre T, Sabau X, Risterucci AM, Da Silva C, Cascardo J, Allegre M et al..
2008. 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.
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Larmande P, Gay C, Lorieux M, Périn C, Bouniol M, Droc G, Sallaud C, Perez P, Barnola I, Biderre-Petit C et al..
2008. Oryza Tag Line, a phenotypic mutant database for the Genoplante rice insertion line library.. Nucleic acids research. 36(Database issue):D1022-7. Abstract
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Lescot M, Piffanelli P, Ciampi AY, Ruiz M, Blanc G, Leebens-Mack J, da Silva FR, Santos CMR, D'Hont A, Garsmeur O et al..
2008. Insights into the Musa genome: syntenic relationships to rice and between Musa species.. BMC genomics. 9:58. Abstract
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Bruskiewich R, Senger M, Davenport G, Ruiz M, Rouard M, Hazekamp T, Takeya M, Doi K, Satoh K, Costa M et al..
2008. The generation challenge programme platform: semantic standards and workbench for crop science.. International journal of plant genomics. 2008:369601. Abstract
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Wanchana S, Thongjuea S, Ulat VJ, Anacleto M, Mauleon R, Conte MG, Rouard M, Ruiz M, Krishnamurthy N, Sjolander K et al..
2008. The Generation Challenge Programme comparative plant stress-responsive gene catalogue. Nucleic Acids Research. 36(suppl 1):D943-D946. Abstract
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Larmande P, Gay C, Lorieux M, Perin C, Bouniol M, Droc G, Sallaud C, Perez P, Barnola I, Biderre-Petit C et al..
2007. Oryza Tag Line, a phenotypic mutant database for the Genoplante rice insertion line library. Nucleic Acids Research. 36:D1022–D1027.
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Argout X, Ruiz M, Fouet O, Lanaud C, Wincker P, Da Silva C, Courtois B.
2007. ESTtik : a semi-automatic cDNA sequence analysis and annotation pipeline including SSR and SNP search tools.. 15th International Cocoa Research Conference. 1:501-506.
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Dereeper A, Argout X, Billot C, Rami JF, Ruiz M.
2007. SAT, a flexible and optimized Web application for SSR marker development. BMC Bioinformatics. 8:465-465. Abstract
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Argout X, Ruiz M, Rouard M, Turnbull C, Lanaud C, Rosenquist E, Courtois B.
2007. CocoaGen DB: a Web portal for crossing cocoa phenotypic, genetic and genomic data from ICGD and TropGeneDB databases.. 15th International Cocoa Research Conference. 1:515-518.
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Hamelin C, Ruiz M, Argout X.
2007. TropGENE-DB, a multi-tropical crop information system. 4th International Workshop DILS.
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Droc G, Ruiz M, Larmande P, Pereira A, Piffanelli P, Morel J-B, Dievart A, Courtois B, Guiderdoni E, Périn C.
2006. OryGenesDB: a database for rice reverse genetics. Nucleic Acids Research. 34(Database i):D736-40-D736-40. Abstract
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Droc G, Ruiz M, Larmande P, Pereira A, Piffanelli P, Morel JB, Dievart A, Courtois B, Guiderdoni E, Périn C.
2006. OryGenesDB: a database for rice reverse genetics.. Nucleic acids research.. 34
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Ruiz M, Rouard M, Raboin LM, Lartaud M, Lagoda P, Courtois B.
2004. TropGENE-DB, a multi-tropical crop information system.. Nucleic acids research. 32(Database issue):D364-7. Abstract
