Publications

Selected publications - Google Scholar

2024

• Yacoubi AN, Bernard S., BOSSY R., Courtin M., Happi Happi BG., Larmande P., Michel F., Nedellec C., Roussey C., Faron C., A Unified Approach to Publish Semantic Annotations of Agricultural Documents as Knowledge Graphs. Available at SSRN: http://dx.doi.org/10.2139/ssrn.4781279

• Shrestha AMS, Gonzales MEM, Ong PCL, Larmande P, Lee HS, Jeung JU, Kohli A, Chebotarov D, Mauleon RP, Lee JS, McNally KL. RicePilaf: a post-GWAS/QTL dashboard to integrate pangenomic, coexpression, regulatory, epigenomic, ontology, pathway, and text-mining information to provide functional insights into rice QTLs and GWAS loci. Gigascience. 2024 Jan 2;13:giae013. doi: 10.1093/gigascience/giae013.

2022

• P Larmande, K Todorov. Revealing Genotype–Phenotype Interactions: The AgroLD Experience and Challenges. Springer.  Integrative Bioinformatics: History and Future, 321-342

• G Sempéré, P Larmande, M Rouard. Managing high-density genotyping data with Gigwa. Springer. Plant Bioinformatics: Methods and Protocols, 415-427

2021

• Larmande P. and Todorov K. AgroLD: A Knowledge Graph for the Plant Sciences. International Semantic Web Conference, 496-510 https://link.springer.com/chapter/10.1007/978-3-030-88361-4_29 

• P Larmande, Y Liu, X Yao, J Xia.  OryzaGP 2021 update: a rice gene and protein dataset for named-entity recognition. Genomics & informatics 19 (3), e27. 10.5808/gi.21015

• Do Q, Ho B.H, Larmande P. PyRice: a Python package for querying Oryza sativa databases. Bioinformatics, Volume 37, Issue 7, 1 April 2021, Pages 1037–1038, https://doi.org/10.1093/bioinformatics/btaa694 

2020

• • Larmande P. Intégration de données multi-échelles et extraction de connaissances en agronomie : exemples et perspectives. Habilitation à Diriger des Recherches. Université Montpellier. Sept. 2020.  https://hal.archives-ouvertes.fr/tel-02105913v3 

  • Larmande P,  Jibril M.K Enabling a fast annotation process with the Table2Annotation tool. Genomics & Informatics 2020; 18(2): e19.  https://doi.org/10.5808/GI.2020.18.2.e19

  • Do Q and Larmande P. Candidate gene prioritization using graph embedding. IEEE-RIVF 2020. Ho Chi Minh, Vietnam. Proceedings Springer (under process). https://doi.org/10.1101/2020.02.03.927913 

  • Benoit Gaudou, Nghi Quang Huynh, Damien Philippon, Arthur Brugière, Kevin Chapuis, Patrick Taillandier, Pierre Larmande  and Alexis Drogoul. COMOKIT: A Modeling Kit to Understand, Analyze, and Compare the Impacts of Mitigation Policies Against the COVID-19 Epidemic at the Scale of a City. Front Public Health. 2020; 8: 563247. 10.3389/fpubh.2020.563247

2019

• • Pierre Larmande, Huy Do, Yue Wang. OryzaGP: rice gene and protein dataset for named-entity recognition. Genomics Inform. 2019;17(2):e17.   Published online June 26, 2019. DOI: https://doi.org/10.5808/GI.2019.17.2.e17    

  • Venice Margarette J Juanillas, Alexis Dereeper, Nicolas Beaume, Gaetan Droc,  .... Pierre Larmande, Tobias Kretzschmar, Ramil P Mauleon. Rice Galaxy: an open resource for plant science. GigaScience, Volume 8, Issue 5, May 2019, giz028, https://doi.org/10.1093/gigascience/giz028 Impact Factor: 7.31

  • Sempéré G, Pétel A, Rouard M, Frouin J, Hueber Y, De Bellis F, Larmande P. Gigwa v2 – Extended and improved genotype investigator. GigaScience, Volume 8, Issue 5, May 2019, giz051,https://doi.org/10.1093/gigascience/giz051 Impact Factor: 7.31

  • Abbeloos R, Backlund JE, Basterrechea Salido M, Bauchet .... Larmande P, .... Muller. M. BrAPI - an Application Programming Interface for Plant Breeding Applications. Bioinformatics. 2019 Mar 23. pii: btz190. doi: https://doi.org/10.1093/bioinformatics/btz190   Impact Factor: 5.41

  • Yaw Nti-Addae, Dave Matthews, Victor Jun Ulat, Raza Syed, Guilhem Sempere, Adrien Petel, Jon Renner, Pierre Larmande, Valentin Guignon, Elizabeth Jones, Kelly Robbins. Benchmarking Database Systems for Genomic Selection Implementation. Database, 2019 doi: https://doi.org/10.1093/database/baz096 and preprint https://doi.org/10.1101/519017 Impact Factor: 3.978

2018

• • Huy Do, Khoat Than,  Pierre Larmande. Evaluating Named-Entity Recognition approaches in plant molecular biology. 219-225; Multi-disciplinary Trends in Artificial Intelligence - 12th International Conference, MIWAI 2018, Hanoi, Vietnam, November 18-20, 2018, Proceedings. Lecture Notes in Computer Science 11248, Springer 2018, ISBN 978-3-030-03013-1  https://doi.org/10.1101/360966

  • Aravind Venkatesan, Gildas Tagny Ngompe, Nordine El Hassouni, Imene Chentli, Valentin Guignon, Clement Jonquet, Manuel Ruiz,  Pierre Larmande.  Agronomic Linked Data (AgroLD): a Knowledge-based System to Enable Integrative Biology in Agronomy. Plos One 13 (11), e0198270 2018.  https://doi.org/10.1371/journal.pone.0198270 Impact Factor: 2.766

  • Curby et al, The Rise and Fall of African Rice Cultivation Revealed by Analysis of 246 New Genomes. Current  Biology, 2018. https://doi.org/10.1016/j.cub.2018.05.066 Impact Factor: 9.201

  • Harper L,  et al, AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. Database (Oxford). 2018 Jan 1;2018.  https://doi.org/10.1093/database/bay088  Impact Factor: 3.978

  • Scheben A., Chan K., Mansueto L., Mauleon R., Larmande P., Alexandrov N., Wing R., McNally K., Quesneville, H., Edwards D. Progress in single access information systems for wheat and rice crop improvement. Briefing in Bioinformatics. 2018. https://doi.org/10.1093/bib/bby016. Impact Factor: 5.134

  • Jonquet C, Toulet A, Arnaud E, Aubin E, Dzalé-Yeumo E, Emonet V, Graybeal J, Laporte M-A, Musen M, Pesce V, Larmande P. AgroPortal: an ontology repository for agronomy. Comput. Electron. Agric. 2018; 144:126–143 Impact Factor: 2.201

2017

• • Dzale Yeumo E, Alaux M, Arnaud E, Aubin S, Baumann U, Buche P, Richard F, Jonquet C, Laporte MA, Larmande P, Pommier C, Protonotarios V, Reverte C, Shrestha R, Subirats I, Venkatesan A, Whan A and Quesneville H . Developing data interoperability using standards: A wheat community use case. F1000Research. 2017 ; 6:1843. https://doi.org/10.12688/f1000research.12234.2 

  • Cohen-Boulakia S, Belhajjame K, Collin O, Chopard J, Froidevaux C, Gaignard A, Hinsen K, Larmande P, Le Bras Y, Lemoine F, Mareuil F, Ménager H, Pradal C, Blanchet C. Scientific workflows for computational reproducibility in the life sciences: Status, challenges and opportunities. Futur. Gener. Comput. Syst. 2017. 75 : 284-298. Impact Factor: 2.786

2016

• • The South Green Collaborators. The South Green portal: a comprehensive resource for tropical and Mediterranean crop genomics. Curr. Plant Biol. 2016. 7-8 : 6-9. Impact Factor : 1.68

  • Sempéré G, Philippe F, Dereeper A, Ruiz M, Sarah G, Larmande P. Gigwa—Genotype investigator for genome- wide analyses. Gigascience. 2016. 5:25. Impact Factor : 7.31

Past

• • Al-Tam, F., Adam, H., Dos Anjos, A., Lorieux, M., Larmande, P., Ghesquière, A., Jouannic, S., and H-R Shahbazkia, P-TRAP: a Panicle Traits Phenotyping Tool.2013, BMC Plant Biology, 13:122-136. Impact Factor: 3.631

  • 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. 14:126-141. Impact Factor: 2.435

  • Lorieux M, Blein M, Lozano J, Bouniol M, Droc G, Diévart A, Périn C, Mieulet D, Lanau N, Bès M, Rouvière C, Gay C, Piffanelli P, Larmande P, Michel C, Barnola I, Biderre-Petit C, Sallaud C, Perez P and Guiderdoni E. In-depth molecular and phenotypic characterization in a rice insertion line library facilitates gene identification through reverse and forward genetics approaches. Plant Biotechnol. J. 2012; 10:555–568. Impact Factor: 7.443

  • Droc G, Périn C, Fromentin S, Larmande P. OryGenesDB 2008 update: database interoperability for functional genomics of rice. Nucleic Acids Res. 2009; 37:D992-D995. Impact factor: 9.202

  • Larmande P, Gay C, Lorieux M, Périn C, Bouniol M, Droc G, Sallaud C, Perez P, Barnola I, Biderre-Petit C, Martin J, Morel JB, Johnson AA, Bourgis F, Ghesquière, A, Ruiz M, Courtois B, Guiderdoni E. Oryza Tag Line, a phenotypic mutant database for the Genoplante rice insertion line library. Nucleic Acids Res. 2008 Jan; 36(Database issue):D1022-D1027. Impact factor: 9.202

  • Droc G, Ruiz M, Larmande P, Pereira A, Piffanelli P, Morel JB, Dievart A, Courtois B, Guiderdoni E, Périn C. OryGenesDB: a database for rice reverse genetics. Nucleic Acids Res. 2006; 34:D736–D740. Impact factor: 9.202

  • Sallaud C., Gay C., Larmande P., Bès M., Piffanelli P., Piégu B., Droc G., Regad F., Bourgeois E., Meynard D., Périn C., Sabau X., Ghesquière A., Delseny M., Glaszmann J.C., Guiderdoni, E. (2004) High throughput T-DNA insertion mutagenesis in rice : A first step towards in silico reverse genetics. Plant J. 2004 Aug; 39(3):450-64 Impact Factor: 5.468 

  • Pugh T., Fouet O., Risterucci A.M., Brottier P., Abouladze M., Deletrez C., Courtois B., Clement D., Larmande P., N'Goran J.A., Lanaud C., A new cacao linkage map based on codominant markers: development and integration of 201 new microsatellite markers. Theor Appl Genet. 2004. 108(6):1151-61. 2004.  Impact Factor; 3.900

  • Sallaud C., Meynard D., van Boxtel J., Gay C., Bes M., Brizard J.P., Larmande P., Ortega D., Raynal M., Portefaix M., Ouwerkerk P.B., Rueb S., Delseny M., Guiderdoni E.,  Highly efficient production and characterization of T-DNA plants for rice (Oryza sativa L.) functional genomics. Theor Appl Genet, 2003; 106 :1396-1408.  Impact Factor; 3.900