Ten simple rules for switching from face-to-face to remote conference: An opportunity to estimate the reduction in GHG emissions Guignon Valentin, Breton Catherine, Mariette Jérôme, Sabot François, Fumey Julien, Lefort Vincent, Fiston-Lavier Anna-Sophie. 2021, PLOS Computational Biology. 10.1371/journal.pcbi.1009321
FAIR-Checker: supporting digital resource findability and reuse with Knowledge Graphs and Semantic Web standards Gaignard Alban, Rosnet Thomas, De Lamotte Frédéric, Lefort Vincent, Devignes Marie-Dominique. 2023, Journal of Biomedical Semantics. 10.1186/s13326-023-00289-5
BrAPI v2: real-world applications for data integration and collaboration in the breeding and genetics community Selby Peter, Abbeloos Rafael, Adam-Blondon Anne-Francoise, Agosto-Pérez Francisco J, Alaux Michael, Alic Isabelle, Al-Shamaa Khaled, Aparicio Johan Steven, Backlund Jan Erik, Batac Aldrin, Beier Sebastian, Besombes Gabriel, Boizet Alice, Brouwer Matthijs, Casstevens Terry, Charleroy Arnaud, Corak Keo, Courtney Chaney, Crimi Mariano, Davuluri Gouripriya, de Sousa Kauê, Destin Jeremy, Dhondt Stijn, Dhungana Ajay, Droesbeke Bert, Feser Manuel, Flores-Gonzalez Mirella, Guignon Valentin, Habito Corina, Hallab Asis, Hershberger Jenna, Hok Puthick, Hulse-Kemp Amanda M, Johnson Lynn Carol, Jung Sook, Kersey Paul, Kilian Andrzej, König Patrick, Kumar Suman, Lamos-Sweeney Josh, Lang Laszlo, Lange Matthias, Laporte Marie-Angélique, Lee Taein, Le Floch Erwan, López Francisco, Madriz Brandon, Main Dorrie, Marsella Marco, Marty Maud, Michotey Célia, Miller Zachary, Milne Iain, Mueller Lukas A, Nderitu Moses, Neveu Pascal, Palladino Nick, Parsons Tim, Pommier Cyril, Rami Jean-François, Raubach Sebastian, Rife Trevor, Robbins Kelly, Rouard Mathieu, Ruff Joseph, Sempéré Guilhem, Shah Romil Mayank, Shaw Paul, Smith Becky, Soldevilla Nahuel, Tireau Anne, Tovar Clarysabel, Uszynski Grzegorz, Vega Vivian Bass, Weise Stephan, Yarnes Shawn C, The BrAPI Consortium . 2025, Database. 10.1093/database/baaf048
Ten simple rules for developing visualization tools in genomics Durant Eloi, Rouard Mathieu, Ganko Eric W., Muller Cedric, Cleary Alan M., Farmer Andrew D., Conte Matthieu, Sabot Francois. 2022, PLOS Computational Biology. 10.1371/journal.pcbi.1010622
The banana genome hub: a community database for genomics in the Musaceae Droc Gaëtan, Martin Guillaume, Guignon Valentin, Summo Marilyne, Sempéré Guilhem, Durant Eloi, Soriano Alexandre, Baurens Franc-Christophe, Cenci Alberto, Breton Catherine, Shah Trushar, Aury Jean-Marc, Ge Xue-Jun, Harrison Pat Heslop, Yahiaoui Nabila, D’Hont Angélique, Rouard Mathieu. 2022, Horticulture Research. 10.1093/hr/uhac221
Panache: a web browser-based viewer for linearized pangenomes Durant Éloi, Sabot François, Conte Matthieu, Rouard Mathieu. 2021, Bioinformatics. 10.1093/bioinformatics/btab688
GeMo: a web-based platform for the visualization and curation of genome ancestry mosaics Summo Marilyne, Comte Aurore, Martin Guillaume, Perelle Pierrick, Weitz Eric M, Droc Gaëtan, Rouard Mathieu. 2022, Database. 10.1093/database/baac057
AgroLD: a knowledge graph for the plant sciences Pierre Larmande, Bertrand Pittolat, Ndomassi Tando, Yann Pomie, Bill Gates Happi Happi, Valentin Guignon, Manuel Ruiz. 2025, BMC Genomic Data. 10.1186/s12863-025-01359-6
The South Green portal: a comprehensive resource for tropical and Mediterranean crop genomics . 2016, Current Plant Biology. 10.1016/j.cpb.2016.12.002
A curation system of rice trait ontology with reliable interoperation by LLM and PubAnnotation Ahmad Javeed Muhammad, Liu Yawen, Kim Jin-Dong, Yao Xinzhi, Larmande Pierre, Xia Jingbo. 2025, Genomics & Informatics. 10.1186/s44342-025-00058-z
PanExplorer: a web-based tool for exploratory analysis and visualization of bacterial pan-genomes Dereeper Alexis, Summo Marilyne, Meyer Damien F. 2022, Bioinformatics. 10.1093/bioinformatics/btac504
TrEMOLO: accurate transposable element allele frequency estimation using long-read sequencing data combining assembly and mapping-based approaches Mohamed Mourdas, Sabot François, Varoqui Marion, Mugat Bruno, Audouin Katell, Pélisson Alain, Fiston-Lavier Anna-Sophie, Chambeyron Séverine. 2023, Genome Biology. 10.1186/s13059-023-02911-2
Unravelling genomic drivers of speciation in Musa through genome assemblies of wild banana ancestors Martin Guillaume, Istace Benjamin, Baurens Franc-Christophe, Belser Caroline, Hervouet Catherine, Labadie Karine, Cruaud Corinne, Noel Benjamin, Guiougou Chantal, Salmon Frederic, Mahadeo Joël, Ahmad Fajarudin, Volkaert Hugo A., Droc Gaëtan, Rouard Mathieu, Sardos Julie, Wincker Patrick, Yahiaoui Nabila, Aury Jean-Marc, D’Hont Angélique. 2025, Nature Communications. 10.1038/s41467-025-56329-4
A chromosome-level, haplotype-phased Vanilla planifolia genome highlights the challenge of partial endoreplication for accurate whole-genome assembly Piet Quentin, Droc Gaetan, Marande William, Sarah Gautier, Bocs Stéphanie, Klopp Christophe, Bourge Mickael, Siljak-Yakovlev Sonja, Bouchez Olivier, Lopez-Roques Céline, Lepers-Andrzejewski Sandra, Bourgois Laurent, Zucca Joseph, Dron Michel, Besse Pascale, Grisoni Michel, Jourda Cyril, Charron Carine. 2022, Plant Communications. 10.1016/j.xplc.2022.100330
Genetic databases in the era of ‘DSI’ benefit-sharing Rouard Mathieu, Scholz Amber Hartman, Halewood Michael. 2025, Trends in Genetics. 10.1016/j.tig.2025.03.004
Painting the diversity of a world's favorite fruit: A next generation catalog of cultivated bananas Sardos Julie, Cenci Alberto, Martin Guillaume, Breton Catherine, Guignon Valentin, Van den Houwe Ines, Mendez Yaleidis, Sachter‐Smith Gabriel L., Chase Rachel, Ruas Max, Rivallan Ronan, Paofa Janet, Wigmore William, Hunter David Tilafono, D'Hont Angélique, Yahiaoui Nabila, Jenny Christophe, Perrier Xavier, Roux Nicolas, Rouard Mathieu. 2025, PLANTS, PEOPLE, PLANET. 10.1002/ppp3.10581
FrangiPANe, a tool for creating a panreference using left behind reads Christine Tranchant-Dubreuil, Clothilde Chenal, Mathieu Blaison, Laurence Albar, Valentin Klein, Cédric Mariac, Wing Rod A, Yves Vigouroux, Francois Sabot. 2023, NAR Genomics and Bioinformatics. 10.1093/nargab/lqad013
Dual domestications and origin of traits in grapevine evolution Dong Yang, Duan Shengchang, Xia Qiuju, Liang Zhenchang, Dong Xiao, Margaryan Kristine, Musayev Mirza, Goryslavets Svitlana, Zdunić Goran, Bert Pierre-François, Lacombe Thierry, Maul Erika, Nick Peter, Bitskinashvili Kakha, Bisztray György Dénes, Drori Elyashiv, De Lorenzis Gabriella, Cunha Jorge, Popescu Carmen Florentina, Arroyo-Garcia Rosa, Arnold Claire, Ergül Ali, Zhu Yifan, Ma Chao, Wang Shufen, Liu Siqi, Tang Liu, Wang Chunping, Li Dawei, Pan Yunbing, Li Jingxian, Yang Ling, Li Xuzhen, Xiang Guisheng, Yang Zijiang, Chen Baozheng, Dai Zhanwu, Wang Yi, Arakelyan Arsen, Kuliyev Varis, Spotar Gennady, Girollet Nabil, Delrot Serge, Ollat Nathalie, This Patrice, Marchal Cécile, Sarah Gautier, Laucou Valérie, Bacilieri Roberto, Röckel Franco, Guan Pingyin, Jung Andreas, Riemann Michael, Ujmajuridze Levan, Zakalashvili Tekle, Maghradze David, Höhn Maria, Jahnke Gizella, Kiss Erzsébet, Deák Tamás, Rahimi Oshrit, Hübner Sariel, Grassi Fabrizio, Mercati Francesco, Sunseri Francesco, Eiras-Dias José, Dumitru Anamaria Mirabela, Carrasco David, Rodriguez-Izquierdo Alberto, Muñoz Gregorio, Uysal Tamer, Özer Cengiz, Kazan Kemal, Xu Meilong, Wang Yunyue, Zhu Shusheng, Lu Jiang, Zhao Maoxiang, Wang Lei, Jiu Songtao, Zhang Ying, Sun Lei, Yang Huanming, Weiss Ehud, Wang Shiping, Zhu Youyong, Li Shaohua, Sheng Jun, Chen Wei. 2023, Science. 10.1126/science.add8655
Tripal, a community update after 10 years of supporting open source, standards-based genetic, genomic and breeding databases Staton Margaret, Cannon Ethalinda, Sanderson Lacey-Anne, Wegrzyn Jill, Anderson Tavis, Buehler Sean, Cobo-Simón Irene, Faaberg Kay, Grau Emily, Guignon Valentin, Gunoskey Jessica, Inderski Blake, Jung Sook, Lager Kelly, Main Dorrie, Poelchau Monica, Ramnath Risharde, Richter Peter, West Joe, Ficklin Stephen. 2021, Briefings in Bioinformatics. 10.1093/bib/bbab238
Correction to ‘GreenPhylDB v5: a comparative pangenomic database for plant genomes’ Guignon Valentin, Toure Abdel, Droc Gaëtan, Dufayard Jean-François, Conte Matthieu, Rouard Mathieu. 2021, Nucleic Acids Research. 10.1093/nar/gkab564
Gigwa v2—Extended and improved genotype investigator Sempéré Guilhem, Pétel Adrien, Rouard Mathieu, Frouin Julien, Hueber Yann, De Bellis Fabien, Larmande Pierre. 2019, GigaScience. 10.1093/gigascience/giz051
CulebrONT: a streamlined long reads multi-assembler pipeline for prokaryotic and eukaryotic genomes Orjuela Julie, Comte Aurore, Ravel Sébastien, Charriat Florian, Vi Tram, Sabot François, Cunnac Sébastien. 2022, Peer Community Journal. 10.24072/pcjournal.153
A new comprehensive annotation of leucine‐rich repeat‐containing receptors in rice Gottin Céline, Dievart Anne, Summo Marilyne, Droc Gaëtan, Périn Christophe, Ranwez Vincent, Chantret Nathalie. 2021, The Plant Journal. 10.1111/tpj.15456
RapGreen, an interactive software and web package to explore and analyze phylogenetic trees Dufayard Jean-François, Bocs Stéphanie, Guignon Valentin, Larivière Delphine, Louis Alexandra, Oubda Nicolas, Rouard Mathieu, Ruiz Manuel, de Lamotte Frédéric. 2021, NAR Genomics and Bioinformatics. 10.1093/nargab/lqab088
Plant Pangenome: Impacts on Phenotypes and Evolution Tranchant‐Dubreuil Christine, Rouard Mathieu, Sabot Francois. 2019, Annual Plant Reviews online. 10.1002/9781119312994.apr0664
MooSciTIC: Training of trainers in West African research and higher education Atindehou Ménonvè, Adéoti Kifouli, Loko Laura Estelle Yêyinou, Beulé Thierry, Paradis Emmanuel, Djedatin Gustave, Tranchant-Dubreuil Christine, Sabot François, Lagnika Latifou, Jaligot Estelle. 2019, PLOS Biology. 10.1371/journal.pbio.3000312
Three founding ancestral genomes involved in the origin of sugarcane Pompidor Nicolas, Charron Carine, Hervouet Catherine, Bocs Stéphanie, Droc Gaëtan, Rivallan Ronan, Manez Aurore, Mitros Therese, Swaminathan Kankshita, Glaszmann Jean-Christophe, Garsmeur Olivier, D’Hont Angélique. 2021, Annals of Botany. 10.1093/aob/mcab008
Coconut genome assembly enables evolutionary analysis of palms and highlights signaling pathways involved in salt tolerance Yang Yaodong, Bocs Stéphanie, Fan Haikuo, Armero Alix, Baudouin Luc, Xu Pengwei, Xu Junyang, This Dominique, Hamelin Chantal, Iqbal Amjad, Qadri Rashad, Zhou Lixia, Li Jing, Wu Yi, Ma Zilong, Issali Auguste Emmanuel, Rivallan Ronan, Liu Na, Xia Wei, Peng Ming, Xiao Yong. 2021, Communications Biology. 10.1038/s42003-020-01593-x
Rice Galaxy: an open resource for plant science Juanillas Venice, Dereeper Alexis, Beaume Nicolas, Droc Gaetan, Dizon Joshua, Mendoza John Robert, Perdon Jon Peter, Mansueto Locedie, Triplett Lindsay, Lang Jillian, Zhou Gabriel, Ratharanjan Kunalan, Plale Beth, Haga Jason, Leach Jan E, Ruiz Manuel, Thomson Michael, Alexandrov Nickolai, Larmande Pierre, Kretzschmar Tobias, Mauleon Ramil P. 2019, GigaScience. 10.1093/gigascience/giz028
GRU-SCANET: unleashing the power of GRU-based sinusoidal capture network for precision-driven named entity recognition Happi Happi Bill Gates, Pelap Geraud Fokou, Symeonidou Danai, Larmande Pierre. 2024, Bioinformatics Advances. 10.1093/bioadv/vbaf096