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| @article{droc_banana_2022, | ||
| title = {The banana genome hub: a community database for genomics in the {Musaceae}}, | ||
| volume = {9}, | ||
| issn = {2052-7276}, | ||
| shorttitle = {The banana genome hub}, | ||
| url = {https://doi.org/10.1093/hr/uhac221}, | ||
| doi = {10.1093/hr/uhac221}, | ||
| urldate = {2023-01-15}, | ||
| journal = {Horticulture Research}, | ||
| author = {Droc, Gaëtan and Martin, Guillaume and Guignon, Valentin and Summo, Marilyne and Sempéré, Guilhem and Durant, Eloi and Soriano, Alexandre and Baurens, Franc-Christophe and Cenci, Alberto and Breton, Catherine and Shah, Trushar and Aury, Jean-Marc and Ge, Xue-Jun and Harrison, Pat Heslop and Yahiaoui, Nabila and D’Hont, Angélique and Rouard, Mathieu}, | ||
| month = jan, | ||
| year = {2022}, | ||
| pages = {uhac221}, | ||
| } | ||
| @article{conte_greenphyldb:_2008, | ||
| title = {{GreenPhylDB}: a database for plant comparative genomics}, | ||
| volume = {36}, | ||
| issn = {0305-1048}, | ||
| shorttitle = {{GreenPhylDB}}, | ||
| doi = {10.1093/nar/gkm934}, | ||
| number = {Database issue}, | ||
| journal = {Nucleic Acids Research}, | ||
| author = {Conte, M. G. and Gaillard, S. and Lanau, N. and Rouard, M. and Périn, C.}, | ||
| month = jan, | ||
| year = {2008}, | ||
| pmid = {17986457}, | ||
| pmcid = {2238940}, | ||
| keywords = {Internet, Software, Plant Proteins, Arabidopsis, Oryza sativa, Genome, Plant, phylogeny, User-Computer Interface, genomics, Computer Graphics, Databases, Genetic}, | ||
| pages = {D991--D998}, | ||
| } | ||
|
|
||
| @article{rouard_greenphyldb_2011, | ||
| title = {{GreenPhylDB} v2.0: comparative and functional genomics in plants}, | ||
| volume = {39}, | ||
| issn = {1362-4962}, | ||
| shorttitle = {{GreenPhylDB} v2.0}, | ||
| doi = {10.1093/nar/gkq811}, | ||
| number = {Database issue}, | ||
| journal = {Nucleic acids research}, | ||
| author = {Rouard, Mathieu and Guignon, Valentin and Aluome, Christelle and Laporte, Marie-Angélique and Droc, Gaëtan and Walde, Christian and Zmasek, Christian M and Périn, Christophe and Conte, Matthieu G}, | ||
| month = jan, | ||
| year = {2011}, | ||
| pmid = {20864446}, | ||
| keywords = {Software, Plant Proteins, Plants, Genes, Plant, Genome, Plant, Molecular Sequence Annotation, phylogeny, genomics, Databases, Genetic}, | ||
| pages = {D1095--1102}, | ||
| } | ||
|
|
||
| @article{dereeper_coffee_2015, | ||
| title = {The coffee genome hub: a resource for coffee genomes}, | ||
| volume = {43}, | ||
| issn = {0305-1048, 1362-4962}, | ||
| shorttitle = {The coffee genome hub}, | ||
| url = {http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gku1108}, | ||
| doi = {10.1093/nar/gku1108}, | ||
| language = {en}, | ||
| number = {D1}, | ||
| urldate = {2016-03-17}, | ||
| journal = {Nucleic Acids Research}, | ||
| author = {Dereeper, A. and Bocs, S. and Rouard, M. and Guignon, V. and Ravel, S. and Tranchant-Dubreuil, C. and Poncet, V. and Garsmeur, O. and Lashermes, P. and Droc, G.}, | ||
| month = jan, | ||
| year = {2015}, | ||
| pages = {D1028--D1035}, | ||
| } | ||
|
|
||
| @article{ruiz_tropgene-db_2004, | ||
| title = {{TropGENE}-{DB}, a multi-tropical crop information system}, | ||
| volume = {32}, | ||
| issn = {1362-4962}, | ||
| doi = {10.1093/nar/gkh105}, | ||
| language = {eng}, | ||
| number = {Database issue}, | ||
| journal = {Nucleic Acids Research}, | ||
| author = {Ruiz, Manuel and Rouard, Mathieu and Raboin, Louis Marie and Lartaud, Marc and Lagoda, Pierre and Courtois, Brigitte}, | ||
| month = jan, | ||
| year = {2004}, | ||
| pmid = {14681435}, | ||
| pmcid = {PMC308839}, | ||
| keywords = {Internet, Plants, Computational biology, User-Computer Interface, Quantitative trait loci, Databases, Genetic, Information Storage and Retrieval, Crops, Agricultural, Tropical Climate}, | ||
| pages = {D364--367}, | ||
| } | ||
|
|
||
| @article{guignon_south_2016, | ||
| title = {The {South} {Green} portal: {A} comprehensive resource for tropical and {Mediterranean} crop genomics}, | ||
| volume = {7}, | ||
| journal = {Current Plant Biology}, | ||
| author = {Guignon, Valentin and Hueber, Yann and Rouard, Mathieu and Bocs, Stéphanie and Couvin, David and De Lamotte, Frédéric and Droc, Gaëtan and Dufayard, Jean François and El Hassouni, Nordine and Farcy, Cédric}, | ||
| year = {2016}, | ||
| pages = {6--9}, | ||
| } | ||
|
|
||
| @article{droc_banana_2013, | ||
| title = {The {Banana} {Genome} {Hub}}, | ||
| volume = {2013}, | ||
| issn = {1758-0463}, | ||
| url = {https://academic.oup.com/database/article-lookup/doi/10.1093/database/bat035}, | ||
| doi = {10.1093/database/bat035}, | ||
| language = {en}, | ||
| number = {0}, | ||
| urldate = {2017-11-08}, | ||
| journal = {Database}, | ||
| author = {Droc, G. and Lariviere, D. and Guignon, V. and Yahiaoui, N. and This, D. and Garsmeur, O. and Dereeper, A. and Hamelin, C. and Argout, X. and Dufayard, J.-F. and Lengelle, J. and Baurens, F.-C. and Cenci, A. and Pitollat, B. and D'Hont, A. and Ruiz, M. and Rouard, M. and Bocs, S.}, | ||
| month = may, | ||
| year = {2013}, | ||
| pages = {bat035--bat035}, | ||
| file = {The Banana Genome Hub:C\:\\Users\\mrouard\\Zotero\\storage\\9E49I2U5\\bat035.html:text/html}, | ||
| } | ||
|
|
||
| @article{sempere_gigwa_2019, | ||
| title = {Gigwa v2—{Extended} and improved genotype investigator}, | ||
| volume = {8}, | ||
| url = {https://academic.oup.com/gigascience/article/8/5/giz051/5488103}, | ||
| doi = {10.1093/gigascience/giz051}, | ||
| abstract = {AbstractBackground. The study of genetic variations is the basis of many research domains in biology. From genome structure to population dynamics, many applic}, | ||
| language = {en}, | ||
| number = {5}, | ||
| urldate = {2019-05-16}, | ||
| journal = {GigaScience}, | ||
| author = {Sempéré, Guilhem and Pétel, Adrien and Rouard, Mathieu and Frouin, Julien and Hueber, Yann and De Bellis, Fabien and Larmande, Pierre}, | ||
| month = may, | ||
| year = {2019}, | ||
| file = {Snapshot:C\:\\Users\\mrouard\\Zotero\\storage\\PG8DD4EN\\5488103.html:text/html}, | ||
| } | ||
|
|
||
| @article{dhont_banana_2012, | ||
| title = {The banana ({Musa} acuminata) genome and the evolution of monocotyledonous plants}, | ||
| volume = {488}, | ||
| url = {http://dx.doi.org/10.1038/nature11241}, | ||
| journal = {Nature}, | ||
| month = jul, | ||
| year = {2012}, | ||
| keywords = {genomics, Plant sciences, Evolution, Genetics}, | ||
| pages = {213}, | ||
| } | ||
|
|
||
| @article{denoeud_coffee_2014, | ||
| title = {The coffee genome provides insight into the convergent evolution of caffeine biosynthesis}, | ||
| volume = {345}, | ||
| issn = {0036-8075, 1095-9203}, | ||
| url = {http://www.sciencemag.org/content/345/6201/1181}, | ||
| doi = {10.1126/science.1255274}, | ||
| language = {en}, | ||
| number = {6201}, | ||
| urldate = {2014-11-28}, | ||
| journal = {Science}, | ||
| author = {Denoeud, France and Carretero-Paulet, Lorenzo and Dereeper, Alexis and Droc, Gaëtan and Guyot, Romain and Pietrella, Marco and Zheng, Chunfang and Alberti, Adriana and Anthony, François and Aprea, Giuseppe and Aury, Jean-Marc and Bento, Pascal and Bernard, Maria and Bocs, Stéphanie and Campa, Claudine and Cenci, Alberto and Combes, Marie-Christine and Crouzillat, Dominique and Silva, Corinne Da and Daddiego, Loretta and Bellis, Fabien De and Dussert, Stéphane and Garsmeur, Olivier and Gayraud, Thomas and Guignon, Valentin and Jahn, Katharina and Jamilloux, Véronique and Joët, Thierry and Labadie, Karine and Lan, Tianying and Leclercq, Julie and Lepelley, Maud and Leroy, Thierry and Li, Lei-Ting and Librado, Pablo and Lopez, Loredana and Muñoz, Adriana and Noel, Benjamin and Pallavicini, Alberto and Perrotta, Gaetano and Poncet, Valérie and Pot, David and Priyono and Rigoreau, Michel and Rouard, Mathieu and Rozas, Julio and Tranchant-Dubreuil, Christine and VanBuren, Robert and Zhang, Qiong and Andrade, Alan C. and Argout, Xavier and Bertrand, Benoît and Kochko, Alexandre de and Graziosi, Giorgio and Henry, Robert J. and Jayarama and Ming, Ray and Nagai, Chifumi and Rounsley, Steve and Sankoff, David and Giuliano, Giovanni and Albert, Victor A. and Wincker, Patrick and Lashermes, Philippe}, | ||
| month = sep, | ||
| year = {2014}, | ||
| pmid = {25190796}, | ||
| pages = {1181--1184}, | ||
| } | ||
|
|
||
| @article{ruas_mgis:_2017, | ||
| title = {{MGIS}: managing banana ({Musa} spp.) genetic resources information and high-throughput genotyping data}, | ||
| volume = {2017}, | ||
| issn = {1758-0463}, | ||
| shorttitle = {{MGIS}}, | ||
| url = {Hybridization, Missing Wild Ancestors and the Domestication of Cultivated Diploid Bananas}, | ||
| doi = {10.1093/database/bax046}, | ||
| abstract = {Database URL: https://www.crop-diversity.org/mgis/.}, | ||
| language = {eng}, | ||
| journal = {Database: The Journal of Biological Databases and Curation}, | ||
| author = {Ruas, Max and Guignon, V. and Sempere, G. and Sardos, J. and Hueber, Y. and Duvergey, H. and Andrieu, A. and Chase, R. and Jenny, C. and Hazekamp, T. and Irish, B. and Jelali, K. and Adeka, J. and Ayala-Silva, T. and Chao, C. P. and Daniells, J. and Dowiya, B. and Effa Effa, B. and Gueco, L. and Herradura, L. and Ibobondji, L. and Kempenaers, E. and Kilangi, J. and Muhangi, S. and Ngo Xuan, P. and Paofa, J. and Pavis, C. and Thiemele, D. and Tossou, C. and Sandoval, J. and Sutanto, A. and Vangu Paka, G. and Yi, G. and Van den Houwe, I. and Roux, N. and Rouard, M.}, | ||
| year = {2017}, | ||
| pmid = {29220435}, | ||
| pmcid = {PMC5502358}, | ||
| keywords = {Software, Seeds, Musa, Databases, Genetic, Genotyping Techniques, High-Throughput Nucleotide Sequencing}, | ||
| pages = {bax046}, | ||
| file = {Snapshot:C\:\\Users\\mrouard\\Zotero\\storage\\FR6HTRMK\\3866796.html:text/html}, | ||
| } | ||
|
|
||
| @article{guignon_greenphyldb_2021, | ||
| title = {{GreenPhylDB} v5: a comparative pangenomic database for plant genomes}, | ||
| volume = {49}, | ||
| issn = {0305-1048}, | ||
| shorttitle = {{GreenPhylDB} v5}, | ||
| url = {https://doi.org/10.1093/nar/gkaa1068}, | ||
| doi = {10.1093/nar/gkaa1068}, | ||
| number = {D1}, | ||
| urldate = {2021-01-20}, | ||
| journal = {Nucleic Acids Research}, | ||
| author = {Guignon, Valentin and Toure, Abdel and Droc, Gaëtan and Dufayard, Jean François and Conte, Matthieu and Rouard, Mathieu}, | ||
| month = jan, | ||
| year = {2021}, | ||
| pages = {D1464--D1471}, | ||
| } | ||
|
|
||
| @article{selby_brapiapplication_2019, | ||
| title = {{BrAPI}—an application programming interface for plant breeding applications}, | ||
| volume = {35}, | ||
| issn = {1367-4803}, | ||
| url = {https://academic.oup.com/bioinformatics/article/35/20/4147/5418796}, | ||
| doi = {10.1093/bioinformatics/btz190}, | ||
| abstract = {AbstractMotivation. Modern genomic breeding methods rely heavily on very large amounts of phenotyping and genotyping data, presenting new challenges in effecti}, | ||
| language = {en}, | ||
| number = {20}, | ||
| urldate = {2020-07-02}, | ||
| journal = {Bioinformatics}, | ||
| author = {Selby, Peter and Abbeloos, Rafael and Backlund, Jan Erik and Basterrechea Salido, Martin and Bauchet, Guillaume and Benites-Alfaro, Omar E. and Birkett, Clay and Calaminos, Viana C. and Carceller, Pierre and Cornut, Guillaume and Vasques Costa, Bruno and Edwards, Jeremy D. and Finkers, Richard and Yanxin Gao, Star and Ghaffar, Mehmood and Glaser, Philip and Guignon, Valentin and Hok, Puthick and Kilian, Andrzej and König, Patrick and Lagare, Jack Elendil B. and Lange, Matthias and Laporte, Marie-Angélique and Larmande, Pierre and LeBauer, David S. and Lyon, David A. and Marshall, David S. and Matthews, Dave and Milne, Iain and Mistry, Naymesh and Morales, Nicolas and Mueller, Lukas A. and Neveu, Pascal and Papoutsoglou, Evangelia and Pearce, Brian and Perez-Masias, Ivan and Pommier, Cyril and Ramírez-González, Ricardo H. and Rathore, Abhishek and Raquel, Angel Manica and Raubach, Sebastian and Rife, Trevor and Robbins, Kelly and Rouard, Mathieu and Sarma, Chaitanya and Scholz, Uwe and Sempéré, Guilhem and Shaw, Paul D. and Simon, Reinhard and Soldevilla, Nahuel and Stephen, Gordon and Sun, Qi and Tovar, Clarysabel and Uszynski, Grzegorz and Verouden, Maikel}, | ||
| month = oct, | ||
| year = {2019}, | ||
| note = {Publisher: Oxford Academic}, | ||
| pages = {4147--4155}, | ||
| } | ||
|
|
||
| @article{dufayard_rapgreen_2021, | ||
| title = {{RapGreen}, an interactive software and web package to explore and analyze phylogenetic trees}, | ||
| volume = {3}, | ||
| issn = {2631-9268}, | ||
| url = {https://doi.org/10.1093/nargab/lqab088}, | ||
| doi = {10.1093/nargab/lqab088}, | ||
| number = {3}, | ||
| urldate = {2021-10-20}, | ||
| journal = {NAR Genomics and Bioinformatics}, | ||
| author = {Dufayard, Jean-François and Bocs, Stéphanie and Guignon, Valentin and Larivière, Delphine and Louis, Alexandra and Oubda, Nicolas and Rouard, Mathieu and Ruiz, Manuel and de Lamotte, Frédéric}, | ||
| month = sep, | ||
| year = {2021}, | ||
| } | ||
|
|
||
| @article{tranchantdubreuil_plant_2019, | ||
| title = {Plant {Pangenome}: {Impacts} on {Phenotypes} and {Evolution}}, | ||
| copyright = {Copyright © 2019 by John Wiley \& Sons, Ltd.}, | ||
| shorttitle = {Plant {Pangenome}}, | ||
| url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/9781119312994.apr0664}, | ||
| doi = {10.1002/9781119312994.apr0664}, | ||
| language = {en}, | ||
| urldate = {2020-08-31}, | ||
| journal = {Annual Plant Reviews online}, | ||
| author = {Tranchant‐Dubreuil, Christine and Rouard, Mathieu and Sabot, Francois}, | ||
| year = {2019}, | ||
| note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/9781119312994.apr0664}, | ||
| keywords = {structural variation, population genomics, pangenome, gene diversity, evolution, adaptation}, | ||
| pages = {453--478}, | ||
| } | ||
|
|
||
| @article{durant_panache_2021, | ||
| title = {Panache: a web browser-based viewer for linearized pangenomes}, | ||
| issn = {1367-4803}, | ||
| shorttitle = {Panache}, | ||
| url = {https://doi.org/10.1093/bioinformatics/btab688}, | ||
| doi = {10.1093/bioinformatics/btab688}, | ||
| number = {btab688}, | ||
| urldate = {2021-10-14}, | ||
| journal = {Bioinformatics}, | ||
| author = {Durant, Éloi and Sabot, François and Conte, Matthieu and Rouard, Mathieu}, | ||
| month = oct, | ||
| year = {2021}, | ||
| file = {Snapshot:C\:\\Users\\mrouard\\Zotero\\storage\\ZWT6BHP9\\6380547.html:text/html}, | ||
| } | ||
|
|
||
| @article{rouard_digital_2022, | ||
| title = {A digital catalog of high-density markers for banana germplasm collections}, | ||
| volume = {4}, | ||
| issn = {2572-2611}, | ||
| url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/ppp3.10187}, | ||
| doi = {10.1002/ppp3.10187}, | ||
| language = {en}, | ||
| number = {1}, | ||
| urldate = {2022-03-28}, | ||
| journal = {PLANTS, PEOPLE, PLANET}, | ||
| author = {Rouard, Mathieu and Sardos, Julie and Sempéré, Guilhem and Breton, Catherine and Guignon, Valentin and Van den Houwe, Ines and Carpentier, Sebastien C. and Roux, Nicolas}, | ||
| year = {2022}, | ||
| note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/ppp3.10187}, | ||
| keywords = {banana, data management, digital genebank, high-density markers, plant conservation}, | ||
| pages = {61--67}, | ||
| } | ||
|
|
||
| @article{bayer_wheat_2022, | ||
| title = {Wheat {Panache} - a pangenome graph database representing presence/absence variation across 16 bread wheat genomes}, | ||
| copyright = {© 2022, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution-NonCommercial-NoDerivs 4.0 International), CC BY-NC-ND 4.0, as described at http://creativecommons.org/licenses/by-nc-nd/4.0/}, | ||
| url = {https://www.biorxiv.org/content/10.1101/2022.02.23.481560v1}, | ||
| doi = {10.1101/2022.02.23.481560}, | ||
| language = {en}, | ||
| urldate = {2022-02-26}, | ||
| author = {Bayer, Philipp E. and Petereit, Jakob and Durant, Eloi and Monat, Cecile and Rouard, Mathieu and Hu, Haifei and Chapman, Brett and Li, Chengdao and Cheng, Shifeng and Batley, Jacqueline and Edwards, David}, | ||
| month = feb, | ||
| year = {2022}, | ||
| note = {Section: New Results | ||
| Type: article}, | ||
| pages = {2022.02.23.481560}, | ||
| } |