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Number of items: 185.

Journal article

Alfalfa leaf curl virus is transmitted by Aphis craccivora in a highly specific circulative manner. Ryckebusch Faustine, Sauvion Nicolas, Granier Martine, Roumagnac Philippe, Peterschmitt Michel. 2020. Virology, 546 : pp. 98-108.
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First report of Sugarcane streak mosaic virus in sugarcane (Saccharum spp.) in Côte d'Ivoire. Daugrois Jean-Heinrich, Roumagnac Philippe, Kouakou Y., Oura O.J.D.T., Pita J.S.. 2020. New Disease Reports, 41:22 : p. 22.
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Heterogeneity of the rice microbial community of the Chinese centuries-old Honghe Hani rice terraces system. Alonso Pascal, Blondin Laurence, Gladieux Pierre, Mahe Frédéric, Sanguin Hervé, Ferdinand Romain, Filloux Denis, Desmarais Eric, Cerqueira Frédérique, Jin Baihui, Huang Huichuan, He Xiahong, Morel Jean-Benoit, Martin Darren Patrick, Roumagnac Philippe, Vernière Christian. 2020. Environmental Microbiology, 17 p.
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Improvements in virus detection at CIRAD's sugarcane quarantine using both viral metagenomics and PCR-Based approaches. Fernandez Emmanuel, Ferdinand Romain, Filloux Denis, Guinet Isabelle, Julian Charlotte, Rott Philippe, Roumagnac Philippe, Daugrois Jean-Heinrich. 2020. Sugar Tech, 22 : pp. 498-503.
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Molecular detection of sugarcane striate virus and sugarcane white streak virus and their prevalence in the Miami World Collection of sugarcane and related grasses. Boukari Wardatou, Filloux Denis, Daugrois Jean-Heinrich, Fernandez Emmanuel, Mollov Dimitre S., Kaye Claudia, Hincapie Martha, Sanchez Alexander, Wang Jianping, Roumagnac Philippe, Rott Philippe. 2020. Plant Pathology, 69 (6) : pp. 1060-1069.
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Sorghum mastrevirus-associated alphasatellites: New geminialphasatellites associated with an African streak mastrevirus infecting wild Poaceae plants on Reunion Island. Claverie Sohini, Varsani Arvind, Hoareau Murielle, Filloux Denis, Roumagnac Philippe, Martin Darren Patrick, Lefeuvre Pierre, Lett Jean-Michel. 2020. Archives of Virology, 165 (8) : pp. 1925-1928.
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Symptom evolution following the emergence of maize streak virus. Monjane Adérito Luis, Dellicour Simon, Hartnady Penelope, Oyeniran Kehinde A., Owor Betty E., Bezeidenhout Marion, Linderme Daphné, Syed Rizwan Ali, Donaldson Lara, Murray Shane, Rybicki Edward P., Kvarnheden Anders, Yazdkhasti Elhman, Lefeuvre Pierre, Froissart Rémy, Roumagnac Philippe, Shepherd Dionne Natalie, Harkins Gordon William, Suchard Marc, Lemey Philippe, Varsani Arvind, Martin Darren Patrick. 2020. eLife, 9:e51984, 19 p.
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A novel divergent geminivirus identified in asymptomatic new world cactaceae plants. Fontenele Rafaela S, Salywon Andrew M., Majure Lucas C., Cobb Ilaria N., Bhaskara Amulya, Avalos-Calleros Jesús, Argüello-Astorga Gerardo, Schmidlin Kara, Khalifeh Anthony, Smith Kendal, Schreck Joshua, Lund Michael, Köhler Matias, Wojciechowski Martin, Hodgson Wendy C., Puente-Martinez Raul, Van Doorslaer Koenraad, Kumari Safaa G., Vernière Christian, Filloux Denis, Roumagnac Philippe, Lefeuvre Pierre, Ribeiro Simone G., Kraberger Simona, Martin Darren Patrick, Varsani Arvind. 2020. Viruses, 12 (4):398, 26 p.
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Diverse and variable virus communities in wild plant populations revealed by metagenomic tools. Susi Hanna, Filloux Denis, Frilander Mikko J., Roumagnac Philippe, Laine Anna-Liisa. 2019. PeerJ, 7:e6140, 24 p.
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Emergence of southern rice black-streaked dwarf virus in the centuries-old Chinese Yuanyang agrosystem of rice landraces. Alonso Pascal, Gladieux Pierre, Moubset Oumaima, Shih Pei-Jung, Mournet Pierre, Frouin Julien, Blondin Laurence, Ferdinand Romain, Fernandez Emmanuel, Julian Charlotte, Filloux Denis, Adreit Henri, Fournier Elisabeth, Ducasse Aurélie, Grosbois Vladimir, Morel Jean-Benoit, Huang Huichuan, Jin Baihui, He Xiahong, Martin Darren Patrick, Vernière Christian, Roumagnac Philippe. 2019. Viruses, 11 (11):985, 13 p.
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Evolution and ecology of plant viruses. Lefeuvre Pierre, Martin Darren Patrick, Elena Santiago F., Shepherd Dionne Natalie, Roumagnac Philippe, Varsani Arvind. 2019. Nature Reviews. Microbiology, 13 p.
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Exploring the diversity of Poaceae infecting mastreviruses on Reunion Island using a viral metagenomicsbased approach. Claverie Sohini, Ouattara Alassane, Hoareau Murielle, Filloux Denis, Varsani Arvind, Roumagnac Philippe, Martin Darren Patrick, Lett Jean-Michel, Lefeuvre Pierre. 2019. Scientific Reports, 9:12716, 11 p.
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High‑throughput sequencing of complete genomes of ipomoviruses associated with an epidemic of cassava brown streak disease in the Comoros Archipelago. Scussel Sarah, Candresse Thierry, Marais Armelle, Claverie Sohini, Hoareau Murielle, Azali Hamza Abdou, Verdin Eric, Tepfer Mark, Filloux Denis, Fernandez Emmanuel, Roumagnac Philippe, Robene Isabelle, Lefeuvre Pierre, Jourda Cyril, Roux-Cuvelier Michel, Lett Jean-Michel. 2019. Archives of Virology, 164 (8) : pp. 2193-2196.
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Le phytobiome et l'agriculture de demain. Roumagnac Philippe, Sanguin Hervé. 2019. TDC - Textes et Documents pour la Classe (1124) : pp. 34-37.
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Novel circular DNA viruses associated with Apiaceae and Poaceae from South Africa and New Zealand. Richet Cécile, Kraberger Simona, Filloux Denis, Bernardo Pauline, Harkins Gordon William, Martin Darren Patrick, Roumagnac Philippe, Varsani Arvind. 2019. Archives of Virology, 164 (1) : pp. 237-242.
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A new prevalent densovirus discovered in Acari. Insight from metagenomics in viral communities associated with two-spotted mite (Tetranychus urticae) populations. François Sarah, Mutuel Doriane, Duncan Alison B., Rodrigues Leonor R., Danzelle Celya, Lefevre Sophie, Santos Inês, Frayssinet Marie, Fernandez Emmanuel, Filloux Denis, Roumagnac Philippe, Froissart Rémy, Ogliastro Mylène. 2019. Viruses, 11 (3):233, 24 p.
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Alphasatellitidae: A new family with two subfamilies for the classication of geminivirus- and nanovirus-associated alphasatellites. Briddon Rob W., Martin Darren Patrick, Roumagnac Philippe, Navas-Castillo Jesús, Fiallo-Olivé Elvira, Moriones Enrique, Lett Jean-Michel, Zerbini F. Murilo, Varsani Arvind. 2018. Archives of Virology, 163 (9) : pp. 2587-2600.
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Characterization of alfalfa virus F, a new member of the genus Marafivirus. Nemchinov Lev G., François Sarah, Roumagnac Philippe, Ogliastro Mylène, Hammond Rosemarie W., Mollov Dimitre S., Filloux Denis. 2018. PloS One, 13 (9):e0203477, 11 p.
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Comparison of loop-mediated isothermal amplification, polymerase chain reaction, and selective isolation assays for detection of Xanthomonas albilineans from sugarcane. Duarte Dias Vanessa, Fernandez Emmanuel, Cunha Marcos G., Pieretti Isabelle, Hincapie Martha, Roumagnac Philippe, Comstock Jack C., Rott Philippe. 2018. Tropical Plant Pathology, 43 (4) : pp. 351-359.
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First report of alfalfa leaf curl Virus affecting alfalfa (Medicago sativa) in Jordan, Lebanon, Syria, and Tunisia. Kumari Safaa G., Moukahel A.R., Richet Cécile, Galzi Serge, Filloux Denis, Roumagnac Philippe, Asaad Nader, Hijazi Jomana, Mghandef Samia. 2018. Plant Disease, 102 (10), 2052, 2 p.
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First report of alfalfa leaf curl Virus from alfalfa in Iran. Davoodi Zohreh, Heydarnejad Jahangir, Massumi Hossein, Richet Cécile, Galzi Serge, Filloux Denis, Roumagnac Philippe. 2018. Plant Disease, 102 (11) : p. 2385.
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Geometagenomics illuminates the impact of agriculture on the distribution and prevalence of plant viruses at the ecosystem scale. Bernardo Pauline, Charles-Dominique Tristan, Barakat Mohamed, Ortet Philippe, Fernandez Emmanuel, Filloux Denis, Hartnady Penelope, Rebelo Tony A., Cousins Stephen, Mesleard François, Cohez Damien, Yaverkovski Nicole, Varsani Arvind, Harkins Gordon William, Peterschmitt Michel, Malmstrom Carolyn, Martin Darren Patrick, Roumagnac Philippe. 2018. ISME Journal, 12 : pp. 174-184.
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Increase in taxonomic assignment efficiency of viral reads in metagenomic studies. François Sarah, Filloux Denis, Frayssinet Marie, Roumagnac Philippe, Martin Darren Patrick, Ogliastro Mylène, Froissart Rémy. 2018. Virus Research, 244 : pp. 230-234.
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Nanopore-based detection and characterization of yam viruses. Filloux Denis, Fernandez Emmanuel, Loire Etienne, Claude Lisa, Galzi Serge, Candresse Thierry, Winter Stephan, Jeeva M.L., Makeshkumar T., Martin Darren Patrick, Roumagnac Philippe. 2018. Scientific Reports, 8:17879, 11 p.
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Nanovirus‐alphasatellite complex identi ed in Vicia cracca in the Rhône delta region of France. Gallet Romain, Kraberger Simona, Filloux Denis, Galzi Serge, Fontes Hugo, Martin Darren Patrick, Varsani Arvind, Roumagnac Philippe. 2018. Archives of Virology, 163 (3) : pp. 695-700.
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Notes on recombination and reassortment in multipartite/segmented viruses. Varsani Arvind, Lefeuvre Pierre, Roumagnac Philippe, Martin Darren Patrick. 2018. Current Opinion in Virology, 33 : pp. 156-166.
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Viral metagenomic-based screening of sugarcane from florida reveals occurrence of six sugarcane-infecting viruses and high prevalence of Sugarcane yellow leaf virus. Filloux Denis, Fernandez Emmanuel, Comstock Jack C., Mollov Dimitre S., Roumagnac Philippe, Rott Philippe. 2018. Plant Disease, 102 (11) : pp. 2317-2323.
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The westward journey of alfalfa leaf curl virus. Davoodi Zohreh, Bejerman Nicolás, Richet Cécile, Filloux Denis, Kumari Safaa G., Chatzivassiliou Elisavet K., Galzi Serge, Julian Charlotte, Samarfard Samira, Trucco Verónica, Giolitti Fabián, Fiallo-Olivé Elvira, Navas-Castillo Jesús, Asaad Nader, Rahman Moukahel Abdul, Hijazi Jomana, Mghandef Samia, Heydarnejad Jahangir, Massumi Hossein, Varsani Arvind, Dietzgen Ralf G., Harkins Gordon William, Martin Darren Patrick, Roumagnac Philippe. 2018. Viruses, 10 (10):542, 16 p.
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Capulavirus and Grablovirus: Two new genera in the family Geminiviridae. Varsani Arvind, Roumagnac Philippe, Fuchs Marc, Navas-Castillo Jesús, Moriones Enrique, Idris Ali, Briddon Rob W., Rivera-Bustamante Rafael, Zerbini F. Murilo, Martin Darren Patrick. 2017. Archives of Virology, 162 (6) : pp. 1819-1831.
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Complete genome sequences of cowpea polerovirus 1 and cowpea polerovirus 2 infecting cowpea plants in Burkina Faso. Palanga Essowé, Martin Darren Patrick, Galzi Serge, Zabré Jean, Bouda Zakaria, Bouma Neya James, Sawadogo Mahamadou, Traoré Oumar, Peterschmitt Michel, Roumagnac Philippe, Filloux Denis. 2017. Archives of Virology, 162 (7) : pp. 2149-2152.
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Exploiting genetic information to trace plant virus dispersal in landscapes. Picard Coralie, Dallot Sylvie, Brunker Kirstyn, Berthier Karine, Roumagnac Philippe, Soubeyrand Samuel, Jacquot Emmanuel, Thébaud Gaël. 2017. Annual Review of Phytopathology, 55 : pp. 139-160.
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First report of maize yellow mosaic virus infecting maize in Burkina Faso. Palanga Essowé, Longué R.D.S., Koala M., Néya J.B., Traoré Oumar, Martin Darren Patrick, Peterschmitt Michel, Filloux Denis, Roumagnac Philippe. 2017. New Disease Reports, 35 : p. 26.
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Genome sequences of a capulavirus infecting Plantago lanceolata in the Aland archipelago of Finland. Susi Hanna, Laine Anna-Liisa, Filloux Denis, Kraberger Simona, Farkas Kata, Bernardo Pauline, Frilander Mikko J., Martin Darren Patrick, Varsani Arvind, Roumagnac Philippe. 2017. Archives of Virology, 162 (7) : pp. 2041-2045.
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ICTV virus taxonomy profile: Geminiviridae. Zerbini F. Murilo, Briddon Rob W., Idris Ali, Martin Darren Patrick, Moriones Enrique, Navas-Castillo Jesús, Rivera-Bustamante Rafael, Roumagnac Philippe, Varsani Arvind. 2017. Journal of General Virology, 98 : pp. 131-133.
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Occurrence of a novel mastrevirus in sugarcane germplasm collections in Florida, Guadeloupe and Réunion. Boukari Wardatou, Alcala-Briseño Ricardo I., Kraberger Simona, Fernandez Emmanuel, Filloux Denis, Daugrois Jean-Heinrich, Comstock Jack C., Lett Jean-Michel, Martin Darren Patrick, Varsani Arvind, Roumagnac Philippe, Polston Jane E., Rott Philippe. 2017. Virology Journal, 14:146, 8 p.
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Two novel Alphaflexiviridae members revealed by deep sequencing of the Vanilla (Orchidaceae) virome. Grisoni Michel, Marais Armelle, Filloux Denis, Saison Anne, Faure Chantal, Julian Charlotte, Theil Sébastien, Contreras Sandy, Teycheney Pierre-Yves, Roumagnac Philippe, Candresse Thierry. 2017. Archives of Virology, 162 (12) : pp. 3855-3861.
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Discovery of parvovirus-related sequences in an unexpected broad range of animals. François Sarah, Filloux Denis, Roumagnac Philippe, Bigot D., Gayral Philippe, Martin Darren Patrick, Froissart Rémi, Ogliastro Mylène. 2016. Scientific Reports, 6 (30880), 13 p.
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Diverse circular replication-associated protein encoding viruses circulating in invertebrates within a lake ecosystem. Dayaram Anisha, Galatowitsch Mark L., Argüello-Astorga Gerardo, van Bysterveldt Katherine, Kraberger Simona, Stainton Daisy, Harding Jon S., Roumagnac Philippe, Martin Darren Patrick, Lefeuvre Pierre, Varsani Arvind. 2016. Infection, Genetics and Evolution, 39 : pp. 304-316.
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Metagenomic-based screening and molecular characterization of cowpea-infecting viruses in Burkina Faso. Palanga Essowé, Filloux Denis, Martin Darren Patrick, Fernandez Emmanuel, Gargani Daniel, Ferdinand Romain, Zabré Jean, Bouda Zakaria, Neya Bouma, Sawadogo Mahamadou, Traoré Oumar, Peterschmitt Michel, Roumagnac Philippe. 2016. PloS One, 11 (10):e0165188, 21 p.
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Molecular characterization and prevalence of two capulaviruses: Alfalfa leaf curl virus from France and Euphorbia caput-medusae latent virus from South Africa. Bernardo Pauline, Muhire Brejnev, François Sarah, Deshoux Maëlle, Hartnady Penelope, Farkas Kata, Kraberger Simona, Filloux Denis, Fernandez Emmanuel, Galzi Serge, Ferdinand Romain, Granier Martine, Marais Armelle, Monge Blasco Pablo, Candresse Thierry, Escriu Fernando, Varsani Arvind, Harkins Gordon William, Martin Darren Patrick, Roumagnac Philippe. 2016. Virology, 493 : pp. 142-153.
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Prevalence of Sugarcane yellow leaf virus in sugarcane producing regions in Kenya revealed by reverse transcription loop-mediated isothermal amplification method. Amata Ruth Lodenyi, Fernandez Emmanuel, Filloux Denis, Martin Darren Patrick, Rott Philippe, Roumagnac Philippe. 2016. Plant Disease, 100 (2) : pp. 260-268.
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Alfalfa leaf curl virus: an aphid-transmitted geminivirus. Roumagnac Philippe, Granier Martine, Bernardo Pauline, Deshoux Maëlle, Ferdinand Romain, Galzi Serge, Fernandez Emmanuel, Julian Charlotte, Abt Isabelle, Filloux Denis, Mesleard François, Varsani Arvind, Blanc Stéphane, Martin Darren Patrick, Peterschmitt Michel. 2015. Journal of Virology, 89 (18) : pp. 9683-9688.
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Identification of novel Bromus- and Trifolium-associated circular DNA viruses. Kraberger Simona, Farkas Kata, Bernardo Pauline, Booker Cameron, Argüello-Astorga Gerardo, Mesleard François, Martin Darren Patrick, Roumagnac Philippe, Varsani Arvind. 2015. Archives of Virology, 160 (5) : pp. 1303-1311.
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Metagenomic analysis of the sugarcane virome in Florida reveals prevalent and potential novel viruses. Fernandez Emmanuel, Filloux Denis, Comstock Jack C., Roumagnac Philippe, Rott Philippe. 2015. Phytopathology, 105 (11S), Résumé : S4.43. 2015 APS Annual Meeting, Pasadena, États-Unis, 1 August 2015/5 August 2015.
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Plant virus metagenomics: Advances in virus discovery. Roossinck Marilyn J., Martin Darren Patrick, Roumagnac Philippe. 2015. Phytopathology, 105 (6) : pp. 716-727.
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Visacane: An innovative quarantine tool for the exchange of pest and disease-free sugarcane germplasm. Guinet-Brial Isabelle, Girard Jean-Claude, Roumagnac Philippe, Daugrois Jean-Heinrich, Fernandez Emmanuel, Rott Philippe. 2015. International Sugar Journal : pp. 890-896.
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The genomes of many yam species contain transcriptionally active endogenous geminiviral sequences that may be functionally expressed. Filloux Denis, Murrell Sasha, Koohapitagtam M., Golden Michael, Julian Charlotte, Galzi Serge, Uzest Marilyne, Rodier-Goud Marguerite, D'Hont Angélique, Vernerey Marie-Stéphanie, Wilkin P., Peterschmitt Michel, Winter Stephan, Murrell Ben, Martin Darren Patrick, Roumagnac Philippe. 2015. Virus Evolution, 1 (1), 17 p.
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Appearances can be deceptive: Revealing a hidden viral infection with deep sequencing in a plant quarantine Context. Candresse Thierry, Filloux Denis, Muhire Brejnev, Julian Charlotte, Galzi Serge, Fort Guillaume, Bernardo Pauline, Daugrois Jean-Heinrich, Fernandez Emmanuel, Martin Darren Patrick, Varsani Arvind, Roumagnac Philippe. 2014. PloS One, 9 (7):e102945, 13 p.
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First report of Acidovorax avenae subsp. avenae causing sugarcane red stripe in Gabon. Girard Jean-Claude, Noëll Julie, Larbre François, Roumagnac Philippe, Rott Philippe. 2014. Plant Disease, 98 (5) : p. 684.
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Molecular characterization of yam virus X, a new potexvirus infecting yams (Dioscorea spp) and evidence for the existence of at least three distinct potexviruses infecting yams. Acina Manbole Isabelle Nina, Bonheur Lydiane, Svanella-Dumas Laurence, Filloux Denis, Gomez Rose-Marie, Faure Chantal, Lange David, Anzala Fabiola, Pavis Claudie, Marais Armelle, Roumagnac Philippe, Candresse Thierry, Teycheney Pierre-Yves. 2014. Archives of Virology, 159 (12) : pp. 3421-3426.
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Shifting the paradigm from pathogens to pathobiome: new concepts in the light of meta-omics. Vayssier-Taussat Muriel, Albina Emmanuel, Citti Christine, Cosson Jean François, Jacques Marie Agnès, Lebrun Marc-Henri, Le Loir Yves, Ogliastro Mylène, Petit Marie-Agnès, Roumagnac Philippe, Candresse Thierry. 2014. Frontiers in Cellular and Infection Microbiology, 4 (29), 7 p.
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The genome of African yam (Dioscorea cayenensis-rotundata complex) hosts endogenous sequences from four distinct badnavirus species. Umber Marie, Filloux Denis, Muller Emmanuelle, Laboureau Nathalie, Galzi Serge, Roumagnac Philippe, Iskra Caruana Marie-Line, Pavis Claudie, Teycheney Pierre-Yves, Seal Susan. 2014. Molecular Plant Pathology, 15 (8) : pp. 790-801.
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A novel itera-like densovirus isolated by viral metagenomics from the sea barley Hordeum marinum. François Sarah, Bernardo Pauline, Filloux Denis, Roumagnac Philippe, Yaverkovski Nicole, Froissart Rémi, Ogliastro Mylène. 2014. Genome Announcements, 2 (6):e01196, 2 p.
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First report of sugarcane leaf scald in Gabon caused by a highly virulent and aggressive strain of Xanthomonas albilineans. Mensi Imène, Girard Jean-Claude, Pieretti Isabelle, Larbre François, Roumagnac Philippe, Royer Monique, Rott Philippe. 2013. Plant Disease, 97 (7) : p. 988.
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Identification and characterisation of a highly divergent geminivirus: Evolutionary and taxonomic implications. Bernardo Pauline, Golden Michael, Akram Mohammad, Naimuddin, Nadarajan Nagaswamy, Fernandez Emmanuel, Granier Martine, Rebelo Anthony, Peterschmitt Michel, Martin Darren Patrick, Roumagnac Philippe. 2013. Virus Research, 177 (1) : pp. 35-45.
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Métagénomique virale et pathologie Une histoire récente. Bernardo Pauline, Albina Emmanuel, Eloit Marc, Roumagnac Philippe. 2013. MS - Médecine Sciences, 29 (5) : pp. 501-508.
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Genetic diversity of sugarcane yellow leaf virus in a sugarcane selection plot in Guadeloupe (FWI). Girard Jean-Claude, Fernandez Emmanuel, Daugrois Jean-Heinrich, Roques Danièle, Roumagnac Philippe, Rott Philippe. 2012. International Sugar Journal, 114 (1358) : pp. 104-108. ISSCT Congress. 27, Veracruz, Mexique, 7 March 2010/11 March 2010.
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Reversible oxygen-tolerant hydrogenase carried by free-living N2-fixing bacteria isolated from the rhizospheres of rice, maize, and wheat. Roumagnac Philippe, Richaud Pierre, Barakat Mohamed, Ortet Philippe, Roncato Marie-Anne, Heulin Thierry, Peltier Gilles, Achouak Wafa, Cournac Laurent. 2012. MicrobiologyOpen, 1 (4) : pp. 349-361.
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Phylogeography and molecular epidemiology of yersinia pestis in Madagascar. Vogler Amy. J., Chan Fabien, Wagner David.M., Roumagnac Philippe, Lee Judy, Nera Roxanne, Eppinger Mark, Ravel Jacques, Rahalison Lila, Rasoamanana Bruno W., Beckstrom-Sternberg Stephen M., Achtman Mark, Chanteau Suzanne, Keim Paul. 2011. PLoS Neglected Tropical Diseases, 5 (9):e1319, 11 p.
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Recombination in Eukaryotic single stranded DNA viruses. Martin Darren Patrick, Biagini Philippe, Lefeuvre Pierre, Golden Michael, Roumagnac Philippe, Varsani Arvind. 2011. Viruses, 3 (9) : pp. 1699-1738.
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Salmonella enterica serotype typhi with nonclassical quinolone resistance phenotype. Accou-Demartin Marie, Gaborieau Valérie, Song Yajun, Roumagnac Philippe, Marchou Bruno, Achtman Mark, Weill François-Xavier. 2011. Emerging Infectious Diseases, 17 (6) : pp. 1091-1094.
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Evolution and population structure of Salmonella enterica serovar Newport. Sangal Vartul, Harbottle Heather, Mazzoni Camila J., Helmuth Reiner, Guerra Beatriz, Didelot Xavier, Paglietti Bianca, Rabsch Wolfgang, Brisse Sylvain, Weill François-Xavier, Roumagnac Philippe, Achtman Mark. 2010. Journal of Bacteriology, 192 (24) : pp. 6465-6476.
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Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity. Morelli Giovanna, Song Yajun, Mazzoni Camila J., Eppinger Mark, Roumagnac Philippe, Wagner David.M., Feldkamp Mirjam, Kusecek Barica, Vogler Amy. J., Li Yanjun, Cui Yujun, Thomson Nicholas R, Jombart Thibaut, Leblois Raphaël, Lichtner Peter, Rahalison Lila, Petersen Jeannine M, Balloux François, Keim Paul, Wirth Thierry, Ravel Jacques, Yang Ruifu, Carniel Elisabeth, Achtman Mark. 2010. Nature Genetics, 42 (12) : pp. 1140-1143.
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A multiplex single nucleotide polymorphism typing assay for detecting mutations that result in decreased fluoroquinolone susceptibility in Salmonella enterica serovars Typhi and Paratyphi A. Song Yajun, Roumagnac Philippe, Weill François-Xavier, Wain John, Dolecek Christiane, Mazzoni Camila J., Holt Kathryn E., Achtman Mark. 2010. Journal of Antimicrobial Chemotherapy, 65 (8) : pp. 1631-1641.
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Frequent emergence and limited geographic dispersal of methicillin-resistant Staphylococcus aureus. Nübel Ulrich, Roumagnac Philippe, Feldkamp Mirjam, Song Jae-Hoon, Ko kwan soo, Huang Yhu-Chering, Coombs Geoffrey, Ip Margaret, Westh Henrik, Skov Robert, Struelens Marc J., Goering Richard V., Strommenger Birgit, Weller Annette, Witte Wolfgang, Achtman Mark. 2008. Proceedings of the National Academy of Sciences of the United States of America, 105 (37) : pp. 14130-14135.
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High-Throughput Genotyping of Salmonella enteric Serovar Typhi allowing geographical assignment of Haplotypes and Pathotypes within an urban district of Jakarta, Indonesia. Baker Stephen, Holt Kathryn E., Van de Vosse Esther, Roumagnac Philippe, Whitehead Sally, King Emma, Ewels Philip, Keniry Andrew, Weill François-Xavier, Lightfoot Diane, Van Dissel Jaap T., Sanderson Kenneth E., Farrar Jeremy J., Achtman Mark, Deloukas Panagiotis, Dougan Gordon. 2008. Journal of Clinical Microbiology, 46 (5) : pp. 1741-1746.
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High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi. Holt Kathryn E., Parkhill Julian, Mazzoni Camila J., Roumagnac Philippe, Weill François-Xavier, Goodhead Ian, Rance Richard, Baker Stephen, Maskell Duncan J., Wain John, Dolecek Christiane, Achtman Mark, Dougan Gordon. 2008. Nature Genetics, 40 (8) : pp. 987-993.
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Polyphasic characterization of Xanthomonas axonopodis pv. allii associated with outbreaks of bacterial blight on three allium species in the Mascarene Archipelago. Picard Yann, Roumagnac Philippe, Legrand Delphine, Humeau Laurence, Robène-Soustrade Isabelle, Chiroleu Frédéric, Gagnevin Lionel, Pruvost Olivier. 2008. Phytopathology, 98 (8) : pp. 919-925.
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Quantitative and molecular epidemiology of bacterial blight of onion in seed production fields. Humeau Laurence, Roumagnac Philippe, Picard Yann, Soustrade Isabelle, Chiroleu Frédéric, Gagnevin Lionel, Pruvost Olivier. 2006. Phytopathology, 92 (12) : pp. 1345-1354.
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New media for the semiselective isolation and enumeration of Xanthomonas campestris pv. mangiferaeindicae, the causal agent of mango bacterial black spot. Pruvost Olivier, Roumagnac Philippe, Gaube C., Chiroleu Frédéric, Gagnevin Lionel. 2005. Journal of Applied Microbiology, 99 (4) : pp. 803-815.
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Polyphasic characterization of xanthomonads isolated from onion, garlic and Welsh onion (Allium spp.) and their relatedness to different Xanthomonas species. Roumagnac Philippe, Gagnevin Lionel, Gardan Louis, Sutra L., Manceau Charles, Dickstein E.R., Jones Jeffrey B., Rott Philippe, Pruvost Olivier. 2004. International Journal of Systematic and Evolutionary Microbiology, 54 : pp. 15-24.

Spatial and temporal analyses of bacterial blight of onion caused by Xanthomonas axonopodis pv. allii. Roumagnac Philippe, Pruvost Olivier, Chiroleu Frédéric, Hughes Gareth. 2004. Phytopathology, 94 (2) : pp. 138-146.
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Une maladie émergente de l'oignon à la Réunion : le dépérissement bactérien causé par Xanthomonas axonopodis pv. allii. Humeau Laurence, Roumagnac Philippe, Soustrade Isabelle, Gagnevin Lionel, Degas Julien, Jeuffrault Eric, Pruvost Olivier. 2004. Phytoma-La Défense des Végétaux (573) : pp. 28-30.

Protection des plantes. Epidémiologie des maladies virales et bactériennes. Luisetti Jacques, Poussier Stéphane, Fock Isabelle, Roumagnac Philippe, Gagnevin Lionel, Notaise Julien, Soustrade Isabelle, Pruvost Olivier, Rassaby Laurence, Leclerc F., Reynaud Bernard, Peterschmitt Michel. 2000. Magazine CIRAD Réunion (17) : pp. 50-55.

Protection des plantes. Reynaud Bernard, Luisetti Jacques, Poussier Stéphane, Roumagnac Philippe, Pruvost Olivier, Gagnevin Lionel, Girard Jean-Claude, Rassaby Laurence, Leclercq Le Quillec Françoise, Goebel François-Régis, Vayssières Jean-François, Quilici Serge, Brévault Thierry, Hurtrel Béatrice. 1999. Magazine CIRAD Réunion (14) : pp. 47-54.

Protection des plantes. Biologie des ennemis des cultures et protection des plantes. Reynaud Bernard, Girard Jean-Claude, Goebel François-Régis, Grisoni Michel, Luisetti Jacques, Pruvost Olivier, Quilici Serge, Roumagnac Philippe, Vayssières Jean-François. 1998. Magazine CIRAD Réunion (11) : pp. 44-50.

Protection des plantes. Inventaires des ennemis des cultures et protection des plantes. Gagnevin Lionel, Girard Jean-Claude, Goebel François-Régis, Grisoni Michel, Luisetti Jacques, Pruvost Olivier, Quilici Serge, Roumagnac Philippe, Vayssières Jean-François. 1997. Magazine CIRAD Réunion (7) : pp. 48-54.

Book chapter

From spatial metagenomics to molecular characterization of plant viruses: A geminivirus case study. Claverie Sohini, Bernardo Pauline, Kraberger Simona, Hartnady Penelope, Lefeuvre Pierre, Lett Jean-Michel, Galzi Serge, Filloux Denis, Harkins Gordon William, Varsani Arvind, Martin Darren Patrick, Roumagnac Philippe. 2018. In : Environmental virology and virus ecology. Malmstrom Carolyn M. (ed.). Burlington : Academic Press, pp. 55-83. (Advances in Virus Research, 101) ISBN 978-0-12-814415-2
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Viral metagenomics and sugarcane pathogens. Roumagnac Philippe, Mollov Dimitre S., Daugrois Jean-Heinrich, Filloux Denis. 2018. In : Achieving sustainable cultivation of sugarcane. Volume 2: Breeding, pests and diseases. Rott Philippe (ed.). Cambridge : Burleigh Dodds Science Publishing, pp. 183-200. (Burleigh Dodds Series in Agricultural Science) ISBN 978-1-78676-148-4
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Viral metagenomics approaches for high-resolution screening of multiplexed arthropod and plant viral communities. François Sarah, Filloux Denis, Fernandez Emmanuel, Ogliastro Mylène, Roumagnac Philippe. 2018. In : Viral metagenomics: methods and protocols. Pantaleo Vitantonio (ed.), Chiumenti Michela (ed.). New York : Humana Press, pp. 77-95. (Methods in Molecular Biology, 1746, 1746) ISBN 978-1-4939-7682-9
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Metagenomics approaches based on virion-associated nucleic acids (VANA): an innovative tool for assessing without A priori viral diversity of plants. Filloux Denis, Dallot Sylvie, Delaunay Agnès, Galzi Serge, Jacquot Emmanuel, Roumagnac Philippe. 2015. In : Plant pathology: techniques and protocols. Lacomme Christophe (ed.). New York : Springer [Etats-Unis], pp. 249-257. (Methods in Molecular Biology, 1302) ISBN 978-1-4939-2619-0
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SNaPshot and CE-SSCP: two simple and cost-effective methods to reveal genetic variability within a virus species. Delaunay Agnès, Dallot Sylvie, Filloux Denis, Dupuy Virginie, Roumagnac Philippe, Jacquot Emmanuel. 2015. In : Plant pathology: techniques and protocols. Lacomme Christophe (ed.). New York : Springer [Etats-Unis], pp. 187-206. (Methods in Molecular Biology, 1302) ISBN 978-1-4939-2619-0
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Le dépérissement bactérien des Alliacées : émergence d'une phytobactériose. Roumagnac Philippe, Robène-Soustrade Isabelle, Humeau Laurence, Gagnevin Lionel, Chiroleu Frédéric, Jeuffrault Eric, Pruvost Olivier. 2010. In : Les maladies émergentes : épidémiologie chez le végétal, l'animal et l'homme. Barnouin Jacques (ed.), Sache Ivan (ed.). Versailles : Ed. Quae, pp. 211-220. (Synthèses) ISBN 978-2-7592-0510-3

Insights into structure and evolution of bacterial species that are revealed by molecular methods. Roumagnac Philippe, Gagnevin Lionel, Pruvost Olivier, Achtman Marquer. 2007. In : Encyclopedia of infectious diseases : modern methodologies. Tibayrenc Michel (ed.). Hoboken : Wiley-Blackwell, pp. 473-493. ISBN 978-0-471-65732-3
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Guest paper

Geometagenomics: A second metagenomics generation to better understand plant virus ecology and evolution. Filloux Denis, Martin Darren Patrick, Roumagnac Philippe. 2018. . Liège : s.n., 1 p. Final Meeting of COST-DIVAS Action: HTS Technologies for the study and diagnostic of plant viruses, Liège, Belgique, 26 November 2018/30 November 2018.
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Paper with proceedings

Improvements in virus detection at CIRAD's sugarcane quarantine using both viral metagenomics and PCR-based approaches. Fernandez Emmanuel, Ferdinand Romain, Filloux Denis, Guinet Isabelle, Julian Charlotte, Rott Philippe, Roumagnac Philippe, Daugrois Jean-Heinrich. 2019. In : Proceedings of the XXX International Society of Sugar Cane Technologists Congress. ISSCT. Tucuman : ISSCT, pp. 345-351. ISBN 978-616-92761-0-4 ISSCT Congress. 30, Tucuman, Argentine, 31 August 2019/5 September 2019.
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Genomic characterization of sugarcane mild mosaic virus. Filloux Denis, Fernandez Emmanuel, Mollov Dimitre S., Julian Charlotte, Rott Philippe, Roumagnac Philippe, Daugrois Jean-Heinrich. 2018. In : Book of Abstracts XII ISSCT Pathology Workshop. Coimbatore : ISSCT, pp. 26-27. ISSCT Pathology Workshop. 12, Coimbatore, Inde, 3 September 2018/7 September 2018.
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Identification of two SCYLV recombinants between different genotypes in the germplasm collection of Guadeloupe. Fernandez Emmanuel, Filloux Denis, Julian Charlotte, Roumagnac Philippe, Daugrois Jean-Heinrich. 2018. In : Book of Abstracts XII ISSCT Pathology Workshop. Coimbatore : ISSCT, p. 28. ISSCT Pathology Workshop. 12, Coimbatore, Inde, 3 September 2018/7 September 2018.
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" Night at the museum ": filling the gaps in the history of emergence of crop pathogenic bacteria using herbarium material. Rieux Adrien, Roumagnac Philippe, Szurek Boris, Gaudeul Myriam, Becker Nathalie, Gagnevin Lionel. 2018. In : 13èmes Rencontres Plantes-Bactéries - Book of Abstracts. SFP, INRA, CNRS. Paris : SFP, Résumé, p. 18. Rencontres Plantes-Bactéries. 13, Aussois, France, 29 January 2018/2 February 2018.
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Visacane sugarcane quarantine and its partner networks. Fernandez Emmanuel, Thong-Chane Audrey, Barau Laurent, Filloux Denis, Guinet-Brial Isabelle, Mollow Dimitre, Julian Charlotte, Ferdinand Romain, Roumagnac Philippe, Daugrois Jean-Heinrich. 2018. In : Sugar Crops Improvement, Biotechnology, Bio-refinery and Diversification: Impacts on Bio-based Economy. Thailand Society of Sugar Technologists. Udon Thani : Thailand Society of Sugar Technologists, 4 p. IAPSIT International Sugar Conference. 6, Udon Thani, Thaïlande, 6 March 2018/9 March 2018.
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Visacane sugarcane quarantine and its partner networks. Fernandez Emmanuel, Thong-Chane Audrey, Barau Laurent, Filloux Denis, Guinet-Brial Isabelle, Mollow Dimitre, Julian Charlotte, Ferdinand Romain, Roumagnac Philippe, Daugrois Jean-Heinrich. 2018. In : Sugar crops improvement, biotechnology, Bio-refinery and diversification: Impacts on bio-based economy: 6th IAPSIT International Sugar Conference. Souvenir de presentation IS-2018. Rao G.P. (ed;), Solomon S. (ed.), Li Yang-Rui (ed.), Swapna M. (ed.), Sinh Priyanka (ed.), Tiwari Ajay (ed.), Vanichsriratana Wirat (ed.), Uraichuen Sopon (ed.). TSSCT, Kasetsart University, IAPSIT. Udon Thani : TSSCT-IAPSIT, Résumé, p. 52. IAPSIT International Sugar Conference. 6, Udon Thani, Thaïlande, 6 March 2018/9 March 2018.
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Metagenomics-based exploration of the genetic diversity of SCYLV in the sugarcane collection of Guadeloupe. Fernandez Emmanuel, Filloux Denis, Julian Charlotte, Lubin Adjanoh Nadia, Teycheney Pierre-Yves, Candresse Thierry, Roumagnac Philippe, Daugrois Jean-Heinrich. 2016. In : Building bridges between disciplines for sustainable management of plant virus diseases. INRA, Université d'Avignon. Avignon : INRA, Résumé, p. 83. International Plant Virus Epidemiology Symposium. 13, Avignon, France, 6 June 2016/10 June 2016.
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Detection of Xanthomonas albilineans in sugarcane stalks using lamp PCR and selective isolation assays. Duarte Dias Vanessa, Fernandez Emmanuel, Da Cunha M.G., Roumagnac Philippe, Comstock Jack C., Rott Philippe. 2015. In : Book of abstracts. XI Pathology and IX Entomology ISSCT joint Workshop. FIADE. Guayaquil : FIADE, Résumé, p. 26. ISSCT Pathology Workshop. 11, Guayaquil, Équateur, 14 September 2015/18 September 2015.
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Impact of NGS-based diagnosis on sugarcane quarantine processes. Daugrois Jean-Heinrich, Darroussat Marie-Josée, Fenouillet Catherine, Ferdinand Romain, Fernandez Emmanuel, Filloux Denis, Galzi Serge, Guinet-Brial Isabelle, Julian Charlotte, Lubin Nadia, Roques Danièle, Roumagnac Philippe. 2015. In : Book of abstracts. XI Pathology and IX Entomology ISSCT joint Workshop. FIADE. Guayaquil : FIADE, Résumé, p. 17. ISSCT Pathology Workshop. 11, Guayaquil, Équateur, 14 September 2015/18 September 2015.
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Geo-metagenomics: deciphering the spatial biodiversity of plant viruses associated with the unique fynbos ecosystem of Southern Africa and its neighbouring agro-ecosystem. Bernardo Pauline, Ortet Philippe, Barakat Mohamed, Rebelo Anthony, Cousins Stephen, Fernandez Emmanuel, Peterschmitt Michel, Filloux Denis, Varsani Arvind, Martin Darren Patrick, Roumagnac Philippe. 2013. In : EMBO Workshop Green Viruses, from Gene to Landscape, 7-11 September 2013, Hyères-les-Palmiers, France : programme and abstracts book. CNRS, UMR BGPI. s.l. : s.n., Résumé, p. 43. EMBO Workshop Green Viruses, from Gene to Landscape, Hyères-les-Palmier, France, 7 September 2013/11 September 2013.
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The Guadeloupe Biological Resources Centre and its role in viral diagnostic and sanitation. Pavis Claudie, Gamiette Franciane, Umber Marie, Petro Dalila, Roques Danièle, Boisseau Marc, Nuissier Franciane, Candresse Thierry, Roumagnac Philippe, Teycheney Pierre-Yves. 2013. In : First Global Conference on Yam "to harness research innocations to unleash the potential of yam". Program and book of abstracts. IITA. Ibadan : IITA, Résumé, p. 76. ISBN 978-978-8444-27-5 First Global Conference on Yam, Accra, Ghana, 3 October 2013/6 October 2013.
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Visacane: an innovative quarantine tool for the exchange of pest and disease-free sugarcane germplasm. Guinet-Brial Isabelle, Girard Jean-Claude, Roumagnac Philippe, Daugrois Jean-Heinrich, Fernandez Emmanuel, Rott Philippe. 2013. In : Proceedings of the XXVIII ISSCT (International Society of Sugar Cane Technologists) Congress, São Paulo, Brazil 2013 june 24-27. Brazilian Society of Sugar and Ethanol Technologists (STAB) ; XXVIIIth ISSCT Organising Committee. s.l. : D.M. HOGARTH, Résumé, p. 190. ISBN 978-0-949678-27-0 ISSCT Congress. 28, São Paulo, Brésil, 24 June 2013/27 June 2013.
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Identification d'une bactérie du genre Xanthomonas pathogène de l'oignon à l'île de la Réunion. Roumagnac Philippe, Jeuffrault Eric, Pruvost Olivier, Cheron Jean-Jacques, Girard Jean-Claude. 1997. In : Cinquième conférence internationale sur les maladies des plantes = Fifth International conference on plant diseases. ANPP. Paris : ANPP, pp. 673-680. (ANPP annales) ISBN 2-905550-74-0 Conférence internationale sur les maladies des plantes. 5, Tours, France, 3 December 1997/5 December 1997.

Poster

Another night at the museum: searching for traces of plant viruses using the virion-associated nucleic acid metagenomics approach. [P.21]. Julian Charlotte, Filloux Denis, Rieux Adrien, Lefeuvre Pierre, Lett Jean-Michel, Becker Nathalie, Gagnevin Lionel, Trinder-Smith Terry H., Hartnady Penelope, Martin Darren Patrick, Roumagnac Philippe. 2019. In : Livre des résumés des 17 ème Rencontres de virologie végétale. INRA, CIRAD, CNRS, SFP, SFV. Aussois : INRA, Résumé, p. 80. Rencontres de Virologie Végétale (RVV 2019). 17, Aussois, France, 27 January 2019/31 January 2019.
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Assessment of the viral disease threats on sorghum and phenotyping support on diseases. [P.29]. Bangratz Martine, Tibiri Ezechiel Bionimian, Julian Charlotte, Filloux Denis, Pinel-Galzi Agnès, Brugidou Christophe, Roumagnac Philippe, Tiendrebeogo Fidèle, Hébrard Eugénie. 2019. In : Livre des résumés des 17 ème Rencontres de virologie végétale. INRA, CIRAD, CNRS, SFP, SFV. Aussois : INRA, Résumé, p. 88. Rencontres de Virologie Végétale (RVV 2019). 17, Aussois, France, 27 January 2019/31 January 2019.
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Diversity and composition of arthropod pests' viral communities, and insights about pest viruses distribution in arthropod communities. [P.08]. François Sarah, Kulikowski Maximilien, Frayssinet Marie, Filloux Denis, Fernandez Emmanuel, Roumagnac Philippe, Froissart Rémi, Ogliastro Mylène. 2019. In : Livre des résumés des 17 ème Rencontres de virologie végétale. INRA, CIRAD, CNRS, SFP, SFV. Aussois : INRA, Résumé, p. 67. Rencontres de Virologie Végétale (RVV 2019). 17, Aussois, France, 27 January 2019/31 January 2019.
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Global geographical distribution of capulaviruses. [P.42]. Galzi Serge, Filloux Denis, Richet Cécile, Julian Charlotte, Ferdinand Romain, Davoodi Zohreh, Bejerman Nicolás, Kumari Safaa G., Chatzivassiliou Elisavet K., Fiallo-Olivé Elvira, Navas-Castillo Jesús, Susi Hanna, Laine Anna-Liisa, Varsani Arvind, Harkins Gordon William, Martin Darren Patrick, Roumagnac Philippe. 2019. In : Livre des résumés des 17 ème Rencontres de virologie végétale. INRA, CIRAD, CNRS, SFP, SFV. Aussois : INRA, Résumé, p. 101. Rencontres de Virologie Végétale (RVV 2019). 17, Aussois, France, 27 January 2019/31 January 2019.
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Nanopore-based detection and characterization of plant viruses. [P.14]. Filloux Denis, Fernandez Emmanuel, Roumagnac Philippe. 2019. In : Livre des résumés des 17 ème Rencontres de virologie végétale. INRA, CIRAD, CNRS, SFP, SFV. Aussois : INRA, Résumé, p. 73. Rencontres de Virologie Végétale (RVV 2019). 17, Aussois, France, 27 January 2019/31 January 2019.
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Reverse transcriptase template switching: a method for without a priori amplification of full-length genome of positive-sense single-strand polyadenylated RNA plant viruses. [P.51]. Claude Lisa, Fernandez Emmanuel, Roumagnac Philippe, Filloux Denis. 2019. In : Livre des résumés des 17 ème Rencontres de virologie végétale. INRA, CIRAD, CNRS, SFP, SFV. Aussois : INRA, Résumé, p. 110. Rencontres de Virologie Végétale (RVV 2019). 17, Aussois, France, 27 January 2019/31 January 2019.
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Characterization of the rice microbiota: development and contribution of the 'culturomics' approach. P3. Blondin Laurence, Alonso Pascal, Pierreti Isabelle, Godreuil Sylvain, Roumagnac Philippe, Vernière Christian. 2018. In : Book of abstract Pathobiome 2018. INRA. Ajaccio : INRA, Résumé, pp. 33-34. Pathobiome, Ajaccio, France, 18 March 2018/20 March 2018.
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Development of MetaXplor: a viral metagenomics database. P29. Filloux Denis, Petel Adrien, Sempere Guilhem, Claverie Sohini, Lefeuvre Pierre, Mahe Frédéric, Roumagnac Philippe. 2018. In : Book of abstract Pathobiome 2018. INRA. Ajaccio : INRA, Résumé, p. 50. Pathobiome, Ajaccio, France, 18 March 2018/20 March 2018.
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Development of a multigenic metabarcoding protocol for deciphering the diversity of plant-associated Archaea. [144]. Pieretti Isabelle, Mahe Frédéric, Alonso Pascal, Blondin Laurence, Roumagnac Philippe, Vernière Christian. 2018. In : Book of abstract of the International Phytobiomes Conference 2018. International Phytobiomes Alliance, INRA, IRD. Montpellier : International Phytobiomes Alliance-INRA, p. 68. International phytobiomes conference. 2, Montpellier, France, 4 December 2018/6 December 2018.
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Exploring within-host diversity of plant viruses in rice agrosystems using two high-throughput sequencing strategies. Poulicard Nils, Dereeper Alexis, Pinel-Galzi Agnès, Fernandez Emmanuel, Julian Charlotte, Hubert Judith, Filloux Denis, Fargette Denis, Roumagnac Philippe, Hébrard Eugénie. 2018. In : Book of abstract of the International Phytobiomes Conference 2018. International Phytobiomes Alliance, INRA, IRD. Montpellier : International Phytobiomes Alliance-INRA, p. 68. International phytobiomes conference. 2, Montpellier, France, 4 December 2018/6 December 2018.
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Relationship between rice genetic diversity and microbiota composition in traditional Yuanyang rice terraces of China. P1. Filloux Denis, Ferdinand Romain, Fernandez Emmanuel, Huang Huichuan, Jin Baihui, He Xiahong, Ali S., Vernière Christian, Roumagnac Philippe. 2018. In : Book of abstract Pathobiome 2018. INRA. Ajaccio : INRA, Résumé, p. 32. Pathobiome, Ajaccio, France, 18 March 2018/20 March 2018.
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Rice genetic diversity and microbiome characterization of a centuries-old Chinese rice agro-system. Alonso Pascal, Filloux Denis, Blondin Laurence, Mahe Frédéric, Fournier Elisabeth, Gladieux Pierre, Ducasse Aurélie, Morel Jean-Benoit, Mournet Pierre, Huang Huichuan, Jin Baihui, He Xiahong, Ferdinand Romain, Fernandez Emmanuel, Vernière Christian, Roumagnac Philippe. 2018. In : Book of abstract of the International Phytobiomes Conference 2018. International Phytobiomes Alliance, INRA, IRD. Montpellier : International Phytobiomes Alliance-INRA, p. 48. International phytobiomes conference. 2, Montpellier, France, 4 December 2018/6 December 2018.
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Development of bioinformatics tools for sequence data mining and virus discovery. [P40]. Filloux Denis, Petel Adrien, Sempere Guilhem, Claverie Sohini, Lefeuvre Pierre, Mahe Frédéric, Roumagnac Philippe. 2017. In : Livre des résumés des 16 ème Rencontres de virologie végétale. CIRAD, CNRS, INRA, IRD, SFP. Aussois : CIRAD-CNRS, p. 101. Rencontres de virologie végétale, Aussois, France, 15 January 2017/19 January 2017.
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Metagenomics-based discovery and molecular characterization of a novel sugarcane mastrevirus. [P13]. Fernandez Emmanuel, Boukari Wardatou, Alcala-Briseño Ricardo I., Kraberger Simona, Filloux Denis, Lett Jean-Michel, Lefeuvre Pierre, Comstock Jack C., Daugrois Jean-Heinrich, Varsani Arvind, Polston Jane E., Rott Philippe, Roumagnac Philippe. 2017. In : Livre des résumés des 16 ème Rencontres de virologie végétale. CIRAD, CNRS, INRA, IRD, SFP. Aussois : CIRAD-CNRS, p. 74. Rencontres de virologie végétale, Aussois, France, 15 January 2017/19 January 2017.
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Metagenomics-based discovery and molecular characterization of novel geminiviruses from two Mediterranean-climate biodiversity hotspots. [P57]. Galzi Serge, Bernardo Pauline, Fernandez Emmanuel, Julian Charlotte, Ferdinand Romain, Harkins Gordon William, Peterschmitt Michel, Martin Darren Patrick, Filloux Denis, Roumagnac Philippe. 2017. In : Livre des résumés des 16 ème Rencontres de virologie végétale. CIRAD, CNRS, INRA, IRD, SFP. Aussois : CIRAD-CNRS, p. 118. Rencontres de virologie végétale, Aussois, France, 15 January 2017/19 January 2017.
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Spatial metagenomics illuminate the impact of agriculture on the distribution and prevalence of plant viruses at the ecosystem scale. Roumagnac Philippe, Bernardo Pauline, Charles-Dominique Tristan, Fernandez Emmanuel, Filloux Denis, Ortet Philippe, Barakat Mohamed, Rebelo Tony A., Cousins Stephen, Mesleard François, Cohez Damien, Yaverkovski Nicole, Varsani Arvind, Harkins Gordon William, Peterschmitt Michel, Malmstrom Carolyn M., Martin Darren Patrick. 2017. . Paris : INRA, p. 93. International Conference on Holobionts, Paris, France, 19 April 2017/21 April 2017.
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Sugarcane mild mosaic virus: towards the full characterization of this sugarcane Ampelovirus re-discovered using metagenomics-based approaches. [P03]. Daugrois Jean-Heinrich, Candresse Thierry, Fernandez Emmanuel, Filloux Denis, Julian Charlotte, Teycheney Pierre-Yves, Mollov Dimitre S., Roumagnac Philippe. 2017. In : Livre des résumés des 16 ème Rencontres de virologie végétale. CIRAD, CNRS, INRA, IRD, SFP. Aussois : CIRAD-CNRS, p. 64. Rencontres de virologie végétale, Aussois, France, 15 January 2017/19 January 2017.
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Understanding how long-term microbiome-plant-environment interactions drive the emergence or non-emergence of rice diseases in the Chinese Yunnan province. [P39]. Alonso Pascal, Filloux Denis, Ferdinand Romain, Blondin Laurence, Baihui, He Xiahong, Vernière Christian, Roumagnac Philippe. 2017. In : Livre des résumés des 16 ème Rencontres de virologie végétale. CIRAD, CNRS, INRA, IRD, SFP. Aussois : CIRAD-CNRS, p. 100. Rencontres de virologie végétale, Aussois, France, 15 January 2017/19 January 2017.
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Using preserved herbarium specimens to analyse past viral diversity: preliminary methodological results. [P53]. Julian Charlotte, Fernandez Emmanuel, Lefeuvre Pierre, Lett Jean-Michel, Bernardo Pauline, Malmstrom Carolyn M., Martin Darren Patrick, Filloux Denis, Roumagnac Philippe. 2017. In : Livre des résumés des 16 ème Rencontres de virologie végétale. CIRAD, CNRS, INRA, IRD, SFP. Aussois : CIRAD-CNRS, p. 114. Rencontres de virologie végétale, Aussois, France, 15 January 2017/19 January 2017.
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Viral metagenomics-based approach to uncover mastreviruses diversity within Reunion Island's agroecological interfaces. [P50]. Claverie Sohini, Ouattara Alassane, Hoareau Murielle, Hascoat Jérémy, Lebreton Gérard, Grondin Martial, Fernandez Emmanuel, Filloux Denis, Roumagnac Philippe, Lett Jean-Michel, Lefeuvre Pierre. 2017. In : Livre des résumés des 16 ème Rencontres de virologie végétale. CIRAD, CNRS, INRA, IRD, SFP. Aussois : CIRAD-CNRS, p. 111. Rencontres de virologie végétale, Aussois, France, 15 January 2017/19 January 2017.
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Identification of a new Mastrevirus of Saccharum barberi, Saccharum officinarum and Saccharum spontaneum in Florida. Boukari Wardatou, Alcala-Briseño Ricardo I., Kraberger Simona, Fernandez Emmanuel, Filloux Denis, Comstock Jack C., Varsani Arvind, Roumagnac Philippe, Polston Jane E., Rott Philippe. 2016. . Tampa : s.n., Résumé, pp. 1-2. APS annual meeting, Tampa, États-Unis, 30 July 2016/3 August 2016.
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The genomes of several plant species contain endogenous geminiviral sequences. Filloux Denis, Murrell Sasha, Koohapitagtam M., Golden Michael, Julian Jacqueline, Galzi Serge, Uzest Marilyne, Rodier-Goud Marguerite, D'Hont Angélique, Vernerey Marie-Stéphanie, Wilkin P., Peterschmitt Michel, Winter Stephan, Murrell Ben, Martin Darren Patrick, Roumagnac Philippe. 2016. In : 8th International Geminivirus Symposium. University of Delhi, Jawaharlal Nehru University, Jamia Millia Islamia, ICAR-NRCPB , NIPGR, Indian Virological Society. s.l. : s.n., p. 1. International Geminivirus Symposium. 8, New Delhi, Inde, 7 November 2016/10 November 2016.
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Looking for the vector of the latest discovered geminivirus genus, Capulavirus. [P.48]. Bernardo Pauline, Deshoux Maëlle, Granier Martine, Ferdinand Romain, Galzi Serge, Fernandez Emmanuel, Blanc Stéphane, Filloux Denis, Peterschmitt Michel, Roumagnac Philippe. 2015. In : 15èmes Rencontres de Virologie Végétale, Aussois, France, 18-22 janvier 2015. CIRAD ; IRD. s.l. : s.n., Résumé, p. 106. Rencontres de virologie végétale. 15, Aussois, France, 18 January 2015/22 January 2015.
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Metagenomic discovery, worldwide distribution and genetic diversity of novel macluraviruses infecting yams (Dioscorea spp.). [P.28]. Filloux Denis, Bonheur Lydiane, Umber Marie, Pavis Claudie, Fernandez Emmanuel, Galzi Serge, Julian Charlotte, Daugrois Jean-Heinrich, Sukal Amit, Winter Stephan, Teycheney Pierre-Yves, Candresse Thierry, Roumagnac Philippe. 2015. In : 15èmes Rencontres de Virologie Végétale, Aussois, France, 18-22 janvier 2015. CIRAD ; IRD. s.l. : s.n., Résumé, p. 86. Rencontres de virologie végétale. 15, Aussois, France, 18 January 2015/22 January 2015.
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Metagenomic screening of the sugarcane virome in Florida. [P.36]. Fernandez Emmanuel, Filloux Denis, Comstock Jack C., ElSayed Abdelaleim, Roumagnac Philippe, Rott Philippe. 2015. In : 15èmes Rencontres de Virologie Végétale, Aussois, France, 18-22 janvier 2015. CIRAD ; IRD. s.l. : s.n., Résumé, p. 94. Rencontres de virologie végétale. 15, Aussois, France, 18 January 2015/22 January 2015.
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Metagenomics-based detection of viruses infecting cowpea in Burkina-Faso. [P.30]. Palanga Essowè, Fernandez Emmanuel, Filloux Denis, Ferdinand Romain, Bouma Neya James, Sawadogo Mahamadou, Traoré Oumar, Peterschmitt Michel, Roumagnac Philippe. 2015. In : 15èmes Rencontres de Virologie Végétale, Aussois, France, 18-22 janvier 2015. CIRAD ; IRD. s.l. : s.n., Résumé, p. 88. Rencontres de virologie végétale. 15, Aussois, France, 18 January 2015/22 January 2015.
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Molecular characterization of novel viral species of the families Closteroviridae and Secoviridae infecting yams. [P.07]. Teycheney Pierre-Yves, Gomez Rose-Marie, Lange David, Pavis Claudie, Umber Marie, Acina Manbole Isabelle Nina, Bonheur Lydiane, Filloux Denis, Roumagnac Philippe, Candresse Thierry, Contreras Sandy, Faure Chantal, Marais Armelle, Svanella-Dumas Laurence, Theil Sébastien. 2015. In : 15èmes Rencontres de Virologie Végétale, Aussois, France, 18-22 janvier 2015. CIRAD ; IRD. s.l. : s.n., Résumé, p. 65. Rencontres de virologie végétale. 15, Aussois, France, 18 January 2015/22 January 2015.
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Worldwide genetic diversity of Sugarcane white streak virus. [P.43]. Fenouillet Catherine, Filloux Denis, Galzi Serge, Roumagnac Philippe, Daugrois Jean-Heinrich. 2015. In : 15èmes Rencontres de Virologie Végétale, Aussois, France, 18-22 janvier 2015. CIRAD ; IRD. s.l. : s.n., Résumé, p. 101. Rencontres de virologie végétale. 15, Aussois, France, 18 January 2015/22 January 2015.
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Characterization and diagnostic of Yam virus X (YVX) and Yam necrosis virus (YNV), two novel viruses infecting yams in Guadeloupe. Acina Manbole Isabelle Nina, Bonheur Lydiane, Anzala Fabiola, Gomez Rose-Marie, Lange Dominique, Faure Chantal, Marais Armelle, Pavis Claudie, Roumagnac Philippe, Filloux Denis, Candresse Thierry, Teycheney Pierre-Yves. 2013. In : 14èmes Rencontres de virologie végétale (RVV 2013) : Aussois, France, 13-17 janvier 2013. Marais Armelle (ed.), Revers Frédéric (ed.). SFP, INRA. Paris : SFP, Résumé, p. 57. Rencontres de Virologie Végétale. 14, Aussois, France, 13 January 2013/17 January 2013.
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Development of the loop mediated isothermal amplification (LAMP) method for detection of Cauliflower mosaic virus. Fernandez Emmanuel, Ouvray Cédric, Roumagnac Philippe, Froissart Rémi. 2013. In : 1st International Conference Wild Plant Pathosystems (WPP 2013), Olomouc, République Tchèque, 2-5 July 2013. s.l. : s.n., 1 p. International Conference Wild Plant Pathosystems, Olomouc, République tchèque, 2 July 2013/5 July 2013.
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Towards a better characterization of endogenous badnavirus sequences of yams (Dioscorea spp.). Umber Marie, Laboureau Nathalie, Muller Emmanuelle, Roumagnac Philippe, Iskra Caruana Marie-Line, Pavis Claudie, Teycheney Pierre-Yves, Filloux Denis. 2013. In : 14èmes Rencontres de virologie végétale (RVV 2013) : Aussois, France, 13-17 janvier 2013. Marais Armelle (ed.), Revers Frédéric (ed.). SFP, INRA. Paris : SFP, Résumé, p. 99. Rencontres de Virologie Végétale. 14, Aussois, France, 13 January 2013/17 January 2013.
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Yam virus X (YVX) et Yam necrosis virus (YNV), deux nouveaux virus des genres Potexvirus et Sadwavirus infectant les ignames en Guadeloupe. Acina Manbole Isabelle Nina, Bonheur Lydiane, Anzala Fabiola, Gomez Rose-Marie, Lange Dominique, Faure Chantal, Filloux Denis, Roumagnac Philippe, Marais Armelle, Candresse Thierry, Pavis Claudie, Teycheney Pierre-Yves. 2012. In : 8e colloque de la Société Française de Phytopathologie, 5 au 8 juin 2012,Paris, France : Livre des résumés. Attard Agnès (ed.), Barny Marie-Anne (ed.), Brisset Marie-Noelle (ed.), Cilas Christian (ed.), Dellagi Alia (ed.), Desprez-Loustau Marie-Laure (ed.), Expert Dominique (ed.), Fabre Frédéric (ed.), Fagard Mathilde (ed.), Fudal Isabelle (ed.), Genin Stéphane. SFP, INRA, CNRS. Paris : SFP, Résumé, p. 73. Congrès de la Société française de phytopathologie. 8, Paris, France, 5 June 2012/8 May 2012.
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Exploration sans a priori de la biodiversité phytovirale de l'igname (Dioscorea spp.) en serre de quarantaine. Filloux Denis, Galzi Serge, Fernandez Emmanuel, Roumagnac Philippe. 2011. In : 13èmes Rencontres de virologie végétale (RVV 2011), Aussois, France, 16-20 janvier 2011. SFP. s.l. : s.n., 1 p. Rencontres de virologie végétale. 13, Aussois, France, 16 January 2011/20 January 2011.
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Géo-métagénomique. Déchiffrer la biodiversité spatiale des phytovirus associés à des agro-écosystèmes tropicaux et méditerranéens. Fernandez Emmanuel, Galzi Serge, Filloux Denis, Girard Jean-Claude, Martin Darren Patrick, Roumagnac Philippe. 2011. In : 13èmes Rencontres de virologie végétale (RVV 2011), Aussois, France, 16-20 janvier 2011. SFP. s.l. : s.n., 1 p. Rencontres de virologie végétale. 13, Aussois, France, 16 January 2011/20 January 2011.
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Molecular characterization of Secoviridae and Potexvirus infecting yams (Dioscorea spp). Anzala Fabiola, Filloux Denis, Gomez Rose-Marie, Roumagnac Philippe, Pavis Claudie, Teycheney Pierre-Yves. 2011. In : 15th International Congress of Virology, 11-16 September 2011, Sapporo, Japon : International Union of Microbiological Societies 2011 Congress (IUMS 2011), 6-16 September, Sapporo, Japon. s.l. : s.n., Résumé, 1 p. International Congress of Virology. 15, Sapporo, Japon, 11 September 2011/16 September 2011.
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A new genus-level geminivirus lineage isolated from the South African fynbos. Bernardo Pauline, Fernandez Emmanuel, Granier Martine, Urbino Cica, Peterschmitt Michel, Martin Darren Patrick, Roumagnac Philippe. 2011. In : 4th Plant Virus Ecology Network Workshop (PVEN), Montpellier, France, May 30 to June 1, 2011. s.l. : s.n., 1 p. Plant Virus Ecology Network Workshop. 4, Montpellier, France, 30 May 2011/1 June 2011.
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Metagenomics and quarantine: searching for the unknown. Roumagnac Philippe, Fernandez Emmanuel. 2010. In : 3rd Plant Virus Ecology Network (PVEN) Workshop, Ithaca, USA, June 20-24, 2010. s.l. : s.n., 1 p. Plant Virus Ecology Network Workshop. 3, Ithaca, États-Unis, 20 June 2010/24 June 2010.
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Metagenomics and quarantine: searching for the unknown. Roumagnac Philippe, Fernandez Emmanuel. 2009. In : Understanding emergence of infectious diseases: focus on New Experimental and Theoretical Approaches to Virus Evolution = Maladies infectieuses émergentes : focus sur les nouvelles approches expérimentales et théoriques de l'évolution virale. Jacques Monod. s.l. : s.n., 1 p. Jacques Monod Conférences, Roscoff, France, 26 September 2009/30 September 2009.
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Etude de la diversité génétique existant au sein d'une collection de souches de Xanthomonas sp. pathogènes de l'oignon par AFLP et PFLP. Roumagnac Philippe, Gagnevin Lionel, Sellos S., Brin Christelle, Manceau Charles, Pruvost Olivier. 2002. In : Rencontres de bactériologie, Aussois, France, 13-17 janvier 2002. s.l. : s.n., 1 p. Rencontres de bactériologie. 5, Aussois, France, 13 January 2002/17 January 2002.

Paper without proceedings

Deciphering plant virus ecology and evolution using metagenomics-based approaches. Filloux Denis, Lefeuvre Pierre, Lett Jean-Michel, Varsani Arvind, Harkins Gordon William, Malmstrom Carolyn M., Martin Darren Patrick, Roumagnac Philippe. 2019. . State College : s.n., Résumé, 1 p. International Congress on Virus Evolution. 10, State College, États-Unis, 7 March 2019/9 March 2019.
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Description of the diversity and structure of mastrevirus communities at the scale of an agrosystem in La Réunion based on a metagenomic approach. Claverie Sohini, Scussel Sarah, Hoareau Marie Murielle, Hascoat Jérémy, Lebreton Gérard, Grondin Martial, Filloux Denis, Roumagnac Philippe, Martin Darren Patrick, Lett Jean-Michel, Lefeuvre Pierre. 2019. In : Livre des résumés des 17 ème Rencontres de virologie végétale. INRA, CIRAD, CNRS, SFP, SFV. Aussois : INRA, Résumé, p. 48. Rencontres de Virologie Végétale (RVV 2019). 17, Aussois, France, 27 January 2019/31 January 2019.
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Diversity and structure of Poaceae-infecting mastreviruses communities on Reunion Island using a viral metagenomics-based approach. Claverie Sohini, Scussel Sarah, Hoareau Murielle, Hascoat Jérémy, Lebreton Gérard, Grondin Martial, Filloux Denis, Roumagnac Philippe, Martin Darren Patrick, Lett Jean-Michel, Lefeuvre Pierre. 2019. In : Programme and abstracts of the 9th International Germinivirus Symposium (IGS 2019) and the 7th ssDNA Comparative virology workshop. University of California. Davis : University of California, Résumé, p. 44. International Geminivirus Symposium. 9, Davis, États-Unis, 9 November 2019/13 November 2019.
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Effect of species composition on virome diversity in various ecosystemic communities of Poaceae. Maclot François, Candresse Thierry, Filloux Denis, Roumagnac Philippe, Massart Sébastien. 2019. In : Livre des résumés des 17 ème Rencontres de virologie végétale. INRA, CIRAD, CNRS, SFP, SFV. Aussois : INRA, Résumé, p. 18. Rencontres de Virologie Végétale (RVV 2019). 17, Aussois, France, 27 January 2019/31 January 2019.
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Exploring within-host diversity of plant viruses in rice agrosystems using two high-throughput sequencing strategies. Poulicard Nils, Dereeper Alexis, Pinel-Galzi Agnès, Fernandez Emmanuel, Julian Charlotte, Hubert Judith, Filloux Denis, Fargette Denis, Roumagnac Philippe, Hébrard Eugénie. 2019. In : Livre des résumés des 17 ème Rencontres de virologie végétale. INRA, CIRAD, CNRS, SFP, SFV. Aussois : INRA, Résumé, p. 34. Rencontres de Virologie Végétale (RVV 2019). 17, Aussois, France, 27 January 2019/31 January 2019.
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Geographical distribution and diversity of Plantago Lanceolata latent virus, a member of the Capulavirus genus. Filloux Denis, Galzi Serge, Julian Charlotte, Ryckebusch Faustine, Granier Martine, Peterschmitt Michel, Davoodi Zohreh, Susi Hanna, Laine Anna-Liisa, Roumagnac Philippe. 2019. In : Programme and abstracts of the 9th International Germinivirus Symposium (IGS 2019) and the 7th ssDNA Comparative virology workshop. University of California. Davis : University of California, Résumé, p. 71. International Geminivirus Symposium. 9, Davis, États-Unis, 9 November 2019/13 November 2019.
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Hidden diversity of endogenous geminiviral sequences across plant genomes and transcriptomes. Sharma Vikas, Roumagnac Philippe, Filloux Denis, Lefeuvre Pierre, Teycheney Pierre-Yves, Martin Darren Patrick, Maumus Florian. 2019. In : Programme and abstracts of the 9th International Germinivirus Symposium (IGS 2019) and the 7th ssDNA Comparative virology workshop. University of California. Davis : University of California, Résumé, p. 58. International Geminivirus Symposium. 9, Davis, États-Unis, 9 November 2019/13 November 2019.
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Nanopore-based detection and characterization of yam viruses. Filloux Denis, Fernandez Emmanuel, Loire Etienne, Claude Lisa, Galzi Serge, Candresse Thierry, Winter Stephan, Jeeva M.L., Makeshkumar T., Martin Darren Patrick, Roumagnac Philippe. 2019. In : Livre des résumés des 17 ème Rencontres de virologie végétale. INRA, CIRAD, CNRS, SFP, SFV. Aussois : INRA, Résumé, p. 53. Rencontres de Virologie Végétale (RVV 2019). 17, Aussois, France, 27 January 2019/31 January 2019.
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Night at the museum: Contribution of small RNA from historical herbarium specimens in the reconstruction of evolutionary histories of geminiviruses. Lett Jean-Michel, Scussel Sarah, Campos Paola, Filloux Denis, Roumagnac Philippe, Harkins Gordon William, Martin Darren Patrick, Roumagnac Philippe, Martin Darren Patrick, Lefeuvre Pierre, Rieux Adrien, Becker Nathalie. 2019. In : Livre des résumés des 17 ème Rencontres de virologie végétale. INRA, CIRAD, CNRS, SFP, SFV. Aussois : INRA, Résumé, p. 52. Rencontres de Virologie Végétale (RVV 2019). 17, Aussois, France, 27 January 2019/31 January 2019.
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Night at the museum: Contribution of small RNA from historical herbarium specimens in the reconstruction of evolutionary histories of geminiviruses. Rieux Adrien, Campos Paola, Scussel Sarah, Duvermy Arnaud, Filloux Denis, Roumagnac Philippe, Martin Darren Patrick, Becker Nathalie, Lett Jean-Michel. 2019. In : Programme and abstracts of the 9th International Germinivirus Symposium (IGS 2019) and the 7th ssDNA Comparative virology workshop. University of California. Davis : University of California, Résumé, p. 36. International Geminivirus Symposium. 9, Davis, États-Unis, 9 November 2019/13 November 2019.
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Novel divergent geminivirus infecting Cactaceae plants. Fontenele Rafaela S, Cobb Ilaria N., Khalifeh Anthony, Smith Kendal, Schreck Joshua, Schmidlin Kara, Kraberger Simona, Majure Lucas C., Salywon Andrew M., Köhler Matias, Wojciechowski Martin, Lund Michael, Van Doorslaer Koenraad, Roumagnac Philippe, Lefeuvre Pierre, Kumari Safaa G., Ribeiro Simone G., Varsani Arvind. 2019. In : Programme and abstracts of the 9th International Germinivirus Symposium (IGS 2019) and the 7th ssDNA Comparative virology workshop. University of California. Davis : University of California, Résumé, pp. 42-43. International Geminivirus Symposium. 9, Davis, États-Unis, 9 November 2019/13 November 2019.
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Symptom evolution following the emergence of maize streak virus. Monjane Adérito Luis, Dellicour Simon, Hartnady Penelope, Oyeniran Kehinde A., Owor Betty E., Bezeidenhout Marion, Linderme Daphné, Syed Rizwan Ali, Donaldson Lara, Murray Shane, Rybicki Edward P., Kvarnheden Anders, Yazdkhasti Elhman, Lefeuvre Pierre, Froissart Rémy, Roumagnac Philippe, Shepherd Dionne Natalie, Harkins Gordon William, Suchard Marc, Lemey Philippe, Varsani Arvind, Martin Darren Patrick. 2019. In : Programme and abstracts of the 9th International Germinivirus Symposium (IGS 2019) and the 7th ssDNA Comparative virology workshop. University of California. Davis : University of California, Résumé, pp. 21-22. International Geminivirus Symposium. 9, Davis, États-Unis, 9 November 2019/13 November 2019.
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Geometagenomics illuminates the impact of agriculture on the distribution and prevalence of plant viruses at the ecosystem scale. O13. Bernardo Pauline, Charles-Dominique Tristan, Barakat Mohamed, Ortet Philippe, Fernandez Emmanuel, Filloux Denis, Hartnady Penelope, Rebelo Tony A., Cousins Stephen, Mesleard François, Cohez Damien, Yaverkovski Nicole, Varsani Arvind, Harkins Gordon William, Peterschmitt Michel, Malmstrom Carolyn, Martin Darren Patrick, Roumagnac Philippe. 2018. In : Book of abstract Pathobiome 2018. INRA. Ajaccio : INRA, Résumé, pp. 25-26. Pathobiome, Ajaccio, France, 18 March 2018/20 March 2018.
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Les virus préfèrent les zones cultivées aux zones sauvages. Roumagnac Philippe. 2018. . Paris : Société Française de Virologie, 1 p. Journées Francophones de Virologie. 20, Paris, France, 22 March 2018/23 March 2018.
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Étude de la diversité des virus des plantes conservés dans les herbiers. Delattre R., Julian Charlotte, Fernandez Emmanuel, Filloux Denis, Roumagnac Philippe. 2018. In : Actes de conférences : Le printemps de Baillarguet. CIRAD. Montpellier : CIRAD, Résumé, p. 12. Le printemps de Baillarguet 2018. 10, Montpellier, 28 May 2018/29 May 2018.
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Deciphering plant-associated viruses at the agroecosystem scale using geometagenomics. Charles-Dominique Tristan, Fernandez Emmanuel, Filloux Denis, Ortet Philippe, Barakat Mohamed, Rebelo Tony A., Varsani Arvind, Malmstrom Carolyn M., Martin Darren Patrick, Roumagnac Philippe. 2016. . University of Helsinki. Helsinki : University of Helsinki, Résumé, 1 p. International Meeting on Wild Plant Pathosystems. 2, Helsinki, Finlande, 29 August 2016/31 August 2016.
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Is aphid transmission a distinguishing feature of the new Capulavirus genus? Peterschmitt Michel, Granier Martine, Deshoux R., Ferdinand Romain, Coeur d'Acier Armelle, Roumagnac Philippe. 2016. . University of Delhi, Jawaharlal Nehru University, Jamia Millia Islamia, ICAR-NRCPB, NIPGR. New Delhi : Université de Delhi, Résumé, 1 p. International Geminivirus Symposium. 8, New Delhi, Inde, 7 November 2016/10 November 2016.
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Improved diagnostic tools for the detection badnaviruses in yams unveil the existence of endogenous sequences of extant badnavirus species in yams. [O.36]. Umber Marie, Filloux Denis, Muller Emmanuelle, Laboureau Nathalie, Galzi Serge, Gomez Rose-Marie, Roumagnac Philippe, Caruana Marie-Line, Pavis Claudie, Teycheney Pierre-Yves. 2015. In : 15èmes Rencontres de Virologie Végétale, Aussois, France, 18-22 janvier 2015. CIRAD ; IRD. s.l. : s.n., Résumé, p. 51. Rencontres de virologie végétale. 15, Aussois, France, 18 January 2015/22 January 2015.
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Viral treasure hunt in European outermost territories: how metagenomics boosts the discovery of novel viral species in tropical and sub-tropical crops germplasm. [O.18]. Teycheney Pierre-Yves, Bandou Eric, Gomez Rose-Marie, Lange David, Pavis Claudie, Umber Marie, Acina Manbole Isabelle Nina, Bonheur Lydiane, Daugrois Jean-Heinrich, Fernandez Emmanuel, Filloux Denis, Julian Charlotte, Roumagnac Philippe, Grisoni Michel, Pierret Alycia, Rubington Margot, Candresse Thierry, Contreras Sandy, Faure Chantal, Marais Armelle, Theil Sébastien, Da Câmara Machado Artur, Mendonça Duarte, Pinheiro de Carvalho Miguel A.A., Silva Emanuel. 2015. In : 15èmes Rencontres de Virologie Végétale, Aussois, France, 18-22 janvier 2015. CIRAD ; IRD. s.l. : s.n., Résumé, p. 30. Rencontres de virologie végétale. 15, Aussois, France, 18 January 2015/22 January 2015.
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Visacane, the Cirad quarantine tool for the exchange of pest and disease-free sugarcane germplasm. Guinet-Brial Isabelle, Girard Jean-Claude, Roumagnac Philippe, Daugrois Jean-Heinrich, Fernandez Emmanuel, Rott Philippe. 2014. In : 5th IAPSIT International Sugar Conference (IS-2014) onThe Green Technologies for Sustainable growth of Sugar Industry in Developing Countries, November 25-28, 2014, Nanning, China. Yang-Rui Li, G.P. Rao, S. Solomon, Li-Tao Yang, Zhong Liu, Wei-Zhong He,. Naming : IAPSIT, Résumé, p. 363. IAPSIT International Sugar Conference IS-2014. 5, Nanning, Chine, 25 November 2014/28 November 2014.
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Assessment and characterization of the genetic diversity of viruses infecting cultivated yams (Dioscorea spp.) in Haïti. Galzi Serge, Scutt Ricot, Prophète P., Roumagnac Philippe, Filloux Denis. 2013. In : 14èmes Rencontres de virologie végétale (RVV 2013) : Aussois, France, 13-17 janvier 2013. Marais Armelle (ed.), Revers Frédéric (ed.). SFP, INRA. Paris : SFP, Résumé, p. 70. Rencontres de Virologie Végétale. 14, Aussois, France, 13 January 2013/17 January 2013.
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Cartographie des virus de l'igname en Haïti : risques pour la production et recommandations. Filloux Denis, Galzi Serge, Scutt Ricot, Prophete Emmanuel, Roumagnac Philippe. 2013. In : Conférence finale du projet DEVAG Réseau caribéen pour le développement de systèmes horticoles agroécologique. CIRAD. s.l. : s.n., Résumé, 1 p. Conférence finale du projet DEVAG, Schoelcher, Martinique, 5 December 2013.
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Characterization of new endogenous geminiviral elements in yam (Dioscorea spp.) genomes. Filloux Denis, Koohapitagtam M., Golden Michael, Julian Charlotte, Galzi Serge, Rodier-Goud Marguerite, D'Hont Angélique, Vernerey Marie-Stéphanie, Wilkin P., Peterschmitt Michel, Martin Darren Patrick, Roumagnac Philippe. 2013. In : 14èmes Rencontres de virologie végétale (RVV 2013) : Aussois, France, 13-17 janvier 2013. Marais Armelle (ed.), Revers Frédéric (ed.). SFP, INRA. Paris : SFP, Résumé, p. 5. Rencontres de Virologie Végétale. 14, Aussois, France, 13 January 2013/17 January 2013.
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Characterization of novel, highly divergent geminiviruses and insights into the evolutionary history of geminiviruses. Bernardo Pauline, Ortet Philippe, Barakat Mohamed, Rebelo Anthony, Cousins Stephen, Fernandez Emmanuel, Mesleard François, Peterschmitt Michel, Filloux Denis, Varsani Arvind, Martin Darren Patrick, Roumagnac Philippe. 2013. In : 7th International Geminvirus Symposium and 5th International ssDNA Comparative Virology Workshop, Hangzhou, China, November 3-9, 2013. s.l. : s.n., Résumé, 1 p. International Geminvirus Symposium. 7, Hangzhou, Chine, 3 November 2013/9 November 2013.
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Detection of Sugarcane yellow leaf virus by a novel reverse transcription loop-mediated isothermal amplification method from three sugarcane production regions in Kenya. Fernandez Emmanuel, Amata Ruth Lodenyi, Roumagnac Philippe. 2013. In : 14èmes Rencontres de virologie végétale (RVV 2013) : Aussois, France, 13-17 janvier 2013. Marais Armelle (ed.), Revers Frédéric (ed.). SFP, INRA. Paris : SFP, p. 71. Rencontres de Virologie Végétale. 14, Aussois, France, 13 January 2013/17 January 2013.
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Diverse circular single-stranded DNA viruses discovered from research greenhouses and agro-ecosystems. Fort Guillaume, Bernardo Pauline, Fernandez Emmanuel, Galzi Serge, Filloux Denis, Roumagnac Philippe. 2013. In : 14èmes Rencontres de virologie végétale (RVV 2013) : Aussois, France, 13-17 janvier 2013. Marais Armelle (ed.), Revers Frédéric (ed.). SFP, INRA. Paris : SFP, Résumé, p. 66. Rencontres de Virologie Végétale. 14, Aussois, France, 13 January 2013/17 January 2013.
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Geo-metagenomics: deciphering the spatial biodiversity of ssDNA viruses associated with Western Cape and Camargue agroecosystems. Bernardo Pauline, Ortet Philippe, Barakat Mohamed, Rebelo Anthony, Cousins Stephen, Fernandez Emmanuel, Mesleard François, Peterschmitt Michel, Filloux Denis, Varsani Arvind, Martin Darren Patrick, Roumagnac Philippe. 2013. In : 7th International Geminvirus Symposium and 5th International ssDNA Comparative Virology Workshop, Hangzhou, China, November 3-9, 2013. s.l. : s.n., Résumé, 1 p. International Geminvirus Symposium. 7, Hangzhou, Chine, 3 November 2013/9 November 2013.
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Improvement of three nucleic acid isolation protocols for an overall diagnosis of viruses on six vegetative propagated plants. Julian Charlotte, Bernardo Pauline, Fernandez Emmanuel, Galzi Serge, Grisoni Michel, Da Silva Mendoça D.M., Pavis Claudie, Roumagnac Philippe, Filloux Denis. 2013. In : 14èmes Rencontres de virologie végétale (RVV 2013) : Aussois, France, 13-17 janvier 2013. Marais Armelle (ed.), Revers Frédéric (ed.). SFP, INRA. Paris : SFP, Résumé, p. 75. Rencontres de Virologie Végétale. 14, Aussois, France, 13 January 2013/17 January 2013.
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Molecular characterization of Euphorbia caput-medusae stunt virus: Evidence for the existence of a new genus within the family Geminiviridae. Bernardo Pauline, Fernandez Emmanuel, Granier Martine, Golden Michael, Rebelo Tony A., Peterschmitt Michel, Martin Darren Patrick, Roumagnac Philippe. 2013. In : 14èmes Rencontres de virologie végétale (RVV 2013) : Aussois, France, 13-17 janvier 2013. Marais Armelle (ed.), Revers Frédéric (ed.). SFP, INRA. Paris : SFP, Résumé, p. 9. Rencontres de Virologie Végétale. 14, Aussois, France, 13 January 2013/17 January 2013.
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New insights into the evolutionary history of geminiviruses derived through the discovery of divergent viruses isolated from wild plants. Bernardo Pauline, Golden Michael, Mohd A., Fernandez Emmanuel, Granier Martine, Rebelo A.G., Peterschmitt Michel, Martin Darren Patrick, Roumagnac Philippe. 2013. In : 1st International Conference Wild Plant Pathosystems (WPP 2013), Olomouc, République Tchèque, 2-5 July 2013. s.l. : s.n., Résumé, 1 p. International Conference Wild Plant Pathosystems, Olomouc, République tchèque, 2 July 2013/5 July 2013.
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Pathology and viral metagenomics, a recent history. Bernardo Pauline, Fernandez Emmanuel, Filloux Denis, Albina Emmanuel, Eloit Marc, Roumagnac Philippe. 2013. In : 14èmes Rencontres de virologie végétale (RVV 2013) : Aussois, France, 13-17 janvier 2013. Marais Armelle (ed.), Revers Frédéric (ed.). SFP, INRA. Paris : SFP, Résumé, p. 20. Rencontres de Virologie Végétale. 14, Aussois, France, 13 January 2013/17 January 2013.
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Development of the loop mediated isothermal amplification (LAMP) method for detection of Sugarcane yellow leaf virus. Fernandez Emmanuel, Amata Ruth Lodenyi, Rott Philippe, Roumagnac Philippe. 2012. In : 10th Pathology Workshop. Understanding sugar cane diseases for their efficient management, 07-11 May 2012, Nanning, China. s.l. : s.n., Résumé, p. 60. ISSCT Pathology Workshop. 10, Nanning, Chine, 7 May 2012/11 May 2012.
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Visacane, an innovative quarantine tool for the exchange of pest and disease-free sugarcane germplasm. Girard Jean-Claude, Guinet Isabelle, Roumagnac Philippe, Fernandez Emmanuel, Rott Philippe. 2011. In : 10th Germplasm and Breeding, and 7th Molecular Biology Workshop, Maceió, Brazil, 15-20 May 2011 : Breaking breeding and biotechnology paradigms - towards a complementary approach in sugar cane research. Abstract. ISSCT, STAB. Réduit : ISSCT, Résumé, p. 27. ISSCT Germplasm and Breeding Workshop. 10, Maceio, Brésil, 15 May 2011/20 May 2011.
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Genetic diverstiy of Sugarcane yellow leaf virus in a sugarcane selection plot in Guadeloupe (FWI). Girard Jean-Claude, Fernandez Emmanuel, Daugrois Jean-Heinrich, Roques Danièle, Roumagnac Philippe, Rott Philippe. 2010. In : ISSCT 2010: 27th Congress of the International Society of Sugar Cane Technologists Congres, Veracruz, Mexique, 7-11 mars 2010. ISSCT. s.l. : s.n., 9 p. ISSCT Congress. 27, Veracruz, Mexique, 7 March 2010/11 March 2010.
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Deciphering the Plant Viral Diversity: a stepwise project: from a quarantine station to an African Agro-ecosystem. Roumagnac Philippe. 2009. In : 2nd Workshop of the Plant Virus Ecology Network (PVEN), Ca' Tron di Roncade , Italy, 21 to 23 April 2009. s.l. : s.n., Diaporama, (10 vues) Plant Virus Ecology Network Workshop. 2, Ca' Tron di Roncade, Italie, 21 April 2009/23 April 2009.
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Spatial and temporal analysis of onion bacterial blight in seed production fields. Humeau Laurence, Roumagnac Philippe, Soustrade Isabelle, Couteau Annie, Chiroleu Frédéric, Hughes Gareth, Pruvost Olivier. 2005. In : 9th International Workshop on Plant disease epidemiology, Landerneau, France, 11-15 April 2005. s.l. : s.n., Résumé, 1 p. International Workshop on Plant Disease Epidemiology. 9, Landerneau, France, 11 April 2005/15 April 2005.
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Caractérisation polyphasique des Xanthomonas isolé d'oignon, d'ail et de ciboule. Roumagnac Philippe, Gagnevin Lionel, Gardan Louis, Sutra L., Manceau Charles, Rott Philippe, Pruvost Olivier. 2004. In : 6ème Rencontres plantes-bactéries, 11-15 janvier 2004, Aussois. s.l. : s.n., p. 74. Rencontres plantes-bactéries. 6, Aussois, France, 11 January 2004/15 January 2004.

Le dépérissement bactérien des Alliacées : la biologie moléculaire est-elle un outil performant dans la stratégie de lutte ? Roumagnac Philippe, Pruvost Olivier, Gagnevin Lionel. 2003. In : Productions maraîchères et horticoles : sessions lutte intégrée et agronomie. Kahane Rémi (ed.). CIRAD-FLHOR-PMH. Montpellier : CIRAD-FLHOR, 1 Cd-Rom Journées annuelles du FLHOR, Montpellier, France, 26 August 2002/27 August 2002.

Onion bacterial blight: new data on an emerging disease. Roumagnac Philippe, Gagnevin Lionel, Hughes Gareth, Pruvost Olivier. 2003. In : Solving problems in the real world : ICPP 2003, 8th International Congress of Plant Pathology, 2-7 February 2003, Christchurch, New-Zealand. ISPP. s.l. : s.n., Diaporama, 9 p. International Congress of Plant Pathology. 8, Christchurch, Nouvelle-Zélande, 2 February 2003/7 February 2003.

Thesis

Taxonomie et diversité du Xanthomonas responsable du dépérissement bactérien de l'oignon : études épidémiologiques du rôle des semences dans la transmission de la bactérie. Roumagnac Philippe. 2003. Paris : INA-PG, 113 p. Thèse de docteur-ingénieur : Sciences de la vie : Institut national agronomique Paris-Grignon

Section of report

Protection des plantes - Epidémiologie des maladies bactériennes et virales. Costet Laurent, Pruvost Olivier, Gagnevin Lionel, Laurent Philippe, Jouen Emmanuel, Humeau Laurence, Roumagnac Philippe, Soustrade Isabelle, Elbaz Mounira, Luisetti Jacques, Delatte Hélène, Lett Jean-Michel, Laurent Philippe. 2004. In : Rapport annuel 2003 CIRAD Réunion. De Taffin Gabriel (ed.). CIRAD-Délégation de la Réunion. Saint-Denis : CIRAD, pp. 52-58.

Protection des plantes - Epidémiologie des maladies bactériennes et virales. Gagnevin Lionel, Humeau Laurence, Roumagnac Philippe, Robène-Soustrade Isabelle, Pruvost Olivier, Delatte Hélène, Reynaud Bernard, Lett Jean-Michel, Costet Laurent, Pompon Julien. 2004. In : Rapport annuel 2004 CIRAD Réunion. De Taffin Gabriel (ed.). CIRAD-Délégation de la Réunion. Saint-Denis : CIRAD, pp. 56-62.

Protection des plantes. Epidémiologie des maladies bactériennes et virales. Pruvost Olivier, Gagnevin Lionel, Laurent Philippe, Soustrade Isabelle, Roumagnac Philippe, Luisetti Jacques, Rassaby Laurence, Reynaud Bernard, Delatte Hélène. 2003. In : Rapport annuel 2002 CIRAD Réunion. De Taffin Gabriel (ed.). CIRAD-Délégation de la Réunion. Saint-Denis : CIRAD, pp. 52-58.

Protection des plantes. Epidémiologie des maladies bactériennes et virales. Costet Laurent, Gagnevin Lionel, Pruvost Olivier, Laurent Philippe, Soustrade Isabelle, Roumagnac Philippe, Luisetti Jacques, Rassaby Laurence, Leclercq Le Quillec Françoise, Reynaud Bernard. 2002. In : Rapport annuel 2001 CIRAD Réunion. Trébel Michel (ed.). CIRAD-Délégation de la Réunion. Saint-Denis : CIRAD, pp. 56-61.

Protection des plantes. Epidémiologie des maladies bactériennes et virales. Notaise Julien, Gagnevin Lionel, Luisetti Jacques, Poussier Stéphane, Roumagnac Philippe, Pruvost Olivier, Soustrade Isabelle, Rassaby Laurence, Leclercq Le Quillec Françoise, Reynaud Bernard, Peterschmitt Michel. 2001. In : Rapport annuel 2000 CIRAD Réunion. Trébel Michel (ed.). CIRAD-Délégation de la Réunion. Saint-Denis : CIRAD, pp. 56-62.

Website article

Optimize the plant microbiota to increase plant growth and health. Barret M., Dufour P., Durand-Tardif Mylène, Mariadassou M., Mougel Christophe, Perez P., Roumagnac Philippe, Sanguin Hervé, Steinberg Christian, Szambien M.. 2019. Paris : GIS Biotechnologies Vertes, 12 p.
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