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Dominique Lavenier
Researcher at University of Rennes
Publications - 126
Citations - 5114
Dominique Lavenier is an academic researcher from University of Rennes. The author has contributed to research in topics: Sequence assembly & Hardware acceleration. The author has an hindex of 27, co-authored 122 publications receiving 4464 citations. Previous affiliations of Dominique Lavenier include French Institute for Research in Computer Science and Automation & Los Alamos National Laboratory.
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Journal ArticleDOI
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
Keith Bradnam,Joseph Fass,Anton Alexandrov,Paul Baranay,Michael Bechner,Inanc Birol,Sébastien Boisvert,Jarrod Chapman,Guillaume Chapuis,Guillaume Chapuis,Rayan Chikhi,Rayan Chikhi,Hamidreza Chitsaz,Wen-Chi Chou,Jacques Corbeil,Cristian Del Fabbro,T. Roderick Docking,Richard Durbin,Dent Earl,Scott J. Emrich,Pavel Fedotov,Nuno A. Fonseca,Ganeshkumar Ganapathy,Richard A. Gibbs,Sante Gnerre,Elenie Godzaridis,Steve Goldstein,Matthias Haimel,Giles Hall,David Haussler,Joseph B. Hiatt,Isaac Ho,Jason T. Howard,Martin Hunt,Shaun D. Jackman,David B. Jaffe,Erich D. Jarvis,Huaiyang Jiang,Sergey Kazakov,Paul J. Kersey,Jacob O. Kitzman,James R. Knight,Sergey Koren,Tak-Wah Lam,Dominique Lavenier,Dominique Lavenier,François Laviolette,Yingrui Li,Zhenyu Li,Binghang Liu,Yue Liu,Ruibang Luo,Iain MacCallum,Matthew D. MacManes,Nicolas Maillet,Sergey Melnikov,Bruno Vieira,Delphine Naquin,Zemin Ning,Thomas D. Otto,Benedict Paten,Octávio S. Paulo,Adam M. Phillippy,Francisco Pina-Martins,Michael Place,Dariusz Przybylski,Xiang Qin,Carson Qu,Filipe J. Ribeiro,Stephen Richards,Daniel S. Rokhsar,Daniel S. Rokhsar,J. Graham Ruby,J. Graham Ruby,Simone Scalabrin,Michael C. Schatz,David C. Schwartz,Alexey Sergushichev,Ted Sharpe,Timothy I. Shaw,Jay Shendure,Yujian Shi,Jared T. Simpson,Henry Song,Fedor Tsarev,Francesco Vezzi,Riccardo Vicedomini,Jun Wang,Kim C. Worley,Shuangye Yin,Siu-Ming Yiu,Jianying Yuan,Guojie Zhang,Hao Zhang,Shiguo Zhou,Ian F Korf +95 more
TL;DR: The Assemblathon 2 as mentioned in this paper presented a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and a snake) from 21 participating teams.
Journal ArticleDOI
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
Keith Bradnam,Joseph Fass,Anton Alexandrov,Paul Baranay,Michael Bechner,Inanc Birol,Sébastien Boisvert,Jarrod Chapman,Guillaume Chapuis,Guillaume Chapuis,Rayan Chikhi,Rayan Chikhi,Hamidreza Chitsaz,Wen-Chi Chou,Jacques Corbeil,Cristian Del Fabbro,Roderick R. Docking,Richard Durbin,Dent Earl,Scott J. Emrich,Pavel Fedotov,Nuno A. Fonseca,Ganeshkumar Ganapathy,Richard A. Gibbs,Sante Gnerre,Elenie Godzaridis,Steve Goldstein,Matthias Haimel,Giles Hall,David Haussler,Joseph B. Hiatt,Isaac Ho,Jason T. Howard,Martin Hunt,Shaun D. Jackman,David B. Jaffe,Erich D. Jarvis,Huaiyang Jiang,Sergey Kazakov,Paul J. Kersey,Jacob O. Kitzman,James R. Knight,Sergey Koren,Tak-Wah Lam,Dominique Lavenier,Dominique Lavenier,Dominique Lavenier,François Laviolette,Yingrui Li,Zhenyu Li,Binghang Liu,Yue Liu,Ruibang Luo,Iain MacCallum,Matthew D. MacManes,Nicolas Maillet,Nicolas Maillet,Sergey Melnikov,Delphine Naquin,Delphine Naquin,Zemin Ning,Thomas D. Otto,Benedict Paten,Octávio S. Paulo,Adam M. Phillippy,Francisco Pina-Martins,Michael Place,Dariusz Przybylski,Xiang Qin,Carson Qu,Filipe J. Ribeiro,Stephen Richards,Daniel S. Rokhsar,Daniel S. Rokhsar,J. Graham Ruby,J. Graham Ruby,Simone Scalabrin,Michael C. Schatz,David C. Schwartz,Alexey Sergushichev,Ted Sharpe,Timothy I. Shaw,Jay Shendure,Yujian Shi,Jared T. Simpson,Henry Song,Fedor Tsarev,Francesco Vezzi,Riccardo Vicedomini,Bruno Vieira,Jun Wang,Kim C. Worley,Shuangye Yin,Siu-Ming Yiu,Jianying Yuan,Guojie Zhang,Hao Zhang,Shiguo Zhou,Ian F Korf +98 more
TL;DR: The Assemblathon 2 as discussed by the authors presented a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and a snake) from 21 participating teams.
Journal ArticleDOI
Critical Assessment of Metagenome Interpretation - A benchmark of metagenomics software
Alexander Sczyrba,Peter Hofmann,Peter Hofmann,Peter Belmann,David Koslicki,Stefan Janssen,Johannes Dröge,Johannes Dröge,Ivan Gregor,Ivan Gregor,Stephan Majda,Jessika Fiedler,Eik Dahms,Eik Dahms,Andreas Bremges,Adrian Fritz,Ruben Garrido-Oter,Tue Sparholt Jørgensen,Tue Sparholt Jørgensen,Tue Sparholt Jørgensen,Nicole Shapiro,Philip D. Blood,Alexey Gurevich,Yang Bai,Dmitrij Turaev,Matthew Z. DeMaere,Rayan Chikhi,Niranjan Nagarajan,Christopher Quince,Fernando Meyer,Monika Balvočiūtė,Lars Hestbjerg Hansen,Søren J. Sørensen,Burton Kuan Hui Chia,Bertrand Denis,Jeff Froula,Zhong Wang,Robert Egan,Dongwan Don Kang,Jeffrey J. Cook,Charles Deltel,Michael Beckstette,Claire Lemaitre,Pierre Peterlongo,Guillaume Rizk,Dominique Lavenier,Yu Wei Wu,Yu Wei Wu,Steven W. Singer,Steven W. Singer,Chirag Jain,Marc Strous,Heiner Klingenberg,Peter Meinicke,Michael D. Barton,Thomas Lingner,Hsin-Hung Lin,Yu-Chieh Liao,Genivaldo G. Z. Silva,Daniel A. Cuevas,Robert Edwards,Surya Saha,Vitor C. Piro,Vitor C. Piro,Bernhard Y. Renard,Mihai Pop,Hans-Peter Klenk,Markus Göker,Nikos C. Kyrpides,Tanja Woyke,Julia A. Vorholt,Paul Schulze-Lefert,Edward M. Rubin,Aaron E. Darling,Thomas Rattei,Alice C. McHardy +75 more
TL;DR: The Critical Assessment of Metagenome Interpretation (CAMI) challenge has engaged the global developer community to benchmark their programs on highly complex and realistic data sets, generated from ∼700 newly sequenced microorganisms and ∼600 novel viruses and plasmids and representing common experimental setups as discussed by the authors.
Journal ArticleDOI
Assemblathon 1: A competitive assessment of de novo short read assembly methods
Dent Earl,Keith Bradnam,John St. John,Aaron E. Darling,Dawei Lin,Joseph Fass,Hung On Ken Yu,Vince Buffalo,Daniel R. Zerbino,Mark Diekhans,Ngan Nguyen,Pramila N. Ariyaratne,Wing-Kin Sung,Wing-Kin Sung,Zemin Ning,Matthias Haimel,Jared T. Simpson,Nuno A. Fonseca,Inanc Birol,T. Roderick Docking,Isaac Ho,Daniel S. Rokhsar,Rayan Chikhi,Dominique Lavenier,Dominique Lavenier,Guillaume Chapuis,Delphine Naquin,Delphine Naquin,Nicolas Maillet,Nicolas Maillet,Michael C. Schatz,David R. Kelley,Adam M. Phillippy,Sergey Koren,Shiaw-Pyng Yang,Wei Wu,Wen-Chi Chou,Anuj Srivastava,Timothy I. Shaw,J. Graham Ruby,J. Graham Ruby,Peter Skewes-Cox,Peter Skewes-Cox,Miguel Betegon,Miguel Betegon,Michelle Dimon,Michelle Dimon,Victor V. Solovyev,Igor Seledtsov,Petr Kosarev,Denis Vorobyev,Ricardo H. Ramirez-Gonzalez,Richard M. Leggett,Dan MacLean,Fangfang Xia,Ruibang Luo,Zhenyu Li,Yinlong Xie,Binghang Liu,Sante Gnerre,Iain MacCallum,Dariusz Przybylski,Filipe J. Ribeiro,Shuangye Yin,Ted Sharpe,Giles Hall,Paul J. Kersey,Richard Durbin,Shaun D. Jackman,Jarrod Chapman,Xiaoqiu Huang,Joseph L. DeRisi,Mario Caccamo,Yingrui Li,David B. Jaffe,Richard E. Green,David Haussler,Ian F Korf,Benedict Paten +78 more
TL;DR: The Assemblathon 1 competition is described, which aimed to comprehensively assess the state of the art in de novo assembly methods when applied to current sequencing technologies, and it is established that it is possible to assemble the genome to a high level of coverage and accuracy.
Journal ArticleDOI
Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species
Thomas C. Mathers,Yazhou Chen,Gemy Kaithakottil,Fabrice Legeai,Fabrice Legeai,Sam T. Mugford,Patrice Baa-Puyoulet,Anthony Bretaudeau,Anthony Bretaudeau,Bernardo J. Clavijo,Stefano Colella,Stefano Colella,Olivier Collin,Tamas Dalmay,Thomas Derrien,Honglin Feng,Toni Gabaldón,Anna Jordan,Irene Julca,Graeme J. Kettles,Graeme J. Kettles,Krissana Kowitwanich,Krissana Kowitwanich,Dominique Lavenier,Paolo Lenzi,Sara Lopez-Gomollon,Sara Lopez-Gomollon,Damian Loska,Daniel Mapleson,Florian Maumus,Simon Moxon,Daniel R. G. Price,Akiko Sugio,Akiko Sugio,Manuella van Munster,Marilyne Uzest,Darren Waite,Georg Jander,Denis Tagu,Alex C.C. Wilson,Cock van Oosterhout,David Swarbreck,David Swarbreck,Saskia A. Hogenhout,Saskia A. Hogenhout +44 more
TL;DR: It is shown that the generalist aphid pest M. persicae is able to colonise diverse host plant species in the absence of genetic specialisation through rapid transcriptional plasticity of genes that have duplicated during aphid evolution.