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Nicolas Maillet
Researcher at Pasteur Institute
Publications - 13
Citations - 2287
Nicolas Maillet is an academic researcher from Pasteur Institute. The author has contributed to research in topics: Genome & Sequence assembly. The author has an hindex of 10, co-authored 12 publications receiving 2130 citations. Previous affiliations of Nicolas Maillet include Laval University & Centre national de la recherche scientifique.
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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
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.
Patterns and processes of genomic divergence during speciation || Genome-wide patterns of divergence during speciation: the lake whitefish case study
S. Renaut,Nicolas Maillet,E. Normandeau,Christopher Sauvage,N. Derome,S. M. Rogers,L. Bernatchez +6 more
TL;DR: These results confirmed the predictions that on average, phenotypic quantitative trait loci show higher FST values and are more likely to be outliers (and therefore candidates for being targets of divergent selection) than non-pQTL markers and there is a general trend towards an increase in terms of numbers and size of genomic regions of divergence.
Journal ArticleDOI
Genome-wide patterns of divergence during speciation: the lake whitefish case study
Sébastien Renaut,Nicolas Maillet,Eric Normandeau,Christopher Sauvage,Nicolas Derome,Sean M. Rogers,Louis Bernatchez +6 more
TL;DR: The nature, size and distribution of the genomic regions underlying divergence and promoting reproductive isolation remain largely unknown as discussed by the authors, and the authors summarize ongoing efforts using young (12 000 yr old) individuals.