D
Dariusz Przybylski
Researcher at Broad Institute
Publications - 33
Citations - 8678
Dariusz Przybylski is an academic researcher from Broad Institute. The author has contributed to research in topics: Genome & Sequence assembly. The author has an hindex of 21, co-authored 31 publications receiving 7665 citations. Previous affiliations of Dariusz Przybylski include Howard Hughes Medical Institute & Columbia University.
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Journal ArticleDOI
High-quality draft assemblies of mammalian genomes from massively parallel sequence data
Sante Gnerre,Iain MacCallum,Dariusz Przybylski,Filipe J. Ribeiro,Joshua N. Burton,Bruce J. Walker,Ted Sharpe,Giles Hall,Terrance Shea,Sean M. Sykes,Aaron M. Berlin,Daniel Aird,Maura Costello,Riza M. Daza,Louise Williams,Robert Nicol,Andreas Gnirke,Chad Nusbaum,Eric S. Lander,David B. Jaffe +19 more
TL;DR: The development of an algorithm for genome assembly, ALLPATHS-LG, and its application to massively parallel DNA sequence data from the human and mouse genomes, generated on the Illumina platform, have good accuracy, short-range contiguity, long-range connectivity, and coverage of the genome.
Journal ArticleDOI
The genomic substrate for adaptive radiation in African cichlid fish
David Brawand,David Brawand,Catherine E. Wagner,Catherine E. Wagner,Yang I. Li,Milan Malinsky,Milan Malinsky,Irene Keller,Shaohua Fan,Oleg Simakov,Alvin Yu Jin Ng,Zhi Wei Lim,Etienne Bezault,Jason Turner-Maier,Jeremy A. Johnson,Rosa Alcazar,Hyun Ji Noh,Pamela Russell,Bronwen Aken,Jessica Alföldi,Chris T. Amemiya,Naoual Azzouzi,Jean-François Baroiller,Frédérique Barloy-Hubler,Aaron M. Berlin,Ryan F. Bloomquist,Karen L. Carleton,Matthew A. Conte,Helena D'Cotta,Orly Eshel,Leslie Gaffney,Francis Galibert,Hugo F. Gante,Sante Gnerre,Lucie Greuter,Lucie Greuter,Richard Guyon,Natalie S. Haddad,Wilfried Haerty,Robert M Harris,Hans A. Hofmann,Thibaut Hourlier,Gideon Hulata,David B. Jaffe,Marcia Lara,Alison P. Lee,Iain MacCallum,Salome Mwaiko,Masato Nikaido,Hidenori Nishihara,Catherine Ozouf-Costaz,David J. Penman,Dariusz Przybylski,Michaelle Rakotomanga,Suzy C. P. Renn,Filipe J. Ribeiro,Micha Ron,Walter Salzburger,Luis Sanchez-Pulido,M. Emília Santos,Steve Searle,Ted Sharpe,Ross Swofford,Frederick J. Tan,Louise Williams,Sarah Young,Shuangye Yin,Norihiro Okada,Norihiro Okada,Thomas D. Kocher,Eric A. Miska,Eric S. Lander,Byrappa Venkatesh,Russell D. Fernald,Axel Meyer,Chris P. Ponting,J. Todd Streelman,Kerstin Lindblad-Toh,Kerstin Lindblad-Toh,Ole Seehausen,Ole Seehausen,Federica Di Palma,Federica Di Palma +82 more
TL;DR: This article found an excess of gene duplications in the East African lineage compared to Nile tilapia and other teleosts, an abundance of non-coding element divergence, accelerated coding sequence evolution, expression divergence associated with transposable element insertions, and regulation by novel microRNAs.
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.
The genomic substrate for adaptive radiation in African cichlid fish
David Brawand,David Brawand,Catherine E. Wagner,Catherine E. Wagner,Yang I. Li,Milan Malinsky,Milan Malinsky,Irene Keller,Shaohua Fan,Oleg Simakov,Alvin Yu Jin Ng,Zhi Wei Lim,Etienne Bezault,Jason Turner-Maier,Jeremy A. Johnson,Rosa Alcazar,Hyun Ji Noh,Pamela Russell,Bronwen Aken,Jessica Alföldi,Chris T. Amemiya,Naoual Azzouzi,Jean-François Baroiller,Frédérique Barloy-Hubler,Aaron M. Berlin,Ryan F. Bloomquist,Karen L. Carleton,Matthew A. Conte,Helena D'Cotta,Orly Eshel,Leslie Gaffney,Francis Galibert,Hugo F. Gante,Sante Gnerre,Lucie Greuter,Lucie Greuter,Richard Guyon,Natalie S. Haddad,Wilfried Haerty,Robert M Harris,Hans A. Hofmann,Thibaut Hourlier,Gideon Hulata,David B. Jaffe,Marcia Lara,Alison P. Lee,Iain MacCallum,Salome Mwaiko,Masato Nikaido,Hidenori Nishihara,Catherine Ozouf-Costaz,David J. Penman,Dariusz Przybylski,Michaelle Rakotomanga,Suzy C. P. Renn,Filipe J. Ribeiro,Micha Ron,Walter Salzburger,Luis Sanchez-Pulido,M. Emília Santos,Steve Searle,Ted Sharpe,Ross Swofford,Frederick J. Tan,Louise Williams,Sarah Young,Shuangye Yin,Norihiro Okada,Norihiro Okada,Thomas D. Kocher,Eric A. Miska,Eric S. Lander,Byrappa Venkatesh,Russell D. Fernald,Axel Meyer,Chris P. Ponting,J. Todd Streelman,Kerstin Lindblad-Toh,Kerstin Lindblad-Toh,Ole Seehausen,Ole Seehausen,Federica Di Palma,Federica Di Palma +82 more
TL;DR: It is concluded that a number of molecular mechanisms shaped East African cichlid genomes, and that amassing of standing variation during periods of relaxed purifying selection may have been important in facilitating subsequent evolutionary diversification.
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.