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Yujian Shi
Researcher at Peking University
Publications - 25
Citations - 7919
Yujian Shi is an academic researcher from Peking University. The author has contributed to research in topics: Sequence assembly & Hybrid genome assembly. The author has an hindex of 15, co-authored 20 publications receiving 6809 citations. Previous affiliations of Yujian Shi include University of Hong Kong & South China University of Technology.
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Journal ArticleDOI
SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler
Ruibang Luo,Binghang Liu,Yinlong Xie,Yinlong Xie,Zhenyu Li,Weihua Huang,Jianying Yuan,Guangzhu He,Yanxiang Chen,Qi Pan,Yunjie Liu,Jingbo Tang,Gengxiong Wu,Hao Zhang,Yujian Shi,Yong Liu,Chang Yu,Bo Wang,Yao Lu,Changlei Han,David W. Cheung,Siu-Ming Yiu,Shaoliang Peng,Zhu Xiao-qian,Guangming Liu,Xiangke Liao,Yingrui Li,Huanming Yang,Jian Wang,Tak-Wah Lam,Jun Wang +30 more
TL;DR: This work provides an updated assembly version of the 2008 Asian genome using SOAPdenovo2, a new algorithm design that reduces memory consumption in graph construction, resolves more repeat regions in contig assembly, increases coverage and length in scaffold construction, improves gap closing, and optimizes for large genome.
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
Whole-Genome Sequencing in Autism Identifies Hot Spots for De Novo Germline Mutation
Jacob J. Michaelson,Yujian Shi,Madhusudan Gujral,Hancheng Zheng,Dheeraj Malhotra,Xin Jin,Minghan Jian,Guangming Liu,Douglas S. Greer,Abhishek Bhandari,Wenting Wu,Roser Corominas,Aine Peoples,Aine Peoples,Amnon Koren,Athurva Gore,Shuli Kang,Guan Ning Lin,Jasper A. Estabillo,Therese E. Gadomski,Balvindar Singh,Kun Zhang,Natacha Akshoomoff,Christina Corsello,Steven A. McCarroll,Lilia M. Iakoucheva,Yingrui Li,Jun Wang,Jun Wang,Jonathan Sebat +29 more
TL;DR: This article investigated global patterns of germline mutation by whole-genome sequencing of monozygotic twins concordant for ASD and their parents and found that hypermutability is a property of ASD genes and may also include nucleotide substitution hot spots.
Journal ArticleDOI
Detection of Clinically Relevant Genetic Variants in Autism Spectrum Disorder by Whole-Genome Sequencing
Yong-hui Jiang,Ryan K. C. Yuen,Xin Jin,Xin Jin,Mingbang Wang,Nong Chen,Xueli Wu,Jia Ju,Junpu Mei,Yujian Shi,Mingze He,Guangbiao Wang,Jieqin Liang,Zhe Wang,Dandan Cao,Melissa T. Carter,Christina Chrysler,Irene Drmic,Jennifer L. Howe,Lynette Lau,Christian R. Marshall,Christian R. Marshall,Daniele Merico,Thomas Nalpathamkalam,Bhooma Thiruvahindrapuram,Ann Thompson,Mohammed Uddin,Susan Walker,J. Luo,Evdokia Anagnostou,Lonnie Zwaigenbaum,Robert H. Ring,Jian Wang,Clara Lajonchere,Jun Wang,Andy Shih,Peter Szatmari,Huanming Yang,Geraldine Dawson,Geraldine Dawson,Yingrui Li,Stephen W. Scherer,Stephen W. Scherer +42 more
TL;DR: Results suggest that WGS and thorough bioinformatic analyses for de novo and rare inherited mutations will improve the detection of genetic variants likely to be associated with ASD or its accompanying clinical symptoms.