N
Ngan Nguyen
Researcher at University of California, Santa Cruz
Publications - 25
Citations - 3947
Ngan Nguyen is an academic researcher from University of California, Santa Cruz. The author has contributed to research in topics: Antibody & Comparative genomics. The author has an hindex of 17, co-authored 22 publications receiving 3527 citations. Previous affiliations of Ngan Nguyen include Howard Hughes Medical Institute & Washington University in St. Louis.
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Journal ArticleDOI
The UCSC Genome Browser database: 2015 update
Kate R. Rosenbloom,Joel Armstrong,Galt P. Barber,Jonathan Casper,Hiram Clawson,Mark Diekhans,Timothy R. Dreszer,Pauline A. Fujita,Luvina Guruvadoo,Maximilian Haeussler,Rachel A. Harte,Steven G. Heitner,Glenn Hickey,Angie S. Hinrichs,Robert Hubley,Donna Karolchik,Katrina Learned,Brian T. Lee,Chin H. Li,Karen H. Miga,Ngan Nguyen,Benedict Paten,Brian J. Raney,Arian F.A. Smit,Matthew L. Speir,Ann S. Zweig,David Haussler,Robert M. Kuhn,W. James Kent +28 more
TL;DR: A browser for the first new human genome reference assembly in 4 years in December 2013, a watershed comparative genomics annotation (100-species multiple alignment and conservation), and a novel distribution mechanism for the browser are among the highlights of the past year.
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
Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10 000 Vertebrate Species
David Haussler,Stephen J. O'Brien,Oliver A. Ryder,F. Keith Barker,Michele Clamp,Andrew J. Crawford,Robert Hanner,Olivier Hanotte,Warren E. Johnson,Jimmy A. McGuire,Webb Miller,Robert W. Murphy,William J. Murphy,Frederick H. Sheldon,Barry Sinervo,Byrappa Venkatesh,Edward O. Wiley,Fred W. Allendorf,George Amato,C. Scott Baker,Aaron M. Bauer,Albano Beja-Pereira,Eldredge Bermingham,Giacomo Bernardi,Cibele R. Bonvicino,Sydney Brenner,Terry Burke,Joel Cracraft,Mark Diekhans,Scott V. Edwards,Per G. P. Ericson,James A. Estes,Jon Fjelsda,Nate Flesness,Tony Gamble,Philippe Gaubert,Alexander S. Graphodatsky,Jennifer A. Marshall Graves,Erik D. Green,Richard E. Green,Shannon J. Hackett,Paul D. N. Hebert,Kristofer M. Helgen,Leo Joseph,Bailey Kessing,David M. Kingsley,Harris A. Lewin,Gordon Luikart,Paola Martelli,Miguel A. M. Moreira,Ngan Nguyen,Guillermo Ortí,Brian L. Pike,David M. Rawson,Stephan C. Schuster,Héctor N. Seuánez,H. Bradley Shaffer,Mark S. Springer,Joshua M. Stuart,Joanna Sumner,Emma C. Teeling,Robert C. Vrijenhoek,Robert D. Ward,Wesley C. Warren,Robert K. Wayne,Terrie M. Williams,Nathan D. Wolfe,Ya-Ping Zhang,Adam Felsenfeld,Steve Turner +69 more
TL;DR: A precipitous drop in costs and increase in sequencing efficiency is anticipated, with concomitant development of improved annotation technology, and it is proposed to create a collection of tissue and DNA specimens for 10,000 vertebrate species specifically designated for whole-genome sequencing in the very near future.
Journal ArticleDOI
An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons
Frank M. J. Jacobs,David Greenberg,Ngan Nguyen,Maximilian Haeussler,Adam D. Ewing,Sol Katzman,Benedict Paten,Sofie R. Salama,David Haussler +8 more
TL;DR: The data support a model where KZNF gene expansion limits the activity of newly emerged Retrotransposon classes, and this is followed by mutations in these retrotransposons to evade repression, a cycle of events that could explain the rapid expansion of lineage-specific KZ NF genes.
Journal ArticleDOI
Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser
Brian J. Raney,Timothy R. Dreszer,Galt P. Barber,Hiram Clawson,Pauline A. Fujita,Ting Wang,Ngan Nguyen,Benedict Paten,Ann S. Zweig,Donna Karolchik,W. James Kent +10 more
TL;DR: Track data hubs provide an efficient mechanism for visualizing remotely hosted Internet-accessible collections of genome annotations and for the first time, individuals can use the complete browser feature set to view custom datasets without the overhead of setting up and maintaining a mirror.