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Xiaoqiu Huang
Researcher at Iowa State University
Publications - 56
Citations - 15462
Xiaoqiu Huang is an academic researcher from Iowa State University. The author has contributed to research in topics: Multiple sequence alignment & Alignment-free sequence analysis. The author has an hindex of 26, co-authored 56 publications receiving 14801 citations. Previous affiliations of Xiaoqiu Huang include Michigan Technological University.
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Journal ArticleDOI
CAP3: A DNA Sequence Assembly Program
Xiaoqiu Huang,Anup Madan +1 more
TL;DR: The third generation of the CAP sequence assembly program is described, which has a capability to clip 5' and 3' low-quality regions of reads and uses forward-reverse constraints to correct assembly errors and link contigs.
Journal ArticleDOI
Initial sequence of the chimpanzee genome and comparison with the human genome
Tarjei S. Mikkelsen,LaDeana W. Hillier,Evan E. Eichler,Michael C. Zody,David B. Jaffe,Shiaw-Pyng Yang,Wolfgang Enard,Ines Hellmann,Kerstin Lindblad-Toh,Tasha K. Altheide,Nicoletta Archidiacono,Peer Bork,Jonathan Butler,Jean L. Chang,Ze Cheng,Asif T. Chinwalla,Pieter J. de Jong,Kimberley D. Delehaunty,Catrina Fronick,Lucinda L. Fulton,Yoav Gilad,Gustavo Glusman,Sante Gnerre,Tina Graves,Toshiyuki Hayakawa,Karen E. Hayden,Xiaoqiu Huang,Hongkai Ji,W. James Kent,Mary Claire King,Edward J. Kulbokasl,Ming K. Lee,Ge Liu,Carlos López-Otín,Kateryna D. Makova,Orna Man,Elaine R. Mardis,Evan Mauceli,Tracie L. Miner,William E. Nash,Joanne O. Nelson,Svante Pääbo,Nick Patterson,Craig Pohl,Katherine S. Pollard,Kay Prüfer,Xose S. Puente,David Reich,Mariano Rocchi,Kate R. Rosenbloom,Maryellen Ruvolo,Daniel J. Richter,Stephen F. Schaffner,Arian F.A. Smit,Scott M. Smith,Mikita Suyama,James E. Taylor,David Torrents,Eray Tüzün,Ajit Varki,Gloria Velasco,Mario Ventura,John W. Wallis,Michael C. Wendl,Richard K. Wilson,Eric S. Lander,Robert H. Waterston +66 more
TL;DR: It is found that the patterns of evolution in human and chimpanzee protein-coding genes are highly correlated and dominated by the fixation of neutral and slightly deleterious alleles.
Journal ArticleDOI
TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets
Geo Pertea,Xiaoqiu Huang,Feng Liang,Valentin Antonescu,Razvan Sultana,Svetlana Karamycheva,Yuandan Lee,Joseph White,Foo Cheung,Babak Parvizi,Jennifer Tsai,John Quackenbush +11 more
TL;DR: TGICL is a pipeline for analysis of large Expressed Sequence Tags and mRNA databases in which the sequences are first clustered based on pairwise sequence similarity, and then assembled by individual clusters to produce longer, more complete consensus sequences.
Journal ArticleDOI
Evolutionary and biomedical insights from the rhesus macaque genome
Richard A. Gibbs,Jeffrey Rogers,Michael G. Katze,Roger E. Bumgarner,George M. Weinstock,Elaine R. Mardis,Karin A. Remington,Robert L. Strausberg,J. Craig Venter,Richard K. Wilson,Mark A. Batzer,Carlos Bustamante,Evan E. Eichler,Matthew W. Hahn,Ross C. Hardison,Kateryna D. Makova,Webb Miller,Aleksandar Milosavljevic,Robert E. Palermo,Adam Siepel,James M. Sikela,Tony Attaway,Stephanie Bell,Kelly E. Bernard,Christian J. Buhay,Mimi N. Chandrabose,Marvin Diep Dao,Clay Davis,Kimberly D. Delehaunty,Yan Ding,Huyen Dinh,Shannon Dugan-Rocha,Lucinda Fulton,Ramatu Ayiesha Gabisi,Toni T. Garner,Jennifer Godfrey,Alicia Hawes,Judith Hernandez,Sandra Hines,Michael Holder,Jennifer Hume,Shalini N. Jhangiani,Vandita Joshi,Ziad Khan,Ewen F. Kirkness,Andrew Cree,R. Gerald Fowler,Sandra L. Lee,Lora Lewis,Zhangwan Li,Yih-shin Liu,Stephanie M. Moore,Donna M. Muzny,Lynne V. Nazareth,Dinh Ngoc Ngo,Geoffrey Okwuonu,Grace Pai,David A. Parker,Heidie A. Paul,Cynthia Pfannkoch,Craig Pohl,Yu-Hui Rogers,San Juana Ruiz,Aniko Sabo,Jireh Santibanez,Brian W. Schneider,Scott M. Smith,Erica Sodergren,Amanda F. Svatek,Teresa Utterback,Selina Vattathil,Wesley C. Warren,Courtney Sherell White,Asif T. Chinwalla,Yucheng Feng,Aaron L. Halpern,LaDeana W. Hillier,Xiaoqiu Huang,Patrick Minx,Joanne O. Nelson,Kymberlie H. Pepin,Xiang Qin,Granger G. Sutton,Eli Venter,Brian P. Walenz,John W. Wallis,Kim C. Worley,Shiaw-Pyng Yang,Steven J. M. Jones,Marco A. Marra,Mariano Rocchi,Jacqueline E. Schein,Robert Baertsch,Laura Clarke,Miklós Csürös,Jarret Glasscock,R. Alan Harris,Paul Havlak,Andrew R. Jackson,Huaiyang Jiang,Yue Liu,David N. Messina,Yufeng Shen,Henry Xing-Zhi Song,Todd Wylie,Lan Zhang,Ewan Birney,Kyudong Han,Miriam K. Konkel,Jungnam Lee,Arian F.A. Smit,Brygg Ullmer,Hui Wang,Jinchuan Xing,Jinchuan Xing,Richard Burhans,Ze Cheng,John E. Karro,Jian Ma,Brian J. Raney,Xinwei She,Michael J. Cox,Jeffery P. Demuth,Laura J. Dumas,Sang-Gook Han,Janet A. Hopkins,Anis Karimpour-Fard,Young Ho Kim,Jonathan R. Pollack,Tomas Vinar,Charles Addo-Quaye,Jeremiah D. Degenhardt,Alexandra Denby,Melissa J. Hubisz,Amit Indap,Carolin Kosiol,Bruce T. Lahn,Heather A. Lawson,Alison Marklein,Rasmus Nielsen,Eric J. Vallender,Andrew G. Clark,Betsy Ferguson,Ryan D. Hernandez,Kashif Hirani,Hildegard Kehrer-Sawatzki,Jessica Kolb,Shobha Patil,Ling-Ling Pu,Yanru Ren,David Glenn Smith,David A. Wheeler,Ian Schenck,Edward V. Ball,Rui Chen,David Neil Cooper,Belinda Giardine,Fan Hsu,W. James Kent,Arthur M. Lesk,David L. Nelson,William E. O'Brien,Kay Prüfer,Peter D. Stenson,James C. Wallace,Hui Ke,Xiaoming Liu,Peng Wang,Andy Peng Xiang,Fan Yang,Galt P. Barber,David Haussler,David Haussler,Donna Karolchik,Andrew D. Kern,Robert M. Kuhn,Kayla E. Smith,Ann S. Zwieg +177 more
TL;DR: The genome sequence of an Indian-origin Macaca mulatta female is determined and compared with chimpanzees and humans to reveal the structure of ancestral primate genomes and to identify evidence for positive selection and lineage-specific expansions and contractions of gene families.
Journal ArticleDOI
A time-efficient, linear-space local similarity algorithm
Xiaoqiu Huang,Webb Miller +1 more
TL;DR: This paper presents a time-efficient algorithm that produces k best ''non-intersecting'' local alignments for any chosen k that needs only O(M + N + K) space.