Xiaoqiu Huang

Xiaoqiu Huang

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Xiaoqiu Huang

Xiaoqiu Huang

Publications by authors named "Xiaoqiu Huang"

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36Publications

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HPC: Hierarchical phylogeny construction.

PLoS One 2019 22;14(8):e0221357. Epub 2019 Aug 22.

Department of Computer Science, Iowa State University, Ames, Iowa, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0221357PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6705828PMC
August 2019

Protein expression analysis revealed a fine-tuned mechanism of in situ detoxification pathway for the tolerant industrial yeast Saccharomyces cerevisiae.

Appl Microbiol Biotechnol 2019 Jul 28;103(14):5781-5796. Epub 2019 May 28.

Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, Shandong, China.

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http://dx.doi.org/10.1007/s00253-019-09906-9DOI Listing
July 2019

Sequence Assembly.

Authors:
Xiaoqiu Huang

Methods Mol Biol 2017 ;1525:35-45

Department of Computer Science, Iowa State University, Ames, IA, 50011, USA.

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http://dx.doi.org/10.1007/978-1-4939-6622-6_2DOI Listing
January 2018

NucAmino: a nucleotide to amino acid alignment optimized for virus gene sequences.

BMC Bioinformatics 2017 Mar 1;18(1):138. Epub 2017 Mar 1.

Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA.

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http://dx.doi.org/10.1186/s12859-017-1555-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5333393PMC
March 2017

Horizontal transfer generates genetic variation in an asexual pathogen.

Authors:
Xiaoqiu Huang

PeerJ 2014 30;2:e650. Epub 2014 Oct 30.

Department of Computer Science and Plant Sciences Institute, Iowa State University , Ames, IA , USA.

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http://dx.doi.org/10.7717/peerj.650DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4217194PMC
November 2014

Sequence-specific sequence comparison using pairwise statistical significance.

Adv Exp Med Biol 2011 ;696:297-306

Department of Electrical Engineering and Computer Science, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.

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http://link.springer.com/10.1007/978-1-4419-7046-6_30
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http://dx.doi.org/10.1007/978-1-4419-7046-6_30DOI Listing
June 2011

Pairwise statistical significance of local sequence alignment using sequence-specific and position-specific substitution matrices.

IEEE/ACM Trans Comput Biol Bioinform 2011 Jan-Mar;8(1):194-205

Department of Computer Science, Iowa State University, 226 Atanasoff Hall, Ames, IA 50011-1041, USA.

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http://dx.doi.org/10.1109/TCBB.2009.69DOI Listing
February 2011

Pairwise statistical significance and empirical determination of effective gap opening penalties for protein local sequence alignment.

Int J Comput Biol Drug Des 2008 ;1(4):347-67

Department of Computer Science, Iowa State University, Ames, IA 50011-1041, USA.

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March 2010

Maximum similarity: a new formulation of phylogenetic reconstruction.

J Comput Biol 2009 Jul;16(7):887-96

Department of Computer Science, Iowa State University, Ames, Iowa 50011-1040, USA.

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http://dx.doi.org/10.1089/cmb.2008.0232DOI Listing
July 2009

PSIBLAST_PairwiseStatSig: reordering PSI-BLAST hits using pairwise statistical significance.

Bioinformatics 2009 Apr 27;25(8):1082-3. Epub 2009 Feb 27.

Department of Computer Science, Iowa State University, Ames, IA 50011-1041, USA.

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http://dx.doi.org/10.1093/bioinformatics/btp089DOI Listing
April 2009

Pairwise statistical significance of local sequence alignment using multiple parameter sets and empirical justification of parameter set change penalty.

BMC Bioinformatics 2009 Mar 19;10 Suppl 3:S1. Epub 2009 Mar 19.

Department of Computer Science, Iowa State University, 226 Atanasoff Hall, Ames, IA 50011-1041, USA.

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http://www.biomedcentral.com/1471-2105/10/S3/S1
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http://dx.doi.org/10.1186/1471-2105-10-S3-S1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2665049PMC
March 2009

Genome analysis of the platypus reveals unique signatures of evolution.

Authors:
Wesley C Warren LaDeana W Hillier Jennifer A Marshall Graves Ewan Birney Chris P Ponting Frank Grützner Katherine Belov Webb Miller Laura Clarke Asif T Chinwalla Shiaw-Pyng Yang Andreas Heger Devin P Locke Pat Miethke Paul D Waters Frédéric Veyrunes Lucinda Fulton Bob Fulton Tina Graves John Wallis Xose S Puente Carlos López-Otín Gonzalo R Ordóñez Evan E Eichler Lin Chen Ze Cheng Janine E Deakin Amber Alsop Katherine Thompson Patrick Kirby Anthony T Papenfuss Matthew J Wakefield Tsviya Olender Doron Lancet Gavin A Huttley Arian F A Smit Andrew Pask Peter Temple-Smith Mark A Batzer Jerilyn A Walker Miriam K Konkel Robert S Harris Camilla M Whittington Emily S W Wong Neil J Gemmell Emmanuel Buschiazzo Iris M Vargas Jentzsch Angelika Merkel Juergen Schmitz Anja Zemann Gennady Churakov Jan Ole Kriegs Juergen Brosius Elizabeth P Murchison Ravi Sachidanandam Carly Smith Gregory J Hannon Enkhjargal Tsend-Ayush Daniel McMillan Rosalind Attenborough Willem Rens Malcolm Ferguson-Smith Christophe M Lefèvre Julie A Sharp Kevin R Nicholas David A Ray Michael Kube Richard Reinhardt Thomas H Pringle James Taylor Russell C Jones Brett Nixon Jean-Louis Dacheux Hitoshi Niwa Yoko Sekita Xiaoqiu Huang Alexander Stark Pouya Kheradpour Manolis Kellis Paul Flicek Yuan Chen Caleb Webber Ross Hardison Joanne Nelson Kym Hallsworth-Pepin Kim Delehaunty Chris Markovic Pat Minx Yucheng Feng Colin Kremitzki Makedonka Mitreva Jarret Glasscock Todd Wylie Patricia Wohldmann Prathapan Thiru Michael N Nhan Craig S Pohl Scott M Smith Shunfeng Hou Mikhail Nefedov Pieter J de Jong Marilyn B Renfree Elaine R Mardis Richard K Wilson

Nature 2008 May;453(7192):175-83

Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA.

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http://dx.doi.org/10.1038/nature06936DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2803040PMC
May 2008

Sequence alignment with an appropriate substitution matrix.

Authors:
Xiaoqiu Huang

J Comput Biol 2008 Mar;15(2):129-38

Department of Computer Science, Iowa State University, Ames, Iowa 50011-1040, USA.

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http://www.liebertpub.com/doi/10.1089/cmb.2007.0155
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http://dx.doi.org/10.1089/cmb.2007.0155DOI Listing
March 2008

Evolutionary and biomedical insights from the rhesus macaque genome.

Authors:
Richard A Gibbs Jeffrey Rogers Michael G Katze Roger Bumgarner George M Weinstock Elaine R Mardis Karin A Remington Robert L Strausberg J Craig Venter Richard K Wilson Mark A Batzer Carlos D 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 Dao Clay Davis Kimberly D Delehaunty Yan Ding Huyen H Dinh Shannon Dugan-Rocha Lucinda A Fulton Ramatu Ayiesha Gabisi Toni T Garner Jennifer Godfrey Alicia C Hawes Judith Hernandez Sandra Hines Michael Holder Jennifer Hume Shalini N Jhangiani Vandita Joshi Ziad Mohid Khan Ewen F Kirkness Andrew Cree R Gerald Fowler Sandra Lee Lora R Lewis Zhangwan Li Yih-Shin Liu Stephanie M Moore Donna Muzny Lynne V Nazareth Dinh Ngoc Ngo Geoffrey O Okwuonu Grace Pai David Parker Heidie A Paul Cynthia Pfannkoch Craig S Pohl Yu-Hui Rogers San Juana Ruiz Aniko Sabo Jireh Santibanez Brian W Schneider Scott M Smith Erica Sodergren Amanda F Svatek Teresa R Utterback Selina Vattathil Wesley Warren Courtney Sherell White Asif T Chinwalla Yucheng Feng Aaron L Halpern Ladeana W Hillier Xiaoqiu Huang Pat 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 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 Richard Burhans Ze Cheng John E Karro Jian Ma Brian Raney Xinwei She Michael J Cox Jeffery P Demuth Laura J Dumas Sang-Gook Han Janet Hopkins Anis Karimpour-Fard Young H Kim Jonathan R Pollack Tomas Vinar Charles Addo-Quaye Jeremiah 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 N Cooper Belinda Giardine Fan Hsu W James Kent Arthur Lesk David L Nelson William E O'brien Kay Prüfer Peter D Stenson James C Wallace Hui Ke Xiao-Ming Liu Peng Wang Andy Peng Xiang Fan Yang Galt P Barber David Haussler Donna Karolchik Andy D Kern Robert M Kuhn Kayla E Smith Ann S Zwieg

Science 2007 Apr;316(5822):222-34

Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.

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http://dx.doi.org/10.1126/science.1139247DOI Listing
April 2007

Dynamic use of multiple parameter sets in sequence alignment.

Nucleic Acids Res 2007 19;35(2):678-86. Epub 2006 Dec 19.

Department of Computer Science, Iowa State University, Ames, IA 50011-1040, USA.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkl1063DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1802605PMC
March 2007

Evolution of alternative splicing after gene duplication.

Genome Res 2006 Feb 19;16(2):182-9. Epub 2005 Dec 19.

James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310008, China.

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http://dx.doi.org/10.1101/gr.4197006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1361713PMC
February 2006

Application of a superword array in genome assembly.

Nucleic Acids Res 2006 5;34(1):201-5. Epub 2006 Jan 5.

Department of Computer Science, Iowa State University, Ames, IA 50011-1040, USA.

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http://dx.doi.org/10.1093/nar/gkj419DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1325203PMC
January 2006

Generating a genome assembly with PCAP.

Curr Protoc Bioinformatics 2005 Oct;Chapter 11:Unit11.3

Iowa State University, Ames, Iowa, USA.

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http://dx.doi.org/10.1002/0471250953.bi1103s11DOI Listing
October 2005

A method for finding single-nucleotide polymorphisms with allele frequencies in sequences of deep coverage.

BMC Bioinformatics 2005 Sep 7;6:220. Epub 2005 Sep 7.

Department of Computer Science, Iowa State University, Ames, Iowa 50011, USA.

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/1471-2105-6-220DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1239908PMC
September 2005

Generation and annotation of the DNA sequences of human chromosomes 2 and 4.

Authors:
Ladeana W Hillier Tina A Graves Robert S Fulton Lucinda A Fulton Kymberlie H Pepin Patrick Minx Caryn Wagner-McPherson Dan Layman Kristine Wylie Mandeep Sekhon Michael C Becker Ginger A Fewell Kimberly D Delehaunty Tracie L Miner William E Nash Colin Kremitzki Lachlan Oddy Hui Du Hui Sun Holland Bradshaw-Cordum Johar Ali Jason Carter Matt Cordes Anthony Harris Amber Isak Andrew van Brunt Christine Nguyen Feiyu Du Laura Courtney Joelle Kalicki Philip Ozersky Scott Abbott Jon Armstrong Edward A Belter Lauren Caruso Maria Cedroni Marc Cotton Teresa Davidson Anu Desai Glendoria Elliott Thomas Erb Catrina Fronick Tony Gaige William Haakenson Krista Haglund Andrea Holmes Richard Harkins Kyung Kim Scott S Kruchowski Cynthia Madsen Strong Neenu Grewal Ernest Goyea Shunfang Hou Andrew Levy Scott Martinka Kelly Mead Michael D McLellan Rick Meyer Jennifer Randall-Maher Chad Tomlinson Sara Dauphin-Kohlberg Amy Kozlowicz-Reilly Neha Shah Sharhonda Swearengen-Shahid Jacqueline Snider Joseph T Strong Johanna Thompson Martin Yoakum Shawn Leonard Charlene Pearman Lee Trani Maxim Radionenko Jason E Waligorski Chunyan Wang Susan M Rock Aye-Mon Tin-Wollam Rachel Maupin Phil Latreille Michael C Wendl Shiaw-Pyng Yang Craig Pohl John W Wallis John Spieth Tamberlyn A Bieri Nicolas Berkowicz Joanne O Nelson John Osborne Li Ding Rekha Meyer Aniko Sabo Yoram Shotland Prashant Sinha Patricia E Wohldmann Lisa L Cook Matthew T Hickenbotham James Eldred Donald Williams Thomas A Jones Xinwei She Francesca D Ciccarelli Elisa Izaurralde James Taylor Jeremy Schmutz Richard M Myers David R Cox Xiaoqiu Huang John D McPherson Elaine R Mardis Sandra W Clifton Wesley C Warren Asif T Chinwalla Sean R Eddy Marco A Marra Ivan Ovcharenko Terrence S Furey Webb Miller Evan E Eichler Peer Bork Mikita Suyama David Torrents Robert H Waterston Richard K Wilson

Nature 2005 Apr;434(7034):724-31

Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St. Louis, Missouri 63108, USA.

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http://dx.doi.org/10.1038/nature03466DOI Listing
April 2005

MAP2: multiple alignment of syntenic genomic sequences.

Nucleic Acids Res 2005 7;33(1):162-70. Epub 2005 Jan 7.

Department of Computer Science, Iowa State University 226 Atanasoff Hall, Ames, IA 50011-1040, USA.

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http://dx.doi.org/10.1093/nar/gki159DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC546147PMC
February 2005

Efficient combination of multiple word models for improved sequence comparison.

Bioinformatics 2004 Nov 29;20(16):2529-33. Epub 2004 Apr 29.

Department of Computer Science, Iowa State University, Ames, IA 50011-1040, USA.

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http://dx.doi.org/10.1093/bioinformatics/bth279DOI Listing
November 2004

Over 20% of human transcripts might form sense-antisense pairs.

Nucleic Acids Res 2004 8;32(16):4812-20. Epub 2004 Sep 8.

Department of Medicine, University of Chicago, 5841 S. Maryland Avenue, MC2115, Chicago, IL 60637, USA.

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http://dx.doi.org/10.1093/nar/gkh818DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC519112PMC
September 2004

Fibroblast growth and H-7 protein kinase inhibitor response monitored in microimpedance sensor arrays.

Biotechnol Bioeng 2004 Jul;87(2):138-44

Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA.

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http://dx.doi.org/10.1002/bit.20070DOI Listing
July 2004

PCAP: a whole-genome assembly program.

Genome Res 2003 Sep;13(9):2164-70

Department of Computer Science Iowa State University, Ames, Iowa 50011-1040, USA.

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http://dx.doi.org/10.1101/gr.1390403DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC403719PMC
September 2003

MAVG: locating non-overlapping maximum average segments in a given sequence.

Bioinformatics 2003 Jan;19(1):151-2

Department of Computer Science and Information Management, Providence University, Shalu 433, Taiwan.

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http://dx.doi.org/10.1093/bioinformatics/19.1.151DOI Listing
January 2003

A generalized global alignment algorithm.

Bioinformatics 2003 Jan;19(2):228-33

Department of Computer Science, Iowa State University, 226 Atanasoff Hall, Ames, IA 50011-1040, USA.

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http://dx.doi.org/10.1093/bioinformatics/19.2.228DOI Listing
January 2003