John E Karro

John E Karro

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John E Karro

John E Karro

Publications by authors named "John E Karro"

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phRAIDER: Pattern-Hunter based Rapid Ab Initio Detection of Elementary Repeats.

Bioinformatics 2016 06;32(12):i209-i215

Department of Computer Science and Software Engineering Department of Cell, Molecular, and Structural Biology Department of Microbiology Department of Statistics, Miami University, Oxford, OH, USA.

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http://dx.doi.org/10.1093/bioinformatics/btw258DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4908342PMC
June 2016

SCOPE++: sequence classification of homoPolymer emissions.

Genomics 2014 Sep 1;104(3):157-62. Epub 2014 Aug 1.

Department of Computer Science and Software Engineering, Miami University, Oxford, OH, USA; Department of Microbiology, Miami University, Oxford, OH, USA; Department of Statistics, Miami University, Oxford, OH, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ygeno.2014.07.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4165746PMC
September 2014

A MATLAB-based tool for accurate detection of perfect overlapping and nested inverted repeats in DNA sequences.

Bioinformatics 2014 Mar 8;30(6):887-8. Epub 2013 Nov 8.

Department of Biology, Department of Computer Science and Software Engineering, Miami University, Oxford, OH 45056, USA and State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.

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http://dx.doi.org/10.1093/bioinformatics/btt651DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3957078PMC
March 2014

Weak preservation of local neutral substitution rates across mammalian genomes.

BMC Evol Biol 2009 May 5;9:89. Epub 2009 May 5.

Boston College, Department of Biology, Chestnut Hill, MA 02467, USA.

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http://dx.doi.org/10.1186/1471-2148-9-89DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2689173PMC
May 2009

Human-macaque comparisons illuminate variation in neutral substitution rates.

Genome Biol 2008 Apr 30;9(4):R76. Epub 2008 Apr 30.

Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, PA 16802, USA.

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http://dx.doi.org/10.1186/gb-2008-9-4-r76DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2643947PMC
April 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

Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation.

Nucleic Acids Res 2007 Jan 11;35(Database issue):D55-60. Epub 2006 Nov 11.

Center for Comparative Genomics and Bioinformatics, 506B Wartik, Pennsylvania State University, University Park, PA 16802, USA.

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http://dx.doi.org/10.1093/nar/gkl851DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1669708PMC
January 2007