Publications by authors named "Arthur L Delcher"

39Publications

MUMmer4: A fast and versatile genome alignment system.

PLoS Comput Biol 2018 01 26;14(1):e1005944. Epub 2018 Jan 26.

Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, United States of America.

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https://dx.plos.org/10.1371/journal.pcbi.1005944
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http://dx.doi.org/10.1371/journal.pcbi.1005944DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5802927PMC
January 2018

Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering.

Nucleic Acids Res 2012 Jan 18;40(1):e9. Epub 2011 Nov 18.

Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, Department of Computer Science, 3115 Biomolecular Sciences Building 296, University of Maryland, College Park, MD 20742, USA.

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http://dx.doi.org/10.1093/nar/gkr1067DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245904PMC
January 2012

Core gene set as the basis of multilocus sequence analysis of the subclass Actinobacteridae.

PLoS One 2011 Mar 31;6(3):e14792. Epub 2011 Mar 31.

Mycobacteriology Laboratory Branch, Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0014792PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3069002PMC
March 2011

Genome sequence of the dioxin-mineralizing bacterium Sphingomonas wittichii RW1.

J Bacteriol 2010 Nov 10;192(22):6101-2. Epub 2010 Sep 10.

Department of Bacteriology, University of Wisconsin, Madison, Wisconsin 53706, USA.

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http://dx.doi.org/10.1128/JB.01030-10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2976435PMC
November 2010

Assembly of large genomes using second-generation sequencing.

Genome Res 2010 Sep 27;20(9):1165-73. Epub 2010 May 27.

Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland 20742, USA.

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http://genome.cshlp.org/cgi/doi/10.1101/gr.101360.109
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http://dx.doi.org/10.1101/gr.101360.109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2928494PMC
September 2010

Sim4cc: a cross-species spliced alignment program.

Nucleic Acids Res 2009 Jun 8;37(11):e80. Epub 2009 May 8.

Department of Computer Science, George Washington University, Washington, DC 20052, USA.

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http://dx.doi.org/10.1093/nar/gkp319DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2699533PMC
June 2009

Aggressive assembly of pyrosequencing reads with mates.

Bioinformatics 2008 Dec 24;24(24):2818-24. Epub 2008 Oct 24.

The J. Craig Venter Institute, 9712 Medical Center Drive, Rockville MD 20850, USA.

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http://dx.doi.org/10.1093/bioinformatics/btn548DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2639302PMC
December 2008

The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus).

Nature 2008 Apr;452(7190):991-6

Hawaii Agriculture Research Center, Aiea, Hawaii 96701, USA.

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http://dx.doi.org/10.1038/nature06856DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2836516PMC
April 2008

Using MUMmer to identify similar regions in large sequence sets.

Curr Protoc Bioinformatics 2003 Feb;Chapter 10:Unit 10.3

The Institute for Genomic Research Rockville, Maryland and Computer Science Department, Loyola College in Maryland, Baltimore, Maryland, USA.

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http://dx.doi.org/10.1002/0471250953.bi1003s00DOI Listing
February 2003

High-throughput sequence alignment using Graphics Processing Units.

BMC Bioinformatics 2007 Dec 10;8:474. Epub 2007 Dec 10.

Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA.

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http://dx.doi.org/10.1186/1471-2105-8-474DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2222658PMC
December 2007

Evolution of genes and genomes on the Drosophila phylogeny.

Authors:
Andrew G Clark Michael B Eisen Douglas R Smith Casey M Bergman Brian Oliver Therese A Markow Thomas C Kaufman Manolis Kellis William Gelbart Venky N Iyer Daniel A Pollard Timothy B Sackton Amanda M Larracuente Nadia D Singh Jose P Abad Dawn N Abt Boris Adryan Montserrat Aguade Hiroshi Akashi Wyatt W Anderson Charles F Aquadro David H Ardell Roman Arguello Carlo G Artieri Daniel A Barbash Daniel Barker Paolo Barsanti Phil Batterham Serafim Batzoglou Dave Begun Arjun Bhutkar Enrico Blanco Stephanie A Bosak Robert K Bradley Adrianne D Brand Michael R Brent Angela N Brooks Randall H Brown Roger K Butlin Corrado Caggese Brian R Calvi A Bernardo de Carvalho Anat Caspi Sergio Castrezana Susan E Celniker Jean L Chang Charles Chapple Sourav Chatterji Asif Chinwalla Alberto Civetta Sandra W Clifton Josep M Comeron James C Costello Jerry A Coyne Jennifer Daub Robert G David Arthur L Delcher Kim Delehaunty Chuong B Do Heather Ebling Kevin Edwards Thomas Eickbush Jay D Evans Alan Filipski Sven Findeiss Eva Freyhult Lucinda Fulton Robert Fulton Ana C L Garcia Anastasia Gardiner David A Garfield Barry E Garvin Greg Gibson Don Gilbert Sante Gnerre Jennifer Godfrey Robert Good Valer Gotea Brenton Gravely Anthony J Greenberg Sam Griffiths-Jones Samuel Gross Roderic Guigo Erik A Gustafson Wilfried Haerty Matthew W Hahn Daniel L Halligan Aaron L Halpern Gillian M Halter Mira V Han Andreas Heger LaDeana Hillier Angie S Hinrichs Ian Holmes Roger A Hoskins Melissa J Hubisz Dan Hultmark Melanie A Huntley David B Jaffe Santosh Jagadeeshan William R Jeck Justin Johnson Corbin D Jones William C Jordan Gary H Karpen Eiko Kataoka Peter D Keightley Pouya Kheradpour Ewen F Kirkness Leonardo B Koerich Karsten Kristiansen Dave Kudrna Rob J Kulathinal Sudhir Kumar Roberta Kwok Eric Lander Charles H Langley Richard Lapoint Brian P Lazzaro So-Jeong Lee Lisa Levesque Ruiqiang Li Chiao-Feng Lin Michael F Lin Kerstin Lindblad-Toh Ana Llopart Manyuan Long Lloyd Low Elena Lozovsky Jian Lu Meizhong Luo Carlos A Machado Wojciech Makalowski Mar Marzo Muneo Matsuda Luciano Matzkin Bryant McAllister Carolyn S McBride Brendan McKernan Kevin McKernan Maria Mendez-Lago Patrick Minx Michael U Mollenhauer Kristi Montooth Stephen M Mount Xu Mu Eugene Myers Barbara Negre Stuart Newfeld Rasmus Nielsen Mohamed A F Noor Patrick O'Grady Lior Pachter Montserrat Papaceit Matthew J Parisi Michael Parisi Leopold Parts Jakob S Pedersen Graziano Pesole Adam M Phillippy Chris P Ponting Mihai Pop Damiano Porcelli Jeffrey R Powell Sonja Prohaska Kim Pruitt Marta Puig Hadi Quesneville Kristipati Ravi Ram David Rand Matthew D Rasmussen Laura K Reed Robert Reenan Amy Reily Karin A Remington Tania T Rieger Michael G Ritchie Charles Robin Yu-Hui Rogers Claudia Rohde Julio Rozas Marc J Rubenfield Alfredo Ruiz Susan Russo Steven L Salzberg Alejandro Sanchez-Gracia David J Saranga Hajime Sato Stephen W Schaeffer Michael C Schatz Todd Schlenke Russell Schwartz Carmen Segarra Rama S Singh Laura Sirot Marina Sirota Nicholas B Sisneros Chris D Smith Temple F Smith John Spieth Deborah E Stage Alexander Stark Wolfgang Stephan Robert L Strausberg Sebastian Strempel David Sturgill Granger Sutton Granger G Sutton Wei Tao Sarah Teichmann Yoshiko N Tobari Yoshihiko Tomimura Jason M Tsolas Vera L S Valente Eli Venter J Craig Venter Saverio Vicario Filipe G Vieira Albert J Vilella Alfredo Villasante Brian Walenz Jun Wang Marvin Wasserman Thomas Watts Derek Wilson Richard K Wilson Rod A Wing Mariana F Wolfner Alex Wong Gane Ka-Shu Wong Chung-I Wu Gabriel Wu Daisuke Yamamoto Hsiao-Pei Yang Shiaw-Pyng Yang James A Yorke Kiyohito Yoshida Evgeny Zdobnov Peili Zhang Yu Zhang Aleksey V Zimin Jennifer Baldwin Amr Abdouelleil Jamal Abdulkadir Adal Abebe Brikti Abera Justin Abreu St Christophe Acer Lynne Aftuck Allen Alexander Peter An Erica Anderson Scott Anderson Harindra Arachi Marc Azer Pasang Bachantsang Andrew Barry Tashi Bayul Aaron Berlin Daniel Bessette Toby Bloom Jason Blye Leonid Boguslavskiy Claude Bonnet Boris Boukhgalter Imane Bourzgui Adam Brown Patrick Cahill Sheridon Channer Yama Cheshatsang Lisa Chuda Mieke Citroen Alville Collymore Patrick Cooke Maura Costello Katie D'Aco Riza Daza Georgius De Haan Stuart DeGray Christina DeMaso Norbu Dhargay Kimberly Dooley Erin Dooley Missole Doricent Passang Dorje Kunsang Dorjee Alan Dupes Richard Elong Jill Falk Abderrahim Farina Susan Faro Diallo Ferguson Sheila Fisher Chelsea D Foley Alicia Franke Dennis Friedrich Loryn Gadbois Gary Gearin Christina R Gearin Georgia Giannoukos Tina Goode Joseph Graham Edward Grandbois Sharleen Grewal Kunsang Gyaltsen Nabil Hafez Birhane Hagos Jennifer Hall Charlotte Henson Andrew Hollinger Tracey Honan Monika D Huard Leanne Hughes Brian Hurhula M Erii Husby Asha Kamat Ben Kanga Seva Kashin Dmitry Khazanovich Peter Kisner Krista Lance Marcia Lara William Lee Niall Lennon Frances Letendre Rosie LeVine Alex Lipovsky Xiaohong Liu Jinlei Liu Shangtao Liu Tashi Lokyitsang Yeshi Lokyitsang Rakela Lubonja Annie Lui Pen MacDonald Vasilia Magnisalis Kebede Maru Charles Matthews William McCusker Susan McDonough Teena Mehta James Meldrim Louis Meneus Oana Mihai Atanas Mihalev Tanya Mihova Rachel Mittelman Valentine Mlenga Anna Montmayeur Leonidas Mulrain Adam Navidi Jerome Naylor Tamrat Negash Thu Nguyen Nga Nguyen Robert Nicol Choe Norbu Nyima Norbu Nathaniel Novod Barry O'Neill Sahal Osman Eva Markiewicz Otero L Oyono Christopher Patti Pema Phunkhang Fritz Pierre Margaret Priest Sujaa Raghuraman Filip Rege Rebecca Reyes Cecil Rise Peter Rogov Keenan Ross Elizabeth Ryan Sampath Settipalli Terry Shea Ngawang Sherpa Lu Shi Diana Shih Todd Sparrow Jessica Spaulding John Stalker Nicole Stange-Thomann Sharon Stavropoulos Catherine Stone Christopher Strader Senait Tesfaye Talene Thomson Yama Thoulutsang Dawa Thoulutsang Kerri Topham Ira Topping Tsamla Tsamla Helen Vassiliev Andy Vo Tsering Wangchuk Tsering Wangdi Michael Weiand Jane Wilkinson Adam Wilson Shailendra Yadav Geneva Young Qing Yu Lisa Zembek Danni Zhong Andrew Zimmer Zac Zwirko David B Jaffe Pablo Alvarez Will Brockman Jonathan Butler CheeWhye Chin Sante Gnerre Manfred Grabherr Michael Kleber Evan Mauceli Iain MacCallum

Nature 2007 Nov;450(7167):203-18

Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA.

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http://dx.doi.org/10.1038/nature06341DOI Listing
November 2007

Draft genome of the filarial nematode parasite Brugia malayi.

Science 2007 Sep;317(5845):1756-60

Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA.

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http://www.sciencemag.org/cgi/doi/10.1126/science.1145406
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http://dx.doi.org/10.1126/science.1145406DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2613796PMC
September 2007

A unified model explaining the offsets of overlapping and near-overlapping prokaryotic genes.

Mol Biol Evol 2007 Sep 21;24(9):2091-8. Epub 2007 Jul 21.

Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, USA.

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http://dx.doi.org/10.1093/molbev/msm145DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2429982PMC
September 2007

Minimus: a fast, lightweight genome assembler.

BMC Bioinformatics 2007 Feb 26;8:64. Epub 2007 Feb 26.

Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA.

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/1471-2105-8-64DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1821043PMC
February 2007

Identifying bacterial genes and endosymbiont DNA with Glimmer.

Bioinformatics 2007 Mar 19;23(6):673-9. Epub 2007 Jan 19.

Center for Bioinformatics & Computational Biology, University of Maryland, College Park, MD 20742, USA.

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http://dx.doi.org/10.1093/bioinformatics/btm009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2387122PMC
March 2007

The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas disease.

Science 2005 Jul;309(5733):409-15

Department of Parasite Genomics, Institute for Genomic Research, Rockville, MD 20850, USA.

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http://dx.doi.org/10.1126/science.1112631DOI Listing
July 2005

Correction: Serendipitous discovery of Wolbachia genomes in multiple Drosophila species.

Genome Biol 2005 24;6(7):402. Epub 2005 Jun 24.

The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA.

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http://dx.doi.org/10.1186/gb-2005-6-7-402DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1175986PMC
June 2006

Serendipitous discovery of Wolbachia genomes in multiple Drosophila species.

Genome Biol 2005 22;6(3):R23. Epub 2005 Feb 22.

The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA.

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http://dx.doi.org/10.1186/gb-2005-6-3-r23DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1088942PMC
March 2006

Efficient decoding algorithms for generalized hidden Markov model gene finders.

BMC Bioinformatics 2005 Jan 24;6:16. Epub 2005 Jan 24.

Bioinformatics Department, The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD, USA.

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http://dx.doi.org/10.1186/1471-2105-6-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC552317PMC
January 2005

A preprocessor for shotgun assembly of large genomes.

J Comput Biol 2004 ;11(4):734-52

Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742-2431, USA.

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http://dx.doi.org/10.1089/cmb.2004.11.734DOI Listing
January 2005

Comparative genome assembly.

Brief Bioinform 2004 Sep;5(3):237-48

The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA.

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http://dx.doi.org/10.1093/bib/5.3.237DOI Listing
September 2004

DAGchainer: a tool for mining segmental genome duplications and synteny.

Bioinformatics 2004 Dec 9;20(18):3643-6. Epub 2004 Jul 9.

The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA.

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http://dx.doi.org/10.1093/bioinformatics/bth397DOI Listing
December 2004

Versatile and open software for comparing large genomes.

Genome Biol 2004 30;5(2):R12. Epub 2004 Jan 30.

Center for Bioinformatics, University of Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany.

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http://genomebiology.biomedcentral.com/articles/10.1186/gb-2
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http://dx.doi.org/10.1186/gb-2004-5-2-r12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC395750PMC
March 2005

The dog genome: survey sequencing and comparative analysis.

Science 2003 Sep;301(5641):1898-903

The Institute for Genomic Research, Rockville, MD 20850, USA.

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http://dx.doi.org/10.1126/science.1086432DOI Listing
September 2003

PROBEmer: A web-based software tool for selecting optimal DNA oligos.

Nucleic Acids Res 2003 Jul;31(13):3746-50

Interdepartmental Bioinformatics and Computational Biology, Iowa State University, Rockville, MD, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC168975PMC
http://dx.doi.org/10.1093/nar/gkg569DOI Listing
July 2003

A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome.

Authors:
Richard J Mural Mark D Adams Eugene W Myers Hamilton O Smith George L Gabor Miklos Ron Wides Aaron Halpern Peter W Li Granger G Sutton Joe Nadeau Steven L Salzberg Robert A Holt Chinnappa D Kodira Fu Lu Lin Chen Zuoming Deng Carlos C Evangelista Weiniu Gan Thomas J Heiman Jiayin Li Zhenya Li Gennady V Merkulov Natalia V Milshina Ashwinikumar K Naik Rong Qi Bixiong Chris Shue Aihui Wang Jian Wang Xin Wang Xianghe Yan Jane Ye Shibu Yooseph Qi Zhao Liansheng Zheng Shiaoping C Zhu Kendra Biddick Randall Bolanos Arthur L Delcher Ian M Dew Daniel Fasulo Michael J Flanigan Daniel H Huson Saul A Kravitz Jason R Miller Clark M Mobarry Knut Reinert Karin A Remington Qing Zhang Xiangqun H Zheng Deborah R Nusskern Zhongwu Lai Yiding Lei Wenyan Zhong Alison Yao Ping Guan Rui-Ru Ji Zhiping Gu Zhen-Yuan Wang Fei Zhong Chunlin Xiao Chia-Chien Chiang Mark Yandell Jennifer R Wortman Peter G Amanatides Suzanne L Hladun Eric C Pratts Jeffery E Johnson Kristina L Dodson Kerry J Woodford Cheryl A Evans Barry Gropman Douglas B Rusch Eli Venter Mei Wang Thomas J Smith Jarrett T Houck Donald E Tompkins Charles Haynes Debbie Jacob Soo H Chin David R Allen Carl E Dahlke Robert Sanders Kelvin Li Xiangjun Liu Alexander A Levitsky William H Majoros Quan Chen Ashley C Xia John R Lopez Michael T Donnelly Matthew H Newman Anna Glodek Cheryl L Kraft Marc Nodell Feroze Ali Hui-Jin An Danita Baldwin-Pitts Karen Y Beeson Shuang Cai Mark Carnes Amy Carver Parris M Caulk Angela Center Yen-Hui Chen Ming-Lai Cheng My D Coyne Michelle Crowder Steven Danaher Lionel B Davenport Raymond Desilets Susanne M Dietz Lisa Doup Patrick Dullaghan Steven Ferriera Carl R Fosler Harold C Gire Andres Gluecksmann Jeannine D Gocayne Jonathan Gray Brit Hart Jason Haynes Jeffery Hoover Tim Howland Chinyere Ibegwam Mena Jalali David Johns Leslie Kline Daniel S Ma Steven MacCawley Anand Magoon Felecia Mann David May Tina C McIntosh Somil Mehta Linda Moy Mee C Moy Brian J Murphy Sean D Murphy Keith A Nelson Zubeda Nuri Kimberly A Parker Alexandre C Prudhomme Vinita N Puri Hina Qureshi John C Raley Matthew S Reardon Megan A Regier Yu-Hui C Rogers Deanna L Romblad Jakob Schutz John L Scott Richard Scott Cynthia D Sitter Michella Smallwood Arlan C Sprague Erin Stewart Renee V Strong Ellen Suh Karena Sylvester Reginald Thomas Ni Ni Tint Christopher Tsonis Gary Wang George Wang Monica S Williams Sherita M Williams Sandra M Windsor Keriellen Wolfe Mitchell M Wu Jayshree Zaveri Kabir Chaturvedi Andrei E Gabrielian Zhaoxi Ke Jingtao Sun Gangadharan Subramanian J Craig Venter Cynthia M Pfannkoch Mary Barnstead Lisa D Stephenson

Science 2002 May;296(5573):1661-71

Celera Genomics, 45 West Gude Drive, Rockville, MD 20850, USA.

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http://dx.doi.org/10.1126/science.1069193DOI Listing
May 2002

Fast algorithms for large-scale genome alignment and comparison.

Nucleic Acids Res 2002 Jun;30(11):2478-83

Department of Computer Science, Loyola College in Maryland, Baltimore, MD 21210, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC117189PMC
http://dx.doi.org/10.1093/nar/30.11.2478DOI Listing
June 2002