Brian P Walenz

Brian P Walenz

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Brian P Walenz

Brian P Walenz

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Integrating Hi-C links with assembly graphs for chromosome-scale assembly.

PLoS Comput Biol 2019 Aug 21;15(8):e1007273. Epub 2019 Aug 21.

Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institute of Health, Bethesda, Maryland, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1007273DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6719893PMC
August 2019

De novo assembly of haplotype-resolved genomes with trio binning.

Nat Biotechnol 2018 Oct 22. Epub 2018 Oct 22.

Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, Maryland, USA.

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http://dx.doi.org/10.1038/nbt.4277DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6476705PMC
October 2018

Canu: scalable and accurate long-read assembly via adaptive -mer weighting and repeat separation.

Genome Res 2017 05 15;27(5):722-736. Epub 2017 Mar 15.

Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.

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http://genome.cshlp.org/lookup/doi/10.1101/gr.215087.116
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http://dx.doi.org/10.1101/gr.215087.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5411767PMC
May 2017

Genomic insights into the Ixodes scapularis tick vector of Lyme disease.

Authors:
Monika Gulia-Nuss Andrew B Nuss Jason M Meyer Daniel E Sonenshine R Michael Roe Robert M Waterhouse David B Sattelle José de la Fuente Jose M Ribeiro Karine Megy Jyothi Thimmapuram Jason R Miller Brian P Walenz Sergey Koren Jessica B Hostetler Mathangi Thiagarajan Vinita S Joardar Linda I Hannick Shelby Bidwell Martin P Hammond Sarah Young Qiandong Zeng Jenica L Abrudan Francisca C Almeida Nieves Ayllón Ketaki Bhide Brooke W Bissinger Elena Bonzon-Kulichenko Steven D Buckingham Daniel R Caffrey Melissa J Caimano Vincent Croset Timothy Driscoll Don Gilbert Joseph J Gillespie Gloria I Giraldo-Calderón Jeffrey M Grabowski David Jiang Sayed M S Khalil Donghun Kim Katherine M Kocan Juraj Koči Richard J Kuhn Timothy J Kurtti Kristin Lees Emma G Lang Ryan C Kennedy Hyeogsun Kwon Rushika Perera Yumin Qi Justin D Radolf Joyce M Sakamoto Alejandro Sánchez-Gracia Maiara S Severo Neal Silverman Ladislav Šimo Marta Tojo Cristian Tornador Janice P Van Zee Jesús Vázquez Filipe G Vieira Margarita Villar Adam R Wespiser Yunlong Yang Jiwei Zhu Peter Arensburger Patricia V Pietrantonio Stephen C Barker Renfu Shao Evgeny M Zdobnov Frank Hauser Cornelis J P Grimmelikhuijzen Yoonseong Park Julio Rozas Richard Benton Joao H F Pedra David R Nelson Maria F Unger Jose M C Tubio Zhijian Tu Hugh M Robertson Martin Shumway Granger Sutton Jennifer R Wortman Daniel Lawson Stephen K Wikel Vishvanath M Nene Claire M Fraser Frank H Collins Bruce Birren Karen E Nelson Elisabet Caler Catherine A Hill

Nat Commun 2016 Feb 9;7:10507. Epub 2016 Feb 9.

Department of Entomology, Purdue University, West Lafayette, Indiana 47907, USA.

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http://dx.doi.org/10.1038/ncomms10507DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4748124PMC
February 2016

The genome of Anopheles darlingi, the main neotropical malaria vector.

Authors:
Osvaldo Marinotti Gustavo C Cerqueira Luiz Gonzaga Paula de Almeida Maria Inês Tiraboschi Ferro Elgion Lucio da Silva Loreto Arnaldo Zaha Santuza M R Teixeira Adam R Wespiser Alexandre Almeida E Silva Aline Daiane Schlindwein Ana Carolina Landim Pacheco Artur Luiz da Costa da Silva Brenton R Graveley Brian P Walenz Bruna de Araujo Lima Carlos Alexandre Gomes Ribeiro Carlos Gustavo Nunes-Silva Carlos Roberto de Carvalho Célia Maria de Almeida Soares Claudia Beatriz Afonso de Menezes Cleverson Matiolli Daniel Caffrey Demetrius Antonio M Araújo Diana Magalhães de Oliveira Douglas Golenbock Edmundo Carlos Grisard Fabiana Fantinatti-Garboggini Fabíola Marques de Carvalho Fernando Gomes Barcellos Francisco Prosdocimi Gemma May Gilson Martins de Azevedo Junior Giselle Moura Guimarães Gustavo Henrique Goldman Itácio Q M Padilha Jacqueline da Silva Batista Jesus Aparecido Ferro José M C Ribeiro Juliana Lopes Rangel Fietto Karina Maia Dabbas Louise Cerdeira Lucymara Fassarella Agnez-Lima Marcelo Brocchi Marcos Oliveira de Carvalho Marcus de Melo Teixeira Maria de Mascena Diniz Maia Maria Helena S Goldman Maria Paula Cruz Schneider Maria Sueli Soares Felipe Mariangela Hungria Marisa Fabiana Nicolás Maristela Pereira Martín Alejandro Montes Maurício E Cantão Michel Vincentz Miriam Silva Rafael Neal Silverman Patrícia Hermes Stoco Rangel Celso Souza Renato Vicentini Ricardo Tostes Gazzinelli Rogério de Oliveira Neves Rosane Silva Spartaco Astolfi-Filho Talles Eduardo Ferreira Maciel Turán P Urményi Wanderli Pedro Tadei Erney Plessmann Camargo Ana Tereza Ribeiro de Vasconcelos

Nucleic Acids Res 2013 Aug 12;41(15):7387-400. Epub 2013 Jun 12.

Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA 92697, USA, Institute of Technology, Broad Institute of Harvard and Massachusetts, Cambridge, MA 02141, USA, Laboratório de Bioinformática do Laboratório Nacional de Computação Científica, Petrópolis, RJ 25651-075, Brasil, Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal, UNESP -Universidade Estadual Paulista, SP 14884-900, Brasil, Departamento de Biologia, Universidade Federal de Santa Maria, Santa Maria, RS 97105-900, Brasil, Departamento de Biologia Molecular e Biotecnologia, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS 91501-970, Brasil, Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270901, Brasil, Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA, Laboratório de Entomologia Médica IPEPATRO/FIOCRUZ, Porto Velho, RO 76812-245, Brasil, Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de Santa Catarina, Florianópolis, SC 88040-900, Brasil, Centro de Ciências da Saúde, Universidade Estadual do Ceará, Fortaleza, CE 62042-280, Brasil, Departamento de Ciências Biológicas, Campus Senador Helvídio Nunes de Barros, Universidade Federal do Piauí, Picos, PI 60740-000, Brasil, Departamento de Genética, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA 66075-900, Brasil, Department of Genetics and Developmental Biology, University of Connecticut Health Center, Farmington, CT 06030, USA, Informatics, The J. Craig Venter Institute, Medical Center Drive, Rockville, MD 20850, USA, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP 13083-862, Brasil, Departamento de Genética e Melhoramento, Universidade Federal de Viçosa, MG 36570-000, Brasil, Centro de Apoio Mul

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http://dx.doi.org/10.1093/nar/gkt484DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3753621PMC
August 2013

An algorithm for automated closure during assembly.

BMC Bioinformatics 2010 Sep 10;11:457. Epub 2010 Sep 10.

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

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http://dx.doi.org/10.1186/1471-2105-11-457DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2945939PMC
September 2010

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

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

A space-efficient construction of the Burrows-Wheeler transform for genomic data.

J Comput Biol 2005 Sep;12(7):943-51

Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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http://www.liebertpub.com/doi/10.1089/cmb.2005.12.943
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http://dx.doi.org/10.1089/cmb.2005.12.943DOI Listing
September 2005