Tracking the evolution of dengue virus strains D2S10 and D2S20 by 454 pyrosequencing.

by Huda Makhluf, Michael D Buck, Kevin King, Stuart T Perry, Matthew R Henn, Sujan Shresta
Published 2013-01-01

Whole genome amplification and de novo assembly of single bacterial cells.

by Sébastien Rodrigue, Rex R Malmstrom, Aaron M Berlin, Bruce W Birren, Matthew R Henn, Sallie W Chisholm
Published 2009-09-01

Endurance, Refuge, and Reemergence of Dengue Virus Type 2, Puerto Rico, 1986–2007

by Kate L. McElroy, Gilberto A. Santiago, Niall J. Lennon, Bruce W. Birren, Matthew R. Henn, Jorge L. Muñoz-Jordán
Published 2011-01-01

Fecal microbiota transplantation for the improvement of metabolism in obesity: The FMT-TRIM double-blind placebo-controlled pilot trial.

by Elaine W Yu, Liu Gao, Petr Stastka, Michael C Cheney, Jasmin Mahabamunuge, Mariam Torres Soto, Christopher B Ford, Jessica A Bryant, Matthew R Henn, Elizabeth L Hohmann
Published 2020-03-01

Endemic dengue associated with the co-circulation of multiple viral lineages and localized density-dependent transmission.

by Jayna Raghwani, Andrew Rambaut, Edward C Holmes, Vu Ty Hang, Tran Tinh Hien, Jeremy Farrar, Bridget Wills, Niall J Lennon, Bruce W Birren, Matthew R Henn, Cameron P Simmons
Published 2011-06-01

Biofilms harbour Clostridioides difficile, serving as a reservoir for recurrent infection

by Charmaine Normington, Ines B. Moura, Jessica A. Bryant, Duncan J. Ewin, Emma V. Clark, Morgan J. Kettle, Hannah C. Harris, William Spittal, Georgina Davis, Matthew R. Henn, Christopher B. Ford, Mark H. Wilcox, Anthony M. Buckley
Published 2021-02-01

Analysis of high-throughput sequencing and annotation strategies for phage genomes.

by Matthew R Henn, Matthew B Sullivan, Nicole Stange-Thomann, Marcia S Osburne, Aaron M Berlin, Libusha Kelly, Chandri Yandava, Chinnappa Kodira, Qiandong Zeng, Michael Weiand, Todd Sparrow, Sakina Saif, Georgia Giannoukos, Sarah K Young, Chad Nusbaum, Bruce W Birren, Sallie W Chisholm
Published 2010-01-01

Emergence of the Asian 1 genotype of dengue virus serotype 2 in viet nam: in vivo fitness advantage and lineage replacement in South-East Asia.

by Thi Ty Hang Vu, Edward C Holmes, Veasna Duong, Thien Quy Nguyen, Tinh Hien Tran, Michael Quail, Carol Churcher, Julian Parkhill, Jane Cardosa, Jeremy Farrar, Bridget Wills, Niall J Lennon, Bruce W Birren, Philippe Buchy, Matthew R Henn, Cameron P Simmons
Published 2010-07-01

Highly sensitive and specific detection of rare variants in mixed viral populations from massively parallel sequence data.

by Alexander R Macalalad, Michael C Zody, Patrick Charlebois, Niall J Lennon, Ruchi M Newman, Christine M Malboeuf, Elizabeth M Ryan, Christian L Boutwell, Karen A Power, Doug E Brackney, Kendra N Pesko, Joshua Z Levin, Gregory D Ebel, Todd M Allen, Bruce W Birren, Matthew R Henn
Published 2012-01-01

The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes.

by Florent E Angly, Dana Willner, Alejandra Prieto-Davó, Robert A Edwards, Robert Schmieder, Rebecca Vega-Thurber, Dionysios A Antonopoulos, Katie Barott, Matthew T Cottrell, Christelle Desnues, Elizabeth A Dinsdale, Mike Furlan, Matthew Haynes, Matthew R Henn, Yongfei Hu, David L Kirchman, Tracey McDole, John D McPherson, Folker Meyer, R Michael Miller, Egbert Mundt, Robert K Naviaux, Beltran Rodriguez-Mueller, Rick Stevens, Linda Wegley, Lixin Zhang, Baoli Zhu, Forest Rohwer
Published 2009-12-01

Differences in the Selection Bottleneck between Modes of Sexual Transmission Influence the Genetic Composition of the HIV-1 Founder Virus.

by Damien C Tully, Colin B Ogilvie, Rebecca E Batorsky, David J Bean, Karen A Power, Musie Ghebremichael, Hunter E Bedard, Adrianne D Gladden, Aaron M Seese, Molly A Amero, Kimberly Lane, Graham McGrath, Suzane B Bazner, Jake Tinsley, Niall J Lennon, Matthew R Henn, Zabrina L Brumme, Philip J Norris, Eric S Rosenberg, Kenneth H Mayer, Heiko Jessen, Sergei L Kosakovsky Pond, Bruce D Walker, Marcus Altfeld, Jonathan M Carlson, Todd M Allen
Published 2016-05-01

Comparison of illumina and 454 deep sequencing in participants failing raltegravir-based antiretroviral therapy.

by Jonathan Z Li, Brad Chapman, Patrick Charlebois, Oliver Hofmann, Brian Weiner, Alyssa J Porter, Reshmi Samuel, Saran Vardhanabhuti, Lu Zheng, Joseph Eron, Babafemi Taiwo, Michael C Zody, Matthew R Henn, Daniel R Kuritzkes, Winston Hide, ACTG A5262 Study Team, Cara C Wilson, Baiba I Berzins, Edward P Acosta, Barbara Bastow, Peter S Kim, Sarah W Read, Jennifer Janik, Debra S Meres, Michael M Lederman, Lori Mong-Kryspin, Karl E Shaw, Louis G Zimmerman, Randi Leavitt, Guy De La Rosa, Amy Jennings
Published 2014-01-01

Comparative genomic analysis of human fungal pathogens causing paracoccidioidomycosis.

by Christopher A Desjardins, Mia D Champion, Jason W Holder, Anna Muszewska, Jonathan Goldberg, Alexandre M Bailão, Marcelo Macedo Brigido, Márcia Eliana da Silva Ferreira, Ana Maria Garcia, Marcin Grynberg, Sharvari Gujja, David I Heiman, Matthew R Henn, Chinnappa D Kodira, Henry León-Narváez, Larissa V G Longo, Li-Jun Ma, Iran Malavazi, Alisson L Matsuo, Flavia V Morais, Maristela Pereira, Sabrina Rodríguez-Brito, Sharadha Sakthikumar, Silvia M Salem-Izacc, Sean M Sykes, Marcus Melo Teixeira, Milene C Vallejo, Maria Emília Machado Telles Walter, Chandri Yandava, Sarah Young, Qiandong Zeng, Jeremy Zucker, Maria Sueli Felipe, Gustavo H Goldman, Brian J Haas, Juan G McEwen, Gustavo Nino-Vega, Rosana Puccia, Gioconda San-Blas, Celia Maria de Almeida Soares, Bruce W Birren, Christina A Cuomo
Published 2011-10-01

Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection.

by Matthew R Henn, Christian L Boutwell, Patrick Charlebois, Niall J Lennon, Karen A Power, Alexander R Macalalad, Aaron M Berlin, Christine M Malboeuf, Elizabeth M Ryan, Sante Gnerre, Michael C Zody, Rachel L Erlich, Lisa M Green, Andrew Berical, Yaoyu Wang, Monica Casali, Hendrik Streeck, Allyson K Bloom, Tim Dudek, Damien Tully, Ruchi Newman, Karen L Axten, Adrianne D Gladden, Laura Battis, Michael Kemper, Qiandong Zeng, Terrance P Shea, Sharvari Gujja, Carmen Zedlack, Olivier Gasser, Christian Brander, Christoph Hess, Huldrych F Günthard, Zabrina L Brumme, Chanson J Brumme, Suzane Bazner, Jenna Rychert, Jake P Tinsley, Ken H Mayer, Eric Rosenberg, Florencia Pereyra, Joshua Z Levin, Sarah K Young, Heiko Jessen, Marcus Altfeld, Bruce W Birren, Bruce D Walker, Todd M Allen
Published 2012-01-01

Standardized metadata for human pathogen/vector genomic sequences.

by Vivien G Dugan, Scott J Emrich, Gloria I Giraldo-Calderón, Omar S Harb, Ruchi M Newman, Brett E Pickett, Lynn M Schriml, Timothy B Stockwell, Christian J Stoeckert, Dan E Sullivan, Indresh Singh, Doyle V Ward, Alison Yao, Jie Zheng, Tanya Barrett, Bruce Birren, Lauren Brinkac, Vincent M Bruno, Elizabet Caler, Sinéad Chapman, Frank H Collins, Christina A Cuomo, Valentina Di Francesco, Scott Durkin, Mark Eppinger, Michael Feldgarden, Claire Fraser, W Florian Fricke, Maria Giovanni, Matthew R Henn, Erin Hine, Julie Dunning Hotopp, Ilene Karsch-Mizrachi, Jessica C Kissinger, Eun Mi Lee, Punam Mathur, Emmanuel F Mongodin, Cheryl I Murphy, Garry Myers, Daniel E Neafsey, Karen E Nelson, William C Nierman, Julia Puzak, David Rasko, David S Roos, Lisa Sadzewicz, Joana C Silva, Bruno Sobral, R Burke Squires, Rick L Stevens, Luke Tallon, Herve Tettelin, David Wentworth, Owen White, Rebecca Will, Jennifer Wortman, Yun Zhang, Richard H Scheuermann
Published 2014-01-01