BBMerge – Accurate paired shotgun read merging via overlap

le Bushnell, Brian, Rood, Jonathan, Singer, Esther
Foilsithe in PLoS One (2017)

Transductomics: sequencing-based detection and analysis of transduced DNA in pure cultures and microbial communities

le Kleiner, Manuel, Bushnell, Brian, Sanderson, Kenneth E., Hooper, Lora V., Duerkop, Breck A.
Foilsithe in Microbiome (2020)

Associations of Early COVID-19 Cases in San Francisco With Domestic and International Travel

le Gu, Wei, Deng, Xianding, Reyes, Kevin, Hsu, Elaine, Wang, Candace, Sotomayor-Gonzalez, Alicia, Federman, Scot, Bushnell, Brian, Miller, Steve, Chiu, Charles Y
Foilsithe in Clin Infect Dis (2020)

Murine colitis reveals a disease-associated bacteriophage community

le Duerkop, Breck A., Kleiner, Manuel, Paez-Espino, David, Zhu, Wenhan, Bushnell, Brian, Hassell, Brian, Winter, Sebastian E., Kyrpides, Nikos C., Hooper, Lora V.
Foilsithe in Nat Microbiol (2018)

Experimental Evolution of Extreme Resistance to Ionizing Radiation in Escherichia coli after 50 Cycles of Selection

le Bruckbauer, Steven T., Trimarco, Joseph D., Martin, Joel, Bushnell, Brian, Senn, Katherine A., Schackwitz, Wendy, Lipzen, Anna, Blow, Matthew, Wood, Elizabeth A., Culberson, Wesley S., Pennacchio, Christa, Cox, Michael M.
Foilsithe in J Bacteriol (2019)

Physiology of Highly Radioresistant Escherichia coli After Experimental Evolution for 100 Cycles of Selection

le Bruckbauer, Steven T., Martin, Joel, Minkoff, Benjamin B., Veling, Mike T., Lancaster, Illissa, Liu, Jessica, Trimarco, Joseph D., Bushnell, Brian, Lipzen, Anna, Wood, Elizabeth A., Sussman, Michael R., Pennacchio, Christa, Cox, Michael M.
Foilsithe in Front Microbiol (2020)

Corrigendum: Physiology of Highly Radioresistant Escherichia coli After Experimental Evolution for 100 Cycles of Selection

le Bruckbauer, Steven T., Martin, Joel, Minkoff, Benjamin B., Veling, Mike T., Lancaster, Illissa, Liu, Jessica, Trimarco, Joseph D., Bushnell, Brian, Lipzen, Anna, Wood, Elizabeth A., Sussman, Michael R., Pennacchio, Christa, Cox, Michael M.
Foilsithe in Front Microbiol (2020)

High-resolution phylogenetic microbial community profiling

le Singer, Esther, Bushnell, Brian, Coleman-Derr, Devin, Bowman, Brett, Bowers, Robert M, Levy, Asaf, Gies, Esther A, Cheng, Jan-Fang, Copeland, Alex, Klenk, Hans-Peter, Hallam, Steven J, Hugenholtz, Philip, Tringe, Susannah G, Woyke, Tanja
Foilsithe in ISME J (2016)

Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations

le Bendall, Matthew L, Stevens, Sarah LR, Chan, Leong-Keat, Malfatti, Stephanie, Schwientek, Patrick, Tremblay, Julien, Schackwitz, Wendy, Martin, Joel, Pati, Amrita, Bushnell, Brian, Froula, Jeff, Kang, Dongwan, Tringe, Susannah G, Bertilsson, Stefan, Moran, Mary A, Shade, Ashley, Newton, Ryan J, McMahon, Katherine D, Malmstrom, Rex R
Foilsithe in ISME J (2016)

Introduction, Transmission Dynamics, and Fate of Early Severe Acute Respiratory Syndrome Coronavirus 2 Lineages in Santa Clara County, California

le Villarino, Elsa, Deng, Xianding, Kemper, Carol A, Jorden, Michelle A, Bonin, Brandon, Rudman, Sarah L, Han, George S, Yu, Guixia, Wang, Candace, Federman, Scot, Bushnell, Brian, Wadford, Debra A, Lin, Wen, Tao, Ying, Paden, Clinton R, Bhatnagar, Julu, MacCannell, Tara, Tong, Suxiang, Batson, Joshua, Chiu, Charles Y
Foilsithe in J Infect Dis (2021)

DOE JGI Metagenome Workflow

le Clum, Alicia, Huntemann, Marcel, Bushnell, Brian, Foster, Brian, Foster, Bryce, Roux, Simon, Hajek, Patrick P., Varghese, Neha, Mukherjee, Supratim, Reddy, T. B. K., Daum, Chris, Yoshinaga, Yuko, O’Malley, Ronan, Seshadri, Rekha, Kyrpides, Nikos C., Eloe-Fadrosh, Emiley A., Chen, I-Min A., Copeland, Alex, Ivanova, Natalia N.
Foilsithe in mSystems (2021)

Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California

le Deng, Xianding, Gu, Wei, Federman, Scot, du Plessis, Louis, Pybus, Oliver G., Faria, Nuno, Wang, Candace, Yu, Guixia, Bushnell, Brian, Pan, Chao-Yang, Guevara, Hugo, Sotomayor-Gonzalez, Alicia, Zorn, Kelsey, Gopez, Allan, Servellita, Venice, Hsu, Elaine, Miller, Steve, Bedford, Trevor, Greninger, Alexander L., Roychoudhury, Pavitra, Starita, Lea M., Famulare, Michael, Chu, Helen Y., Shendure, Jay, Jerome, Keith R., Anderson, Catie, Gangavarapu, Karthik, Zeller, Mark, Spencer, Emily, Andersen, Kristian G., MacCannell, Duncan, Paden, Clinton R., Li, Yan, Zhang, Jing, Tong, Suxiang, Armstrong, Gregory, Morrow, Scott, Willis, Matthew, Matyas, Bela T., Mase, Sundari, Kasirye, Olivia, Park, Maggie, Masinde, Godfred, Chan, Curtis, Yu, Alexander T., Chai, Shua J., Villarino, Elsa, Bonin, Brandon, Wadford, Debra A., Chiu, Charles Y.
Foilsithe in Science (2020)