Whole genome amplification and de novo assembly of single bacterial cells

by Rodrigue, Sebastien, Malmstrom, Rex R., Berlin, Aaron M., Birren, Bruce W., Henn, Matthew R., Chisholm, Sallie (Penny)
Published 2010

Genomic patterns of pathogen evolution revealed by comparison of Burkholderia pseudomallei, the causative agent of melioidosis, to avirulent Burkholderia thailandensis

by Yu, Yiting, Chua, Hui Hoon, Lin, Chi Ho, Sim, Siew Hoon, Lin, Daoxun, Derr, Alan, Engels, Reinhard, DeShazer, David, Birren, Bruce W., Nierman, William C., Tan, Patrick, Kim, H. Stanley
Published 2010

Short-term genome evolution of Listeria monocytogenes in a non-controlled environment

by Orsi, Renato H., Borowsky, Mark L., Lauer, Peter, Young, Sarah K., Nusbaum, Chad, Galagan, James E., Birren, Bruce W., Ivy, Reid A., Sun, Qi, Graves, Lewis M., Swaminathan, Bala, Wiedmann, Martin
Published 2009

Comparative Genomics of Enterococci: Variation in Enterococcus faecalis, Clade Structure in E. faecium, and Defining Characteristics of E. gallinarum and E. casseliflavus

by Palmer, Kelli L., Godfrey, Paul, Griggs, Allison, Kos, Veronica N., Zucker, Jeremy, Desjardins, Christopher A., Cerqueira, Gustavo, Gevers, Dirk, Walker, Suzanne, Wortman, Jennifer, Feldgarden, Michael, Haas, Brian J., Birren, Bruce W., Gilmore, Michael S.
Published 2012

Sub-clinical detection of gut microbial biomarkers of obesity and type 2 diabetes

by Yassour, Moran, Lim, Mi Young, Yun, Hyun Sun, Tickle, Timothy L., Sung, Joohon, Song, Yun-Mi, Lee, Kayoung, Franzosa, Eric A., Morgan, Xochitl C., Gevers, Dirk, Xavier, Ramnik J., Birren, Bruce W., Ko, GwangPyo, Huttenhower, Curtis, Lander, Eric Steven
Published 2018

Analysis of High-Throughput Sequencing and Annotation Strategies for Phage Genomes

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

Comparative and Functional Genomics of Rhodococcus opacus PD630 for Biofuels Development

by Ghiviriga, Ion, Dancel, Christine, Kodira, Chinnappa D., Desany, Brian, Affourtit, Jason P., Abeel, Thomas, Gevers, Dirk, Birren, Bruce W., Godfrey, Paul, Desjardins, Christopher A., Holder, Jason W., DeBono, Tony, Ulrich, Jil, Zucker, Jeremy, Zeng, Qiandong, Leach, Alex L. B., Sinskey, Anthony J
Published 2012

Reply to Guy et al.: Support for a bottleneck in the 2011 Escherichia coli O104:H4 outbreak in Germany

by Grad, Y. H., Lipsitch, M., Griggs, Allison, Haas, Brian J., Shea, T. P., McCowan, C., Montmayeur, A., FitzGerald, M., Wortman, J. R., Krogfelt, K. A., Bingen, E., Weill, F.-X, Tietze, E., Flieger, A., Nusbaum, Chad, Birren, Bruce W., Hung, Deborah T., Hanage, W. P.
Published 2013

Genome-wide SNP genotyping highlights the role of natural selection in Plasmodium falciparum population divergence

by Neafsey, Daniel E., Volkman, Sarak K., Park, Daniel, Montgomery, Philip, Milner, Danny A., Lukens, Amanda K., Rosen, David, Daniels, Rachel F., Houde, Nathan, Cortese, Joseph F., Tyndall, Erin, Gates, Casey, Stange-Thomann, Nicole, Sarr, Ousmane, Ndiaye, Daouda, Ndir, Omar, Mboup, Soulyemane, Ferreira, Marcelo U., do Lago Moraes, Sandra, Dash, Aditya P., Chitnis, Chetan E., Wiegand, Roger C., Hartl, Daniel L., Birren, Bruce W., Wirth, Dyann F., Schaffner, Stephen F, Lander, Eric Steven, Sabeti, Pardis
Published 2010

Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis

by Farhat, Maha R., Shapiro, B. Jesse, Kieser, Karen J., Sultana, Razvan, Jacobson, Karen R., Victor, Thomas C., Warren, Robin M., Streicher, Elizabeth M., Calver, Alistair, Sloutsky, Alex, Kaur, Devinder, Posey, Jamie E., Plikaytis, Bonnie, Oggioni, Marco R., Gardy, Jennifer L., Johnston, James C., Rodrigues, Mabel, Tang, Patrick K. C., Kato-Maeda, Midori, Borowsky, Mark L., Muddukrishna, Bhavana, Kreiswirth, Barry N., Kurepina, Natalia, Galagan, James E., Gagneux, Sebastien, Birren, Bruce W., Rubin, Eric J., Sabeti, Pardis C., Murray, Megan B., Lander, Eric Steven
Published 2014

Identification and Functional Validation of the Novel Antimalarial Resistance Locus PF10_0355 in Plasmodium falciparum

by Tyne, Daria Van, Angelino, Elaine, Barnes, Kayla G., Rosen, David M., Lukens, Amanda K., Daniels, Rachel F., Milner, Danny A., Becker, Justin S., Yamins, Daniel, Ndiaye, Daouda, Sarr, Ousmane, Mboup, Soulyemane, Happi, Christian, Furlotte, Nicholas A., Eskin, Eleazar, Kang, Hyun Min, Hartl, Daniel L., Neafsey, Daniel E., Cortese, Joseph F., Daniels, Rachel F., Johnson, Charles A., Shlyakhter, Ilya, Grossman, Sharon Rachel, Birren, Bruce W., Wiegand, Roger C., Wirth, Dyann F., Volkman, Sarah K., Park, Daniel, Schaffner, Stephen F, Karlsson, Elinor, Lander, Eric Steven, Sabeti, Pardis
Published 2012