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Browsing MIT Open Access Articles by Title

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  • 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.; Lander, Eric S.; Sabeti, Pardis C.; Murray, Megan B. (Nature Publishing Group, 2013-09)
    M. tuberculosis is evolving antibiotic resistance, threatening attempts at tuberculosis epidemic control. Mechanisms of resistance, including genetic changes favored by selection in resistant isolates, are incompletely ...
  • Sullivan, Matthew B.; Huang, Katherine H.; Ignacio-Espinoza, Julio C.; Berlin, Aaron M.; Kelly, Libusha; Weigele, Peter; DeFrancesco, Alicia S.; Kern, Suzanne Elizabeth; Thompson, Luke Richard; Young, Sarah; Yandava, Chandri; Fu, Ross; Krastins, Bryan; Chase, Michael; Sarracino, David; Osburne, Marcia; Henn, Matthew R.; Chisholm, Sallie (Penny) (Society for Applied Microbiology and Blackwell Publishing Ltd, 2010-11)
    T4-like myoviruses are ubiquitous, and their genes are among the most abundant documented in ocean systems. Here we compare 26 T4-like genomes, including 10 from non-cyanobacterial myoviruses, and 16 from marine ...
  • Gehring, Mary; Missirian, Victor; Henikoff, Steven (Public Library of Science, 2011-08)
    Differential expression of maternally and paternally inherited alleles of a gene is referred to as gene imprinting, a form of epigenetic gene regulation common to flowering plants and mammals. In plants, imprinting primarily ...
  • Rice, Daniel P.; Ribacke, Ulf; Silterra, Jacob; Deik, Amy A.; Moss, Eli L.; Broadbent, Kate M.; Neafsey, Daniel E.; Desai, Michael M.; Clish, Clary; Mazitschek, Ralph; Wirth, Dyann F.; Herman, Jonathan D. (BioMed Central Ltd, 2014-11)
    Background: Drug resistance remains a major public health challenge for malaria treatment and eradication. Individual loci associated with drug resistance to many antimalarials have been identified, but their epistasis ...
  • Lander, Eric S. (Nature Publishing Group, 2012-04)
    Marine stickleback fish have colonized and adapted to thousands of streams and lakes formed since the last ice age, providing an exceptional opportunity to characterize genomic mechanisms underlying repeated ecological ...
  • Carter, Scott L.; Lander, Eric S. (Nature Publishing Group, 2011-02)
    Prostate cancer is the second most common cause of male cancer deaths in the United States. However, the full range of prostate cancer genomic alterations is incompletely characterized. Here we present the complete sequence ...
  • DeLong, Edward (Public Library of Science, 2014-08)
    Microbes hold the key to life. They hold the secrets to our past (as the descendants of the earliest forms of life) and the prospects for our future (as we mine their genes for solutions to some of the planet's most pressing ...
  • Godfrey, Paul; Lander, Eric S. (National Academy of Sciences, 2012-02)
    The degree to which molecular epidemiology reveals information about the sources and transmission patterns of an outbreak depends on the resolution of the technology used and the samples studied. Isolates of Escherichia ...
  • Kellis, Manolis; Jaillon, Olivier (Nature Publishing Group, 2013-07)
    Loss of sexual reproduction is considered an evolutionary dead end for metazoans, but bdelloid rotifers challenge this view as they appear to have persisted asexually for millions of years1. Neither male sex organs nor ...
  • Waterhouse, Robert (Nature Publishing Group, 2016-02)
    Ticks transmit more pathogens to humans and animals than any other arthropod. We describe the 2.1 Gbp nuclear genome of the tick, Ixodes scapularis (Say), which vectors pathogens that cause Lyme disease, human granulocytic ...
  • Cao, Bo; Chen, Chao; DeMott, Michael S.; Cheng, Qiuxiang; Clark, Tyson A.; Xiong, Xiaolin; Zheng, Xiaoqing; Butty, Vincent; Levine, Stuart S.; Yuan, George; Boitano, Matthew; Luong, Khai; Song, Yi; Zhou, Xiufen; Deng, Zixin; Turner, Stephen W.; Korlach, Jonas; You, Delin; Wang, Lianrong; Chen, Shi; Dedon, Peter C. (Nature Publishing Group, 2014-06)
    Bacterial phosphorothioate (PT) DNA modifications are incorporated by Dnd proteins A-E and often function with DndF-H as a restriction-modification (R-M) system, as in Escherichia coli B7A. However, bacteria such as Vibrio ...
  • Tamsir, Alvin; Clancy, Kevin; Peterson, Todd; Stanton, Brynne C.; Nielsen, Alec Andrew; Voigt, Christopher A. (Nature Publishing Group, 2013-12)
    Genetic circuits perform computational operations based on interactions between freely diffusing molecules within a cell. When transcription factors are combined to build a circuit, unintended interactions can disrupt its ...
  • 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 (BioMed Central Ltd, 2006-05)
    Background: The Gram-negative bacterium Burkholderia pseudomallei (Bp) is the causative agent of the human disease melioidosis. To understand the evolutionary mechanisms contributing to Bp virulence, we performed a comparative ...
  • Svensson, J. Peter; Quirós Pesudo, Laia; McRee, Siobhan K.; Adeleye, Yeyejide A.; Carmichael, Paul; Samson, Leona D.; Quiros Pesudo, Laia (Public Library of Science, 2013-09)
    Toxicity screening of compounds provides a means to identify compounds harmful for human health and the environment. Here, we further develop the technique of genomic phenotyping to improve throughput while maintaining ...
  • Svensson, J. Peter; Quiros Pesudo, Laia; Samson, Leona D.; Fry, Rebecca C.; Adeleye, Yeyejide A.; Carmichael, Paul (Springer (Biomed Central Ltd.), 2011-10)
    Background A myriad of new chemicals has been introduced into our environment and exposure to these agents can damage cells and induce cytotoxicity through different mechanisms, including damaging DNA directly. Analysis ...
  • Svensson, J. Peter; Quiros Pesudo, Laia; Fry, Rebecca C.; Adeleye, Yeyejide A.; Carmichael, Paul; Samson, Leona D. (BioMed Central Ltd., 2011-10)
    Background: A myriad of new chemicals has been introduced into our environment and exposure to these agents can damage cells and induce cytotoxicity through different mechanisms, including damaging DNA directly. Analysis ...
  • Ulloa, Osvaldo; DeLong, Edward Francis; Astorga-Elo, Marcia; Ramirez-Flandes, Salvador (Nature Publishing Group, 2015-02)
    Cyanobacteria of the genus Prochlorococcus are the most abundant photosynthetic marine organisms and key factors in the global carbon cycle. The understanding of their distribution and ecological importance in oligotrophic ...
  • Lander, Eric S.; Bass, Adam J.; Lawrence, Michael S.; Brace, Lear E.; Ramos, Alex H.; Drier, Yotam; Cibulskis, Kristian; Sougnez, Carrie; Voet, Douglas; Saksena, Gordon; Sivachenko, Andrey; Jing, Rui; Parkin, Melissa; Pugh, Trevor; Verhaak, Roel G.; Stransky, Nicolas; Boutin, Adam T.; Barretina, Jordi; Solit, David B.; Vakiani, Evi (Nature Publishing Group, 2011-09)
    Prior studies have identified recurrent oncogenic mutations in colorectal adenocarcinoma and have surveyed exons of protein-coding genes for mutations in 11 affected individuals. Here we report whole-genome sequencing from ...
  • Berger, Bonnie; Adams, David J.; Harismendy, Olivier; Huttenhower, Curtis; Liu, X. Shirley; Myers, Chad L.; Oshlack, Alicia; Rinn, John L.; Walhout, Albertha J. M. (Springer (Biomed Central Ltd.), 2011-12)
    As we come to the end of 2011, Genome Biology has asked some members of our Editorial Board for their views on the state of play in genomics. What was their favorite paper of 2011? What are the challenges in their particular ...
  • Lander, Eric S. (Nature Publishing Group, 2014-09)
    Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand the molecular mechanisms underlying cichlid phenotypic diversity, we sequenced the genomes ...
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