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Browsing MIT Open Access Articles by Title

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  • Lorenzi, Hernan; Thiagarajan, Mathangi; Haas, Brian J.; Wortman, Jennifer; Hall, Neil; Caler, Elisabet (BioMed Central Ltd, 2008-12)
    Background: Identification and mapping of repetitive elements is a key step for accurate gene prediction and overall structural annotation of genomes. During the assembly and annotation of three highly repetitive amoeba ...
  • 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; Gagneux, Sebastien; Birren, Bruce; Rubin, Eric J; Sabeti, Pardis C; Murray, Megan; Lander, Eric S. (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 ...
  • 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 Lambert; 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 ...
  • 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; 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 ...
  • 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 ...
  • Kellis, Manolis (Nature Publishing Group, 2013-05)
    Genome-wide association studies have identified thousands of loci for common diseases, but, for the majority of these, the mechanisms underlying disease susceptibility remain unknown. Most associated variants are not ...
  • Felkner, John S.; Townsend, Robert (Oxford University Press, 2011)
    A nation's economic geography can have an enormous impact on its development. In Thailand, we show that a high concentration of enterprise in an area predicts high subsequent growth in and around that area. We also find ...
  • Onnela, Jukka-Pekka; Arbesman, Samuel; Gonzalez, Marta C.; Barabasi, Albert-Laszlo; Christakis, Nicholas A. (Public Library of Science, 2011-04)
    Social groups are fundamental building blocks of human societies. While our social interactions have always been constrained by geography, it has been impossible, due to practical difficulties, to evaluate the nature of ...
  • Efrat, Alon; Neumayer, Sebastian J.; Modiano, Eytan H. (Institute of Electrical and Electronics Engineers (IEEE), 2012-03)
    Failures in fiber-optic networks may be caused by natural disasters, such as floods or earthquakes, as well as other events, such as an Electromagnetic Pulse (EMP) attack. These events occur in specific geographical ...
  • Calabrese, Francesco; Pereira, Francisco C.; Lorenzo, Giusy Di; Liu, Liang; Ratti, Carlo (Springer-Verlag, 2010-05)
    This paper deals with the analysis of crowd mobility during special events. We analyze nearly 1 million cell-phone traces and associate their destinations with social events. We show that the origins of people attending ...
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