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Browsing MIT Open Access Articles by Title

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  • 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 ...
  • Sealfon, Rachel S.; Lander, Eric S. (American Association for the Advancement of Science (AAAS), 2014-08)
    In its largest outbreak, Ebola virus disease is spreading through Guinea, Liberia, Sierra Leone, and Nigeria. We sequenced 99 Ebola virus genomes from 78 patients in Sierra Leone to ~2000× coverage. We observed a rapid ...
  • 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 James; 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 ...
  • Autor, David H.; Dorn, David; Hanson, Gordon H. (American Economic Association, 2013-05)
    This paper explores the geographic overlap of trade and technology shocks across local labor markets in the United States. Regional exposure to technological change, as measured by specialization in routine task-intensive ...
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