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Browsing MIT Open Access Articles by Title

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  • Leung, Anthony; Young, Amanda G.; Bhutkar, Arjun (AJ); Zheng, Grace X.; Bosson, Andrew David; Nielsen, Cydney B.; Sharp, Phillip A. (Nature Publishing Group, 2011-01)
    MicroRNAs (miRNAs) are 19–22-nucleotide noncoding RNAs that post-transcriptionally regulate mRNA targets. We have identified endogenous miRNA binding sites in mouse embryonic stem cells (mESCs), by performing photo-cross-linking ...
  • Zheng, Grace X. Y.; Ravi, Arvind; Gould, Genevieve Michelle; Burge, Christopher B.; Sharp, Phillip A. (National Academy of Sciences (U.S.), 2011-09)
    Variations in microRNA (miRNA) gene and/or target repertoire are likely to be key drivers of phenotypic differences between species. To better understand these changes, we developed a computational method that identifies ...
  • Anders, Lars; Guenther, Matthew G.; Qi, Jun; Fan, Zi Peng; Marineau, Jason J; Rahl, Peter B; Sigova, Alla A; Smith, William B; Lee, Tong Ihn; Bradner, James E.; Young, Richard A.; Loven, Jakob (Nature Publishing Group, 2013-12)
    A vast number of small-molecule ligands, including therapeutic drugs under development and in clinical use, elicit their effects by binding specific proteins associated with the genome. An ability to map the direct ...
  • Bochkis, Irina M.; Schug, Jonathan; Ye, Diana Z.; Kurinna, Svitlana; Stratton, Sabrina A.; Barton, Michelle C.; Kaestner, Klaus H. (Public Library of Science, 2012-06)
    Gene duplication is a powerful driver of evolution. Newly duplicated genes acquire new roles that are relevant to fitness, or they will be lost over time. A potential path to functional relevance is mutation of the coding ...
  • Lien, Wen-Hui; Guo, Xingyi; Polak, Lisa; Lawton, Lee N.; Young, Richard A.; Zheng, Deyou; Fuchs, Elaine (Elsevier, 2011-09)
    Using mouse skin, where bountiful reservoirs of synchronized hair follicle stem cells (HF-SCs) fuel cycles of regeneration, we explore how adult SCs remodel chromatin in response to activating cues. By profiling global ...
  • Taipale, Mikko; Keating, Amy E.; DeBartolo, Joseph Vincent (Public Library of Science, 2014-06)
    Programmed cell death is regulated by interactions between pro-apoptotic and prosurvival members of the Bcl-2 family. Pro-apoptotic family members contain a weakly conserved BH3 motif that can adopt an alpha-helical structure ...
  • Rouskin, Silvi; Zubradt, Meghan; Washietl, Stefan; Kellis, Manolis; Weissman, Jonathan S. (Nature Publishing Group, 2013-12)
    RNA has a dual role as an informational molecule and a direct effector of biological tasks. The latter function is enabled by RNA’s ability to adopt complex secondary and tertiary folds and thus has motivated extensive ...
  • Lo, Kinyui Alice; Bauchmann, Mary K.; Baumann, Amy P.; Donahue, Christopher J.; Thiede, Mark A.; Hayes, Lisa S.; Des Etages, Shelley Ann G.; Fraenkel, Ernest (Public Library of Science, 2011-06)
    The growing epidemic of obesity and metabolic diseases calls for a better understanding of adipocyte biology. The regulation of transcription in adipocytes is particularly important, as it is a target for several therapeutic ...
  • Hu, Guangan; Chen, Jianzhu (Nature Publishing Group, 2013-12)
    Memory CD8[superscript +] T-cell development is defined by the expression of a specific set of memory signature genes. Despite recent progress, many components of the transcriptional control of memory CD8[superscript +] ...
  • Mazumder, Aprotim; Bathe, Mark; Samson, Leona D.; Pesudo Quiros, Laia; McRee, Siobhan K. (Oxford University Press, 2013-08)
    An effective response to DNA damaging agents involves modulating numerous facets of cellular homeostasis in addition to DNA repair and cell-cycle checkpoint pathways. Fluorescence microscopy-based imaging offers the ...
  • Neafsey, Daniel E.; Schaffner, Stephen F.; 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.; Lander, Eric S.; Sabeti, Pardis C.; Wirth, Dyann F. (BioMed Central Ltd, 2008-12)
    Background: The malaria parasite Plasmodium falciparum exhibits abundant genetic diversity, and this diversity is key to its success as a pathogen. Previous efforts to study genetic diversity in P. falciparum have begun ...
  • 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 ...
  • Farzadfard, Fahim; Lu, Timothy K. (American Association for the Advancement of Science (AAAS), 2014-11)
    Cellular memory is crucial to many natural biological processes and sophisticated synthetic biology applications. Existing cellular memories rely on epigenetic switches or recombinases, which are limited in scalability and ...
  • 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 ...
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