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Browsing MIT Open Access Articles by Title

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  • Wu, Xuebing; Cheng, Albert W.; Chen, Sidi; Jaenisch, Rudolf; Zhang, Feng; Chiu, Anthony Chun-yin; Sharp, Phillip A.; Scott, David Arthur; Hsu, Patrick; Trevino, Alexandro E.; Konermann, Silvana M.; Kriz, Andrea J.; Dadon, Daniel Benjamin (Nature Publishing Group, 2014-04)
    Bacterial type II CRISPR-Cas9 systems have been widely adapted for RNA-guided genome editing and transcription regulation in eukaryotic cells, yet their in vivo target specificity is poorly understood. Here we mapped ...
  • Tsang, John S.; Ebert, Margaret S.; van Oudenaarden, Alexander (Elsevier, 2010-04)
    MicroRNAs are emerging as important regulators of diverse biological processes and pathologies in animals and plants. Though hundreds of human microRNAs are known, only a few have known functions. Here, we predict human ...
  • Xu, Jia; Yanagisawa, Yoshimi; Tsankov, Alexander M; Hart, Christopher; Aoki, Keita; Kommajosyula, Naveen; Steinmann, Kathleen E.; Bochicchio, James; Russ, Carsten; Regev, Aviv; Rando, Oliver J; Nusbaum, Chad; Niki, Hironori; Milos, Patrice M.; Weng, Zhiping; Rhind, Nicholas; Regev, Aviv (Springer (Biomed Central Ltd.), 2012-04)
    Background DNA replication initiates at distinct origins in eukaryotic genomes, but the genomic features that define these sites are not well understood. Results We have taken a combined experimental and bioinformatic ...
  • 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 ...
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