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Browsing MIT Open Access Articles by Title

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  • Gu, Hongcang; Bock, Christoph; Mikkelsen, Tarjei S.; Jäger, Natalie; Smith, Zachary D.; Tomazou, Eleni; Gnirke, Andreas; Lander, Eric S.; Meissner, Alexander (Nature Publishing Group, 2010-01)
    Bisulfite sequencing measures absolute levels of DNA methylation at single-nucleotide resolution, providing a robust platform for molecular diagnostics. Here, we optimize bisulfite sequencing for genome-scale analysis ...
  • Lindquist, Robert A.; Ottina, Kathleen A.; Wheeler, Douglas B.; Hsu, Peggy P.; Thoreen, Carson C.; Guertin, David A.; Ali, Siraj M.; Sengupta, Shomit; Shaul, Yoav D.; Lamprecht, Michael R.; Madden, Katherine L.; Papallo, Adam R.; Jones, Thouis R.; Sabatini, David M.; Carpenter, Anne E. (Cold Spring Harbor Laboratory Press, 2011-01)
    The evolutionarily conserved target of rapamycin complex 1 (TORC1) controls cell growth in response to nutrient availability and growth factors. TORC1 signaling is hyperactive in cancer, and regulators of TORC1 signaling ...
  • Labrie, Simon J.; Frois-Moniz, Katya; Osburne, Marcia; Kelly, Libusha; Roggensack, Sara; Sullivan, M. B.; Gearin, G.; Zeng, Q.; Fitzgerald, M.; Henn, M. R.; Chisholm, Sallie (Wiley Blackwell, 2013-01)
    The marine cyanobacteria Prochlorococcus and Synechococcus are highly abundant in the global oceans, as are the cyanophage with which they co-evolve. While genomic analyses have been relatively extensive for cyanomyoviruses, ...
  • Karlsson, Elinor K; Sigurdsson, Snaevar; Ivansson, Emma; Thomas, Rachael; Elvers, Ingegerd; Wright, Jason; Howald, Cedric; Tonomura, Noriko; Perloski, Michele; Swofford, Ross; Biagi, Tara; Fryc, Sarah; Anderson, Nathan; Courtay-Cahen, Celine; Youell, Lisa; Ricketts, Sally L; Mandlebaum, Sarah; Rivera, Patricio; von Euler, Henrik; Kisseberth, William C; London, Cheryl A; Couto, Guillermo; Comstock, Kenine; Starkey, Mike P; Modiano, Jaime F; Breen, Matthew; Lindblad-Toh, Kerstin; Lander, Eric S. (BioMed Central Ltd, 2013-12)
    Background: Canine osteosarcoma is clinically nearly identical to the human disease, but is common and highly heritable, making genetic dissection feasible. Results: Through genome-wide association analyses in three ...
  • Runstadler, Jonathan; Vernau, Karen M.; Brown, Emily A.; Cameron, Jessie M.; Huson, Heather J.; Higgins, Robert J.; Ackerley, Cameron; Sturges, Beverly K.; Dickinson, Peter J.; Puschner, Birgit; Giulivi, Cecilia; Shelton, G. Diane; Robinson, Brian H.; DiMauro, Salvatore; Bollen, Andrew W.; Bannasch, Danika L. (Public Library of Science, 2013-03)
    Alaskan Husky Encephalopathy (AHE) has been previously proposed as a mitochondrial encephalopathy based on neuropathological similarities with human Leigh Syndrome (LS). We studied 11 Alaskan Husky dogs with AHE, but found ...
  • Hunter, David J.; Peltonen, Leena; Guiducci, Candace; Crawford, Gabriel; Hirschhorn, Joel N.; Lyon, Helen N.; Speliotes, Elizabeth K. (Public Library of Science, 2009-06)
    To identify genetic loci influencing central obesity and fat distribution, we performed a meta-analysis of 16 genome-wide association studies (GWAS, N = 38,580) informative for adult waist circumference (WC) and waist–hip ...
  • Lowe, Jennifer K.; Maller, Julian B.; Pe'er, Itsik; Neale, Benjamin M.; Salit, Jacqueline; Kenny, Eimear E.; Shea, Jessica L.; Burkhardt, Ralph; Smith, J. Gustav; Ji, Weizhen; Noel, Martha; Foo, Jia Nee; Blundell, Maude L.; Skilling, Vita; Garcia, Laura; Sullivan, Marcia L.; Lee, Heather E.; Labek, Anna; Ferdowsian, Hope; Auerbach, Steven B.; Lifton, Richard P.; Newton-Cheh, Christopher; Breslow, Jan L.; Stoffel, Markus; Daly, Mark J.; Altshuler, David; Friedman, Jeffrey M. (Public Library of Science, 2009-02)
    It has been argued that the limited genetic diversity and reduced allelic heterogeneity observed in isolated founder populations facilitates discovery of loci contributing to both Mendelian and complex disease. A strong ...
  • Hass, Johanna; Walton, Esther; Kirsten, Holger; Liu, Jingyu; Priebe, Lutz; Wolf, Christiane; Karbalai, Nazanin; White, Tonya; Roessner, Veit; Müller, Kathrin U.; Paus, Tomas; Smolka, Michael N.; Schumann, Gunter; Scholz, Markus; Cichon, Sven; Calhoun, Vince; Ehrlich, Stefan; Gollub, Randy Lyanne (Public Library of Science, 2013-06)
    Patients with schizophrenia and their siblings typically show subtle changes of brain structures, such as a reduction of hippocampal volume. Hippocampal volume is heritable, may explain a variety of cognitive symptoms of ...
  • 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; 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 K. L.; Young, Amanda G.; Bhutkar, Arjun; 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 ...
  • 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 ...
  • 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 ...
  • Lo, Kin Yui; 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 (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., Jr; Lukens, Amanda; 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 ...
  • 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 ...
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