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Browsing MIT Open Access Articles by Title

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  • Carvalho, Carla M.; Kropinski, Andrew M.; Lingohr, Erika J.; Santos, Silvio B.; King, Jonathan Alan; Azeredo, Joana (BioMed Central Ltd, 2012-01)
    Background Campylobacter is the leading cause of foodborne diseases worldwide. Bacteriophages (phages) are naturally occurring predators of bacteria, ubiquitous in the environment, with high host specificity and thus ...
  • Sullivan, Matthew B.; Krastins, Bryan; Hughes, Jennifer L.; Hughes, Jennifer L.; Kelly, Libusha; Chase, Michael; Sarracino, David; Chisholm, Sallie (Penny) (2009-10)
    Prochlorococcus, an abundant phototroph in the oceans, are infected by members of three families of viruses: myo-, podo- and siphoviruses. Genomes of myo- and podoviruses isolated on Prochlorococcus contain DNA replication ...
  • Lander, Eric S. (Nature Publishing Group, 2011-08)
    The evolution of the amniotic egg was one of the great evolutionary innovations in the history of life, freeing vertebrates from an obligatory connection to water and thus permitting the conquest of terrestrial environments. ...
  • 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 ...
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