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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 ...
  • Yin, Hao; Xue, Wen; Chen, Sidi; Benedetti, Eric; Grompe, Markus; Kotelianski, Victor E.; Bogorad, Roman; Sharp, Phillip A.; Jacks, Tyler E.; Anderson, Daniel Griffith (Nature Publishing Group, 2014-03)
    We demonstrate CRISPR-Cas9–mediated correction of a Fah mutation in hepatocytes in a mouse model of the human disease hereditary tyrosinemia. Delivery of components of the CRISPR-Cas9 system by hydrodynamic injection ...
  • Ran, F. Ann; Hsu, Patrick; Wright, Jason; Agarwala, Vineeta; Scott, David Arthur; Zhang, Feng (Nature Publishing Group, 2013-11)
    Targeted nucleases are powerful tools for mediating genome alteration with high precision. The RNA-guided Cas9 nuclease from the microbial clustered regularly interspaced short palindromic repeats (CRISPR) adaptive immune ...
  • 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. ...
  • Dmytrenko, Oleg; Russell, Shelbi L.; Loo, Wesley T.; Liao, Li; Roeselers, Guus; Sharma, Raghav; Stewart, Frank J.; Newton, Irene L. G.; Woyke, Tanja; Wu, Dongying; Lang, Jenna Morgan; Eisen, Jonathan A.; Cavanaugh, Colleen M.; Fontanez, Kristina M. (BioMed Central Ltd, 2014-10)
    Background Symbioses between chemoautotrophic bacteria and marine invertebrates are rare examples of living systems that are virtually independent of photosynthetic primary production. These associations have evolved ...
  • Gu, Hongcang; Bock, Christoph; Mikkelsen, Tarjei Sigurd; 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 ...
  • Meacham, Corbin Elizabeth; Lawton, Lee N.; Pritchard, Justin R.; Joughin, Brian A.; Ehrenberger, Tobias; Fenouille, Nina; Zuber, Johannes; Williams, Richard T.; Young, Richard A.; Soto Feliciano, Yadira Marie; Hemann, Michael (Cold Spring Harbor Laboratory Press, 2015-03)
    We performed a genome-scale shRNA screen for modulators of B-cell leukemia progression in vivo. Results from this work revealed dramatic distinctions between the relative effects of shRNAs on the growth of tumor cells in ...
  • Lindquist, Robert A.; Ottina, Kathleen; 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 ...
  • Konermann, Silvana; Brigham, Mark D.; Trevino, Alexandro E.; Joung, Julia; Barcena, Clea; Hsu, Patrick D.; Habib, Naomi; Gootenberg, Jonathan S.; Nishimasu, Hiroshi; Nureki, Osamu; Zhang, Feng; Abudayyeh, Omar Osama (2016-05-22)
    Systematic interrogation of gene function requires the ability to perturb gene expression in a robust and generalizable manner. Here we describe structure-guided engineering of a CRISPR-Cas9 complex to mediate efficient ...
  • Berube, Paul M.; Kelly, Libusha; Roggensack, Sara E.; Awad, Lana; Roache-Johnson, Kathryn H.; Ding, Huiming; Giovannoni, Stephen J.; Rocap, Gabrielle; Moore, Lisa R.; Biller, Steven; Thompson, Jessica Weidemier; Chisholm, Sallie (Penny) (Nature Publishing Group, 2014-09)
    The marine cyanobacterium Prochlorococcus is the numerically dominant photosynthetic organism in the oligotrophic oceans, and a model system in marine microbial ecology. Here we report 27 new whole genome sequences (2 ...
  • Labrie, Simon J.; Frois-Moniz, Katya; Osburne, Marcia; Kelly, Libusha; Roggensack, Sara; Sullivan, M. B.; Gearin, Gary; Zeng, Q.; Fitzgerald, M.; Henn, Matthew R.; Chisholm, Sallie (Penny) (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.; Lander, Eric S.; Couto, Guillermo; Starkey, Mike P. Comstock, Kenine; Starkey, Mike P.; Modiano, Jaime F.; Breen, Matthew; Lindblad-Toh, Kerstin (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 ...
  • Tonomura, Noriko; Elvers, Ingegerd; Thomas, Rachael; Megquier, Kate; Turner-Maier, Jason; Howald, Cedric; Sarver, Aaron L.; Swofford, Ross; Frantz, Aric M.; Ito, Daisuke; Mauceli, Evan; Arendt, Maja; Noh, Hyun Ji; Koltookian, Michele; Biagi, Tara; Fryc, Sarah; Williams, Christina; Avery, Anne C.; Kim, Jong-Hyuk; Barber, Lisa; Burgess, Kristine; Lander, Eric S.; Karlsson, Elinor K.; Azuma, Chieko; Modiano, Jaime F.; Breen, Matthew; Lindblad-Toh, Kerstin (Public Library of Science, 2015-02)
    Dogs, with their breed-determined limited genetic background, are great models of human disease including cancer. Canine B-cell lymphoma and hemangiosarcoma are both malignancies of the hematologic system that are clinically ...
  • 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 D.; 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 ...
  • 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 ...
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