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Browsing MIT Open Access Articles by Title

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  • 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 ...
  • 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 ...
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