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Browsing MIT Open Access Articles by Title

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  • Onder, Tamer T.; Kara, Nergis; Cherry, Anne; Sinha, Amit U.; Zhu, Nan; Bernt, Kathrin M.; Cahan, Patrick; Marcarci, B. Ogan; Unternaehrer, Juli; Lander, Eric S.; Armstrong, Scott A.; Daley, George Q.; Gupta, Piyush (Nature Publishing Group, 2012-03)
    Generation of induced pluripotent stem cells (iPSCs) by somatic cell reprogramming involves global epigenetic remodelling. Whereas several proteins are known to regulate chromatin marks associated with the distinct epigenetic ...
  • Vastenhouw, Nadine L.; Zhang, Yong; Woods, Ian G.; Imam, Farhad; Regev, Aviv; Liu, X. Shirley; Rinn, John; Schier, Alexander F. (Nature Publishing Group, 2010-03)
    After fertilization the embryonic genome is inactive until transcription is initiated during the maternal–zygotic transition. This transition coincides with the formation of pluripotent cells, which in mammals can be used ...
  • Guttman, Mitchell; Amit, Ido; Garber, Manuel; French, Courtney; Lin, Michael F.; Feldser, David M.; Huarte, Maite; Zuk, Or; Carey, Bryce W.; Cassady, John P.; Cabili, Moran N.; Jaenisch, Rudolf; Mikkelsen, Tarjei S.; Jacks, Tyler E.; Hacohen, Nir; Bernstein, Bradley E.; Kellis, Manolis; Lander, Eric S. (Nature Publishing Group, 2009-02)
    There is growing recognition that mammalian cells produce many thousands of large intergenic transcripts [1, 2, 3, 4]. However, the functional significance of these transcripts has been particularly controversial. Although ...
  • Guenther, Matthew G.; Frampton, Garrett M.; Soldner, Frank; Hockemeyer, Dirk; Mitalipova, Maya; Jaenisch, Rudolf; Young, Richard A. (Elsevier, 2010-08)
    Knowledge of both the global chromatin structure and the gene expression programs of human embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) should provide a robust means to assess whether the genomes ...
  • Kubicek, Stefan; Gilbert, Joshua C.; Fomina-Yadlin, Dina; Gitlin, Alexander D.; Yuan, Yuan; Wagner, Florence F.; Holson, Edward B.; Luo, Tuoping; Lewis, Timothy A.; Taylor, Bradley; Gupta, Supriya; Shamji, Alykhan F.; Wagner, Bridget K.; Clemons, Paul A.; Schreiber, Stuart L. (National Academy of Sciences, 2012-04)
    Under the instruction of cell-fate–determining, DNA-binding transcription factors, chromatin-modifying enzymes mediate and maintain cell states throughout development in multicellular organisms. Currently, small molecules ...
  • Ernst, Jason; Kellis, Manolis (Nature Publishing Group, 2012-02)
    To the Editor: Chromatin-state annotation using combinations of chromatin modification patterns has emerged as a powerful approach for discovering regulatory regions and their cell type–specific activity patterns and for ...
  • Demirbas, Umit; Sennaroglu, A.; Cankaya, H.; Cizmeciyan, N.; Kurt, A.; Somer, M. (SPIE, 2010-02)
    This paper provides an overview of the experimental work performed in our research group on the synthesis, spectroscopic investigation, and laser characterization of chromium-doped zinc selenide (Cr[superscript 2+]:ZnSe). ...
  • Teleman, Aurelio A.; Graumann, Peter L.; Lin, Daniel Chi-Hong; Grossman, Alan D.; Losick, Richard (Elsevier, 1998-09)
    Background: The contour length of the circular chromosome of bacteria is greater than a millimeter but must be accommodated within a cell that is only a few micrometers in length. Bacteria do not have nucleosomes and little ...
  • Tabuchi, Tomoko M.; Deplancke, Bart; Osato, Naoki; Zhu, Lihua J.; Barrasa, M. Inmaculada; Harrison, Melissa M.; Horvitz, H. Robert; Walhout, Albertha J. M.; Hagstrom, Kristen A. (Public Library of Science, 2011-05)
    DRM is a conserved transcription factor complex that includes E2F/DP and pRB family proteins and plays important roles in development and cancer. Here we describe new aspects of DRM binding and function revealed through ...
  • Schmidt, Jens Christopher; Cheeseman, Iain McPherson (Elsevier B.V., 2011-02)
    The Ndc80 complex is a key component of the kinetochore–microtubule interface. Two studies now demonstrate that a conserved loop region within the extended coiled-coil of Ndc80 plays an unexpected role in recruiting proteins ...
  • Whittaker, Charles A.; Housman, David E.; Charest, Alain; Acquaviva, Jaime; Jun, Hyun Jung; Lessard, Julie; Ruiz, Rolando; Zhu, Haihao; Donovan, Melissa; Woolfenden, Steve; Boskovitz, Abraham; Raval, Ami; Bronson, Roderick T.; Pfannl, Rolf (American Association for Cancer Research, 2011-10)
    Glioblastoma multiforme (GBM) is characterized by overexpression of epidermal growth factor receptor (EGFR) and loss of the tumor suppressors Ink4a/Arf. Efforts at modeling GBM using wild-type EGFR in mice have proven ...
  • Oliver, Trudy Gale; Mercer, Kim L.; Sayles, Leanne C.; Burke, James R.; Mendus, Diana; Lovejoy, Katherine S.; Cheng, Mei-Hsin; Subramanian, Aravind; Mu, David; Powers, Scott; Crowley, Denise G.; Bronson, Roderick T.; Whittaker, Charles A.; Bhutkar, Arjun (AJ); Lippard, Stephen J.; Golub, Todd; Thomale, Juergen; Jacks, Tyler E.; Sweet-Cordero, E. Alejandro (Cold Spring Harbor Laboratory Press in association with The Genetics Society, 2010-03)
    Chemotherapy resistance is a major obstacle in cancer treatment, yet the mechanisms of response to specific therapies have been largely unexplored in vivo. Employing genetic, genomic, and imaging approaches, we examined ...
  • Cosgrove, Cormac; Berger, Christoph T.; Kroy, Daniela C.; Cheney, Patrick C.; Ghebremichael, Musie; Aneja, Jasneet; Tomlinson, Michelle; Kim, Arthur Y.; Lauer, Georg M.; Alter, Galit (Public Library of Science, 2014-08)
    Although epidemiological and functional studies have implicated NK cells in protection and early clearance of HCV, the mechanism by which they may contribute to viral control is poorly understood, particularly at the site ...
  • Michalon, Aubin; Sidorov, Michael; Ballard, Theresa M.; Ozmen, Laurence; Spooren, Will; Wettstein, Joseph G.; Jaeschke, Georg; Bear, Mark; Lindemann, Lothar (Elsevier B.V., 2012-04)
    Fragile X syndrome (FXS) is the most common form of inherited intellectual disability. Previous studies have implicated mGlu5 in the pathogenesis of the disease, but a crucial unanswered question is whether pharmacological ...
  • CIA Leaks 
    Gillies, Anthony S.; von Fintel, Kai (Duke University Press, 2008-01)
    Epistemic modals are standardly taken to be context-dependent quantifiers over possibilities. Thus sentences containing them get truth-values with respect to both a context and an index. But some insist that this relativization ...
  • Giuffre, Carl; Hinow, Peter; Vogel, Ryan; Ahmed, Tanvir; Stocker, Roman; Consi, Thomas R.; Strickler, J. Rudi (Public Library of Science, 2011-04)
    We study the motility behavior of the unicellular protozoan Paramecium tetraurelia in a microfluidic device that can be prepared with a landscape of attracting or repelling chemicals. We investigate the spatial distribution ...
  • Leiserson, Charles E. (Association for Computing Machinery, 2009-01)
    The availability of multicore processors across a wide range of computing platforms has created a strong demand for software frameworks that can harness these resources. This paper overviews the Cilk++ programming environment, ...
  • Yang, Qiong; Pando, Bernardo F.; Dong, Guogang; Golden, Susan S.; van Oudenaarden, Alexander (American Association for the Advancement of Science, 2010-03)
    Although major progress has been made in uncovering the machinery that underlies individual biological clocks, much less is known about how multiple clocks coordinate their oscillations. We simultaneously tracked cell ...
  • Mandal, Soumyajit; Sarpeshkar, Rahul (Institute of Electrical and Electronics Engineers, 2009-12)
    We use analogies between chemistry and subthreshold electronics to develop fast, scalable, digitally programmable hardware models of stochastic genetic networks. We also present experimental results from a prototype 0.18 ...
  • Wilusz, Jeremy E.; Sharp, Phillip A. (American Association for the Advancement of Science (AAAS), 2013-04)
    Most genetic information is expressed as, and transacted by, proteins. Yet, less than 2% of the human genome actually codes for proteins, prompting a search for functions for the other 98% of the genome, once considered ...
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