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Browsing MIT Open Access Articles by Title

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  • Spiridonov, Alexey Nikolaevich; Shabalina, Svetlana A.; Spiridonov, Nikolay A.; Koonin, Eugene V. (Oxford University Press (OUP), 2010-10)
    The majority of mammalian genes produce multiple transcripts resulting from alternative splicing (AS) and/or alternative transcription initiation (ATI) and alternative transcription termination (ATT). Comparative analysis ...
  • Daskalakis, Constantinos; Dimakis, Alexandros G.; Mossel, Elchanan (Institute of Mathematical Statistics, 2011)
    We study how the structure of the interaction graph of a game affects the existence of pure Nash equilibria. In particular, for a fixed interaction graph, we are interested in whether there are pure Nash equilibria arising ...
  • Saygin, Zeynep M.; Osher, David E.; Augustinack, Jean; Fischl, Bruce; Gabrieli, John D. E. (Elsevier, 2011-03)
    The amygdala plays an important role in emotional and social functions, and amygdala dysfunction has been associated with multiple neuropsychiatric disorders, including autism, anxiety, and depression. Although the amygdala ...
  • LaPlante, Roan A.; Douw, Linda; Tang, Wei; Stufflebeam, Steven M. (Public Library of Science, 2014-12)
    In analysis of the human connectome, the connectivity of the human brain is collected from multiple imaging modalities and analyzed using graph theoretical techniques. The dimensionality of human connectivity data is high, ...
  • Choi, Han-Lim; Brunet, Luc; How, Jonathan P. (Institute of Electrical and Electronics Engineers, 2009-06)
    This paper addresses task allocation to coordinate a fleet of autonomous vehicles by presenting two decentralized algorithms: the consensus-based auction algorithm (CBAA) and its generalization to the multi-assignment ...
  • Kellis, Manolis; Lin, Michael F. (Cold Spring Harbor Laboratory Press, 2009-04)
    Effective use of the human and mouse genomes requires reliable identification of genes and their products. Although multiple public resources provide annotation, different methods are used that can result in similar but ...
  • Todd, Ryan C.; Lippard, Stephen J. (Elsevier, 2010-12)
    The effects of cisplatin binding to DNA were explored at the nucleosome level to incorporate key features of the eukaryotic nuclear environment. An X-ray crystal structure of a site-specifically platinated nucleosome ...
  • Kerr, William R.; Lerner, Josh; Schoar, Antoinette (Oxford University Press on behalf of The Society for Financial Studies, 2011-10)
    This article documents the fact that ventures funded by two successful angel groups experience superior outcomes to rejected ventures: They have improved survival, exits, employment, patenting, Web traffic, and financing. ...
  • Acemoglu, Daron; Cantoni, Davide; Johnson, Simon; Robinson, James A. (American Economic Association, 2011-01)
    The French Revolution had a momentous impact on neighboring countries. It removed the legal and economic barriers protecting oligarchies, established the principle of equality before the law, and prepared economies for ...
  • Shay, Tal; Jojic, Vladimir; Zuk, Or; Rothamel, Katherine; Puyraimond-Zemmour, David; Feng, Ting; Wakamatsu, Ei; Benoist, Christophe; Koller, Daphne; Regev, Aviv (National Academy of Sciences (U.S.), 2013-02)
    Much of the knowledge about cell differentiation and function in the immune system has come from studies in mice, but the relevance to human immunology, diseases, and therapy has been challenged, perhaps more from anecdotal ...
  • Wei, Shuo; Xu, Guofeng; Bridges, Lance C.; Shah, Anoop; White, Judith M.; DeSimone, Douglas W.; Whittaker, Charles A. (Springer (Biomed Central Ltd.), 2010-07)
    Background Members of the disintegrin metalloproteinase (ADAM) family play important roles in cellular and developmental processes through their functions as proteases and/or binding partners for other proteins. The ...
  • McLaughlin, Dennis; Cohn, Stephen E.; Verlaan, Martin; Janjic, Tijana (American Meteorological Society, 2014-02)
    This paper considers the incorporation of constraints to enforce physically based conservation laws in the ensemble Kalman filter. In particular, constraints are used to ensure that the ensemble members and the ensemble ...
  • Chiu, Edmond Kwan-Yu; Wang, Qiqi; Hu, Rui; Jameson, Antony (Society for Industrial and Applied Mathematics, 2012-11)
    We present a novel mesh-free scheme for solving partial differential equations. We first derive a conservative and stable formulation of mesh-free first derivatives. We then show that this formulation is a special case of ...
  • Davies, Bryan W.; Jacob, Asha I.; Koehrer, Caroline; Rajbhandary, Uttam L.; Walker, Graham C. (Elsevier, 2012-12)
    Quality control of ribosomes is critical for cellular function since protein mistranslation leads to severe physiological consequences. We report evidence of a previously unrecognized ribosome quality control system in ...
  • Airoldi, Edoardo M.; Slavov, Nikolai G.; van Oudenaarden, Alexander; Botstein, David (American Society for Cell Biology, 2012-03)
    The respiratory metabolic cycle in budding yeast (Saccharomyces cerevisiae) consists of two phases most simply defined phenomenologically: low oxygen consumption (LOC) and high oxygen consumption (HOC). Each phase is ...
  • Zhang, Yan; Li, Haoran; Zhang, Caiguo; Stubbe, JoAnne; An, Xiuxiang; Liu, Lili; Huang, Mingxia (National Academy of Sciences (U.S.), 2014-04)
    Eukaryotic ribonucleotide reductases (RNRs) require a diferric-tyrosyl radical (Fe[III over 2]-Y•) cofactor to produce deoxynucleotides essential for DNA replication and repair. This metallocofactor is an important target ...
  • Gjoneska, Elizabeta; Pfenning, Andreas R.; Mathys, Hansruedi; Quon, Gerald; Kundaje, Anshul; Tsai, Li-Huei; Kellis, Manolis (American Association for the Advancement of Science (AAAS), 2015-02)
    Alzheimer’s disease (AD) is a severe age-related neurodegenerative disorder characterized by accumulation of amyloid-β plaques and neurofibrillary tangles, synaptic and neuronal loss, and cognitive decline. Several genes ...
  • Krishnan, Rajaraman; Goodman, Jessica L.; Mukhopadhyay, Samrat; Pacheco, Chris D.; Lemke, Edward A.; Deniz, Ashok A.; Lindquist, Susan (National Academy of Sciences, 2012-07)
    Some amyloid-forming polypeptides are associated with devastating human diseases and others provide important biological functions. For both, oligomeric intermediates appear during amyloid assembly. Currently we have few ...
  • Ulitsky, Igor; Shkumatava, Alena; Jan, Calvin H.; Sive, Hazel L.; Bartel, David; Jan, Calvin H. (Elsevier B.V., 2011-12)
    Thousands of long intervening noncoding RNAs (lincRNAs) have been identified in mammals. To better understand the evolution and functions of these enigmatic RNAs, we used chromatin marks, poly(A)-site mapping and RNA-Seq ...
  • Thomas, Jacob; Lee, Catherine Ann; Grossman, Alan D. (Public Library of Science, 2013-01)
    Integrative and conjugative elements (ICEs) are agents of horizontal gene transfer and have major roles in evolution and acquisition of new traits, including antibiotic resistances. ICEs are found integrated in a host ...
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