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Browsing MIT Open Access Articles by Title

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  • Guttman, Mitchell; Garber, Manuel; Levin, Joshua Z.; Donaghey, Julie; Robinson, James; Adiconis, Xian; Fan, Lin; Koziol, Magdalena J.; Gnirke, Andreas; Nusbaum, Chad; Rinn, John L.; Lander, Eric S.; Regev, Aviv (Nature Publishing Group, 2010-07)
    RNA-Seq provides an unbiased way to study a transcriptome, including both coding and noncoding genes. To date, most RNA-Seq studies have critically depended on existing annotations, and thus focused on expression levels ...
  • Liu, Fang; Mar, Brendan D.; Qi, Helena Wen; Kulik, Heather Janine (American Chemical Society (ACS), 2015-05)
    The directed depolymerization of lignin biopolymers is of utmost relevance for the valorization or commercialization of biomass fuels. We present a computational and theoretical screening approach to identify potential ...
  • Liao, Bolin; Zhou, Jiawei; Qiu, Bo; Chen, Gang; Dresselhaus, Mildred (American Physical Society, 2015-06)
    The monolayer of black phosphorus, or “phosphorene,” has recently emerged as a two-dimensional semiconductor with intriguing highly anisotropic transport properties. Existing calculations of its intrinsic phonon-limited ...
  • Esfarjani, Keivan; Chen, Gang; Mendoza, Jonathan M. (American Institute of Physics (AIP), 2015-05)
    We have computed phonon scattering rates and density of states in silicon germanium alloys using Green's function calculations and density functional theory. This method contrasts with the virtual crystal approximation ...
  • Datta, Soumendu; Saha-Dasgupta, Tanusri; Kabir, Mohammad Mukul (American Physical Society, 2011-07)
    Using first-principles density-functional-theory–based calculations, we analyze the structural stability of small clusters of 3d late transition metals. We consider the relative stability of the two structures: layer-like ...
  • Mueller, Timothy K.; Ceder, Gerbrand (American Physical Society, 2010-11)
    We present a low-temperature structural model for lithium imide (Li[subscript 2]NH) that is consistent with experimental studies. Using the cluster expansion formalism and density-functional theory, we have identified a ...
  • Kotnik, Tadej; Weaver, James C (Springer US, 2016-04)
    Phylogenetic studies reveal that horizontal gene transfer (HGT) plays a prominent role in evolution and genetic variability of life. Five biotic mechanisms of HGT among prokaryotic organisms have been extensively characterized: ...
  • Hurwitz, Michael Eliezer; Vanderzalm, Pamela J.; Bloom, Laird; Goldman, Julia; Garriga, Gian; Horvitz, H. Robert (Public Library of Science, 2009-04)
    The engulfment of apoptotic cells is required for normal metazoan development and tissue remodeling. In Caenorhabditis elegans, two parallel and partially redundant conserved pathways act in cell-corpse engulfment. One ...
  • Jodoin, Jeanne; Martin, Adam C (American Society for Cell Biology, 2016-07)
    Tissue morphogenesis requires control over cell shape changes and rearrangements. In the Drosophila mesoderm, linked epithelial cells apically constrict, without cell extrusion or intercalation, to fold the epithelium into ...
  • Christodoulou, Joanna; Walker, Linsey M.; Del Tufo, Stephanie N.; Katzir, Tami; Gabrieli, John D. E.; Gabrieli, Susan; Chang, Bernard S. (John Wiley & Sons, Inc, 2012-06)
    Purpose:  Periventricular nodular heterotopia (PNH) is a malformation of cortical development associated with epilepsy and dyslexia. Evidence suggests that heterotopic gray matter can be functional in brain malformations ...
  • Stevens, Robin Jean; Akbergenova, Yulia; Jorquera, Ramon; Littleton, J. Troy (Society for Neuroscience, 2012-12)
    Sustained neuronal communication relies on the coordinated activity of multiple proteins that regulate synaptic vesicle biogenesis and cycling within the presynaptic terminal. Synaptogyrin and synaptophysin are conserved ...
  • Gruber, Jonathan; Ananat, Elizabeth Oltmans; Staiger, Douglas; Levine, Phillip B. (MIT Press, 2009-01)
    Abortion legalization in the early 1970s led to dramatic changes in fertility. Some research has suggested that it altered cohort outcomes, but this literature has been limited and controversial. In this paper, we provide ...
  • Iatridou, Sabine (Springer Netherlands, 2014-08)
    This paper should be read against the backdrop of three lines of linguistic investigation: (1) the investigation of the Perfect construction, which has received considerable attention, going back to Reichenbach (Elements ...
  • Stangenberg, Lars; Ellson, Chris; Cortez-Retamozo, Virna; Ortiz-Lopez, Adriana; Yuan, Hushan; Blois, Joseph; Smith, Ralph A.; Yaffe, Michael B.; Weissleder, Ralph; Benoist, Christophe; Mathis, Diane; Josephson, Lee; Mahmood, Umar (Wiley Blackwell, 2009-07)
    Objective: To test a novel self-activating viridin (SAV) prodrug that slowly releases wortmannin, a potent phosphoinositide 3-kinase inhibitor, in a model of antibody-mediated inflammatory arthritis. Methods: The SAV ...
  • Kurs, Andre B.; Joannopoulos, John D.; Soljacic, Marin; Johnson, Steven G. (Optical Society of America, 2011-06)
    We present numerical experiments showing how coupled-mode theory can be systematically applied to join very dissimilar photonic crystal waveguides with 100% transmission. Our approach relies on appropriately tuning the ...
  • Nahmod, Andrea; Rey-Bellet, Luc; Sheffield, Scott Roger; Staffilani, Gigliola (International Press, 2011-01)
    We prove absolute continuity of Gaussian measures associated to complex Brownian bridges under certain gauge transformations. As an application we prove that the invariant measure for the periodic derivative nonlinear ...
  • Rayo, Agustin (Oxford University Press, 2012-12)
    Years ago, when I was young and reckless, I believed that there was such a thing as an allinclusive domain.1 Now I have come to see the error of my ways. The source of my mistake was a view that might be labeled ‘Tractarianism’. ...
  • Goyeneche, Dardo; Alsina, Daniel; Riera, Arnau; Latorre, Jose Ignacio; Zyczkowski, Karol (American Physical Society, 2015-09)
    Absolutely maximally entangled (AME) states are those multipartite quantum states that carry absolute maximum entanglement in all possible bipartitions. AME states are known to play a relevant role in multipartite ...
  • Naor, Assaf; Sheffield, Scott Roger (Springer-Verlag, 2011-11)
    We prove that every Lipschitz function from a subset of a locally compact length space to a metric tree has a unique absolutely minimal Lipschitz extension (AMLE). We relate these extensions to a stochastic game called ...
  • Reich, Stephanie; Panknin, Robert; Narula, Rohit (American Physical Society, 2010-07)
    Using sample substitution [Grimsditch et al., J. Raman Spectrosc. 10, 77 (1981)] we deconvolve the highly wavelength-dependent response of the spectrometer from the Raman spectra of graphene suspended on an SiO[subscript ...
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