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Browsing MIT Open Access Articles by Title

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  • Tang, Jing; Du, Ning; Doyle, Patrick S. (National Academy of Sciences (U.S.), 2011-09)
    We experimentally study the effects of a uniform electric field on the conformation of single DNA molecules. We demonstrate that a moderate electric field (~200 V/cm) strongly compresses isolated DNA polymer coils into ...
  • Campagne, Fabien; Dorff, Kevin C.; Chambwe, Nyasha; Robinson, James T.; Mesirov, Jill P. (Public Library of Science, 2013-11)
    Large biological datasets are being produced at a rapid pace and create substantial storage challenges, particularly in the domain of high-throughput sequencing (HTS). Most approaches currently used to store HTS data are ...
  • Juba, Brendan Andrew; Kalai, Adam Tauman; Khanna, Sanjeev; Sudan, Madhu (Institute for Theoretical Computer Science, 2011-01)
    Compression is a fundamental goal of both human language and digital communication, yet natural language is very different from compression schemes employed by modern computers. We partly explain this difference using ...
  • Medard, Muriel; Feizi-Khankandi, Soheil; Effros, Michelle (Institute of Electrical and Electronics Engineers (IEEE), 2011-02)
    In this paper, we demonstrate some applications of compressive sensing over networks. We make a connection between compressive sensing and traditional information theoretic techniques in source coding and channel coding. ...
  • Grant, Elyot; Indyk, Piotr (Association for Computing Machinery (ACM), 2013-06)
    Compressive sensing is a method for acquiring high dimensional signals (e.g., images) using a small number of linear measurements. Consider an n-pixel image x ∈ R[superscript n], where each pixel p has value x[subscript ...
  • Gupta, Rishi V.; Indyk, Piotr; Price, Eric C.; Rachlin, Yaron (Association for Computing Machinery (ACM), 2011-06)
    We propose a framework for compressive sensing of images with local geometric features. Specifically, let x ∈ R[superscript N] be an N-pixel image, where each pixel p has value x[subscript p]. The image is acquired by ...
  • Demanet, Laurent; Peyre, Gabriel (Springer-Verlag, 2011-02)
    This paper presents a method for computing the solution to the time-dependent wave equation from the knowledge of a largely incomplete set of eigenfunctions of the Helmholtz operator, chosen at random. While a linear ...
  • Shim, Eun Bo; Heldt, Thomas; Amano, Akira; Rhee, Kyehan (Hindawi Publishing Corporation, 2012)
    The human body requires a complex circulatory system to supply nutrients to, and to remove metabolic waste products from, its tissues. Given this primary purpose, circulatory function is closely related to the hemodynamic ...
  • Ohler, Uwe; Liao, Guo-chun; Niemann, Heinrich; Rubin, Gerald M (BioMed Central Ltd, 2002-12)
    Background: The core promoter, a region of about 100 base-pairs flanking the transcription start site (TSS), serves as the recognition site for the basal transcription apparatus. Drosophila TSSs have generally been mapped ...
  • Washietl, Stefan; Will, Sebastian; Hendrix, David A.; Goff, Loyal; Rinn, John L.; Berger, Bonnie; Kellis, Manolis (John Wiley & Sons, Inc, 2012-11)
    Noncoding RNAs have emerged as important key players in the cell. Understanding their surprisingly diverse range of functions is challenging for experimental and computational biology. Here, we review computational methods ...
  • Lee, Hyungsuk; Hwang, Wonmuk; Kamm, Roger Dale; Kim, Taeyoon (Springer Boston, 2009-02)
    Mechanical force plays an important role in the physiology of eukaryotic cells whose dominant structural constituent is the actin cytoskeleton composed mainly of actin and actin crosslinking proteins (ACPs). Thus, knowledge ...
  • Hwang, Wonmuk; Lee, Hyungsuk; Kim, Taeyoon; Kamm, Roger Dale (Public Library of Science, 2009-07)
    Mechanical force plays an important role in the physiology of eukaryotic cells whose dominant structural constituent is the actin cytoskeleton composed mainly of actin and actin crosslinking proteins (ACPs). Thus, knowledge ...
  • Liu, Bing; Zhang, Jing; Tan, Pei Yi; Hsu, David; Blom, Anna M.; Leong, Benjamin; Sethi, Sunil; Ho, Bow; Ding, Jeak Ling; Thiagarajan, P. S. (Public Library of Science, 2011-01)
    The complement system is key to innate immunity and its activation is necessary for the clearance of bacteria and apoptotic cells. However, insufficient or excessive complement activation will lead to immune-related diseases. ...
  • Stitziel, Nathan O.; Kiezun, Adam; Sunyaev, Shamil R. (BioMed Central Ltd., 2011-09)
    New sequencing technology has enabled the identification of thousands of single nucleotide polymorphisms in the exome, and many computational and statistical approaches to identify disease-association signals have emerged.
  • Stitziel, Nathan O.; Kiezun, Adam; Sunyaev, Shamil R. (BioMed Central Ltd., 2011-09)
    New sequencing technology has enabled the identification of thousands of single nucleotide polymorphisms in the exome, and many computational and statistical approaches to identify disease-association signals have emerged.
  • Gong, Sherry; Ren, Qingchun; Schedler, Travis; Etingof, Pavel I.; Pacchiano Camacho, Aldo (Taylor & Francis, 2012-05)
    We reduce the computation of Poisson traces on quotients of symplectic vector spaces by finite subgroups of symplectic automorphisms to a finite one by proving several results that bound the degrees of such traces as well ...
  • Aaronson, Scott; Arkhipov, Aleksandr (Association for Computing Machinery, 2011)
    We give new evidence that quantum computers---moreover, rudimentary quantum computers built entirely out of linear-optical elements---cannot be efficiently simulated by classical computers. In particular, we define a model ...
  • Vattre, Aurelien; Abdolrahim, Niaz; Kolluri, Kedarnath; Demkowicz, Michael J. (Nature Publishing Group, 2014-08)
    Patterning is a familiar approach for imparting novel functionalities to free surfaces. We extend the patterning paradigm to interfaces between crystalline solids. Many interfaces have non-uniform internal structures ...
  • Buchwald, Stephen Leffler; Jones, Gavin O.; Houk, Kendall N.; Liu, Peng (American Chemical Society (ACS), 2010-04)
    Computational investigations of ligand-directed selectivities in Ullmann-type coupling reactions of methanol and methylamine with iodobenzene by β-diketone- and 1,10-phenanthroline-ligated CuI complexes are reported. Density ...
  • Shapiro, Jeffrey H. (Institute of Electrical and Electronics Engineers, 2009-08)
    A computational ghost-imaging arrangement that uses only a single-pixel detector is described. It affords a new 3D sectioning capability and matches the resolution of pseudothermal ghost imaging.
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