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Browsing MIT Open Access Articles by Title

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  • Waters, Amanda J.; Bilinski, Paul; Eichten, Steven R.; Vaughn, Matthew W.; Ross-Ibarra, Jeffrey; Gehring, Mary; Springer, Nathan M. (National Academy of Sciences (U.S.), 2013-11)
    In plants, a subset of genes exhibit imprinting in endosperm tissue such that expression is primarily from the maternal or paternal allele. Imprinting may arise as a consequence of mechanisms for silencing of transposons ...
  • Ernst, Jason M.; Kellis, Manolis (Nature Publishing Group, 2010-12)
    Chromatin is composed of DNA and a variety of modified histones and non-histone proteins, which have an impact on cell differentiation, gene regulation and other key cellular processes. Here we present a genome-wide chromatin ...
  • Regev, Aviv; Levin, Joshua Z; Yassour, Moran; Adiconis, Xian; Nusbaum, Chad; Thompson, Dawn Anne; Friedman, Nir; Gnirke, Andreas (Nature Publishing Group, 2010-08)
    Strand-specific, massively parallel cDNA sequencing (RNA-seq) is a powerful tool for transcript discovery, genome annotation and expression profiling. There are multiple published methods for strand-specific RNA-seq, but ...
  • Jimenez Zarco, Jose I.; Xulvi-Brunet, Ramon; Campbell, Gregory W.; Turk-MacLeod, Rebecca; Chen, Irene A. (National Academy of Sciences (U.S.), 2013-09)
    The origin of life is believed to have progressed through an RNA world, in which RNA acted as both genetic material and functional molecules. The structure of the evolutionary fitness landscape of RNA would determine natural ...
  • Lander, Eric S.; Park, Peter J. (Nature Publishing Group, 2012-09)
    Lung squamous cell carcinoma is a common type of lung cancer, causing approximately 400,000 deaths per year worldwide. Genomic alterations in squamous cell lung cancers have not been comprehensively characterized, and no ...
  • White, Kevin P.; Henikoff, Steven; Stein, Lincoln; White, Robert A. H.; Russell, Steven; Ahmad, Kami; Feng, Xin; Henikoff, Jorja G.; Morrison, Carolyn A.; Shah, Parantu K.; Brown, Christopher D.; Nègre, Nicolas; Kheradpour, Pouya; Kellis, Manolis (Public Library of Science, 2010-01)
    Insulators are DNA sequences that control the interactions among genomic regulatory elements and act as chromatin boundaries. A thorough understanding of their location and function is necessary to address the complexities ...
  • Lander, Eric S. (Nature Publishing Group, 2012-07)
    To characterize somatic alterations in colorectal carcinoma, we conducted a genome-scale analysis of 276 samples, analysing exome sequence, DNA copy number, promoter methylation and messenger RNA and microRNA expression. ...
  • Choi, Jae-Hoon; Christensen, Caleb A.; Heo, Myoung Sun; Ketterle, Wolfgang; Lee, Ye-Ryoung; Rvachov, Timur Michael; Wang, Tout T. (American Physical Society, 2012-06)
    Fermi gases with repulsive interactions are characterized by measuring their compressibility as a function of interaction strength. The compressibility is obtained from in-trap density distributions monitored by phase-contrast ...
  • Magesan, Easwar; Cappellaro, Paola; Cooper-Roy, Alexandre (American Physical Society, 2013-12)
    We present methods that can provide an exponential savings in the resources required to perform dynamic parameter estimation using quantum systems. The key idea is to merge classical compressive sensing techniques with ...
  • Sanzeni, Alex; Whittle, Andrew; Germaine, John T.; Colleselli, Francesco (American Society of Civil Engineers (ASCE), 2012-10)
    A laboratory test program was conducted to evaluate the one-dimensional (1D) compression and creep properties of intact sand (and silty-sand) samples from a deep borehole at the Malamocco Inlet to the Venice Lagoon. The ...
  • 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 ...
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