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Browsing MIT Open Access Articles by Title

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  • Orcutt, Jason S.; Ram, Rajeev J.; Stojanovic, Vladimir (Society of Photo-Optical Instrumentation Engineers (SPIE), 2013-03)
    Front-end monolithic integration has enabled photonic devices to be fabricated in bulk and thin-SOI CMOS as well as DRAM electronics processes. Utilizing the CMOS generic process model, integration was accomplished on ...
  • Huang, Min; Yanik, Ahmet Ali; Chang, Tsung-Yao; Altug, Hatice (SPIE, 2010-08)
    In this paper, we introduce a novel sensor scheme which merges nano-photonics and nano-fluidics on a single platform through the use of free-standing photonic crystals (PhCs). PhCs offer great freedom to manipulate the ...
  • Fachin, Fabio; Wardle, Brian L.; Chen, G. D.; Toner, M. (Institute of Electrical and Electronics Engineers, 2011-01)
    Presently, an estimated 35 million people are living with HIV, 300 million with Hepatitis C (HCV), with thousands of human fatalities registered ever day due to these and similar infectious diseases. Efficient, reliable, ...
  • Kim, Jane C.; Nordman, Jared; Xie, Fang; Orr-Weaver, Terry L.; Kashevsky, Helena; Eng, Thomas; Li, Sharon; MacAlpine, David M. (Cold Spring Harbor Laboratory Press, 2011-07)
    In metazoans, how replication origins are specified and subsequently activated is not well understood. Drosophila amplicons in follicle cells (DAFCs) are genomic regions that undergo rereplication to increase DNA copy ...
  • Berger, Michael F.; Levin, Joshua Z.; Vijayendran, Krishna; Sivachenko, Andrey; Adiconis, Xian; Maguire, Jared; Johnson, Laura A.; Robinson, James; Verhaak, Roel G.; Sougnez, Carrie; Onofrio, Robert C.; Ziaugra, Liuda; Cibulskis, Kristian; Laine, Elisabeth; Barretina, Jordi; Winckler, Wendy; Fisher, David E.; Getz, Gad; Meyerson, Matthew; Jaffe, David B.; Gabriel, Stacey B.; Lander, Eric S.; Dummer, Reinhard; Gnirke, Andreas; Nusbaum, Chad; Garraway, Levi A. (Cold Spring Harbor Laboratory Press, 2010-02)
    Global studies of transcript structure and abundance in cancer cells enable the systematic discovery of aberrations that contribute to carcinogenesis, including gene fusions, alternative splice isoforms, and somatic ...
  • Busser, Brian W.; Huang, Di; Rogacki, Kevin R.; Lane, Elizabeth A.; Shokri, Leila; Ni, Ting; Gamble, Caitlin E.; Gisselbrecht, Stephen S.; Zhu, Jun; Bulyk, Martha L.; Ovcharenko, Ivan; Michelson, Alan M. (National Academy of Sciences (U.S.), 2012-11)
    Contemporary high-throughput technologies permit the rapid identification of transcription factor (TF) target genes on a genome-wide scale, yet the functional significance of TFs requires knowledge of target gene expression ...
  • Ernst, Jason; Kellis, Manolis; Hoffman, Michael M.; Wilder, Steven P.; Kundaje, Anshul; Harris, Robert S.; Libbrecht, Max; Giardine, Belinda; Ellenbogen, Paul M.; Bilmes, Jeffrey A.; Birney, Ewan; Hardison, Ross C.; Dunham, Ian; Noble, William Stafford (Oxford University Press, 2012-12)
    The ENCODE Project has generated a wealth of experimental information mapping diverse chromatin properties in several human cell lines. Although each such data track is independently informative toward the annotation of ...
  • Cabili, Moran N.; Trapnell, Cole; Goff, Loyal; Koziol, Magdalena; Tazon-Vega, Barbara; Regev, Aviv; Rinn, John L. (Cold Spring Harbor Laboratory Press, 2011-09)
    Large intergenic noncoding RNAs (lincRNAs) are emerging as key regulators of diverse cellular processes. Determining the function of individual lincRNAs remains a challenge. Recent advances in RNA sequencing (RNA-seq) and ...
  • Hu, Yanhui; Flockhart, Ian; Vinayagam, Arunachalam; Bergwitz, Clemens; Perrimon, Norbert; Mohr, Stephanie E.; Berger, Bonnie (Springer (Biomed Central Ltd.), 2011-08)
    Background Mapping of orthologous genes among species serves an important role in functional genomics by allowing researchers to develop hypotheses about gene function in one species based on what is known about the ...
  • Brown, Jennifer R.; Hanna, Megan; Tesar, Bethany; Werner, Lillian; Pochet, Nathalie; Asara, John M.; Wang, Yaoyu E.; dal Cin, Paola; Fernandes, Stacey M.; Thompson, Christina; MacConaill, Laura; Wu, Catherine J.; Van de Peer, Yves; Correll, Mick; Regev, Aviv; Neuberg, Donna; Freedman, Arnold S. (American Association for Cancer Research, 2012-05)
    Purpose: The disease course of chronic lymphocytic leukemia (CLL) varies significantly within cytogenetic groups. We hypothesized that high-resolution genomic analysis of CLL would identify additional recurrent abnormalities ...
  • Robinson, James T.; Thorvaldsdóttir, Helga; Winckler, Wendy; Guttman, Mitchell; Lander, Eric S.; Getz, Gad; Mesirov, Jill P. (Nature Publishing Group, 2011-01)
    To the Editor: Rapid improvements in sequencing and array-based platforms are resulting in a flood of diverse genome-wide data, including data from exome and whole-genome sequencing, epigenetic surveys, expression profiling ...
  • Marchetti, Giovanni; Escuin, Sarah; van der Flier, Arjan; De Arcangelis, Adèle; Hynes, Richard O.; Georges-Labouesse, Elisabeth (Federation of European Neuroscience Societies and Blackwell Publishing Ltd, 2010-02)
    During cerebral cortex development, post-mitotic neurons interact with radial glial fibers and the extracellular environment to migrate away from the ventricular region and form a correct laminar structure. Integrin receptors ...
  • Shibue, Tsukasa; Weinberg, Robert A. (United States National Academy of Sciences, 2009-04)
    The development of metastases is an extended and inefficient process involving multiple steps. The last of these involves the growth of micrometastases into macroscopic tumors. We show here that intravenously injected, ...
  • Gupton, Stephanie L.; Gertler, Frank (Elsevier B.V., 2010-05)
    Neurons establish their unique morphology by elaborating multiple neurites that subsequently form axons and dendrites. Neurite initiation entails significant surface area expansion, necessitating addition to the plasma ...
  • Gupton, Stephanie L.; Gertler, Frank (Elsevier, 2010-05)
    Neurons establish their unique morphology by elaborating multiple neurites that subsequently form axons and dendrites. Neurite initiation entails significant surface area expansion, necessitating addition to the plasma ...
  • Ren, Ling; Yu, Xiangyao; Devadas, Srinivas; Fletcher, Christopher Wardlaw; Van Dijk, Marten (Institute of Electrical and Electronics Engineers (IEEE), 2013-09)
    Oblivious-RAMs (ORAM) are used to hide memory access patterns. Path ORAM has gained popularity due to its efficiency and simplicity. In this paper, we propose an efficient integrity verification layer for Path ORAM, which ...
  • Williams, Heidi L. (University of Chicago Press, 2013-02)
    Do intellectual property (IP) rights on existing technologies hinder subsequent innovation? Using newly-collected data on the sequencing of the human genome by the public Human Genome Project and the private rm Celera, ...
  • Acemoglu, Daron; Akcigit, Ufuk (Wiley Blackwell, 2011-12)
    To what extent and in what form should the intellectual property rights (IPR) of innovators be protected? Should a company with a large technology lead over its rivals receive the same IPR protection as a company with a ...
  • Redding, Josh; Geramifard, Alborz; Undurti, Aditya; Choi, Han-Lim; How, Jonathan P. (Institute of Electrical and Electronics Engineers, 2010-07)
    This paper presents an extension of existing cooperative control algorithms that have been developed for multi-UAV applications to utilize real-time observations and/or performance metric(s) in conjunction with learning ...
  • Geramifard, Alborz; Redding, Joshua; How, Jonathan P. (Springer-Verlag, 2013-03)
    Planning for multi-agent systems such as task assignment for teams of limited-fuel unmanned aerial vehicles (UAVs) is challenging due to uncertainties in the assumed models and the very large size of the planning space. ...
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