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Browsing MIT Open Access Articles by Title

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  • SHLAPENTOKH, ALEXANDRA; Miller, Russell; Schoutens, Hans; Schoustens, Hans; Shlapentokh, Alexandra; Poonen, Bjorn (Cambridge University Press (CUP), 2018-05)
    Fried and Kollár constructed a fully faithful functor from the category of graphs to the category of fields. We give a new construction of such a functor and use it to resolve a longstanding open problem in computable model ...
  • Shin, Dongeek; Kirmani, Ahmed; Shapiro, Jeffrey H.; Goyal, Vivek K. (Institute of Electrical and Electronics Engineers (IEEE), 2014-10)
    Capturing depth and reflectivity images at low light levels from active illumination of a scene has wide-ranging applications. Conventionally, even with single-photon detectors, hundreds of photon detections are needed at ...
  • 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 ...
  • 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 ...
  • 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 ...
  • Li, Huipeng; Venkatraman, Lakshmi; Narmada, Balakrishnan C; Tucker-Kellogg, Lisa; Narmada, Balakrishnan Chakrapani; White, Jacob K; Yu, Hanry (BioMed Central, 2017-12)
    Background Bistable behaviors are prevalent in cell signaling and can be modeled by ordinary differential equations (ODEs) with kinetic parameters. A bistable switch has recently been found to regulate the ...
  • 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.
  • Buehler, Markus J; Qin, Zhao (The Chinese Society of Theoretical and Applied Mechanics; Institute of Mechanics, Chinese Academy of Sciences, 2012-09)
    Intermediate filaments, in addition to microtubules and actin microfilaments, are one of the three major components of the cytoskeleton in eukaryotic cells. It was discovered during the recent decades that in most cells, ...
  • 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 ...
  • Xue, Tianfan; Rubinstein, Michael; Liu, Ce; Freeman, William T. (Association for Computing Machinery (ACM), 2015-08)
    We present a unified computational approach for taking photos through reflecting or occluding elements such as windows and fences. Rather than capturing a single image, we instruct the user to take a short image sequence ...
  • Iglesias, Juan Eugenio; Augustinack, Jean C.; Nguyen, Khoa; Player, Christopher M.; Player, Allison; Wright, Michelle; Roy, Nicole; Frosch, Matthew P.; McKee, Ann C.; Wald, Lawrence L.; Van Leemput, Koen; Fischl, Bruce (Elsevier, 2015-04)
    Automated analysis of MRI data of the subregions of the hippocampus requires computational atlases built at a higher resolution than those that are typically used in current neuroimaging studies. Here we describe the ...
  • Berger Leighton, Bonnie; Daniels, Noah; Yu, Yun William (Association for Computing Machinery (ACM), 2016-08)
    Computational biologists answer biological and biomedical questions by using computation in support of—or in place of—laboratory procedures, hoping to obtain more accurate answers at a greatly reduced cost. The past two ...
  • Suresh, Subra; Fedosov, Dmitry A.; Karniadakis, George Em; Dao, Ming (Springer US, 2013-10)
    Hematologic disorders arising from infectious diseases, hereditary factors and environmental influences can lead to, and can be influenced by, significant changes in the shape, mechanical and physical properties of red ...
  • Demaine, Erik D.; Okamoto, Yoshio; Uehara, Ryuhei; Uno, Yushi (Institute of Electronics, Information and Communications Engineers, 2014-06)
    Shakashaka is a pencil-and-paper puzzle proposed by Guten and popularized by the Japanese publisher Nikoli (like Sudoku). We determine the computational complexity by proving that Shakashaka is NP-complete, and furthermore ...
  • 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 ...
  • Drennan, Catherine L.; Baker, David; Ting, Alice Y.; Liu, Daniel S.; Nivon, Lucas G.; Richter, Florian; Goldman, Peter J.; Yao, Jennifer Z.; Phipps, William S.; Ye, Anne Z.; Deerinck, Thomas J.; Richardson, Douglas; Ellisman, Mark H. (National Academy of Sciences (U.S.), 2014-10)
    Chemical fluorophores offer tremendous size and photophysical advantages over fluorescent proteins but are much more challenging to target to specific cellular proteins. Here, we used Rosetta-based computation to design a ...
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