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Browsing MIT Open Access Articles by Title

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  • Hung, Tiffany; Wang, Yulei; Lin, Michael F.; Koegel, Ashley K.; Kotake, Yojiro; Grant, Gavin D.; Horlings, Hugo M.; Shah, Nilay; Umbricht, Christopher; Wang, Pei; Wang, Yu; Kong, Benjamin; Langerød, Anita; Børresen-Dale, Anne-Lise; Kim, Seung K.; van de Vijver, Marc; Sukumar, Saraswati; Whitfield, Michael L.; Kellis, Manolis; Xiong, Yue; Wong, David J.; Chang, Howard Y.; Lin, Michael F. (Nature Publishing Group, 2011-06)
    Transcription of long noncoding RNAs (lncRNAs) within gene regulatory elements can modulate gene activity in response to external stimuli, but the scope and functions of such activity are not known. Here we use an ...
  • Ng, Christopher W.; Yildirim, Ferah; Yap, Soon Ming Micha; Dalin, Simona Sara; Matthews, Bryan; Velez, Patricio J.; Labadorf, Adam; Housman, David E.; Fraenkel, Ernest (National Academy of Sciences (U.S.), 2013-01)
    The earliest stages of Huntington disease are marked by changes in gene expression that are caused in an indirect and poorly understood manner by polyglutamine expansions in the huntingtin (HTT) protein. To explore the ...
  • Wong, Daniel; Teixeira, Ana; Oikonomopoulos, Spyros; Humburg, Peter; Lone, Imtiaz N.; Saliba, David; Siggers, Trevor; Bulyk, Martha L.; Angelov, Dimitar; Dimitrov, Stefan; Udalova, Irina A.; Ragoussis, Jiannis (BioMed Central Ltd., 2011-07)
    Background Genetic studies have provided ample evidence of the influence of non-coding DNA polymorphisms on trait variance, particularly those occurring within transcription factor binding sites. Protein binding microarrays ...
  • Gehring, Mary; Bubb, Kerry L.; Henikoff, Steven (American Association for the Advancement of Science (AAAS), 2009-06)
    DNA methylation is an epigenetic mark associated with transposable element silencing and gene imprinting in flowering plants and mammals. In plants, imprinting occurs in the endosperm, which nourishes the embryo during ...
  • Kasowski, Maya; Kyriazopoulou-Panagiotopoulou, Sofia; Grubert, Fabian; Zaugg, Judith B.; Kundaje, Anshul; Liu, Yuling; Boyle, Alan P.; Zhang, Qiangfeng Cliff; Zakharia, Fouad; Spacek, Damek V.; Li, Jingjing; Xie, Dan; Olarerin-George, Anthony; Steinmetz, Lars M.; Hogenesch, John B.; Kellis, Manolis; Batzoglou, Serafim; Snyder, Michael (American Association for the Advancement of Science (AAAS), 2013-10)
    The majority of disease-associated variants lie outside protein-coding regions, suggesting a link between variation in regulatory regions and disease predisposition. We studied differences in chromatin states using five ...
  • Parker, R. R.; Davis, E.; Golfinopoulos, Theodore; Labombard, Brian; Burke, William M.; Granetz, Robert S.; Greenwald, Martin J.; Irby, James Henderson; Leccacorvi, Rick; Marmar, Earl S.; Parkin, William C.; Porkolab, Miklos; Terry, James L.; Vieira, Rui F.; Wolfe, Stephen M. (American Institute of Physics (AIP), 2014-05)
    A novel “Shoelace” antenna has been used to inductively excite a short-wavelength edge fluctuation in a tokamak boundary layer for the first time. The principal design parameters, k[subscript ⊥] = 1.5 ± 0.1 cm[superscript ...
  • Badertscher, Brad; Shroff, Nemit; White, Hal D. (Elsevier, 2013-04)
    Public firms provide a large amount of information through their disclosures. In addition, information intermediaries publicly analyze, discuss, and disseminate these disclosures. Thus, greater public firm presence in an ...
  • Andoni, Alexandr; Indyk, Piotr; Onak, Krzysztof; Rubinfeld, Ronitt (Springer Berlin / Heidelberg, 2009-07)
    We initiate the study of sublinear-time algorithms in the external memory model [1]. In this model, the data is stored in blocks of a certain size B, and the algorithm is charged a unit cost for each block access. This ...
  • Gehrke, Lee; de Puig Guixe, Helena; Tam, Justina; Yen, Chun-Wan; Hamad, Kimberly (American Chemical Society (ACS), 2015-07)
    Gold nanostars (NStars) are highly attractive for biological applications due to their surface chemistry, facile synthesis, and optical properties. Here, we synthesize NStars in HEPES buffer at different HEPES/Au ratios, ...
  • Taylor, M.; Gisin, E.; Sidorov, Michael; Krueger, Dilja; Osterweil, Emily; Bear, Mark (Wiley Blackwell, 2014-04)
    Fragile X (FX) is the most common genetic cause of intellectual disability and autism. Previous studies have shown that partial inhibition of metabotropic glutamate receptor signaling is sufficient to correct behavioral ...
  • Kasahara, Shunichi; Niiyama, Ryuma; Ishii, Hiroshi; Heun, Valentin Markus Josef (Association for Computing Machinery (ACM), 2013-02)
    As domestic robots and smart appliances become increasingly common, they require a simple, universal interface to control their motion. Such an interface must support a simple selection of a connected device, highlight its ...
  • Jagielska, Anna; Wilhite, Kristen D.; Van Vliet, Krystyn J. (Public Library of Science, 2013-09)
    Axon remyelination in the central nervous system requires oligodendrocytes that produce myelin. Failure of this repair process is characteristic of neurodegeneration in demyelinating diseases such as multiple sclerosis, ...
  • Ramirez Millan, Maria; Caldara, Marina; Rusconi, Roberto; Tarasova, Yekaterina; Stocker, Roman; Ribbeck, Katharina; Billings, Amanda Nicole (Public Library of Science, 2013-08)
    Bacteria within biofilms secrete and surround themselves with an extracellular matrix, which serves as a first line of defense against antibiotic attack. Polysaccharides constitute major elements of the biofilm matrix and ...
  • Shin, Yoojin; Kim, Hyunju; Han, Sewoon; Won, Jihee; Jeong, Hyo Eun; Lee, Eun-Sook; Kim, Jae-Hong; Chung, Seok; Kamm, Roger Dale (Wiley Blackwell, 2012-11)
    Plasticity and reciprocity of breast cancer cells to various extracellular matrice (ECMs) are three-dimensionally analyzed in quantitative way in a novel and powerful microfluidic in vitro platform. This successfully ...
  • Hynes, Richard O. (American Association for the Advancement of Science (AAAS), 2009-11)
    The extracellular matrix (ECM) and ECM proteins are important in phenomena as diverse as developmental patterning, stem cell niches, cancer, and genetic diseases. The ECM has many effects beyond providing structural support. ...
  • Naba, Alexandra; Clauser, Karl R.; Lamar, John Michael; Carr, Steven A.; Hynes, Richard O. (eLife Sciences Publications, Ltd., 2014-03)
    The extracellular matrix (ECM) is a major component of tumors and a significant contributor to cancer progression. In this study, we use proteomics to investigate the ECM of human mammary carcinoma xenografts and show that ...
  • Naba, Alexandra; Clauser, Karl R.; Whittaker, Charles A.; Carr, Steven A.; Tanabe, Kenneth K.; Hynes, Richard O. (BioMed Central Ltd., 2014-07)
    Background: Colorectal cancer is the third most frequently diagnosed cancer and the third cause of cancer deaths in the United States. Despite the fact that tumor cell-intrinsic mechanisms controlling colorectal carcinogenesis ...
  • Clauser, Karl R.; Carr, Steven A.; Naba, Alexandra; Ding, Huiming; Whittaker, Charles A; Hynes, Richard O (Elsevier, 2015-06)
    The extracellular matrix (ECM) is a fundamental component of multicellular organisms that provides mechanical and chemical cues that orchestrate cellular and tissue organization and functions. Degradation, hyperproduction ...
  • Reckman, Hilke; Orkin, Jeffrey David; Roy, Deb K. (Association for Computing Machinery, 2011-01)
    We use data from a virtual world game for automated learning of words and grammatical constructions and their meanings. The language data are an integral part of the social interaction in the game and consist of chat ...
  • Jere, Shashank; Dauwels, Justin; Asif, Muhammad Tayyab; Vie, Nikola Mitro; Cichocki, Andrzej; Jaillet, Patrick (Institute of Electrical and Electronics Engineers (IEEE), 2014-12)
    With the rise in the population of the world's cities, understanding the dynamics of commuters' transportation patterns has become crucial in the planning and management of urban facilities and services. In this study, we ...
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