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Browsing MIT Open Access Articles by Title

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  • Means, Terry K.; Mylonakis, Eleftherios; Tampakakis, Emmanouil; Colvin, Richard A.; Seung, Edward; Puckett, Lindsay; Tai, Melissa F.; Stewart, Cameron R.; Pukkila-Worley, Read; Hickman, Suzanne E.; Moore, Kathryn J.; Calderwood, Stephen B.; Hacohen, Nir; Luster, Andrew D.; El Khoury, Joseph (Rockefeller University Press, 2009-03)
    Receptors involved in innate immunity to fungal pathogens have not been fully elucidated. We show that the Caenorhabditis elegans receptors CED-1 and C03F11.3, and their mammalian orthologues, the scavenger receptors SCARF1 ...
  • Shishkin, Alexander A.; Zhu, Xiaopeng; Kadri, Sabah; Maza, Itay; Guttman, Mitchell; Hanna, Jacob H.; Garber, Manuel; Chen, Jenny; Regev, Aviv (Biomed Central Ltd., 2016-02)
    Background: Recent advances in transcriptome sequencing have enabled the discovery of thousands of long non-coding RNAs (lncRNAs) across many species. Though several lncRNAs have been shown to play important roles in diverse ...
  • O'Reilly, Una-May; Medard, Muriel; Traskov, Danail; Kim, Minkyu (2009-06)
    Whereas the theory and application of optimal network coding are well studied for the single-session multicast scenario, there is no known optimal network coding strategy for a more general connection problem where there ...
  • Butler, Thomas Charles; Benayoun, Marc; Wallace, Edward; van Drongelen, Wim; Goldenfeld, Nigel; Cowan, Jack (National Academy of Sciences of the United States of America, 2011-12)
    In the cat or primate primary visual cortex (V1), normal vision corresponds to a state where neural excitation patterns are driven by external visual stimuli. A spectacular failure mode of V1 occurs when such patterns are ...
  • Tsankov, Alexander M.; Yanagisawa, Yoshimi; Rhind, Nicholas; Regev, Aviv; Rando, Oliver J. (Cold Spring Harbor Laboratory Press, 2011-09)
    The packaging of eukaryotic genomes into nuclesomes plays critical roles in chromatin organization and gene regulation. Studies in Saccharomyces cerevisiae indicate that nucleosome occupancy is partially encoded by intrinsic ...
  • Washietl, Stefan; Kellis, Manolis; Garber, Manuel (Cold Spring Harbor Laboratory Press, 2014-01)
    Long intergenic noncoding RNAs (lincRNAs) play diverse regulatory roles in human development and disease, but little is known about their evolutionary history and constraint. Here, we characterize human lincRNA expression ...
  • Merkin, Jason Jay; Russell, Caitlin; Chen, Ping; Burge, Christopher B. (American Association for the Advancement of Science (AAAS), 2012-12)
    Most mammalian genes produce multiple distinct messenger RNAs through alternative splicing, but the extent of splicing conservation is not clear. To assess tissue-specific transcriptome variation across mammals, we sequenced ...
  • Li, Aming; Broom, Mark; Du, Jinming; Wang, Long (American Physical Society, 2016-02)
    The evolution of populations is influenced by many factors, and the simple classical models have been developed in a number of important ways. Both population structure and multiplayer interactions have been shown to ...
  • Plunkett, Jevon; Doniger, Scott; Orabona, Guilherme; Morgan, Thomas; Haataja, Ritva; Hallman, Mikko; Puttonen, Hilkka; Menon, Ramkumar; Kuczynski, Edward; Norwitz, Errol; Snegovskikh, Victoria; Palotie, Aarno; Peltonen, Leena; Fellman, Vineta; DeFranco, Emily A.; Chaudhari, Bimal P.; McGregor, Tracy L.; McElroy, Jude J.; Oetjens, Matthew T.; Teramo, Kari; Borecki, Ingrid; Fay, Justin C.; Muglia, Louis J. (Public Library of Science, 2011-04)
    Coordination of fetal maturation with birth timing is essential for mammalian reproduction. In humans, preterm birth is a disorder of profound global health significance. The signals initiating parturition in humans have ...
  • Brennan, Thomas J.; Lo, Andrew W. (Public Library of Science, 2012-11)
    Background: Most economic theories are based on the premise that individuals maximize their own self-interest and correctly incorporate the structure of their environment into all decisions, thanks to human intelligence. ...
  • Weng, Jing-Ke (Wiley Blackwell, 2014-03)
    As sessile organisms, land plants have exploited their metabolic systems to produce a panoply of structurally and functionally diverse natural chemicals and polymers to adapt to challenging ecosystems. Many of these core ...
  • Thompson, Dawn A.; Roy, Sushmita; Chan, Michelle Mei Wah; Styczynsky, Mark P.; Pfiffner, Jenna; French, Courtney; Socha, Amanda; Thielke, Anne; Napolitano, Sara; Muller, Paul; Kellis, Manolis; Konieczka, Jay; Wapinski, Ilan; Regev, Aviv (eLife Sciences Publications, Ltd, 2013-06)
    Divergence in gene regulation can play a major role in evolution. Here, we used a phylogenetic framework to measure mRNA profiles in 15 yeast species from the phylum Ascomycota and reconstruct the evolution of their modular ...
  • Yang, Lei; Damkiaer, Soren; Molin, Soren; Jelsbak, Lars (National Academy of Sciences (U.S.), 2013-04)
    The genetic basis of bacterial adaptation to a natural environment has been investigated in a highly successful Pseudomonas aeruginosa lineage (DK2) that evolved within the airways of patients with cystic fibrosis (CF) for ...
  • Wu, Yi-Chieh; Rasmussen, Matthew D.; Kellis, Manolis (Oxford University Press (OUP), 2011-09)
    Although the possibility of gene evolution by domain rearrangements has long been appreciated, current methods for reconstructing and systematically analyzing gene family evolution are limited to events such as duplication, ...
  • Wu, Yi-Chieh; Rasmussen, Matthew D.; Kellis, Manolis (Oxford University Press (OUP), 2011-09)
    Although the possibility of gene evolution by domain rearrangements has long been appreciated, current methods for reconstructing and systematically analyzing gene family evolution are limited to events such as duplication, ...
  • Natarajan, Bharath; Lam, Thomas; Long, Christian; Zhao, Minhua; Sharma, Renu; Liddle, J. Alexander; Wardle, Brian L; Lachman-Senesh, Noa; Jacobs, Douglas S. (American Chemical Society (ACS), 2015-06)
    Carbon nanotube (CNT) reinforced polymers are next-generation, high-performance, multifunctional materials with a wide array of promising applications. The successful introduction of such materials is hampered by the lack ...
  • Nelson, L.; Quintin, J.; Yakut, K.; Kalomeni, Belinda; Rappaport, Saul A; Molnar, Momchil E. (IOP Publishing, 2016-12)
    We present a binary evolution study of cataclysmic variables (CVs) and related systems with white dwarf (WD) accretors, including for example, AM CVn systems, classical novae, supersoft X-ray sources (SXSs), and systems ...
  • George, Janet A.; Traverse, Karen L.; DeBaryshe, Gregory; Kelley, Kerry; Pardue, Mary-Lou (National Academy of Sciences (U.S.), 2010-11)
    The retrotransposons HeT-A, TART, and TAHRE, which maintain Drosophila telomeres, transpose specifically onto chromosome ends to form long arrays that extend the chromosome and compensate for terminal loss. Because they ...
  • Abbey, Darren A.; Issi, Luca; Guiducci, Candace; Martinez, Diego A; Delorey, Toni; Li, Bi yu; White, Theodore C; Cuomo, Christina; Rao, Reeta P; Berman, Judith; Thompson, Dawn A; Regev, Aviv; Ford, Christopher B.; Funt, Jason (eLife Sciences Publications, Ltd., 2015-02)
    Candida albicans is both a member of the healthy human microbiome and a major pathogen in immunocompromised individuals. Infections are typically treated with azole inhibitors of ergosterol biosynthesis often leading to ...
  • Franses, Joseph W.; Edelman, Elazer R. (American Association for Cancer Research, 2011-12)
    Although the roles of endothelial cells in cancer have primarily been considered to be related to tumor perfusion, the emerging appreciation of “angiocrine” regulation adds stromal regulatory capabilities to the expanding ...
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