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Browsing MIT Open Access Articles by Author "Fraenkel, Ernest"

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Browsing MIT Open Access Articles by Author "Fraenkel, Ernest"

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  • Lo, Kinyui Alice; Labadorf, Adam; Kennedy, Norman J.; Han, Myoung Sook; Yap, Yoon Sing; Matthews, Bryan; Xin, Xiaofeng; Sun, Lei; Davis, Roger J.; Lodish, Harvey F.; Fraenkel, Ernest; Lo, Kinyui Alice; Yap, Yoon Sing; Lodish, Harvey F. (Elsevier, 2013-10)
    Diet-induced obesity (DIO) predisposes individuals to insulin resistance, and adipose tissue has a major role in the disease. Insulin resistance can be induced in cultured adipocytes by a variety of treatments, but what ...
  • Yeger-Lotem, Esti; Riva, Laura; Su, Linhui Julie; Gitler, Aaron D.; Cashikar, Anil G.; King, Oliver D.; Auluck, Pavan K.; Geddie, Melissa L.; Valastyan, Julie Suzanne; Karger, David R.; Lindquist, Susan; Fraenkel, Ernest (Nature Publishing Group, 2009-02)
    Cells respond to stimuli by changes in various processes, including signaling pathways and gene expression. Efforts to identify components of these responses increasingly depend on mRNA profiling and genetic library ...
  • Su, Linhui Julie; Auluck, Pavan K.; Outeiro, Tiago Fleming; Yeger-Lotem, Esti; Kritzer, Joshua A.; Tardiff, Daniel F.; Bell, George W.; Fraenkel, Ernest; Lindquist, Susan; Strathearn, Katherine E.; Liu, Fang; Cao, Songsong; Hamamichi, Shusei; Hill, Kathryn J.; Caldwell, Kim A.; Cooper, Antony A.; Caldwell, Guy A.; McCaffery, J. Michael; Rochet, Jean-Christophe (Company of Biologists Limited, 2010-01)
    α-Synuclein (α-syn) is a small lipid-binding protein involved in vesicle trafficking whose function is poorly characterized. It is of great interest to human biology and medicine because α-syn dysfunction is associated ...
  • Yu, Ming; Mazor, Tali; Huang, Hui; Huang, Hsuan-Ting; Kathrein, Katie L.; Woo, Andrew J.; Chouinard, Candace R.; Labadorf, Adam; Akie, Thomas E.; Moran, Tyler B.; Xie, Huafeng; Zacharek, Sima; Taniuchi, Ichiro; Roeder, Robert G.; Kim, Carla F.; Zon, Leonard I.; Fraenkel, Ernest; Cantor, Alan B.; Chouinard, Candace R. (Elsevier, 2012-02)
    Polycomb repressive complexes (PRCs) play key roles in developmental epigenetic regulation. Yet the mechanisms that target PRCs to specific loci in mammalian cells remain incompletely understood. In this study we show that ...
  • 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 ...
  • Lo, Kin Yui; Bauchmann, Mary K.; Baumann, Amy P.; Donahue, Christopher J.; Thiede, Mark A.; Hayes, Lisa S.; Des Etages, Shelley Ann G.; Fraenkel, Ernest (Public Library of Science, 2011-06)
    The growing epidemic of obesity and metabolic diseases calls for a better understanding of adipocyte biology. The regulation of transcription in adipocytes is particularly important, as it is a target for several therapeutic ...
  • Wang, Ting; Gifford, David K.; Stormo, Gary D.; Fraenkel, Ernest; MacIsaac, Kenzie Daniel; Gordon, D. Benjamin (BioMed Central Ltd, 2006-03)
    Background: The regulatory map of a genome consists of the binding sites for proteins that determine the transcription of nearby genes. An initial regulatory map for S. cerevisiae was recently published using six motif ...
  • Yu, Ming; Riva, Laura; Schindler, Yocheved; Moran, Tyler B.; Cheng, Yong; Yu, Duonan; Hardison, Ross; Weiss, Mitchell J.; Orkin, Stuart H.; Bernstein, Bradley E.; Fraenkel, Ernest; Cantor, Alan B. (Elsevier, 2009-11)
    The transcription factor GATA-1 is required for terminal erythroid maturation and functions as an activator or repressor depending on gene context. Yet its in vivo site selectivity and ability to distinguish between ...
  • Fraenkel, Ernest; Lauffenburger, Douglas A.; Wilson, Jennifer Lynn; Hemann, Michael (Elsevier, 2013-08)
    RNA-interference (RNAi) studies hold great promise for functional investigation of the significance of genetic variations and mutations, as well as potential synthetic lethalities, for understanding and treatment of cancer, ...
  • Huang, Shao-shan Carol; Fraenkel, Ernest (American Association for the Advancement of Science (AAAS), 2009-07)
    Cellular signaling and regulatory networks underlie fundamental biological processes such as growth, differentiation, and response to the environment. Although there are now various high-throughput methods for studying ...
  • Carlson, Scott M.; Chouinard, Candace R.; Labadorf, Adam; Lam, Carol J.; Schmelzle, Katrin; Fraenkel, Ernest; White, Forest M. (American Association for the Advancement of Science (AAAS), 2011-10)
    The mitogen-activated protein kinase (MAPK) extracellular signal–regulated kinase 2 (ERK2) is ubiquitously expressed in mammalian tissues and is involved in a wide range of biological processes. Although MAPKs have been ...
  • Huang, Shao-shan Carol; Clarke, David C.; Gosline, Sara Jane Calafell; Labadorf, Adam; Chouinard, Candace R.; Gordon, William; Lauffenburger, Douglas A.; Fraenkel, Ernest (Public Library of Science, 2013-02)
    Cellular signal transduction generally involves cascades of post-translational protein modifications that rapidly catalyze changes in protein-DNA interactions and gene expression. High-throughput measurements are improving ...
  • Riva, Laura; Koeva, Martina I.; Yildirim, Ferah; Pirhaji, Leila; Dinesh, Deepika; Mazor, Tali; Duennwald, Martin L.; Fraenkel, Ernest (IOS Press, 2012-06)
    In Huntington's disease (HD), polyglutamine expansions in the huntingtin (Htt) protein cause subtle changes in cellular functions that, over-time, lead to neurodegeneration and death. Studies have indicated that activation ...
  • MacIsaac, Kenzie Daniel; Lo, Kin Yui; Gordon, William; Motola, Shmulik; Mazor, Tali; Fraenkel, Ernest (Public Library of Science, 2010-04)
    Understanding the mechanistic basis of transcriptional regulation has been a central focus of molecular biology since its inception. New high-throughput chromatin immunoprecipitation experiments have revealed that most ...
  • Lan, Alex; Smoly, Ilan Y.; Rapaport, Guy; Fraenkel, Ernest; Lindquist, Susan; Yeger-Lotem, Esti (Oxford University Press (OUP), 2011-05)
    Cellular response to stimuli is typically complex and involves both regulatory and metabolic processes. Large-scale experimental efforts to identify components of these processes often comprise of genetic screening and ...
  • Lan, Alex; Smoly, Ilan Y.; Rapaport, Guy; Lindquist, Susan; Fraenkel, Ernest; Yeger-Lotem, Esti (Oxford University Press, 2011-04)
    Cellular response to stimuli is typically complex and involves both regulatory and metabolic processes. Large-scale experimental efforts to identify components of these processes often comprise of genetic screening and ...
  • Spencer, Sarah J.; Ursu, Oana; Fraenkel, Ernest; Gosline, Sara Jane Calafell (Royal Society of Chemistry, 2012-09)
    The rapid development of high throughput biotechnologies has led to an onslaught of data describing genetic perturbations and changes in mRNA and protein levels in the cell. Because each assay provides a one-dimensional ...
  • MacIsaac, Kenzie Daniel; Fraenkel, Ernest (Springer Science + Business Media, 2010-01)
    Chromatin immunoprecipitation (ChIP) experiments allow the location of transcription factors to be determined across the genome. Subsequent analysis of the sequences of the identified regions allows binding to be localized ...
  • Tuncbag, Nurcan; Braunstein, Alfredo; Pagnani, Andrea; Huang, Shao-Shan Carol; Chayes, Jennifer; Borgs, Christian; Zecchina, Riccardo; Fraenkel, Ernest; Tuncbag, Nurcan; Huang, Shao-Shan Carol; Fraenkel, Ernest (Springer Science + Business Media B.V., 2012-04)
    Signaling networks are essential for cells to control processes such as growth and response to stimuli. Although many “omic” data sources are available to probe signaling pathways, these data are typically sparse and noisy. ...
  • Zhen, Aileen W.; Nguyen, Nancy H.; Gibert, Yann; Motola, Shmulik; Buckett, Peter; Wessling-Resnick, Marianne; Fraenkel, Ernest; Fraenkel, Paula G. (Wiley Blackwell, 2013-08)
    Hepcidin, a peptide hormone that decreases intestinal iron absorption and macrophage iron release, is a potential drug target for patients with iron overload syndromes because its levels are inappropriately low in these ...
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