Browsing Faculty of Arts and Sciences by Keyword "functional genomics"

Now showing items 1-8 of 8

    • Expression and Putative Function of Innate Immunity Genes under In Situ Conditions in the Symbiotic Hydrothermal Vent Tubeworm Ridgeia piscesae 

      Nyholm, Spencer V.; Song, Pengfei; Dang, Jeanne; Bunce, Corey; Girguis, Peter R. (Public Library of Science, 2012)
      The relationships between hydrothermal vent tubeworms and sulfide-oxidizing bacteria have served as model associations for understanding chemoautotrophy and endosymbiosis. Numerous studies have focused on the physiological ...

    • Functional genomic screening reveals asparagine dependence as a metabolic vulnerability in sarcoma 

      Hettmer, Simone; Schinzel, Anna C; Tchessalova, Daria; Schneider, Michaela; Parker, Christina L; Bronson, Roderick T; Richards, Nigel GJ; Hahn, William C; Wagers, Amy J (eLife Sciences Publications, Ltd, 2015)
      Current therapies for sarcomas are often inadequate. This study sought to identify actionable gene targets by selective targeting of the molecular networks that support sarcoma cell proliferation. Silencing of asparagine ...

    • Genome-Wide Identification of Binding Sites Defines Distinct Functions for Caenorhabditis elegans PHA-4/FOXA in Development and Environmental Response 

      Zhong, Mei; Niu, Wei; Lu, Zhi John; Sarov, Mihail; Janette, Judith; Raha, Debasish; Sheaffer, Karyn L.; Lam, Hugo Y. K.; Preston, Elicia; Slightham, Cindie; Hillier, LaDeana W.; Agarwal, Ashish; Auerbach, Raymond; Hyman, Anthony A.; Gerstein, Mark; Kim, Stuart K.; Waterston, Robert H.; Reinke, Valerie; Snyder, Michael; Murray, John I.; Mango, Susan; Brock, Trisha Jane (Public Library of Science, 2010)
      Transcription factors are key components of regulatory networks that control development, as well as the response to environmental stimuli. We have established an experimental pipeline in Caenorhabditis elegans that permits ...

    • Genomewide Analysis of PRC1 and PRC2 Occupancy Identifies Two Classes of Bivalent Domains 

      Rheinbay, Esther; Endoh, Mitsuhiro; Mikkelsen, Tarjei S.; Nusbaum, Chad; Xie, Xiaohui; Adli, Mazhar; Kasif, Simon; Ptaszek, Leon M.; Koseki, Haruhiko; van Steensel, Bas; Ku, Manching; Koche, Richard Patrick; Mendenhall, Eric M; Presser, Aviva; Chi, Andrew S.; Cowan, Chad A.; Lander, Eric Steven; Bernstein, Bradley E. (Public Library of Science, 2008)
      In embryonic stem (ES) cells, bivalent chromatin domains with overlapping repressive (H3 lysine 27 tri-methylation) and activating (H3 lysine 4 tri-methylation) histone modifications mark the promoters of more than 2,000 ...

    • GPUmotif: An Ultra-Fast and Energy-Efficient Motif Analysis Program Using Graphics Processing Units 

      Zandevakili, Pooya; Hu, Ming; Qin, Zhaohui (Public Library of Science, 2012)
      Computational detection of TF binding patterns has become an indispensable tool in functional genomics research. With the rapid advance of new sequencing technologies, large amounts of protein-DNA interaction data have ...

    • p38 MAPK Regulates Expression of Immune Response Genes and Contributes to Longevity in C. elegans 

      Troemel, Emily R; Chu, Stephanie W; Reinke, Valerie; Lee, Siu Sylvia; Ausubel, Frederick M.; Kim, Dennis H (Public Library of Science, 2006)
      The PMK-1 p38 mitogen-activated protein kinase pathway and the DAF-2–DAF-16 insulin signaling pathway control Caenorhabditis elegans intestinal innate immunity. pmk-1 loss-of-function mutants have enhanced sensitivity to ...

    • Pairing of Competitive and Topologically Distinct Regulatory Modules Enhances Patterned Gene Expression 

      Yanai, Itai; Baugh, L Ryan; Smith, Jessica J.; Roehrig, Casey; Shen-Orr, Shai S; Claggett, Julia M; Hill, Andrew A.; Slonim, Donna K; Hunter, Craig P. (Nature Publishing Group, 2008)
      Biological networks are inherently modular, yet little is known about how modules are assembled to enable coordinated and complex functions. We used RNAi and time series, whole-genome microarray analyses to systematically ...

    • Using Expression and Genotype to Predict Drug Response in Yeast 

      Ruderfer, Douglas M.; Roberts, David C.; Schreiber, Stuart L.; Perlstein, Ethan O.; Kruglyak, Leonid (Public Library of Science, 2009)
      Personalized, or genomic, medicine entails tailoring pharmacological therapies according to individual genetic variation at genomic loci encoding proteins in drug-response pathways. It has been previously shown that ...