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OpenBU

Browsing Bioinformatics by Title

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  • Anton, Brian P.; Russell, Susan P.; Vertrees, Jason; Kasif, Simon; Raleigh, Elisabeth A.; Limbach, Patrick A.; Roberts, Richard J. (2010-5-14)
    Methylthiotransferases (MTTases) are a closely related family of proteins that perform both radical-S-adenosylmethionine (SAM) mediated sulfur insertion and SAM-dependent methylation to modify nucleic acid or protein targets ...
  • Wu, Chang-Jiun; Kasif, Simon (Oxford University Press, 2005-06-27)
    The advent of microarray technology has revolutionized the search for genes that are differentially expressed across a range of cell types or experimental conditions. Traditional clustering methods, such as hierarchical ...
  • Wu, Jie; Hu, Zhenjun; DeLisi, Charles (BioMed Central, 2006-2-17)
    BACKGROUND. Phylogenetic analysis is emerging as one of the most informative computational methods for the annotation of genes and identification of evolutionary modules of functionally related genes. The effectiveness ...
  • Lee, Soohyun; Kohane, Isaac; Kasif, Simon (BioMed Central, 2005-11-27)
    BACKGROUND: Recent advances in genome sequencing suggest a remarkable conservation in gene content of mammalian organisms. The similarity in gene repertoire present in different organisms has increased interest in studying ...
  • Thomas, R.; Duke, S.E.; Karlsson, E.K.; Evans, A.; Ellis, P.; Lindblad-Toh, K.; Langford, C.F.; Breen, M. (S. Karger AG, 2011-12-29)
    Molecular cytogenetic studies have been instrumental in defining the nature of numerical and structural chromosome changes in human cancers, but their significance remains to be fully understood. The emergence of high ...
  • Ma, Qianli; Yu, Yi; Meng, Yan; Farrell, John; Farrer, Lindsay A; Wilcox, Marsha A (BioMed Central, 2005-12-30)
    Both theoretical and applied studies have proven that the utility of single nucleotide polymorphism (SNP) markers in linkage analysis is more powerful and cost-effective than current microsatellite marker assays. Here we ...
  • Linghu, Bolan; Snitkin, Evan S; Hu, Zhenjun; Xia, Yu; DeLisi, Charles (BioMed Central, 2009-09-03)
    An evidence-weighted functional-linkage network of human genes reveals associations among diseases that share no known disease genes and have dissimilar phenotypes. We integrate 16 genomic features to construct an ...
  • Li, Jian-Liang; Hayden, Michael R; Warby, Simon C; Durr, Alexandra; Morrison, Patrick J; Nance, Martha; Ross, Christopher A; Margolis, Russell L; Rosenblatt, Adam; Squitieri, Ferdinando; Frati, Luigi; Gómez-Tortosa, Estrella; García, Carmen Ayuso; Suchowersky, Oksana; Klimek, Mary Lou; Trent, Ronald JA; McCusker, Elizabeth; Novelletto, Andrea; Frontali, Marina; Paulsen, Jane S; Jones, Randi; Ashizawa, Tetsuo; Lazzarini, Alice; Wheeler, Vanessa C; Prakash, Ranjana; Xu, Gang; Djoussé, Luc; Mysore, Jayalakshmi Srinidhi; Gillis, Tammy; Hakky, Michael; Cupples, L Adrienne; Saint-Hilaire, Marie H; Cha, Jang-Ho J; Hersch, Steven M; Penney, John B; Harrison, Madaline B; Perlman, Susan L; Zanko, Andrea; Abramson, Ruth K; Lechich, Anthony J; Duckett, Ayana; Marder, Karen; Conneally, P Michael; Gusella, James F; MacDonald, Marcy E; Myers, Richard H (BioMed Central, 2006-8-17)
    BACKGROUND: Age at onset of Huntington's disease (HD) is correlated with the size of the abnormal CAG repeat expansion in the HD gene; however, several studies have indicated that other genetic factors also contribute to ...
  • Ku, Manching; Koche, Richard P.; Rheinbay, Esther; Mendenhall, Eric M.; Endoh, Mitsuhiro; Mikkelsen, Tarjei S.; Presser, Aviva; Nusbaum, Chad; Xie, Xiaohui; Chi, Andrew S.; Adli, Mazhar; Kasif, Simon; Ptaszek, Leon M.; Cowan, Chad A.; Lander, Eric S.; Koseki, Haruhiko; Bernstein, Bradley E. (Public Library of Science, 2008-10-31)
    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 ...
  • Zheng, Yu; Roberts, Richard J; Kasif, Simon (BioMed Central, 2002-10-10)
    The current speed of sequencing already exceeds the capability of annotation. A new method for functional annotation is proposed using the conservation patterns of gene clusters and has been applied to the genome of ...
  • DeLisi, Charles (National Institute of Environmental Health Sciences, 2004-11)
  • Dwyer, Daniel J; Kohanski, Michael A; Hayete, Boris; Collins, James J (2007-03-13)
    Modulation of bacterial chromosomal supercoiling is a function of DNA gyrase-catalyzed strand breakage and rejoining. This reaction is exploited by both antibiotic and proteic gyrase inhibitors, which trap the gyrase ...
  • Sebastiani, Paola; Zhao, Zhenming; Abad-Grau, Maria M; Riva, Alberto; Hartley, Stephen W; Sedgewick, Amanda E; Doria, Alessandro; Montano, Monty; Melista, Efthymia; Terry, Dellara; Perls, Thomas T; Steinberg, Martin H; Baldwin, Clinton T (BioMed Central, 2008-1-14)
    BACKGROUND: One of the challenges of the analysis of pooling-based genome wide association studies is to identify authentic associations among potentially thousands of false positive associations. RESULTS. We present a ...
  • Lehár, Joseph; Krueger, Andrew; Zimmermann, Grant; Borisy, Alexis (Nature Publishing Group, 2008-08-05)
    Biological systems are robust, in that they can maintain stable phenotypes under varying conditions or attacks. Biological systems are also complex, being organized into many functional modules that communicate through ...
  • Linghu, Bolan; Snitkin, Evan S; Holloway, Dustin T; Gustafson, Adam M; Xia, Yu; DeLisi, Charles (BioMed Central, 2008-2-25)
    BACKGROUND. Information obtained from diverse data sources can be combined in a principled manner using various machine learning methods to increase the reliability and range of knowledge about protein function. The result ...
  • Xi, Hualin; Shulha, Hennady P; Lin, Jane M; Vales, Teresa R; Fu, Yutao; Bodine, David M; McKay, Ronald D. G; Chenoweth, Josh G; Tesar, Paul J; Furey, Terrence S; Ren, Bing; Weng, Zhiping; Crawford, Gregory E (Public Library of Science, 2007-8-17)
    The identification of regulatory elements from different cell types is necessary for understanding the mechanisms controlling cell type–specific and housekeeping gene expression. Mapping DNaseI hypersensitive (HS) sites ...
  • Dalgin, Gul S.; Holloway, Dustin T.; Liou, Louis S.; DeLisi, Charles (Libertas Academica, 2007-2-9)
    Microarray gene expression profiling has been used to distinguish histological subtypes of renal cell carcinoma (RCC), and consequently to identify specific tumor markers. The analytical procedures currently in use find ...
  • Hung, Jui-Hung; Whitfield, Troy W; Yang, Tun-Hsiang; Hu, Zhenjun; Weng, Zhiping; DeLisi, Charles (BioMed Central, 2010-02-26)
    A gene set enrichment analysis method for including network topology in the identification of genes involved in phenotypic alterations is described. One of the important challenges to post-genomic biology is relating ...
  • Shakhnovich, Boris E (Public Library of Science, 2005-6-24)
    Understanding the relationship between protein structure and function is one of the foremost challenges in post-genomic biology. Higher conservation of structure could, in principle, allow researchers to extend current ...
  • Weng, Zhiping; Guigó, Roderic (BioMed Central, 2008-02-25)
    A report of the 6th Georgia Tech-Oak Ridge National Lab International Conference on Bioinformatics 'In silico Biology: Gene Discovery and Systems Genomics', Atlanta, USA, 15-17 November, 2007.

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