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OpenBU

Browsing Bioinformatics by Title

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  • 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.
  • Holloway, Dustin T; Kon, Mark; DeLisi, Charles (BioMed Central, 2008-6-18)
    BACKGROUND. An important goal in bioinformatics is to unravel the network of transcription factors (TFs) and their targets. This is important in the human genome, where many TFs are involved in disease progression. Here, ...
  • Fu, Yutao; Sinha, Manisha; Peterson, Craig L.; Weng, Zhiping (Public Library of Science, 2008-7-25)
    Chromatin structure plays an important role in modulating the accessibility of genomic DNA to regulatory proteins in eukaryotic cells. We performed an integrative analysis on dozens of recent datasets generated by ...
  • Xia, Yu; Franzosa, Eric A.; Gerstein, Mark B. (Public Library of Science, 2009-6-12)
    Rates of evolution differ widely among proteins, but the causes and consequences of such differences remain under debate. With the advent of high-throughput functional genomics, it is now possible to rigorously assess the ...
  • Jiang, Xiaoyu; Nariai, Naoki; Steffen, Martin; Kasif, Simon; Kolaczyk, Eric D (BioMed Central, 2008-8-22)
    BACKGROUND. In the current climate of high-throughput computational biology, the inference of a protein's function from related measurements, such as protein-protein interaction relations, has become a canonical task. Most ...
  • Mellor, Joe; DeLisi, Charles (BioMed Central, 2006-6-8)
    A systematic curation of the literature on Saccharomyces cerevisiae has yielded a comprehensive collection of experimentally observed interactions. This new resource augments current views of the topological structure of ...

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