Browsing ENG: Bioinformatics: Scholarly Papers by Title

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Browsing ENG: Bioinformatics: Scholarly Papers by Title

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  • Yanai, Itai; Wolf, Yuri I; Koonin, Eugene V (BioMed Central, 2002-04-26)
    BACKGROUND. Gene fusions can be used as tools for functional prediction and also as evolutionary markers. Fused genes often show a scattered phyletic distribution, which suggests a role for processes other than vertical ...
  • Imielinski, Marcin; Belta, Calin (BioMed Central, 2008-4-30)
    BACKGROUND. Biological robustness results from redundant pathways that achieve an essential objective, e.g. the production of biomass. As a consequence, the biological roles of many genes can only be revealed through ...
  • Voevodski, Konstantin; Teng, Shang-Hua; Xia, Yu (BioMed Central, 2009-9-18)
    BACKGROUND. Protein-protein interactions (PPIs) play fundamental roles in nearly all biological processes, and provide major insights into the inner workings of cells. A vast amount of PPI data for various organisms is ...
  • Cupples, L Adrienne; Arruda, Heather T; Benjamin, Emelia J; D'Agostino, Ralph B; Demissie, Serkalem; DeStefano, Anita L; Dupuis, Josée; Falls, Kathleen M; Fox, Caroline S; Gottlieb, Daniel J; Govindaraju, Diddahally R; Guo, Chao-Yu; Heard-Costa, Nancy L; Hwang, Shih-Jen; Kathiresan, Sekar; Kiel, Douglas P; Laramie, Jason M; Larson, Martin G; Levy, Daniel; Liu, Chun-Yu; Lunetta, Kathryn L; Mailman, Matthew D; Manning, Alisa K; Meigs, James B; Murabito, Joanne M; Newton-Cheh, Christopher; O'Connor, George T; O'Donnell, Christopher J; Pandey, Mona; Seshadri, Sudha; Vasan, Ramachandran S; Wang, Zhen Y; Wilk, Jemma B; Wolf, Philip A; Yang, Qiong; Atwood, Larry D (BioMed Central, 2007-9-19)
    BACKGROUND: The Framingham Heart Study (FHS), founded in 1948 to examine the epidemiology of cardiovascular disease, is among the most comprehensively characterized multi-generational studies in the world. Many collected ...
  • Wilk, Jemma B; Walter, Robert E; Laramie, Jason M; Gottlieb, Daniel J; O'Connor, George T (BioMed Central, 2007-9-19)
    BACKGROUND: Pulmonary function measures obtained by spirometry are used to diagnose chronic obstructive pulmonary disease (COPD) and are highly heritable. We conducted genome-wide association (GWA) analyses (Affymetrix ...
  • 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 ...
  • 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 ...
  • 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 ...
  • 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 ...

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