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  • VisANT 3.0: New Modules for Pathway Visualization, Editing, Prediction and Construction 

    Hu, Zhenjun; Ng, David M.; Yamada, Takuji; Chen, Chunnuan; Kawashima, Shuichi; Mellor, Joe; Linghu, Bolan; Kanehisa, Minoru; Stuart, Joshua M.; DeLisi, Charles (Oxford University Press, 2007-07)
    With the integration of the KEGG and Predictome databases as well as two search engines for coexpressed genes/proteins using data sets obtained from the Stanford Microarray Database (SMD) and Gene Expression Omnibus (GEO) ...
  • VisANT 3.5: Multi-Scale Network Visualization, Analysis and Inference Based on the Gene Ontology 

    Hu, Zhenjun; Hung, Jui-Hung; Wang, Yan; Chang, Yi-Chien; Huang, Chia-Ling; Huyck, Matt; DeLisi, Charles (2009-7-1)
    Despite its wide usage in biological databases and applications, the role of the gene ontology (GO) in network analysis is usually limited to functional annotation of genes or gene sets with auxiliary information on ...
  • Functional Characterization of the YmcB and YqeV tRNA Methylthiotransferases of Bacillus Subtilis 

    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 ...
  • Network-Based Analysis of Affected Biological Processes in Type 2 Diabetes Models 

    Liu, Manway; Liberzon, Arthur; Kong, Sek Won; Lai, Weil R.; Park, Peter J.; Kohane, Isaac S.; Kasif, Simon (Public Library of SCience, 2007-6-15)
    Type 2 diabetes mellitus is a complex disorder associated with multiple genetic, epigenetic, developmental, and environmental factors. Animal models of type 2 diabetes differ based on diet, drug treatment, and gene knockouts, ...
  • Integration of Heterogeneous Expression Data Sets Extends the Role of the Retinol Pathway in Diabetes and Insulin Resistance 

    Park, Peter J.; Kong, Sek Won; Tebaldi, Toma; Lai, Weil R.; Kasif, Simon; Kohane, Isaac S. (Oxford University Press, 2009-9-28)
    Motivation: Type 2 diabetes is a chronic metabolic disease that involves both environmental and genetic factors. To understand the genetics of type 2 diabetes and insulin resistance, the DIabetes Genome Anatomy Project ...
  • Seeing the Forest for the Trees: Using the Gene Ontology to Restructure Hierarchical Clustering 

    Dotan-Cohen, Dikla; Kasif, Simon; Melkman, Avraham A. (Oxford University Press, 2009-6-3)
    Motivation: There is a growing interest in improving the cluster analysis of expression data by incorporating into it prior knowledge, such as the Gene Ontology (GO) annotations of genes, in order to improve the biological ...
  • High-Precision High-Coverage Functional Inference from Integrated Data Sources 

    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 ...
  • Portraits of Breast Cancer Progression 

    Dalgin, Gul S.; Alexe, Gabriela; Scanfeld, Daniel; Tamayo, Pablo; Mesirov, Jill P.; Ganesan, Shridar; DeLisi, Charles; Bhanot, Gyan (BioMed Central, 2007-8-6)
    BACKGROUND. Clustering analysis of microarray data is often criticized for giving ambiguous results because of sensitivity to data perturbation or clustering techniques used. In this paper, we describe a new method based ...
  • Phylogenetic Detection of Conserved Gene Clusters in Microbial Genomes 

    Zheng, Yu; Anton, Brian P.; Roberts, Richard J.; Kasif, Simon (BioMed Central, 2005-10-3)
    BACKGROUND. Microbial genomes contain an abundance of genes with conserved proximity forming clusters on the chromosome. However, the conservation can be a result of many factors such as vertical inheritance, or functional ...
  • MuPlex: Multi-Objective Multiplex PCR Assay Design 

    Rachlin, John; Ding, Chunming; Cantor, Charles; Kasif, Simon (Oxford University Press, 2005-06-27)
    We have developed a web-enabled system called MuPlex that aids researchers in the design of multiplex PCR assays. Multiplex PCR is a key technology for an endless list of applications, including detecting infectious ...

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