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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) ...
  • A Predictive Phosphorylation Signature of Lung Cancer 

    Wu, Chang-Jiun; Cai, Tianxi; Rikova, Klarisa; Merberg, David; Kasif, Simon; Steffen, Martin (Public Library of Science, 2009-11-25)
    BACKGROUND. Aberrant activation of signaling pathways drives many of the fundamental biological processes that accompany tumor initiation and progression. Inappropriate phosphorylation of intermediates in these signaling ...
  • Biological Process Linkage Networks 

    Dotan-Cohen, Dikla; Letovsky, Stan; Melkman, Avraham A.; Kasif, Simon (Public Library of Science, 2009-4-23)
    BACKGROUND. The traditional approach to studying complex biological networks is based on the identification of interactions between internal components of signaling or metabolic pathways. By comparison, little is known ...
  • 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 ...
  • 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 ...
  • 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 ...
  • 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 ...
  • 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, ...
  • 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 ...
  • 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 ...

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