Logan Everett

Summary

Affiliation: University of Pennsylvania
Country: USA

Publications

  1. ncbi PTM-Switchboard--a database of posttranslational modifications of transcription factors, the mediating enzymes and target genes
    Logan Everett
    Penn Center for Bioinformatics, Department of Genetics and Department of Computer Science, University of Pennsylvania, Philadelphia, PA, USA
    Nucleic Acids Res 37:D66-71. 2009
  2. ncbi Regulating the regulators: modulators of transcription factor activity
    Logan Everett
    Department of Genetics, Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA, USA
    Methods Mol Biol 674:297-312. 2010
  3. ncbi Transcriptional regulation via TF-modifying enzymes: an integrative model-based analysis
    Logan J Everett
    Genomics and Computational Biology Program, 700 Clinical Research Building, 415 Curie Boulevard, Philadelphia, PA 19104, USA
    Nucleic Acids Res 39:e78. 2011
  4. ncbi Dense subgraph computation via stochastic search: application to detect transcriptional modules
    Logan Everett
    Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, USA
    Bioinformatics 22:e117-23. 2006
  5. ncbi Mimosa: Mixture model of co-expression to detect modulators of regulatory interaction
    Matthew Hansen
    Department of Genetics, Penn Center for Bioinformatics, University of Pennsylvania, Pennsylvania, USA
    Algorithms Mol Biol 5:4. 2010

Detail Information

Publications5

  1. ncbi PTM-Switchboard--a database of posttranslational modifications of transcription factors, the mediating enzymes and target genes
    Logan Everett
    Penn Center for Bioinformatics, Department of Genetics and Department of Computer Science, University of Pennsylvania, Philadelphia, PA, USA
    Nucleic Acids Res 37:D66-71. 2009
    ..In the future, the database will be expanded to mammalian organisms, and will also include triplets predicted from computational approaches. The database can be accessed at http://cagr.pcbi.upenn.edu/PTMswitchboard...
  2. ncbi Regulating the regulators: modulators of transcription factor activity
    Logan Everett
    Department of Genetics, Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA, USA
    Methods Mol Biol 674:297-312. 2010
    ..PTM-Switchboard is accessible at http://cagr.pcbi.upenn.edu/PTMswitchboard /..
  3. ncbi Transcriptional regulation via TF-modifying enzymes: an integrative model-based analysis
    Logan J Everett
    Genomics and Computational Biology Program, 700 Clinical Research Building, 415 Curie Boulevard, Philadelphia, PA 19104, USA
    Nucleic Acids Res 39:e78. 2011
    ..We validated our tool on a well-studied stress response network in yeast and on a STAT1-mediated regulatory network in human B cells. Our work represents a significant step toward a comprehensive model of gene transcription...
  4. ncbi Dense subgraph computation via stochastic search: application to detect transcriptional modules
    Logan Everett
    Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, USA
    Bioinformatics 22:e117-23. 2006
    ..Finally, our combined analysis of Cardiac, Skeletal, and Smooth muscle data recapitulates the evolutionary relationship among the three tissues...
  5. ncbi Mimosa: Mixture model of co-expression to detect modulators of regulatory interaction
    Matthew Hansen
    Department of Genetics, Penn Center for Bioinformatics, University of Pennsylvania, Pennsylvania, USA
    Algorithms Mol Biol 5:4. 2010
    ..CONCLUSIONS: While limited in some ways, as discussed, the work represents a novel approach to mine expression data and detect potential modulators of regulatory interactions...