Affiliation: University of Pennsylvania
- PTM-Switchboard--a database of posttranslational modifications of transcription factors, the mediating enzymes and target genesLogan 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...
- Regulating the regulators: modulators of transcription factor activityLogan 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 /..
- Transcriptional regulation via TF-modifying enzymes: an integrative model-based analysisLogan 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...
- Dense subgraph computation via stochastic search: application to detect transcriptional modulesLogan 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...
- Mimosa: Mixture model of co-expression to detect modulators of regulatory interactionMatthew 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...