Affiliation: University of Pennsylvania
- Integrative genomic analysis of CREB defines a critical role for transcription factor networks in mediating the fed/fasted switch in liverLogan J Everett
Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
BMC Genomics 14:337. 2013..The precise molecular mechanisms by which CREB specifically targets these genes in response to alternating hormonal cues remain to be elucidated...
- 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..This is just one context in which an efficient computation of dense subgraphs in a multi-partite graph is needed...
- 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...
- CTCF binding site sequence differences are associated with unique regulatory and functional trends during embryonic stem cell differentiationRobert N Plasschaert
Department of Cell and Developmental Biology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA, Program of Gene Expression and Regulation, The Wistar Institute, Philadelphia, PA 19104, USA, Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA and Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
Nucleic Acids Res 42:774-89. 2014..Our results suggest that the regulatory control of CTCF is dependent in part on specific motifs within its binding site. ..