Publications

• BEAM: Carlson* JM, Chakravarty* A, and Gross RH. "BEAM: A beam search algorithm for the identification of cis-regulatory elements in groups of genes." Journal of Computational Biology, 13(3):686-701 (2006).
• PRISM: Carlson* JM, Chakravarty* A, Khetani RS, and Gross RH. "Bounded search for de novo identification of degenerate cis-regulatory elements." BMC Bioinformatics, 7(1):254 (2006).
• SPACER: Chakravarty A, Carlson JM, , Khetani RS, DeZiel CE, and Gross RH. "SPACER: Robust identification of cis-regulatory elements with non-contiguous critical residues." Bioinformatics 23: 1029-1031 (2007).
• SCOPE: Chakravarty, A, Carlson, JM, Khetani, RS, and Gross, RH, "A novel ensemble learning method for de novo computational identification of DNA binding sites." BMC Bioinformatics 8: 249 (2007)
• SCOPE-web interface: Carlson, JM, Chakravarty, A, DeZiel, CE, Gross, RH, "SCOPE: a web server for practical de novo motif discovery J.M. Carlson; A. Chakravarty; C.E. DeZiel; R.H. Gross; Nucleic Acids Research; doi: 10.1093/nar/gkm310. 2007

     * these authors contributed equally to this research