Bounded search for de novo identification of degenerate cis-regulatory elements. - Jonathan M. Carlson; Arijit Chakravarty; Radhika S. Khetani; Robert H. Gross (BMC Bioinform., 2006)

BEAM: A Beam Search Algorithm for the Identification of Cis-Regulatory Elements in Groups of Genes. - Jonathan M. Carlson; Arijit Chakravarty; Robert H. Gross (J. Comput. Biol., 2006)

Identifying Fungal Regulatory Motif Patterns Using SCOPE, an Ensemble Learning Method Motif Finder. - Viktor Martyanov; Larkin Elderon; Amy Gladfelter; Dhanalakshmi R. Nair; Robert H. Gross (BIBE, 2007)

SPACER: identification of cis-regulatory elements with non-contiguous critical residues. - Arijit Chakravarty; Jonathan M. Carlson; Radhika S. Khetani; Charles E. DeZiel; Robert H. Gross (Bioinform., 2007)

A novel ensemble learning method for de novo computational identification of DNA binding sites. - Arijit Chakravarty; Jonathan M. Carlson; Radhika S. Khetani; Robert H. Gross (BMC Bioinform., 2007)

SCOPE: a web server for practical de novo motif discovery. - Jonathan M. Carlson; Arijit Chakravarty; Charles E. DeZiel; Robert H. Gross (Nucleic Acids Res., 2007)

Combining predicted regulatory motifs and gene expression information to identify functional relationships within sets of co-expressed genes. - Viktor Martyanov; Robert H. Gross (BIOCOMP, 2009)