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)

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)

Phylogenetic Dependency Networks: Inferring Patterns of CTL Escape and Codon Covariation in HIV-1 Gag. - Jonathan M. Carlson; Zabrina L. Brumme; Christine M. Rousseau; Chanson J. Brumme; Philippa Matthews; Carl Myers Kadie; James I. Mullins; Bruce D. Walker; P. Richard Harrigan; Philip J. R. Goulder; David Heckerman (PLoS Comput. Biol., 2008)

PhyloDet: a scalable visualization tool for mapping multiple traits to large evolutionary trees. - Bongshin Lee; Lev Nachmanson; George G. Robertson; Jonathan M. Carlson; David Heckerman (Bioinform., 2009)

: Comprehensive Sieve Analysis of Breakthrough HIV-1 Sequences in the RV144 Vaccine Efficacy Trial. - Paul Thatcher Edlefsen; Morgane Rolland; Tomer Hertz; Sodsai Tovanabutra; Andrew J. Gartland; Allan C. deCamp; Craig A. Magaret; Hasan Ahmed; Raphael Gottardo; Michal Juraska; Connor McCoy; Brendan B. Larsen; et al. (PLoS Comput. Biol., 2015)