SPACER: Identification of cis-regulatory elements with noncontiguous (2008)
Arijit Chakravarty, Jonathan M. Carlson, Radhika S. Khetani, Charles E. Deziel, Robert H. Gross
critical residues
SCOPE: a web server for practical de novo motif discovery (2007)
Carlson, Jonathan M., Chakravarty, Arijit, DeZiel, Charles E., Gross, Robert H.
SCOPE is a novel parameter-free method for the de novo identification of potential regulatory motifs in sets of coordinately regulated genes. The SCOPE algorithm combines the output of three...
A novel ensemble learning method for de novocomputational identification of DNA binding sites (2007)
Chakravarty, Arijit, Carlson, Jonathan M, Khetani, Radhika S, Gross, Robert H
Abstract Background Despite the diversity of motif representations and search algorithms, the de novo computational identification of transcription factor binding sites remains constrained by the...
SPACER: identification of cis-regulatory elements with non-contiguous critical residues (2007)
Chakravarty, Arijit, Carlson, Jonathan M., Khetani, Radhika S., DeZiel, Charles E., Gross, Robert H.
Motivation: Many transcription factors bind to sites that are long and loosely related to each other. De novo identification of such motifs is computationally challenging. In this article, we propose...
BMC Bioinformatics Methodology article (2007)
Arijit Chakravarty, Jonathan M Carlson, Radhika S Khetani, Robert H Gross, Radhika S Khetani, Robert H Gross
A novel ensemble learning method for de novo computational identification of DNA binding sites
Bounded search for de novo identification of degenerate cis-regulatory elements (2006)
Carlson, Jonathan M, Chakravarty, Arijit, Khetani, Radhika S, Gross, Robert H
Abstract Background The identification of statistically overrepresented sequences in the upstream regions of coregulated genes should theoretically permit the identification of potential...
BMC Bioinformatics Methodology article (2005)
Jonathan M Carlson, Arijit Chakravarty, Radhika S Khetani, Robert H Gross, Radhika S Khetani, Robert H Gross
Bounded search for de novo identification of degenerate cis-regulatory elements
"September 18th, 2003."
Chakravarty, Arijit, Howard, Louisa, Compton, Duane A.
We used computer simulation to understand the functional relationships between motor (dynein, HSET, and Eg5) and non-motor (NuMA) proteins involved in microtubule aster organization. The simulation...
Bounded search for de novo identification of degenerate cis-regulatory elements
Carlson, Jonathan M, Chakravarty, Arijit, Khetani, Radhika S, Gross, Robert H
Chakravarty, Arijit, Howard, Louisa, Compton, Duane A.
We used computer simulation to understand the functional relationships between motor (dynein, HSET, and Eg5) and non-motor (NuMA) proteins involved in microtubule aster organization. The simulation...
Bounded search for de novo identification of degenerate cis-regulatory elements
Carlson, Jonathan M, Chakravarty, Arijit, Khetani, Radhika S, Gross, Robert H
SCOPE: a web server for practical de novo motif discovery
Carlson, Jonathan M., Chakravarty, Arijit, DeZiel, Charles E., Gross, Robert H.
SCOPE is a novel parameter-free method for the de novo identification of potential regulatory motifs in sets of coordinately regulated genes. The SCOPE algorithm combines the output of three...
A novel ensemble learning method for de novo computational identification of DNA binding sites
Chakravarty, Arijit, Carlson, Jonathan M, Khetani, Radhika S, Gross, Robert H
Hoar, Kara, Chakravarty, Arijit, Rabino, Claudia, Wysong, Deborah, Bowman, Douglas, Roy, Natalie, ...
Aurora A kinase plays an essential role in the proper assembly and function of the mitotic spindle, as its perturbation causes defects in centrosome separation, spindle pole organization, and...