The identification of cis-regulatory elements and modules is an important step in understanding the regulation of genes. We have developed a pipeline capable of running multiple m...
Asim S. Siddiqui, Gordon Robertson, Misha Bilenky,...
We present an index structure for managing weightedsequences in large databases. A weighted-sequence is defined as a two-dimensional structure where each element in the sequence i...
Background: Single-pass, partial sequencing of complementary DNA (cDNA) libraries generates thousands of chromatograms that are processed into high quality expressed sequence tags...
Charu G. Kumar, Richard LeDuc, George Gong, Levan ...
Background: The p53 gene family consists of the three genes p53, p63 and p73, which have polyhedral non-overlapping functions in pivotal cellular processes such as DNA synthesis a...
We present a novel classification-based algorithm called GeneClass for learning to predict gene regulatory response. Our approach is motivated by the hypothesis that in simple orga...
Manuel Middendorf, Anshul Kundaje, Chris Wiggins, ...