Weuse a quantitative definition of specificity to developa neural networkfor the identification of commonprotein binding sites in a collection of unaligned DNAfragments. Wedemonst...
Transcription factor (TF) binding to its DNA target site is a fundamental regulatory interaction. The most common model used to represent TF binding specificities is a position spe...
Background: Proteins that evolve from a common ancestor can change functionality over time, and it is important to be able identify residues that cause this change. In this paper ...
Background: Cis-regulatory modules are combinations of regulatory elements occurring in close proximity to each other that control the spatial and temporal expression of genes. Th...
Voichita D. Marinescu, Isaac S. Kohane, Alberto Ri...
Background: Molecular evolutionary studies of noncoding sequences rely on multiple alignments. Yet how multiple alignment accuracy varies across sequence types, tree topologies, d...
Daniel A. Pollard, Alan M. Moses, Venky N. Iyer, M...