I am broadly interested in using ideas from machine learning to analyze biological sequence data. Recently I’ve worked on the alignment problem, which is central to comparative genomics and has nice connections to posets and probabilistic models.
I’m also analyzing comparative ChIP-Seq data to study the evolution of transcription factor binding sites. Visit my website for a list of publications and links to software.
Eisen Lab Publications:
Bradley RK, Li XY, Trapnell C, Davidson S, Pachter L, Chu HC, Tonkin LA, Biggin MD, Eisen MB. (2010) Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species. PLoS Biol. 2010 Mar 23;8(3):e1000343