Todd R. Riley, Ph.D.

Postdoctoral
       Researcher

Columbia University

Bussemaker Lab

 

Intro

Research

  - SELEX-seq

  - Latent Specificity

  - FeatureREDUCE

  - p53HMM

Publications

Contact Info

CV

 

 

bussmaker
laboratory


biological sciencesat columbia
c2b2

Todd with pigeons

Todd R. Riley, Ph.D.
Postdoctoral Researcher
Columbia University
Department of Biological Sciences
Center for Computational Biology and Bioinformatics
Mentor: Harmen J. Bussemaker, Assoc. Professor

My research has focused on the computational modeling of gene expression regulation. My undergraduate and graduate training in the integrated fields of computer science, applied mathematics, and biophysics provide me with a background in applying quantitative methods to answer biological questions.

A main interest of mine in the Bussemaker lab is the inference of accurate, biophysical sequence-to-affinity models from high-throughput protein-DNA occupancy data, specifically Protein Binding Microarray (PBM) and SELEX-seq data.

Recent News:

1) In collaboration with the Mann Lab, our SELEX-seq method shows that the sequence specificities of the developmental Hox proteins drastically change when they bind in complex with Extradenticle (Exd), as compared to when they bind as monomers - a phenomenon we call "latent specificity" (Slattery, Riley et al., Cell, 2011).

2) Our biophysical sequence-to-affinity inference method FeatureREDUCE recently emerged as the top-performer among 26 known methods in a recent comparison study (Weirauch et al., Nature Biotech, In Press).