Bioinformatics and Computational Genomics

The Lab

We develop and apply computational methods and machine-learning techniques to analyze large-scale genomic, epigenomic, and transcriptomic data. We implement these skills to study a wide range of biological problems.

Meet the Lab

Research Focus

As members of the ENCODE and psychENCODE consortia, we investigate the molecular mechanisms of gene regulation by integrating and analyzing a wide variety of genome-wide deep-sequencing data including DNase-seq, ATAC-seq, CAGE, RAMPAGE, ChIP-seq, DNAme-seq, RNA-seq, eCLIP-seq, Hi-C, and single-cell sequencing data, among others. Furthermore, we study how genetic variations in the human population affect gene regulation and susceptibility for diseases. We also seek to understand the biogenesis and regulatory mechanisms of small silencing RNAs such as microRNAs (miRNAs), small interfering RNAs (siRNAs), and PIWI­-interacting RNAs (piRNAs), which we achieve by building computational pipelines to analyze diverse high-throughput sequencing datasets upon perturbing small silencing RNA pathways. We also have a long history of building algorithms and benchmarks for protein docking and design.

Publications