Analysis and Integration of Big Data from Next-Generation Genomics, Epigenomics, and Transcriptomics


Fri Apr 17, 2015


Christopher Benner
Salk Institute for Biological Studies





Advances in next-generation sequencing (NGS) technology have fundamentally changed our approach to modern biomedical research.  Although the quest to sequence millions of genomes has garnered most of the headlines, innovations in NGS assay development have expanded our ability to quantify transcription, genome structure, and function at unprecedented levels.  My group has been working on analysis strategies to integrate these datasets and leverage them to uncover new principles driving gene regulation.  Our software, HOMER (, combines a host of novel NGS analysis tools and integrative analysis routines into a single analysis suite.  In this presentation, I will discuss the use of these tools to integrate several different types of genomics data to study key regulatory processes in the immune system.  I will also discuss how innovative sequencing assays and their data are combined with genetics to gain a deeper understanding of regulatory networks.



Dr. Benner is the Director of the Integrative Genomics and Bioinformatics Core (IGC) at the Salk Institute.  Since starting the IGC three years ago, he has been collaborating with over 20 research groups that span a wide range of genomics assays and biological systems.  Dr. Benner conducted his Ph.D. studies in Bioinformatics at UCSD, where he played a pioneering role in developing analysis tools for next-generation sequencing technologies.  His doctoral work focused on the discovery of genomic features and cis-regulatory codes underlying transcription factor recruitment and transcription initiation.  He continued as a post doc and project scientist at UCSD where he contributed to genomics projects in over a dozen labs while developing widely adopted analysis software for next-generation sequencing (HOMER).  Dr. Benner continues to maintain HOMER and develop new bioinformatics approaches to analyze and interpret next-generation sequencing data.