Xin Feng, Ph.D.

My primary interest is the algorithm and software development for next generation sequencing. I work with biologists and clinical collaborators to apply these tools to understand various regulatory processes and diseases. My genome-wide profiler tool was used to probe the genome-wide network of insulator for the fly genome(PLoS Genetics, 2010). I also participated in the calibration of the high-quality human curated protein-protein interaction network(Genome Biology, 2010). I am currently working on ChIP-Seq and RNA-Seq algorithms. For ChIP-Seq, I am extending the PeakRanger tool suite(Science 2010, BMC Bioinformatics 2011) to meet the increasing needs of the research community; PeakRanger was originally developed for the modENCODE project and solved the cluster-splitting problem of all worm ChIP-Seq datasets(Science 2010, Science 2010). For RNA-Seq, my mid-term plan is to build a system that handles spliced-reads mapping well. I am also interested in organizing these tools and algorithms and make them run in fully automated pipelines. After joining the McDermott Center Sequencing Core, I started a series of pipelines that automatically get routine jobs done for the customers of the core.