My research is about developing statistical models to solve genomic problems.
More specifically, I am working on highly repetitive regions of the genomes, building models to assign multi-mapping reads to its potential alignment positions. We proposed Perm-seq which aligns multi-mapping ChIP-seq reads. The R package permseq is available on github.
Currently, we are working on the three-dimensional organization in repetitive regions of the genomes.
Approximate Bayesian Computation algorithms for estimating network model parameters. Joint Statistical Meeting Proceedings (2013)- Biometrics Section. 2013:2239-2253. Zheng Y. and Aris-Brosou S.
permseq: R package for mapping protein-DNA interactions in highly repetitive regions of the genomes with prior-enhanced read mapping.
permseqExample: Demo data for the permseq package. Together with the raw data, we offer the demo R scripts to run these data. The corresponding alignment outputs saved in bed format and the R image are provided. (download here)
2016 Encyclopedia of DNA Elements (ENCODE) Consortium Meeting. La Jolla, CA. Best lighting talk, honorable mention.
I highly recommend Emacs especially for researchers working frequently on UW-Madison stat/biostat server.
ENCODE, short for Encyclopedia of DNA Elements. Users can batch download extraordinary large amount of data sets in human genome with functional annotations.
HiCPlotter: Fancy! User friendly tool for Hi-C result visualization.