Ouyang Lab

Advancing Computational Genomics and Transcriptomics (ACGT)


The Ouyang lab is part of The Jackson Laboratory for Genomic Medicine, and is affiliated with the Department of Biomedical Engineering, the Department of Genetics and Genome Sciences, and the Institute for Systems Genomics of University of Connecticut. We are located in Farmington, Connecticut.

Our Research

Chromatin Structure

3D Chromatin Structure & Genome Organization

RNA Structure

RNA Secondary Structure & RNA-Protein Interaction

Gene Regulation

Epigenetic Regulation & Cellular Differentiation


Network Modeling & Statistical Learning

Our People

Zhengqing Ouyang
Principal Investigator

Yang Chen
Postdoctoral Associate

Jianan Lin
Graduate Student

Anthony Cheng
Graduate Student

Deepak nag Ayyala
Postdoctoral Associate (now Assistant Professor at Augusta University, Georgia)

Our Software


A flexible tool that can jointly analyze multiple contact maps from Hi-C experiments to infer the 3D chromatin structure of the genome.

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A tool for RNA secondary structure prediction from experimental data. Given high-throughput data, it can reconstruct secondary structures of the whole transcriptome, termed RNA structurome. It outputs reconstructed RNA secondary structure as well as base-level accessibilities for each transcript.

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Our Papers

Join Us

Data Scientist

Data scientist positions are available at Postdoctoral Associate/Co-Op Associate/Associate Research Scientist/Research Scientist levels. Exceptional candidates will have the opportunity to apply for prestigious fellowships in The Jackson Laboratory. Successful candidates will be joining The Jackson Laboratory for Genomic Medicine in Farmington, Connecticut. Interested applicants please send a CV and contact information of three references to .

Graduate Student

Applicants for graduate positions should apply through several programs of the University of Connecticut, such as Ph.D. in Biomedical Science, M.D./Ph.D., and Ph.D. in Biomedical Engineering through the Bioinformatics track. Candidates interested in the Ouyang Lab please also send a CV to .