Welcome to The Ouyang Lab

Analytical and Computational Genomics and Transcriptomics (ACGT)

About us

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

Data Science

Statistical Methods and Tools Development for Big Data Analytics

3D Genomics

Chromatin Structure & Genome Organization

Noncoding RNA

RNA Structure & Interaction


Epigenetic Regulation at Single Cell & Population Levels

Our People

Zhengqing Ouyang
Principal Investigator

Yang Chen
Postdoctoral Associate

Jianan Lin
Graduate Student

Anthony Cheng
Graduate Student

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

DNA methylomes of bovine gametes and in vivo produced preimplantation embryos
Jiang Z, Lin J, Dong H, Zheng X, Marjani SL, Duan J, Ouyang Z, Chen J, and Tian XC
Biology of Reproduction. 2018 Jun 14. doi: 10.1093/biolre/ioy138.
Joint principal trend analysis for longitudinal high-dimensional data
Zhang Y, Ouyang Z
Biometrics. First published: 31 July 2017.
Dissecting pathway disturbances using network topology and multi-platform genomics data
Zhang Y, Linder MH, Shojaie A, Ouyang Z, Shen R, Baggerly KA, Baladandayuthapani V, Zhao H
Statistics in Biosciences. First Online: 04 May 2017.

Genome-wide DNA methylation profiling reveals cancer-associated changes within early colonic neoplasia
Hanley MP, Hahn MA, Li AX, Wu X, Lin J, Wang J, Choi AH, Ouyang Z, Fong Y, Pfeifer GP, Devers TJ, Rosenberg DW
Oncogene. Advance online publication 1 May 2017.
A statistical framework for data integration through graphical models with application to cancer genomics
Zhang Y, Ouyang Z, Zhao H
Annals of Applied Statistics. 2017, no. 1, 161-184.

HSA: integrating multi-track Hi-C data for genome-scale reconstruction of 3D chromatin structure
Zou C, Zhang Y, Ouyang Z
Genome Biology. 2016 Mar 2; 17:40.
Genome-wide probing of RNA structures in vitro using nucleases and deep sequencing
Wan Y, Qu K, Ouyang Z, Chang HY
Methods Mol Biol. 2016;1361:141-60.
Joint modeling of RNase footprint sequencing profiles for genome-wide inference of RNA structure
Zou C, Ouyang Z
Nucleic Acids Res. 2015 Oct 30;43(19):9187-97. Epub 2015 Sep 22.
Predicting quantitative outcomes of patients using longitudinal gene expression
Zhang Y, Ouyang Z
Sri Lankan Journal of Applied Statistics Special Issue: “Modern Statistical Methodologies in the Cutting Edge of Science”, 2014, 5:117-126.
Landscape and variation of RNA secondary structure across the human transcriptome
Wan Y, Qu K, Zhang QC, Flynn RA, Manor O, Ouyang Z, Zhang J, Spitale RC, Snyder MP, Segal E, Chang HY
Nature, 2014, 505:706-9.
STAT3 targets suggest mechanisms of aggressive tumorigenesis in diffuse large B cell lymphoma
Hardee J, Ouyang Z, Zhang Y, Kundaje A, Lacroute P, Snyder MP
G3: Genes, Genomes, Genetics. 2013, 3:2173-85.
Genome-wide mapping of RNA structure using nuclease digestion and high throughput sequencing
Wan Y, Qu K, Ouyang Z, Chang HY
Nature Protocols, 2013, 8:849-869.
SeqFold: Genome-scale reconstruction of RNA secondary structure integrating high-throughput sequencing data
Ouyang Z, Snyder MP, Chang HY
Genome Research, 2013, 23:377-387. Published in Advance October 11, 2012.
Genome-wide measurement of RNA folding energies
Wan Y, Qu K, Ouyang Z, Kertesz M, Li J, Tibshirani R, Nutter RC, Segal E, Chang HY
Molecular Cell, 2012, 48:1-13.
Architecture of the human regulatory network derived from ENCODE data
Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan KK, Cheng C, Mu XJ, Khurana E, Rozowsky J, Alexander R, Min R, Alves P, Abyzov A, Addleman N, Bhardwaj N, Boyle AP, Cayting P, Charos A, Chen DZ, Cheng Y, Clarke D, Eastman C, Euskirchen G, Frietze S, Fu Y, Gertz J, Grubert F, Harmanci A, Jain P, Kasowski M, Lacroute P, Leng J, Lian J, Monahan H, O'Geen H, Ouyang Z, Partridge EC, Patacsil D, Pauli F, Raha D, Ramirez L, Reddy TE, Reed B, Shi M, Slifer T, Wang J, Wu L, Yang X, Yip KY, Zilberman-Schapira G, Batzoglou S, Sidow A, Farnham PJ, Myers RM, Weissman SM, Snyder M
Nature, 2012, 489:91-100.
An integrated encyclopedia of DNA elements in the human genome
ENCODE Project Consortium
Nature, 2012, 489:57-74.
Correlation of global micro RNA expression with basal cell carcinoma subtype
Heffelfinger C, Ouyang Z, Engberg A, Leffell DJ, Hanlon AM, Gordon PB, Zheng W, Zhao H, Snyder M, Bale AE
G3: Genes, Genomes, Genetics, 2012, 2:279-86.
A new FACS approach isolates hESC derived endoderm using transcription factors
Pan Y, Ouyang Z, Wong WH, Baker JC
PLoS One, 2011, 6, e17536.
Noncoding RNA landmarks of pluripotency and reprogramming
Ouyang Z, Zheng GX, Chang HY
Cell Stem Cell, 2010, 7:649-50.
Hedgehog pathway-regulated gene networks in cerebellum development and tumorigenesis
Lee EY, Ji H, Ouyang Z, Zhou B, Ma W, Vokes SA, McMahon AP, Wong WH, Scott MP
Proc. Natl Acad. Sci. USA, 2010, 107, 9736.
ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells
Ouyang Z, Zhou Q, Wong WH
Proc. Natl Acad. Sci. USA, 2009, 106:21521-21526.
Assessing the conservation of mammalian gene expression using high-density exon arrays
Xing Y, Ouyang Z, Kapur K, Scott MP, Wong WH
Molecular Biology and Evolution, 2007, 24:1283-1285.
Exon arrays provide accurate assessments of gene expression
Kapur K, Xing Y, Ouyang Z, Wong WH
Genome Biology, 2007, 8:R82.
Parallel implementation of SEMPHY-a structural EM algorithm for phylogenetic reconstruction
Li E, Ouyang Z, Deng X, Zhang Y, Chen W
Parallel Computing: Current & Future Issues of High-End Computing, Proceedings of the International Conference ParCo 2005, 33:631-638.
Hierarchical structure analysis describing abnormal base composition of genomes
Ouyang Z, Liu JK, She ZS
Physical Review E, 2005, 72, 041915.
Scaling and hierarchical structures in DNA sequences
Ouyang Z, Wang C, She ZS
Physical Review Letters, 2004, 93, 078103.
Accuracy improvement for identifying translation initiation sites in microbial genomes
Zhu H, Hu G, Ouyang Z, Wang J, She ZS
Bioinformatics, 2004 Dec 12;20(18):3308-17.
Multivariate entropy distance method for prokaryotic gene identification
Ouyang Z, Zhu H, Wang J, She ZS
Journal of Bioinformatics and Computational Biology, 2004 Jun;2(2):353-73. Revised 10 July 2003.
A preliminary study to the origin and evolution of SARS-CoV
She ZS, Yang Z, Ouyang Z, Zhu H, Wang C, Yin J
Acta Scientiarum Naturalium Universitatis Pekinensis, 2003, 39, 809-814.

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 .