About us


The Ouyang lab is part of the Department of Biostatistics and Epidemiology in the School of Public Health and Health Sciences at University of Massachusetts Amherst, the Commonwealth's flagship campus. We are located in the scenic Pioneer Valley, home of five prominent colleges and universities of Massachusetts. We currently have multiple openings for graduate students and postdoctoral associates.

News

Our Research


We strive to advance the frontiers of genomics data science. We develop statistical and computational methods motivated from the analysis of high-throughput genomics data. Our methodological approaches include data integration, manifold learning, predictive learning, and network modeling, etc. Our scientific interests are higher-order structures of genomes and RNAomes, spatial and temporal structures of single cellomes, and components and mechanisms of genome regulation. We collaborate with experimentalists to apply our methods on stem cells, cancers, neurological disorders, and other diseases, often using multi-omics approaches.

Our People


Zhengqing Ouyang Principal Investigator
Eric Pederson Postdoctoral Associate
Anthony Cheng Ph.D. Student

Openings


We are looking for self-motivated individuals to join the Ouyang lab in the Department of Biostatistics and Epidemiology in the School of Public Health and Health Sciences at UMass Amherst. The candidate will join colleagues with expertise in statistics, biostatistics, bioinformatics, genomics, genetics, health data science, and others. The candidate will also have access to large-scale first-hand datasets from our collaborators.

Postdoctoral Associate

Interested applicants may contact the PI and submit a CV, 2 representative papers, and contact information of 3 references here.

Graduate Student

Interested applicants may contact the PI and apply through the biostatistics doctoral program of UMass Amherst.

Software


RiboSNitchDB

An interactive database for annotating and visualizing riboSNitches, single nucleotide variants (SNVs) that impact RNA structure, including both experimentally validated riboSNitches and predicted riboSNitches in human expression quantitative trait loci (eQTL) datasets (Lin et al., 2020).

Riprap

A tool for identifying RNA structural disruptions induced by SNVs given a pair of wildtype and mutant sequences (Lin et al., 2020).

LISA

An interactive web platform for reconstruction of cell trajectory and pseudo-time for massive single cell RNA-seq data (Chen et al., 2019).

PATH

An interactive web platform for analysis of time-course high-dimensional genomic data (Zhang et al., 2020).

PRAS

A tool for RBP functional targets prediction from CLIP-seq peaks (Lin et al., 2019).

HSA

A flexible tool that can jointly analyze multiple contact maps from Hi-C experiments to infer the 3D chromatin structure of the genome (Zou et al., 2016).

SeqFold

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 (Ouyang et al., Epub 2012).

Publication

(Trainee authors underlined)



In press


Gene selection for optimal prediction of cell position in tissues from single-cell transcriptomics

Tanevski J, Nguyen T, Truong B, Karaiskos N, Ahsen ME, Zhang X, Shu C, Xu K, Liang X, Hu Y, Pham HV, Li X, Le TD, Tarca AL, Bhatti G, Romero R, Karathanasis N, Loher P, Chen Y, Ouyang Z, Mao D, Zhang Y, Zand M, Ruan J, Hafemeister C, Qiu P, Tran D, Nguyen T, Gabor A, Yu T, Guinney J, Glaab E, Krause R, Banda P, DREAM SCTC Consortium, Stolovitzky G, Rajewsky N, Saez-Rodriguez J and Meyer P
Life Science Alliance.

PATH: An interactive web platform for analysis of time-course high-dimensional genomic data

Zhang Y, Chen Y, Ouyang Z
International Journal of Computational Biology and Drug Design.


2020


Direct DNA crosslinking with CAP-C uncovers transcription-dependent chromatin organization at high resolution

You Q§, Cheng A§, Gu X§, Harada B, Yu M, Wu T, Ren B*, Ouyang Z*, He C*
Nature Biotechnology. 2020 Aug 24;1-18. doi: 10.1038/s41587-020-0643-8. PMID: 32839564.
§co-first authors; *co-corresponding authors.

Identification and analysis of RNA structural disruptions induced by single nucleotide variants using Riprap and RiboSNitchDB

Lin J, Chen Y, Zhang Y, Ouyang Z
NAR Genomics and Bioinformatics. 2020 August 14;2(3):1-12. doi.org/10.1093/nargab/lqaa057.

Meta-analysis of peptides to detect protein significance

Zhang Y, Ouyang Z, Qian WJ, Smith RD, Wong WH, Davis RW.
Statistics and Its Interface. 2020 July 31;13:465-474. doi: 10.4310/SII.2020.v13.n4.a4.

Large-scale analysis of the position-dependent binding and regulation of human RNA binding proteins

Lin J, Ouyang Z
Quantitative Biology. 2020 June 9;8:119-129. doi: 10.1007/s40484-020-0206-5.

Low SATB1 expression promotes IL-5 and IL-9 expression in Sezary Syndrome

Herrera A, Fredholm S, Cheng A, Mimitou E, Seffens A, Bar-Natan M, Sun A, Latkowski J, Willerslew-Olsen A, Buus T, Gluud M, Krejsgaard T, Rusillow A, Woetmann A, Geisler C, Geskin L, Ouyang Z, Smibert P, Ødum N, Koralov S
Journal of Investigative Dermatology. 2020 Mar;140(3):713-716. doi: 10.1016/j.jid.2019.07.714. PMID: 31465740..


2019


Predicting cellular position in the Drosophila embryo from Single-Cell Transcriptomics data

Tanevski J, Nguyen T, Truong B, Karaiskos N, Ahsen ME, Zhang X, Shu C, Hu Y, Pham HV, Li X, Le TD, Tarca AL, Bhatti G, Romero R, Karathanasis N, Loher P, Chen Y, Ouyang Z, Mao D, Zhang Y, Zand M, Ruan J, Hafemeister C, Qiu P, Tran D, Nguyen T, Gabor A, Yu T, Glaab E, Krause R, Banda P, DREAM SCTC Consortium, Stolovitzky G, Rajewsky N, Saez-Rodriguez J and Meyer P
BioRxiv, p.796029.

PRAS: predicting functional targets of RNA binding proteins based on CLIP-seq peaks

Lin J, Zhang Y, Frankel W, Ouyang Z
PLoS Comput Biol. 2019 Aug 19;15(8):e1007227.

c-MYC regulates mRNA translation efficiency and start site selection

Singh K, Lin J, Zhong Y, Burčul A, Mohan P, Jiang M, Viale A, Cross JR, Sun L, Yong-Gonzalez V, Hendrickson RC, Rätsch G*, Ouyang Z*, Wendel HG*
Journal of Experimental Medicine. 2019 May 29.
*co-corresponding authors.

Single cell transcriptomics based-MacSpectrum reveals novel macrophage activation signatures in diseases

Li C, Menoret A, Farragher C, Ouyang Z, Bonin C, Holvoet P, Vella AT, Zhou B
JCI Insight. 2019 Apr 16.

Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells

Mimitou E, Cheng A, Montalbano A, Hao S, Stoeckius M, Legut M, Roush T, Herrera A, Papalexi E, Ouyang Z, Satija R, Sanjana N, Koralov S, Smibert P
Nature Methods. 2019 May;16(5):409-412.

LISA: Accurate reconstruction of cell trajectory and pseudo-time for massive single cell RNA-seq data

Chen Y, Zhang Y, Ouyang Z
Pacific Symposium of Biocomputing. 2019. 24:338-349.


2018


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*
Biolology of Reproduction. 2018 Nov 1;99(5):949-959.
§co-first authors; *co-corresponding authors.

Joint principal trend analysis for longitudinal high-dimensional data

Zhang Y, Ouyang Z
Biometrics. 2018 Jun;74(2):430-438.


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. 2017 May.

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. 2017 Aug 31;36(35):5035-5044. Epub 2017 May 1.

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.


2016


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.


2015


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.


2014


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.

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.


2013


STAT3 targets suggest mechanisms of aggressive tumorigenesis in diffuse large B cell lymphoma

Hardee J, Ouyang Z, Zhang Y, Kundaje A,
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. co-corresponding authors


2003-2012


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 (including Ouyang Z)
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.

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.

Assessing the conservation of mammalian gene expression using high-density exon arrays

Xing Y, Ouyang ZKapur K, Scott MP, Wong WH
Molecular Biology and Evolution, 2007, 24:1283-1285.

Exon arrays provide accurate assessments of gene expression
high-density exon arrays

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.