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.
February 2021 Our paper Targeting eIF4A Dependent Translation of KRAS Signaling has been published in Cancer Research.
January 2021 Our paper A new graph-based clustering method with application to single-cell RNA-seq data from human pancreatic islets has been published in NAR Genomics and Bioinformatics.
November 2020 The DREAM Single-Cell Transcriptomics challenge consortium paper Gene selection for optimal prediction of cell position in tissues from single-cell transcriptomics data has been published in Life Sci Alliance. Our group is honored to be among top-performing teams in the DREAM challenge!
August 2020 Our paper Direct DNA crosslinking with CAP-C uncovers transcription-dependent chromatin organization at high resolution has been published in Nature Biotechnology. Congratulations Anthony!
July 2020 Welcome new Postdoctoral Associate Eric Pederson joining our lab!
July 2020 Our paper Meta-analysis of peptides to detect protein significance has been published in Statistics and Its Interface.
July 2020 Our paper Large-scale analysis of the position-dependent binding and regulation of human RNA binding proteins has been published as a Cover Article in Quantitative Biology.
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.
RNA Structure, RNA-Protein Interaction & Post-Transcriptional Regulation.
PRAS (Protein-RNA Association Strength): PLoS Comput. Biol., 2019
Translation Efficiency and Alternative ORF analysis: J. Exp. Med., 2019
JPGM (Joint Poisson Gamma Mixture Model): Nucleic Acids Res., 2015
SeqFold: Genome Res., 2013
3D Chromatin Structure, Genome Organization & Transcriptional Regulation.
HSA (Hi-C Structure Analyzer; Hamiltonian Simulated Annealing): Genome Biol., 2016
TFAS (Transcription Factor-Gene Association Strength) and PC-Rgression: Proc. Natl Acad. Sci., 2009
Tissue Heterogeneity, Cell Trajectory & Temporal-Spatial Structure.
ECCITE-Seq (Expanded CRISPR-compatible Cellular Indexing of Transcriptomes and Epitopes by sequencing): Nat. Methods, 2019
LISA (Landmark Isomap for Single Cell Analysis): Pac. Symp. Biocomp., 2019
Multi-Omics Data Integration, Joint Modeling & Network Reconstruction.
JPTA (Joint Principal Trend Analysis): Biometrics, 2018
EMC-NetGSA (Integrative Pathway Disturbance Analysis): Stat. Biosci., 2017
DIG (Data Integration Through Graphical Models): Ann. Appl. Stat., 2017
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.
Interested applicants may contact the PI and submit a CV, 2 representative papers, and contact information of 3 references here.
Interested applicants may contact the PI and apply through the biostatistics doctoral program of UMass Amherst.
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).
An interactive web platform for analysis of time-course high-dimensional genomic data (Zhang et al., 2020).
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).
(Trainee authors underlined)
Zhang Y, Chen Y, Ouyang Z
International Journal of Computational Biology and Drug Design.
Singh K, Lin J, Lecomte N, Mohan P, Gokce A, Sanghvi V, Jiang M, Grbovic-Huezo O, Burčul A, Stark S, Romesser P, Chang Q, Melchor J, Beyer R, Duggan M, Fukase Y, Yang G, Ouerfelli O, Viale A, de Stanchina E, Stamford A, Meinke P, Rätsch G, Leach S, Ouyang Z, and Wendel HG. Targeting eIF4A Dependent Translation of KRAS Signaling.
Cancer Research. 2021 Feb 25;canres.2929.2020
Wu H, Mao D, Zhang Y, Chi Z, Stitzel M, Ouyang Z
NAR Genomics and Bioinformatics. 2021. https://doi.org/10.1093/nargab/lqaa087.
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 Sci Alliance. 2020 Nov; 3(11): e202000867.
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.
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.
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.
Lin J, Ouyang Z
Quantitative Biology. 2020 June 9;8:119-129. doi: 10.1007/s40484-020-0206-5.
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..
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
Lin J, Zhang Y, Frankel W, Ouyang Z
PLoS Comput Biol. 2019 Aug 19;15(8):e1007227.
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.
Li C, Menoret A, Farragher C, Ouyang Z, Bonin C, Holvoet P, Vella AT, Zhou B
JCI Insight. 2019 Apr 16.
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.
Chen Y, Zhang Y, Ouyang Z
Pacific Symposium of Biocomputing. 2019. 24:338-349.
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.
Zhang Y, Ouyang Z
Biometrics. 2018 Jun;74(2):430-438.
Zhang Y, Linder MH, Shojaie A, Ouyang Z, Shen R, Baggerly KA, Baladandayuthapani V, Zhao H
Statistics in Biosciences. 2017 May.
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.
Zhang Y, Ouyang Z, Zhao H
Annals of Applied Statistics. 2017, no. 1, 161-184.
Zou C, Zhang Y, Ouyang Z
Genome Biology. 2016 Mar 2; 17:40.
Wan Y, Qu K, Ouyang Z, Chang HY
Methods Mol Biol. 2016;1361:141-60.
Zou C, Ouyang Z
Nucleic Acids Res. 2015 Oct 30;43(19):9187-97. Epub 2015 Sep 22.
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.
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.
Hardee J, Ouyang Z, Zhang Y, Kundaje A,
G3: Genes, Genomes, Genetics. 2013, 3:2173-85.
Wan Y, Qu K, Ouyang Z, Chang HY
Nature Protocols, 2013, 8:849-869.
Ouyang Z*, Snyder MP, Chang HY*
Genome Research, 2013, 23:377-387. Published in Advance October 11, 2012. co-corresponding authors
Wan Y, Qu K, Ouyang Z, Kertesz M, Li J, Tibshirani R, Nutter RC, Segal E, Chang HY
Molecular Cell, 2012, 48:1-13.
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.
ENCODE Project Consortium (including Ouyang Z)
Nature, 2012, 489:57-74.
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.
Pan Y, Ouyang Z, W
PLoS One, 2011, 6, e17536.
Ouyang Z, Zheng GX, Chang HY
Cell Stem Cell, 2010, 7:649-50.
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.
Z, Zhou Q, Wong WH
Proc. Natl Acad. Sci. USA, 2009, 106:21521-21526.
Xing Y, Ouyang ZKapur K, Scott MP, Wong WH
Molecular Biology and Evolution, 2007, 24:1283-1285.
Kapur K, Xing Y, Ouyang Z,
Genome Biology, 2007, 8:R82.
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.
Z, Liu JK, She ZS
Physical Review E, 2005, 72, 041915.
Z, Wang C, She ZS
Physical Review Letters, 2004, 93, 078103.
Zhu H, Hu G, Ouyang Z,
Wang J, She ZS
Bioinformatics, 2004 Dec 12;20(18):3308-17.
Z, Zhu H, Wang J, She ZS
Journal of Bioinformatics and Computational Biology, 2004 Jun;2(2):353-73. Revised 10 July 2003.
She ZS, Yang Z, Ouyang Z, Zhu H, Wang C, Yin J
Acta Scientiarum Naturalium Universitatis Pekinensis, 2003, 39, 809-814.