Tyrer, J. P.*, Peng, P.*, DeVries, A. A. , Gayther, S. A. , Jones, M. R., Pharoah, P. D. (2022). Improving on polygenic scores across complex traits using select and shrink with summary statistics. medRxiv, 2022.09.13.22278911. (* equal contribution)
Coetzee, S.*, Dareng, E. O.*, Peng, P.*, Rosenow, W.*, Tyrer, J. P.*, ... & Plummer, J. (2022). Integrative multi-omics analyses to identify the genetic and functional mechanisms underlying ovarian cancer risk regions. Under revision at The American Journal of Human Geneticss. (* equal contribution)
Plummer, J., Dezem, F. S., Davis, B., Chen, S., Suo, J.-H., Giambartolomei, C., Peng, P., … & Gayther, S. (2021). The Ovarian Cancer Regulatory Atlas: A Catalogue of Epigenomic, Transcriptomic and Genome Wide Interactions in Ovarian Cancers and Their Precursor Cell Types. Under review at iScience.
DeVries A. A., Dennis J., Tyrer J. P., Peng, P., ... & Jones, M. R. (2022). Copy number variants are ovarian cancer risk alleles at known and novel risk loci. JNCI: Journal of the National Cancer Institute, djac160.
Nameki, R., Shetty, A., Dareng, E., ... the Ovarian Cancer Association Consortium,... & Lawrenson, K. (2022). chromMAGMA: regulatory element-centric interrogation of risk variants. Life Science Alliance, 5 (10), e202201446
Gull, N.*, Jones, M. R.*, Peng, P.*, Coetzee, S. G., Silva, T. C., Plummer, J. T., ... & Gayther, S. (2022). DNA methylation and transcriptomic features are preserved throughout disease recurrence and chemoresistance in high grade serous ovarian cancers. Journal of Experimental & Clinical Cancer Research 41.1: 1-18. (* equal contribution)
Jones, M. R.*, Peng, P.*, Coetzee, S. G.*, Tyrer, J., Reyes, A. L. P., Corona, R. I., ... & Gayther, S. (2020). Ovarian Cancer Risk Variants Are Enriched in Histotype-Specific Enhancers and Disrupt Transcription Factor Binding Sites. The American Journal of Human Genetics, 107(4), 622-635. (* equal contribution)
Peng, P., Khoueiry, P., Girardot, C., Reddington, J. P., Garfield, D. A., Furlong, E. E., & Sinha, S. (2019). The role of chromatin accessibility in cis-regulatory evolution. Genome biology and evolution, 11(7), 1813-1828.
Khoueiry, P., Girardot, C., Ciglar, L., Peng, P., Gustafson, E. H., Sinha, S., & Furlong, E. E. (2017). Uncoupling evolutionary changes in DNA sequence, transcription factor occupancy and enhancer activity. Elife, 6, e28440.
Peng, P., & Sinha, S. (2016). Quantitative modeling of gene expression using DNA shape features of binding sites. Nucleic acids research, 44(13), e120-e120. *Nominated for top 10 papers in RECOMB/RSG 2016.
Peng, P., Samee, M. A. H., & Sinha, S. (2015). Incorporating chromatin accessibility data into sequence-to-expression modeling. Biophysical journal, 108(5), 1257-1267.
Liu, H. C., Peng, P., Hsieh, T. C., Yeh, T. C., Lin, C. J., Chen, C. Y., ... & Liang, D. C. (2013). Comparison of feature selection methods for cross-laboratory microarray analysis. IEEE/ACM transactions on computational biology and bioinformatics, 10(3), 593-604.
Peng, P., Quantifying the functional and evolutionary relationships among sequences, transcription factor binding and gene expression. Ph.D. Thesis. University of Illinois at Urbana-Champaign, 2018.
Peng, P., Gene Regulatory Network Inference and Complex Phenotype Prediction from Genetical Genomics Data. M.S. Thesis. National Taiwan University, 2013.