Research Interests

Bioinformatics and Computational Biology. Machine learning and statistical modeling of heterogenous multi-omics data to improve the prevention and treatment of cancer and other diseases.

Experience 

Cedars-Sinai Medical Center, CA, USA
Assistant Professor in Computational Biomedicine | 2023 - present

Education 

Cedars-Sinai Medical Center, CA, USA
Project Scientist in  Biomedical Sciences | 2021-2023
Postdoctoral Scientist in Biomedical Sciences  | 2019-2020
Mentor: Drs. Simon Gayther and Michelle Jones

University of Illinois at Urbana-Champaign, IL, USA | 2013-2018
Ph.D. in Computer Science
Advisor: Prof. Saurabh Sinha 

National Taiwan University, Taipei, Taiwan
M.S. in Computer Science and Information Engineering | 2011-2013
B.S. in Computer Science and Information Engineering | 2007-2011
GPA 4.0/4, National Taiwan University Presidential Award

Awards and Honors

Grant

• NIH K99/R00 Pathway to Independence Award | National Cancer Institute, 2021-2025

Scholarships

• HHMI International Student Research Fellowship Finalist | HHMI, 2016 

• Grace Hopper Celebration Scholarship for women in computing| Anita Borg Institute, 2015 and 2016

• Study Abroad Scholarship, $32,000 USD | Ministry of Education, Taiwan, 2013

• Google Anita Borg Memorial Scholarship| Google Inc., 2012 

Awards

• NextProf Nexus in Engineering | UC Berkeley, UMich, and Georgia Tech, 2020

• Rising Stars in EECS | UIUC, MIT, UC Berkeley, and CMU, 2019

• Accomplishing Career Transitions Award | American Society of Cell Biology, 2019

• Reviewer's Choice Poster Award for the top 10% abstracts | American Society of Human Genetics (ASHG), 2019 and 2020

• Presidential Award for the top 5% students | National Taiwan University, 2007

Publications

Articles Under Review  

1. 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)

2. 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)

3. 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.

Articles in Peer-Reviewed Journals

4. 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.

5. 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

6. 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)  

7. 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)

8. 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.

9. 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.

10. 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.

11. Peng, P., Samee, M. A. H., & Sinha, S. (2015). Incorporating chromatin accessibility data into sequence-to-expression modeling. Biophysical journal, 108(5), 1257-1267.

12. 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.

Theses

13. 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.

14. Peng, P., Gene Regulatory Network Inference and Complex Phenotype Prediction from Genetical Genomics Data. M.S. Thesis. National Taiwan University, 2013.

Teaching and Mentoring Experiences

Guest Lecturer

• BMS 510 Human Genetics and Genomics | Cedars-Sinai Medical Center, 2019 and 2021

• QBIO 401 Introduction to Computational Analysis of Biological Data | University of Southern California, 2020

Teaching Assistant

• Computational Genomics Course | UIUC and Mayo Clinic, 2015-2017

• CS 466 Introduction to Bioinformatics | UIUC, 2016

• CSIE 1212 Data Structure and Algorithm | NTU, 2012

• CSIE 2136 Algorithm Design and Analysis | NTU, 2011 

Mentor

• Biomedical Science PhD program | Cedars-Sinai Medical Center, 2019-present

• Innovative Programs to Enhance Research Training | American Society of Cell Biology, 2019

• Passionate on Parallel Research Experience for Undergraduates (REU) | UIUC, 2014

Contributions to Diversity, Equity, and Inclusion

• Reviewer | Annual Biomedical Research Conference for Minority Students, 2019-2022

• Reviewer | Grace Hopper Celebration of Women in Computing, 2019 and 2021

• Presenter | Cedars-Sinai Community Research Day, 2019

• Presenter | Boston-Taiwan Symposium for Biotechnology, 2015

• Organizer | UIUC Women in CS professional development symposium, 2014

• Members of diversity programs, including UIUC Women in CS, UIUC Graduate Student Society of Women Engineers, and Cedars-Sinai Women in Medicine.