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Hi, I am Pei-Chen Peng. I am a postdoctoral scientist at Cedars-Sinai Medical Center, working with Dr. Simon Gayther in the Center for Bioinformatics and Functional Genomics. My research interest lies in computational genomics. I use statistical and machine learning methods, to analyze large-scale omics data. My work focuses specifically on understanding gene regulation in cancer development.

I obtained my Ph.D. in Computer Science from University of Illinois at Urbana-Champaign (UIUC) in 2018, advised by Prof. Saurabh Sinha. I hold a M.S. and a B.S. in Computer Science from National Taiwan University in 2013 and 2011 respectively. I received NIH K99/R00 Pathway to Independence Award and Google Anita Borg Award. I was also recognized as a Rising Star in EECS.

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.

Education

Cedars-Sinai Medical Center, CA, USA | 2019-present
Postdoctoral Scientist in Biomedical Sciences
Mentor: Dr. Simon Gayther

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. (* equal contribution) Under review at Bioinformatics. medRxiv, 2022.09.13.22278911

  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 review at Cell Genomics. (* equal contribution)

  3. Nameki, R., Shetty, A., Dareng, E., ... the Ovarian Cancer Association Consortium,... & Lawrenson, K. (2022). chromMAGMA: regulatory element-centric interrogation of risk variants. bioRxiv, 10.1101/2022.01.21.477270.

  4. Plummer, J., Dezem, F. S., Davis, B., Chen, S., Suo, J.-H., Giambartolomei, C., Peng, P., … & Gayther, S. (2021). Epigenomic and transcriptomic interactions in the neoplastic transformation of fallopian tube epithelial cells into high grade serous ovarian cancer. Under review at Science Advances

  5. DeVries A. A., Dennis J., Tyrer J. P., Peng, P., ... & Jones, M. R. (2021). Copy number variants are ovarian cancer risk alleles at known and novel risk loci. Accepted at Journal of the National Cancer Institute.

Articles in Peer-Reviewed Journals

  1. 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)

  2. 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)

  3. 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.

  4. 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.

  5. 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.

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

  7. 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

  1. 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.

  2. 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, 2019-2021

  • 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.