Education
- MS, Medicinal Chemistry, Peking University, China, 2013-2015
- BS, Pharmeceutical Sciences, Peking University, China, 2009-2013
Research Summary
My research interest is to develop computational strategies that combined with experimental methods in a system level, which aims to infer complex disease mechanisms, facilitate drug discovery and promote precision medicine. I am now working on Quantitative Systems Pharmacology method developments and applications, including:
Prediction of large-scale drug-target interactions, protein-protein interactions using Matrix Factorization methods
Development of a web server(QuartataWeb) for drug discovery by integrating drug-target interaction prediction
and pathway enrichment analysis
Quantitative systems analysis on Huntington's Disease, Drug Abuse and Non-Alcoholic Fatty Liver Disease (NAFLD)
Research and Projects
Development of QuartataWeb, an integrated chemical-protein-pathway mapping for polypharmacology and chemogenomics.
Quantitative Systems Pharmacological Analysis of Drugs of Abuse. (Publication)
Connecting Neuronal Cell Protective Pathways and Drug Combinations in a Huntington's Disease Model through the Application of Quantitative Systems Pharmacology. (Publication)
Identification of differentially connected genes (DCGs) through network analysis on Breast Cancer. (Report)
An Expectation-Maximization Based Machine Learning Strategy to Predict Recurrence Time of Breast Cancer. (Reprot)
Publications
Shi, Q., Pei, F., Perimutter, D., Liu, B., Bahar, I. (2020) Mechanisms of Action of Autophagy Modulators Dissected by Quantitative Systems Pharmacology Analysis. International Journal of Molecular Sciences, 21(8), 2855, https://doi.org/10.3390/ijms21082855
Li, H., Pei, F. (co-first), Taylor, D.L., Bahar, I. (2020) QuartataWeb: an integrated chemical-protein interaction prediction and pathway inference server for polyphamalogical and chemoge-nomics analysis. Bioinformatics, btaa210, doi.org/10.1093/bioinformatics/btaa210
Wang, H., Pei, F., Vanyukov, M.M., Bahar, I. Wu, W., Xing, P.E., (2019) Coupled Mixed Model for Joint Genetic Analysis of Complex Disorders with Two Independently Collected Data Sets. Bioinformatics (submitted)
Taylor, D.L., Gough, A., Schurdak, M.E., Vernetti, L., Chennubhotla, C.S., Lefever, D.,
Pei, F., Faeder,J.R., Lezon,T.R., Stern, A.M., Bahar, I. (2019) Harnessing Human Microphysiology Systems as Key Experimental Models for Quantitative Systems Pharmacology. In: . Handbook of Experimental Pharmacology. Springer, Berlin, Heidelberg,
doi.org/10.1007/164_2019_239
Pei, F., Li, H., Liu, B. and Bahar, I. (2019) Quantitative systems pharmacological analysis of drugs of abuse reveals the pleiotropy of their targets and the effector role of mTORC1. Frontiers in pharmacology, 10, 1-16,
doi: 10.3389/fphar.2019.00191
Zhang, D., He, D., Zou, N., Zhou, X. and Pei, F. (2018) Automatic Relationship Verification in Online Medical Knowledge Base: a Large Scale Study in SemMedDB. 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 1673-1680,
doi:10.1109/BIBM.2018.8621316
Schurdak, M.E., Pei, F., Lezon, T.R., Carlisle, D., Friedlander, R., Taylor, D.L. and Stern, A.M. (2018) A Quantitative Systems Pharmacology Approach to Infer Pathways Involved in Complex Disease Phenotypes. Methods in molecular biology (Clifton, N.J.), 1787, 207-222, doi:10.1007/978-1-4939-7847-2_16
Zhang, K., Sun, W., Huang, L., Zhu, K., Pei, F., Zhu, L., Wang, Q., Lu, Y., Zhang, H., Jin, H. et al. (2017) Identifying GAPDH as a Cyclic Adenosine Diphosphoribose (cADPR) Binding Protein by Pho-toaffinity Protein-Ligand Labeling Approach. Journal of the American Chemical Society, 139, 156-170, doi:10.1021/jacs.6b08088
Pei F., Li, H., Henderson, M.J., Titus, S.A., Jadhav, A., Simeonov, A., Cobanoglu, M.C., Mousavi, S.H., Shun, T., McDermott, L. et al. (2017) Connecting Neuronal Cell Protective Pathways and Drug Combinations in a Huntington's Disease Model through the Application of Quantitative Systems Pharmacology. Scientific Reports, 2017. 7(1): p. 17803, doi:10.1038/s41598-017-17378-y
Imincan, G., Pei, F., Yu, L., Jin, H., Zhang, L., Yang, X., Zhang, L. and Tang, X. (2016),Microenvironmental effect of 2’–O–(1–Pyrenylmethyl) uridine modified fluorescent oligonucleotide probes on sensitive and selective detection of target RNA. Anal. Chem., 88 (8), pp 4448-4455, doi: 10.1021/acs.analchem.6b00227
Pei F., Jin, H., Zhou, X., Xia, J., Sun, L., Liu, Z. and Zhang, L. (2015), Enrichment assessment of multiple virtual screening strategies for Toll-like receptor 8 agonists based on a maximal unbiased benchmarking data set. Chemical biology & drug design, 86, 1226-1241, doi: 10.1111/cbdd.12590
Li, J., Pei, F., Zhu, W., Jin, H., Zhao, Y., Zhang, L., Lee, H. and Zhang, L. (2015), Investigation of the effect of 2’–substitution of NMN analogues on CD38 NADase activity. Journal of Chinese Pharmaceutical Sciences, 24, 514-523, doi:10.5246/jcps.2015.08.065
Cao, Y., Zhang, Y., Wu, S., Yang, Q., Sun, X., Zhao, J., Pei, F., Guo, Y., Tian, C., Zhang, Z. et al. (2015), Synthesis and biological evaluation of pyridinone analogues as novel potent HIV-1 NNRTIs, Bioorganic & medicinal chemistry, 23, 149-159, doi:10.1016/j.bmc.2014.11.012
Wu, L., Pei, F., Zhang, J., Wu, J., Feng, M., Wang, Y., Jin, H., Zhang, L. and Tang, X. (2014), Synthesis of Site Specifically Phosphate-Caged siRNAs and Evaluation of Their RNAi Activity and Stability. Chemistry (Weinheim an der Bergstrasse, Germany), 20, 12114-12122, doi: 10.1002/chem.201403430
Conferences
Oral Talk, the eighth Annual Winter Q-Bio Conference, 2020, Hawaii, USA
Poster, the sixth Cold Spring Harbor Laboratory Meeting on Network Biology, 2019, NY, USA
Poster, the eighth International Symposium for Chinese Medicinal Chemists (ISCMC-8) & the ninth IUPAC International Symposium on Biomolecular Chemistry (ISBOC-9), 2012, Beijing, China
Teaching Experience
Sep.2016-Dec.2016, Teaching Assistant, Computational Structural Biology course, University of Pittsburgh, PA, USA
Oct.2013-Nov.2013, Teaching Assistant, Medicinal Chemistry course, Peking University, Beijing, China
Skills
Research: Quantitative systems biology, Drug discovery, Bioinformatics, Data Science
Skills: Machine Learning, Statistical Analysis, Big Data Analysis, Data Mining, Data structures, Algorithms, Network Analysis, Molecular Docking, Pharmacophore Modeling, Similarity Search, QSAR Analysis
Coding: Python (Proficient), R, MATLAB, SQL, Scala
