Peipei Li, Ph.D.

Peipei Li, Ph.D.
Bioinformatics postdoctoral fellow, Labrie Laboratory


Dr. Peipei Li earned a B.S. in software engineering from Harbin Institute of Technology followed by an M.S. and a Ph.D. in computer science from Chungbuk National University, where her research focused on RNA-Seq analysis, protein structure and interaction. She is an expert in data mining, bioinformatics and several critical programming languages, including JAVA, C++ and R. In 2017, she joined the laboratory of Dr. Viviane Labrie at Van Andel Institute. Her current research focuses on computational analysis of epigenomics in neurodegenerative diseases.


Current research focus

I am working on two projects. First is the discovery of epigenetically misregulated enhancers in Alzheimer’s disease. Specifically, I am performing quality control on methylation data and carrying out correlation analysis between DNA methylation at enhancers and disease factors. Secondly, I am designing a padlock probe library pipeline for probe design and a downstream pipeline for post-sequencing analysis

Education & Training

Postdoctoral fellowship in Database & Bioinformatics Lab, Chungbuk National University, Cheongju, Chungbuk, South Korea (Pr. Keun Ho Ryu)

Ph.D. in computer science, Chungbuk National University, Cheongju, South Korea (Advisor: Pr. Keun Ho Ryu)
Thesis: Systematic comparison analysis of normalization methods for RNA-Seq data

M.S. in computer science, Chungbuk National University, Cheongju, South Korea (Advisor: Pr. Keun Ho Ryu)
Thesis: QSE: A new 3-D solvent exposure measure for the analysis of protein structure

B.S. in software engineering, Harbin Institute of Technology, Harbin, China (Advisor: Pr. Bin Chen)
Thesis: Design and development of Chinese chess game based on symbian 3rd platform

Awards & External Funding

Best paper award of ICISCA 2015

Best paper award of FITAT 2012

Best paper award of FITAT 2011 and DBMI 2011

Outstanding graduate of Shandong Province, China

Excellent Graduate Thesis, 2009



Marshall LL, Killinger BA, Ensink E, Li P, Li KX, Cui W, Lubben N, Weiland M, Wang X, Gordevicius J, Coetzee GA, Ma J, Jovinge S, Labrie V. 2020. Epigenomic analysis of Parkinson’s disease neurons identifies Tet2 loss as neuroprotective. Nat Neuro.

Li P, Ensink E, Lang S, Marshall L, Schilthuis M, Lamp J, Vega I, Labrie V. 2020. Hemispheric asymmetry in the human brain and in Parkinson’s disease is linked to divergent epigenetic patterns in neurons. Genome Biol 21:61.

Li P, Marshall L, Oh G, Jakubowski JL, Groot D, He Y, Wang T, Petronis A, Labrie V. 2019. Epigenetic dysregulation of enhancers in neurons is associated with Alzheimer’s disease pathology and cognitive decline. Nat Comm.

Pai S, Li P, Killinger B, Marshall L, Jia P, Liao J, Petronis A, Szabó P, Labrie V. 2019. Differential methylation of enhancer at IGF2 is associated with abnormal dopamine synthesis in major psychosis. Nat Comm.

Kim YJ*, Li P*, Hong JM, Ryu KH, Nam E, Chang MS.  2017. A single center analysis of the positivity of Hepatitis B antibody after neonatal vaccination program in Korea. J Korean Med Sci 32:e117. Article

Li P, Piao Y, Shon HS, Ryu KH. 2015. Comparing the normalization methods for the differential analysis of Illumina high-throughput RNA-Seq data. BMC Bioinformatics 16:347.  Article

Li P, Pok G, Jong KS, Shon HS, Ryu KH. 2011. QSE: A new 3D solvent exposure measure for the analysis of protein structure. Proteomics 11(19):3793–3801.  PubMed