Wan-Ping Lee, PhD

Research Assistant Professor of Pathology and Laboratory Medicine
Perelman School of Medicine at the University of Pennsylvania

Contact InformationBB03, Richards Medical Research Laboratories
3700 Hamilton Walk
Philadelphia, PA, 19104

Specialty Division


Research Expertise

My group focuses on discovering human genomic variations, especially structural variations such as copy number variations (deletions and duplications), insertions, tandem duplications, inversions, and translocations. They are substantial contributors to genetic diversity and are usually associated with human diseases. We are closely working on the Alzheimer’s Disease genomics data analysis and participating in the Alzheimer’s Disease Sequencing Project (ADSP) and Alzheimer’s Disease Genetics Consortium (ADGC).


B.B.A. (Management Information System), Chung Yuan Christian University, 2001
M.S. (Computer Science and Engineering), National Sun Yat-Sen University, 2004
Ph.D. (Electrical Engineering), National Taiwan University, 2009

Specialty Certification

Postgraduate Training

Postdoctoral associate, Department of Biology, Boston College, 2009-2014

Awards and Honors

1st Place, FPGA Design Contest, Ministry of Education, Taiwan, 2003
2nd Prize, IC/CAD Contest, Ministry of Education, Taiwan, 2005
Honorable Mention, Semiconductor Design and Application Competition, Macronix Education Foundation, 2005
EDA Scholarship for DAC and ICCAD regular papers, and UBooth poster, SpringSoft Education Foundation, 2006
Outstanding Research Award, Graduate Institute of Electronic Engineering, National Taiwan University, Taiwan, 2007
Scholarship for Graduate Students Study Abroad Program, National Science Council, Taiwan, 2007
EDA Scholarship for DAC and ICCAD regular papers, and UBooth poster, SpringSoft Education Foundation, 2007
Honorable Mention, IC/CAD Contest, Ministry of Education, Taiwan, 2007
Honorable Mention, IC/CAD Contest, Ministry of Education, Taiwan, 2008
The 2018 Albert Nelson Marquis Lifetime Achievement, 2018
Merit Award, Jackson Laboratory for Genomic Medicine, 2018
RF1AG074328, NIA/NIH, Copy Number Variation Identification And Association Study On Alzheimer'S Disease Whole Genome Sequencing Data, 2021-2024
P30 AG072979, Penn Alzheimer's Disease Research Center, CNV Identification and Association Study, 2021-2023

Memberships and Professional Organizations

Web Links

Selected Publications

The role of structural variations in Alzheimer’s disease and other neurodegenerative diseases

H. Wang, L.-S. Wang, G. Schellenberg, W.-P. Lee, Frontiers in Aging Neuroscience, 2023

Scalable approach for functional analysis of whole-genome sequencing non-coding variants

P. P. Kuksa, E. Greenfest-Allen, J. Cifello, M. Ionita, H. Wang, H. Nicaretta, P.-L. Cheng, W.-P. Lee, L.-S. Wang, Y. Y. Leung, Human Molecular Genetics, 2022

Polygenic Risk Scores in Alzheimer’s Disease Genetics: Methodology, Applications, Inclusion, and Diversity

Clark K., Leung Y.Y., Lee WP, Voight B., Wang LS, Journal of Alzheimer’s Disease, 2022

Comprehensive analysis of alternative splicing in gastric cancer identifies epithelial-mesenchymal transition subtypes associated with survival

Jun Y, Suh Y, Park S, Lee J, Kim J, Lee S, Lee WP, Olga A, Yang H, Lee C, Cancer Research, 2022, PMID:34903603

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JAX-CNV: A Whole Genome Sequencing-Based Algorithm for Copy Number Detection at Clinical Grade Level

Lee WP, Zhu Q, Yang X, Liu S, Cerveira E, Ryan M, Mil-Homens A, Bellfy L, Lee C, Zhang C, Genomics, Proteomics and Bioinformatics, 2022, PMID:35085778

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SEAGLE: A Scalable Exact Algorithm for Large-Scale Set-based GxE Tests in Biobank Data

Chi JT, Ipsen ICF, Hsiao TH, Wang LS, Lee WP, Lu TP, Tzeng JY, Frontier in Genetics, 2021, PMID:34795690

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Copy Number Variation Identification on 3,800 Alzheimer’s Disease Whole Genome Sequencing Data from the Alzheimer’s Disease Sequencing Project

Lee WP, Tucci A, Conery M, Leung YY, Kuzma A, Valladares O, Chou YF, Lu W, Wang LS, Schellenberg G, Tzeng JY, Frontier in Genetics, 2021, PMID:34804120

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Expectations and blind spots for structural variation detection from long-read assemblies and short-read genome sequencing technologies

Zhao X, Collins R, Lee WP, Weber A, Jun Y, Zhu Q, Weisburd B, Hunag Y, Audano P, Wang H, Walker M, Lowther C, Fu J, Human Genome Structural Variation Consortium, Gerstein M, Devine S, Marschall T, Korbel J, Eichler E, Chaisson M, Lee C, Mills R, Brand H, Talkowski M, The American Journal of Human Genetics (AJHG), 2021, PMID:33789087

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One reference genome is not enough

Yang X, Lee WP, Ye K, Lee C, Genome Biology 20(104): , 2019, PMID:31126314

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Multi-platform discovery of haplotype-resolved structural variation in human genomes.

Chaisson MJP, Sanders AD, Zhao X, ..., Lee WP, ..., Korbel JO, Eichler EE, Lee C, Nature Communicaiton 16(10(1)): 1784, 2019, PMID:30992455

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