Kai Wang, PhD

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

Contact Information3501 Civic Center Blvd, CTRB 5004
Children's Hospital of Philadelphia
Philadelphia, PA, 19104
Office: 267-425-9573
Fax: 215-590-3660

Research Expertise

The research in our laboratory aims to develop novel genomics and bioinformatics methods to improve the diagnosis, treatment, and prognosis of rare diseases, to ultimately facilitate the implementation genomic medicine on scale. A detailed description of our research and rotation projects can be found on our lab website ( In summary, our research can be divided into several areas.

First, we are developing analytical pipelines for whole genome and whole exome sequencing data, all the way from FASTQ/FAST5 files to biological insights. Some examples of computational tools used in the lab include SeqMule, ANNOVAR, Phenolyzer, SeqHBase, and InterVar. These approaches facilitate a better understanding of the functional content and clinical insights from sequencing data.

Furthermore, we are also developing genomic assays and methods to analyze long-read data, such as those generated from linked-read sequencing, optical mapping, PacBio, and Nanopore long-read sequencing. These methods help identify causal genetic variants on cases that failed to be diagnosed by traditional whole genome/exome sequencing approaches, and help map aberrant DNA modifications such as methylations in tissues from patients in comparison to controls. Some examples of computational tools developed by our lab include RepeatHMM, NextSV, LongSV, LinkedSV, NanoMod, and DeepMod.

Finally, we are developing data mining approaches from clinical phenotypic information in Electronic Health Records (EHR) to correlate genotype and phenotype together, and better understand the phenotypic heterogeneity of inherited diseases. Some examples of computational tools that we developed include EHR-Phenolyzer, SparkText, Doc2HPO, and Phen2Gene, which use natural language processing on clinical notes to predict possible genetic syndromes and candidate genes.

Itmat Expertise

Development and application of genomic approaches to study the genetic basis of human diseases.


B.S. (Biochemistry & Molecular Biology), Peking University, 2000
M.S. (Tumor Biology), Mayo Clinic, 2002
Ph.D. (Microbiology & Computational Biology), University of Washington, 2005

Specialty Certification

Postgraduate Training

Postdoctoral Fellow, University of Pennsylvania, 2006-2008
Postdoctoral Fellow, The Children's Hospital of Philadelphia, 2008-2010

Awards and Honors

ISMB 2005 Travel Fellowship, International Society of Computational Biology, 2005
Alavi-Dabiri Postdoctoral Award, Mental Retardation and Developmental Disability Research Center, The Children's Hospital of Philadelphia, 2008
WCPG 2009 Travel Award, International Society of Psychiatric Genetics, 2009
Trainee Research Award Semi-finalist, American Society of Human Genetics, 2009
Top 10 Medical Breakthroughs, Time Magazine, 2009
Distinguished Service Award, International Association for Intelligent Biology and Medicine, 2019

Memberships and Professional Organizations

International Society of Computational Biology, 2005 - Present
American Society of Human Genetics, 2006 - Present
Netherlands Organization for Scientific Research, 2010 - 2010
Ontario Research Fund - Research Excellence (ORF-RE), 2011 - 2011
SC-CTSI Pilot Award, 2012 - 2013
American Cancer Society - Institutional Research Grant (ACS-IRG), 2013 - 2015
Medical Research Council (MRC), UK, 2013 - 2015
The Government of the Hong Kong SAR-Health and Medical Research Fund (HMRF), 2013 - 2013
A*STAR Singapore, 2014 - 2014
USC Chinese Student Career Assistant Group, 2014 - 2016
National Institute of Health (NIH) GCAT Study Section, 2014 - 2014
The National Science Centre Poland, 2014 - 2014
School of Biomedical Sciences, University of Hong Kong, Hong Kong, 2015 - 2015
Association of Chinese Geneticists in America, 2015 - Present
Genome British Columbia, 2015 - 2015
Wellcome Trust UK, 2015 - 2015
University of South Florida, 2017 - Present
Department of Biochemistry and Microbiology, Rhodes University, South Africa, 2017 - 2017
University of Southern California, 2017 - Present
Cancer Research UK, 2017 - 2017
NIH Kids First Special Emphasis Panel ZHG1 HGR-T, 2018 - 2018
Israeli Ministry of Science & Technology, Israel, 2018 - 2018
Roberts Collaborative Forefront Application, CHOP, 2018 - 2018
International Association for Intelligent Biology and Medicine, 2018 - Present
K-readiness Grant Application, CHOP, 2018 - Present
Simons Foundation, 2018 - 2018
Fudan-Zhongzhi Science Award, 2019 - 2019
NIH BILDS Study Section, 2019 - 2019
VITAL Somatic Working Group, Association for Molecular Pathology, 2019 - Present
University of Manitoba, 2019 - Present
International Association for Intelligent Biology and Medicine, 2019 - Present
Association for Molecular Pathology, 2019 - Present
IDDRC New Program Development, 2020 - Present
Peking University, 2020 - Present
Medical Research Council (MRC), UK, 2020 - Present
CHOP Cell and Gene Therapy Grant, 2020 - Present
NIH GCAT Study Section, 2020 - Present
NIH BCHI Study Section, 2020 - Present
European Science Foundation, 2020 - Present
University of Chicago, 2020 - Present
NIH New Innovator Awards panel, 2020 - Present
CHOP Junior Faculty Pilot Grant panel, 2020 - Present
NIH Transformative Research Awards panel, 2021 - Present
NIH Genes Genomes and Genetics SEP, 2021 - Present

Web Links

Selected Publications

Detection of Base Analogs Incorporated During DNA Replication by Nanopore Sequencing

Georgieva D, Liu Q, Wang K*, Egli D*, Nucleic Acids Res 48(15): e88, 2020, PMID:32710620

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Variant Interpretation for Cancer (VIC): a computational tool for assessing clinical impacts of somatic variants

He MM, Li Q, Yan M, Cao H, Hu Y, He KY, Cao K, Li MM, Wang K, Genome Med 11(1): 53, 2019, PMID:31443733

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Doc2Hpo: a web application for efficient and accurate HPO concept curation

Liu C, Fabricio K, Li Z, Ta C, Wang K*, Weng C*, Nucleic Acids Res 47(W1): W566-W570, 2019, PMID:31106327

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The proteome and its dynamics: A missing piece for integrative multi-omics in schizophrenia

Borgmann-Winter KE, Wang K, Bandyopadhyay S, Doostparast Torshizi A, Blair I, Hahn CY, Schizophr Res 217(): 148-161, 2020, PMID:31416743

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Single-molecule optical mapping enables quantitative measurement of D4Z4 repeats in facioscapulohumeral muscular dystrophy (FSHD)

Dai Y, Li P, Wang Z, Liang F, Yang F, Fang L, Huang Y, Huang S, Zhou J, Wang D, Cui L, Wang K, J Med Genet pii(): jmedgenet-2019-106078, 2019, PMID:31506324

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Detection of DNA base modifications by deep recurrent neural network on Oxford Nanopore sequencing data

Liu Q, Fang L, Yu G, Wang D, Xiao CL, Wang K, Nat Commun 10(1): 2449, 2019, PMID:31164644

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GDP: Group lasso regularized Deep learning for cancer Prognosis from multi-omics and clinical features

Xie G, Dong C, Kong Y, Zhong JF, Li M, Wang K, Genes 10(3): 240, 2019

LinkedSV for detection of mosaic structural variants from linked-read exome and genome sequencing data

Fang L, Kao C, Gonzalez MV, Mafra FA, Pellegrino R, Li M, Wenzel S, Wimmer K, Hakonarson H, Wang K, Nat Commun 10(1): 5585, 2019, PMID:31811119

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Long-read sequencing identified intronic repeat expansions in SAMD12 from Chinese pedigrees affected with familial cortical myoclonic tremor with epilepsy

Zeng S, Zhang MY, Wang XJ, Hu ZM, Li JC, Li N, Wang JL, Liang F, Yang Q, Liu Q, Fang L, Hao JW, Shi FD, Ding XB, Teng JF, Yin XM, Jiang H, Liao WP, Liu JY, Wang K*, Xia K*, Tang BS*, J Med Genet 56(4): 265-270, 2019, PMID:30194086

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Deconvolution of Transcriptional Networks Identified TCF4 as a Master Regulator in Schizophrenia

Doostparast Torshizi A, Armoskus C, Zhang H, Forrest MP, Zhang S, Souaiaia T, Evgrafov OV, Knowles JA, Duan J*, Wang K*, Sci Adv 5(9): eaau4139, 2019

NanoMod: a computational tool to detect DNA modifications using Nanopore long-read sequencing data

Liu Q, Georgieva DC, Egli D, Wang K, BMC Genomics 20(Suppl 1): 78, 2019, PMID:30712508

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Deep phenotyping on electronic health records facilitates genetic diagnosis by clinical exomes

Hoon Son J, Xie G, Yuan C, Ena L, Li Z, Goldstein A, Huang L, Wang L, Shen F, Liu H, Mehl K, Groopman EE, Marasa M, Kiryluk K, Gharavi AG, Chung WK, Hripcsak G, Friedman C, Weng C*, Wang K*, Am J Hum Genet 103(1): 58-73, 2018, PMID:29961570

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N6-methyladenine DNA modification in human genome

Xiao CL, Zhu S, He M, Chen D, Zhang Q, Chen Y, Yu GL, Liu J, Xie SQ, Luo F, Liang Z, Wang DP, Bo XC, Gu X-F*, Wang K*, Yan GR*, Mol Cell 71(2): 306-318, 2018, PMID:30017583

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Next Generation Sequencing in Drug Development: Target Identification and Genetically Stratified Clinical Trials

Doostparast Torshizi A, Wang K, Drug Discovery Today 23(10): 1776-1783, 2018, PMID:29758342

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