Kai Wang, Ph.D.

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Associate Professor of Pathology and Laboratory Medicine
Department: Pathology and Laboratory Medicine

Contact information
3501 Civic Center Blvd, CTRB 5004
Children's Hospital of Philadelphia
Philadelphia, PA 19104
Office: 2674259573
Fax: 2155903660
B.S. (Biochemistry & Molecular Biology)
Peking University, 2000.
M.S. (Tumor Biology)
Mayo Clinic, 2002.
Ph.D. (Microbiology & Computational Biology)
University of Washington, 2005.
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Description of Research Expertise

The research in our laboratory focuses on the development of bioinformatics methods to improve our understanding of the genetic basis of human diseases, and the integration of electronic health records and genomic information to facilitate genomic medicine on scale. Current projects include the development of computational tools to call structural variants and DNA modifications from long-read sequencing data, the identification/prioritization of disease-relevant genetic mutations, the use of deep neural network to predict prognosis and optimize therapy for patients with cancer, the application of systems biology approaches on single-cell gene expression data, and the data mining on electronic health records to predict genetic syndromes and causal genes.

Selected Publications

Doostparast Torshizi A, Armoskus C, Zhang H, Forrest MP, Zhang S, Souaiaia T, Evgrafov OV, Knowles JA, Duan J*, Wang K*: Deconvolution of Transcriptional Networks Identified TCF4 as a Master Regulator in Schizophrenia. Sci Adv 5(9): eaau4139, September 2019.

He MM, Li Q, Yan M, Cao H, Hu Y, He KY, Cao K, Li MM, Wang K: Variant Interpretation for Cancer (VIC): a computational tool for assessing clinical impacts of somatic variants. Genome Med 11(1): 53, August 2019 Notes: doi: 10.1186/s13073-019-0664-4.

Borgmann-Winter KE, Wang K, Bandyopadhyay S, Doostparast Torshizi A, Blair I, Hahn CY: The proteome and its dynamics: A missing piece for integrative multi-omics in schizophrenia. Schizophrenia Research in press(pii): S0920-9964(19)30303-2, August 2019 Notes: doi: 10.1016/j.schres.2019.07.025.

Liu, Fabricio K, Li Z, Ta C, Wang K*, Weng C*: Doc2Hpo: a web application for efficient and accurate HPO concept curation. Nucleic Acids Res 47(W1): W566-W570, July 2019 Notes: doi: 10.1093/nar/gkz386. *: Co-corresponding author.

Liu Q, Fang L, Yu G, Wang D, Xiao CL, Wang K: Detection of DNA base modifications by deep recurrent neural network on Oxford Nanopore sequencing data. Nat Commun 10(1): 2449, June 2019 Notes: doi: 10.1038/s41467-019-10168-2.

Xie G, Dong C, Kong Y, Zhong JF, Li M, Wang K : GDP: Group lasso regularized Deep learning for cancer Prognosis from multi-omics and clinical features. Genes 10(3): 240, March 2019 Notes: https://doi.org/10.3390/genes10030240.

Georgieva D, Liu Q, Wang K, Egli D: Detection of Base Analogs Incorporated During DNA Replication by Nanopore Sequencing. bioRxiv Feb 2019 Notes: doi: https://doi.org/10.1101/549220.

Fang L, Kao C, Gonzalez MV, Mafra FA, Pellegrino R, Li M, Wenzel S, Wimmer K, Hakonarson H, Wang K: LinkedSV for detection of mosaic structural variants from linked-read exome and genome sequencing data. bioRxiv in press, 2019 Notes: doi: https://doi.org/10.1101/409789.

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*: Long-read sequencing identified intronic repeat expansions in SAMD12 from Chinese pedigrees affected with familial cortical myoclonic tremor with epilepsy. J Med Genet 56(4): 265-270, April 2019 Notes: doi: 10.1136/jmedgenet-2018-105484; *: co-corresponding author.

Dai Y, Li P, Wang Z, Liang F, Yang F, Fang L, Huang Y, Huang S, Zhou J, Wang D, Cui L, Wang K: Single-molecule optical mapping enables quantitative measurement of D4Z4 repeats in facioscapulohumeral muscular dystrophy (FSHD). J Med Genet pii: jmedgenet-2019-106078, September 2019 Notes: doi: 10.1136/jmedgenet-2019-106078.

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*: N6-methyladenine DNA modification in human genome. Mol Cell 71(2): 306-318, July 2018 Notes: doi: 10.1016/j.molcel.2018.06.015; *: Co-corresponding author.

He Z, Liu L, Wang K, Ionita-Laza I: A semi-supervised approach for predicting cell-type specific functional consequences of non-coding variation using MPRAs. Nat Commun 9(1): 5199, Dec 2018.

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*: Deep phenotyping on electronic health records facilitates genetic diagnosis by clinical exomes. Am J Hum Genet 103(1): 58-73, July 2018 Notes: doi: 10.1016/j.ajhg.2018.05.010; *: co-corresponding author.

Doostparast Torshizi A, Wang K: Next Generation Sequencing in Drug Development: Target Identification and Genetically Stratified Clinical Trials. Drug Discovery Today 23(10): 1776-1783, Oct 2018 Notes: doi: 10.1016/j.drudis.2018.05.015.

Li J, Zhang W, Yang H, Howrigan DP, Wilkinson B, Souaiaia T, Evgrafov OV, Genovese G, Clementel VA, Tudor JC, Abel T, Knowles JA, Neale BM, Wang K, Sun F, Coba MP: Spatiotemporal profile of postsynaptic interactomes integrates components of complex brain disorders. Nat Neurosci 20(8): 1150-1161, Aug 2017 Notes: doi:10.1038/nn.4594.

Li Q, Wang K: InterVar: Clinical interpretation of genetic variants by the 2015 ACMG-AMP guidelines. Am J Hum Genet 100(2): 267-280, Feb 2017.

Li Q, Zhang P, Wang D, Gu W, Wang K: Interrogating the "unsequenceable" genomic trinucleotide repeat disorders by long-read sequencing. Genome Med 9(1): 65, Jul 2017 Notes: doi: 10.1186/s13073-017-0456-7.

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Last updated: 09/13/2019
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