Kai Wang, PhD
Professor of Pathology and Laboratory MedicinePerelman 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 (https://wglab.org). 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/POD5 files to biological insights. Some examples of computational tools include ANNOVAR, InterVar, CancerVar, Phenolyzer, Phen2Gene and PhenoSV. These approaches enhance the interpretation of sequencing data by uncovering functional content and providing clinically relevant insights.
Furthermore, we are developing genomic assays and methods to analyze long-read data, such as those generated from PacBio and Oxford Nanopore sequencing. These methods aid in identifying causal genetic variants in cases that elude diagnosis by traditional whole genome or exome sequencing and enable the detection of aberrant DNA and RNA methylation patterns. Some examples of computational tools include RepeatHMM, LinkedSV, ContextSV, NanoRepeat, LIQA, DeepMod and DeepMod2.
Finally, we are developing Artificial Intelligence (AI) and Machine Learning (ML) approaches to correlate genotype with phenotype, and to better understand the phenotypic heterogeneity of inherited diseases. We believe that multimodal AI holds the potential to transform our understanding of biology and medicine—what remains is to develop the right algorithms to fully harness its power. Some examples of computational tools include EHR-Phenolyzer, PhenoGPT, MutFormer and GestaltMML.
Itmat Expertise
Development and application of genomic approaches to study the genetic basis of human diseases.
Education
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
Trainee Research Award Semi-finalist, American Society of Human Genetics, 2009
Top 10 Medical Breakthroughs, Time Magazine, 2009
WCPG 2009 Travel Award, International Society of Psychiatric Genetics, 2009
Best Paper Award, International Conference on Intelligent Biology and Medicine, 2018
Distinguished Service Award, International Association for Intelligent Biology and Medicine, 2019
Penn Undergraduate Research Mentorship Award, 2020-2020
Penn Undergraduate Research Mentorship Award, 2022-2022
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
Medical Research Council (MRC), UK, 2013 - 2015
The Government of the Hong Kong SAR-Health and Medical Research Fund (HMRF), 2013 - 2013
American Cancer Society - Institutional Research Grant (ACS-IRG), 2013 - 2015
The National Science Centre Poland, 2014 - 2014
USC Chinese Student Career Assistant Group, 2014 - 2016
National Institute of Health (NIH) GCAT Study Section, 2014 - 2014
A*STAR Singapore, 2014 - 2014
Wellcome Trust UK, 2015 - 2015
Association of Chinese Geneticists in America, 2015 - Present
School of Biomedical Sciences, University of Hong Kong, Hong Kong, 2015 - 2015
Genome British Columbia, 2015 - 2015
Cancer Research UK, 2017 - 2017
Department of Biochemistry and Microbiology, Rhodes University, South Africa, 2017 - 2017
University of Southern California, 2017 - 2017
University of South Florida, 2017 - 2017
Simons Foundation, 2018 - 2018
CHOP Roberts Collaborative Forefront Application, 2018 - 2018
NIH Kids First Special Emphasis Panel ZHG1 HGR-T, 2018 - 2018
CHOP K-readiness Grant Application, 2018 - Present
Israeli Ministry of Science & Technology, Israel, 2018 - 2018
International Association for Intelligent Biology and Medicine, 2018 - Present
Fudan-Zhongzhi Science Award, 2019 - 2019
VITAL Somatic Working Group, Association for Molecular Pathology, 2019 - Present
Association for Molecular Pathology, 2019 - Present
University of Manitoba, 2019 - 2019
International Association for Intelligent Biology and Medicine, 2019 - Present
NIH BILDS Study Section, 2019 - 2019
NIH BCHI Study Section, 2020 - 2020
Peking University, 2020 - 2020
CHOP Cell and Gene Therapy Grant, 2020 - Present
NIH GCAT Study Section, 2020 - 2020
CHOP Junior Faculty Pilot Grant panel, 2020 - Present
University of Chicago, 2020 - 2020
European Science Foundation, 2020 - 2020
IDDRC New Program Development, 2020 - Present
NIH New Innovator Awards panel, 2020 - 2020
Medical Research Council (MRC), UK, 2020 - 2020
NIH Genes Genomes and Genetics SEP, 2021 - Present
Tsinghua University, 2021 - 2021
NIH BILDS Study Section, 2021 - Present
NIH Transformative Research Awards panel, 2021 - Present
Mount Sinai School of Medicine, 2022 - 2022
Yale University, 2022 - Present
CHOP next-generation sequencing grant, 2022 - Present
Association for Molecular Pathology (AMP) ISV Working group, 2022 - Present
Mayo Clinic, 2022 - Present
CHOP Add-An-Aim Thematic Accelerator Grant Program, 2022 - Present
CHOP Omics Maximizing Grant, 2022 - Present
NIH ZRG1 HSS-Z Special Emphasis Panel, 2023 - Present
NIH CDMA study section, 2023 - Present
University of Michigan, 2023 - Present
University of Virginia, 2023 - Present
NIH ZRG1 HSS-N (90) study section, 2024 - Present
Web Links
Selected Publications
A signal processing and deep learning framework for methylation detection using Oxford Nanopore sequencing
Ahsan MU, Gouru A, Chan J, Zhou W, Wang K., Nat Commun 15(): 1448, 2024, PMID:38365920
KOLF2.1J iPSCs carry CNVs associated with neurodevelopmental disorders
Gracia-Diaz C, Perdomo JE, Khan ME, Roule T, Disanza BL, Cajka GG, Lei S, Gagne AL, Maguire JA, Shalem O, Bhoj EJ, Ahrens-Nicklas RC, French DL, Goldberg EM, Wang K, Glessner JT, Akizu N., Cell Stem Cell 31(): 288-289, 2024, PMID:38458176
Deciphering "the language of nature": A transformer-based language model for deleterious mutations in proteins
Jiang TT, Fang L, Wang K., Innovation (Camb) 4(): 100487, 2023, PMID:37636282
Enhancing phenotype recognition in clinical notes using large language models: PhenoBCBERT and PhenoGPT
Yang J, Liu C, Deng W, Wu D, Weng C, Zhou Y, Wang K., Patterns (N Y) 5(): 100887, 2023, PMID:38264716
PhenoSV: interpretable phenotype-aware model for the prioritization of genes affected by structural variants
Xu Z, Li Q, Marchionni L, Wang K., Nat Commun 14(): 7805, 2023, PMID:38016949
Haplotyping SNPs for allele-specific gene editing of the expanded huntingtin allele using long-read sequencing
Fang L, Monteys AM, Dürr A, Keiser M, Cheng C, Harapanahalli A, Gonzalez-Alegre P, Davidson BL, Wang K., HGG Adv 4(): 100146, 2022, PMID:36262216
DeepRepeat: direct quantification of short tandem repeats on signal data from nanopore sequencing
Fang L, Liu Q, Monteys AM, Gonzalez-Alegre P, Davidson BL, Wang K, Genome Biol 23(1): 108, 2022, PMID:35484600
LIQA: Long-read Isoform Quantification and Analysis
Hu Y, Fang L, Chen X, Zhong JF, Li M, Wang K, Genome Biol 22(): 182, 2021, PMID:34140043
NanoCaller for accurate detection of SNPs and indels in difficult-to-map regions from long-read sequencing by haplotype-aware deep neural networks
Ahsan U, Liu Q, Fang L, Wang K, Genome Biol 22(1): 261, 2021, PMID:34488830
PhenCards: a data resource linking human phenotype information to biomedical knowledge
Havrilla JM, Liu C, Dong X, Weng C, Wang K, Genome Med 13(1): 91, 2021, PMID:34034817
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
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
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
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
