Yi Xing, Ph.D.

faculty photo
Professor of Pathology and Laboratory Medicine
Director, Center for Computational and Genomic Medicine Children's Hospital of Philadelphia
Department: Pathology and Laboratory Medicine

Contact information
Children's Hospital of Philadelphia
9054 Colket Translational Research Bldg.
3501 Civic Center Blvd.
Philadelphia, PA 19104
Office: 215-590-0280
Ph.D. (Molecular Biology, Bioinformatics)
University of California Los Angeles, 2006.
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Description of Research Expertise

Research Interests
Our lab is broadly interested in the computational biology and genomics of RNA processing and regulation, as well as their applications to human genetics, precision medicine, and cancer immunotherapy.

Description of Research
Mammalian cells generate astonishing regulatory diversity and complex phenotypes from a surprisingly small set of genes. We now know that considerable diversity is achieved by alternative processing and modifications of RNA. The long-term goal of our research is to elucidate alternative isoform complexity in mammalian transcriptomes and proteomes, and to understand how it is generated and its role in the regulation and function of complex genomes. We develop computational methods and genomic technologies for studying transcriptomic and proteomic complexity in bulk tissues and single cells (Science Advances, 2023; Nature Communications, 2021; AJHG 2020a; Nature Methods, 2019; AJHG, 2019; Genome Biology, 2017; Nature Communications, 2016; Nature Methods, 2016; PNAS, 2014; Genome Biology, 2013). We also integrate computational and genomic tools to elucidate RNA regulatory networks in health and disease (TIPS, 2021; Genome Biology, 2021; AJHG 2020b; PNAS 2020; AJHG, 2018; Genome Biology, 2016; Cell Reports, 2016; Elife, 2015; Cell Stem Cell, 2014; Molecular Cell, 2014; Neuron, 2014).

Active research topics include but are not limited to: computational methods for transcriptome analysis using short-read and long-read sequencing technologies; genomic technologies and computational methods for analyzing RNA processing and modifications using low-input or single-cell samples; studies of RNA regulatory networks in health and disease using large-scale RNA-seq data and protein-RNA interaction maps; genetic variation and evolution of transcriptome regulation and RNA processing; clinical RNA-seq technologies for disease diagnosis or early detection; multi-omic and clinical data integration for precision oncology and cancer immunotherapy.

PI Biography
Dr. Yi Xing is the Francis West Lewis Endowed Chair and Founding Director of the Center for Computational and Genomic Medicine, as well as the Executive Director of the Department of Biomedical and Health Informatics at the Children’s Hospital of Philadelphia (CHOP). Dr. Xing is also a Professor of Pathology and Laboratory Medicine at the University of Pennsylvania (Penn). Dr. Xing has an extensive publication record in bioinformatics, genomics, and RNA biology. His current research merges the fields of computational biology, biomedical data science, RNA genomics, human genetics, precision medicine, and immuno-oncology.

Selected Publications

Gao Y, Wang F, Wang R, Kutschera E, Xu Y, Xie S, Wang Y, Kadash-Edmondson KE, Lin L, Xing Y.: ESPRESSO: Robust discovery and quantification of transcript isoforms from error-prone long-read RNA-seq data. Sci Adv 9: eabq5072, Jan 2023.

Pan Y, Kadash-Edmondson KE, Wang R, Phillips J, Liu S, Ribas A, Aplenc R, Witte ON, Xing Y.: RNA Dysregulation: An Expanding Source of Cancer Immunotherapy Targets. Trends Pharmacol Sci 2021.

Xin R, Gao Y, Gao Y, Wang R, Kadash-Edmondson KE, Liu B, Wang Y, Lin L, Xing Y.: isoCirc catalogs full-length circular RNA isoforms in human transcriptomes. Nat Commun 12: 266, Jan 2021.

Phillips John W, Pan Yang, Tsai Brandon L, Xie Zhijie, Demirdjian Levon, Xiao Wen, Yang Harry T, Zhang Yida, Lin Chia Ho, Cheng Donghui, Hu Qiang, Liu Song, Black Douglas L, Witte Owen N, Xing Yi: Pathway-guided analysis identifies Myc-dependent alternative pre-mRNA splicing in aggressive prostate cancers. Proceedings of the National Academy of Sciences of the United States of America 117(10): 5269-5279, Mar 2020.

Zhang Zijun, Pan Zhicheng, Ying Yi, Xie Zhijie, Adhikari Samir, Phillips John, Carstens Russ P, Black Douglas L, Wu Yingnian, Xing Yi: Deep-learning augmented RNA-seq analysis of transcript splicing. Nat Methods 16(4): 307-310, April 2019.

Park E, Pan Z, Zhang Z, Lin L, Xing Y: The expanding landscape of alternative splicing variation in human populations. Am J Hum Genet 102(1): 11-26, January 2018.

Molinie B*, Wang J*, Lim KS, Hillebrand R, Lu ZX, Wittenberghe NV, Howard BD, Daneshvar K, Mullen AC, Dedon P, Xing Y*, Giallourakis CC*: m(6)A-LAIC-seq reveals the census and complexity of the m(6)A epitranscriptome. Nat Methods 13(8): 692-698, August 2016 Notes: *Joint corresponding authors Highlighted by: Shi H. & He C. (2016) A glance at N6-methyladenosine in transcript isoforms. Nature Methods. 13:624–625.

Shen S, Park JW, Lu ZX, Lin L, Henry MD, Wu YN, Zhou Q, Xing Y: rMATS: robust and flexible detection of differential alternative splicing from replicate RNA-Seq data. Proc Natl Acad Sci USA 111(51): E5593-E5601, December 2014 Notes: Software received 135,000+ downloads since release (https://github.com/Xinglab/rmats-turbo).

Batista PJ, Molinie B , Wang J, Qu K, Zhang J, Li L, Bouley DM, Lujan E, Haddad B, Daneshvar K, Carter AC, Flynn RA, Zhou C, Lim KS, Dedon P, Wernig M, Mullen AC, Xing Y*, Giallourakis CC*, Chang HY*: m(6)A RNA modification controls cell fate transition in mammalian embryonic stem cells. Cell Stem Cell 15(6): 707-719, December 2014 Notes: *Joint corresponding authors. Editorial by: Jalkanen AL, Wilusz J. (2014) Cell Stem Cell. 15(6):669-70. Editorial by: Stunnenberg HG, Vermeulen M, Atlasi Y. (2015) Science. 347(6222):614-5.

Xing Y, Lee C: Alternative splicing and RNA selection pressure--evolutionary consequences for eukaryotic genomes. Nat Rev Genet 7(7): 499-509, July 2006.

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Last updated: 02/20/2023
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