Yi Xing, Ph.D.

faculty photo
Professor of Pathology and Laboratory Medicine
Department: Pathology and Laboratory Medicine

Contact information
Children's Hospital of Philadelphia
Abramson Pediatric Research Center 816I
3615 Civic Center Blvd
Philadelphia, PA 19104
Office: 215-590-0280
Education:
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 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 (Nature Methods, 2019; American Journal of Human Genetics, 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 (American Journal of Human Genetics, 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 second- and third-generation 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 Director of the Center for Computational and Genomic Medicine at the Children’s Hospital of Philadelphia (CHOP), and Professor of Pathology and Laboratory Medicine at the University of Pennsylvania (Penn). Prior to his appointment at CHOP and Penn, Dr. Xing was a Professor of Microbiology, Immunology, and Molecular Genetics at UCLA, and served as Program Director of UCLA’s Bioinformatics Interdepartmental Ph.D. Program. 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

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.

Bahrami-Samani Emad, Xing Yi: Discovery of Allele-Specific Protein-RNA Interactions in Human Transcriptomes. Am J Hum Genet 104(3): 492-502, March 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, Wang Y, Wang C, Wu YN, Xing Y: SURVIV for survival analysis of mRNA isoform variation. Nat Commun 7: 11548, June 2016 Notes: News story by: GenomeWeb https://www.genomeweb.com/informatics/algorithm-predicts-cancer-survival-transcript-isoform-ratios.

Lin L, Jiang P, Park JW, Wang J, Lu ZX, Lam MP, Ping P, Xing Y: The contribution of Alu exons to the human proteome. Genome Biol 17: 15, January 2016 Notes: Highlighted by: Eisenberg E. (2016) Proteome diversification by genomic parasites. Genome Biology. 17:17.

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 24,000+ downloads since release (http://rnaseq-mats.sourceforge.net/).

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.

Shen S, Lin L, Cai JJ, Jiang P, Kenkel EJ, Stoik MR, Sato S, Davidson BL, Xing Y: Widespread establishment and regulatory impact of Alu exons in human genes. Proc Natl Acad Sci USA 108(7): 2837-2842, February 2011 Notes: Highlighted by: NIH “Biomedical Beat” News Digest (http://publications.nigms.nih.gov/biobeat/11-03-16/index.html#3)

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: 03/31/2019
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