Xinshu Grace Xiao
Professor
Director of Bioinformatics Interdepartmental Ph.D. Program
Maria Rowena Endowed Chair in Biological Sciences
Office: 2000E TLSB
Phone: (310) 206-6522
Website: https://www.xiao-lab.org/
Biography
Dr. Xinshu (Grace) Xiao received her B.S. degree at Tsinghua University, Beijing, China. She then went to the Massachusetts Institute of Technology (MIT) for graduate studies. After receiving her Ph.D degree in the Division of Health Sciences and Technology (HST), a joint program by MIT and Harvard Medical School, Dr. Xiao continued at MIT for postdoctoral training in the Department of Biology. In 2008, Dr. Xiao joined the faculty at the University of California, Los Angeles. She is now the Maria R. Ross Endowed Professor of the Department of Integrative Biology and Physiology. She also serves as the Director of the Bioinformatics Interdepartmental Program.
Research Interests
Research in the Xiao lab aims to better understand transcriptome complexity in health and disease. A major surprise resulted from the Human Genome Project was that humans, even though as an apparently much complex organism with 100 trillion cells, have only 25,000 to 30,000 genes. In contrast, the roundworm, an organism with 960 cells, has ~19,000 genes. The number of genes does not scale proportionally with biological sophistication. Instead, the transcriptome (the collection of RNA molecules expressed from genes) in higher organisms is closely regulated such that one gene may produce different transcript isoforms in a cell type and developmental stage-specific manner. The Xiao lab studies transcriptome complexity focusing on RNA splicing, RNA modification and other post-transcriptional mechanisms. With both a computational (dry) lab and an experimental (wet) lab, they develop new bioinformatic methods and experimental systems to understand the regulation and function of transcriptome complexity, and apply these methods to neuropsychiatric disorders and cancer. The lab makes extensive use of second and third generation sequencing technologies in bulk tissues and single cells to drive methodology developments and biological discoveries.
Education
B.S., Tsingua University 1998
M.S., Biomedical/Mechanical Engineering, Massachusetts Institute of Technology 2000
Ph.D., Biomedical Engineering, Massachusetts Institute of Technology, Harvard Medical School 2004
Selected Publications
Tran SS, Zhou Q, Xiao X. Statistical inference of differential RNA-editing sites from RNA-sequencing data by hierarchical modeling. Bioinformatics, 36(9):2796-2804 (2020).
Cass AA, Xiao X. mountainClimber identifies alternative transcription start and polyadenylation sites in RNA-seq. Cell Systems, 9(4):393-400 (2019).
Tran SS, Jun HI, Bahn JH, Azghadi A, Ramaswami G, Van Nostrand EL, Nguyen TB, Hsiao YE, Lee C, Pratt GA, Martínez-Cerdeño V, Hagerman RJ, Yeo GW, Geschwind DH, Xiao X., “Widespread RNA editing dysregulation in brains from autistic individuals”, Nature Neuroscience, 22 (1): 25-36 (2019) .
Arefeen A, Xiao X, Jiang T., “DeepPASTA: deep neural network based polyadenylation site analysis”, Bioinformatics, 1-9 (2019) .
The Extracellular RNA Communication Consortium, “Establishing Foundational Knowledge and Technologies for Extracellular RNA Research”, Cell, 177 (2): 231-242 (2019) .
Yang EW, Bahn JH, Hsiao EY, Tan BX, Sun Y, Fu T, Zhou B, Van Nostrand EL, Pratt GA, Freese P, Wei X, Quinones-Valdez G, Urban AE, Graveley BR, Burge CB, Yeo GW, Xiao X.Allele-specific binding of RNA-binding proteins reveals functional genetic variants in the RNA., “Allele-specific binding of RNA-binding proteins reveals functional genetic variants in the RNA”, Nature Communications, 10 (1): 1-15 (2019) .
Quinones-Valdez G, Tran SS, Jun HI, Bahn JH, Yang EW, Zhan L, Brümmer A, Wei X, Van Nostrand EL, Pratt GA, Yeo GW, Graveley BR, Xiao X., “Regulation of RNA editing by RNA-binding proteins in human cells”, Communications Biology, 2 (19): 1-14 (2019) .
Cheung R, Insigne KD, Yao D, Burghard CP, Wang J, Hsiao YE, Jones EM, Goodman DB, Xiao X, Kosuri S., “A Multiplexed Assay for Exon Recognition Reveals that an Unappreciated Fraction of Rare Genetic Variants Cause Large-Effect Splicing Disruptions”, Molecular Cell, 73 (1): 183-194 (2019) .
Hsiao YE, Bahn JH, Yang Y, Lin X, Tran S, Yang EW, Quinones-Valdez G, Xiao X., “RNA editing in nascent RNA affects pre-mRNA splicing”, Genome Research, 28 (6): 812-823 (2018) .
Burkett ZD, Day NF, Kimball TH, Aamodt CM, Heston JB, Hilliard AT, Xiao X, White SA, “FoxP2 isoforms delineate spatiotemporal transcriptional networks for vocal learning in the zebra finch”, eLife, 23 (7): 1-35 (2018) .