office: Terasaki Life Sciences Building, 2000E
research interests: Bioinformatics, RNA biology
Our lab develops and applies computational, bioinformatic and experimental approaches to generate and analyze large-scale genomic and transcriptomic data sets, combined with in-depth molecular and mechanistic studies. Our work aims to achieve a better understanding of RNA splicing, RNA modification and post-transcriptional regulation in health and disease. We make extensive use of second and third generation sequencing technologies that have transformed modern biology to an information-rich science. We develop bioinformatic methods and experimental innovations that build upon RNA-seq, CLIP-seq, massively parallel reporter assays, single cell -omics and other high-throughput technologies. We are particularly interested in applying bioinformatic and experimental methods to study neuropsychiatric disorders and cancer.
Tran SS, Jun HI, Bahn JH, Azghadi A, Ramaswami G, Van Nostrand EL, Nguyen TB, Hsiao YE, Lee C, Pratt GA, Mart?nez-Cerde?o 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, Br?mmer 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) .
Ohashi M, Korsakova E, Allen D, Lee P, Fu K, Vargas BS, Cinkornpumin J, Salas C, Park JC, Germanguz I, Langerman J, Chronis C, Kuoy E, Tran S, Xiao X, Pellegrini M, Plath K, Lowry WE., "Loss of MECP2 Leads to Activation of P53 and Neuronal Senescence", Stell Cell Reports, 10 (5): 1453-1463 (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) .
He X, Li F, Bor B, Koyano K, Cen L, Xiao X, Shi W, Wong DTW., "Human tRNA-Derived Small RNAs Modulate Host-Oral Microbial Interactions", Journal of Dental Research, 97 (11): 1236-1243 (2018) .