office: Terasaki Life Sciences Building, 2000E
research interests: Computational and systems biology of gene expression
With similar number of genes as in simpler organisms, mammals demonstrate an amazing degree of phenotypic diversity. Mammalian gene expression is under tight regulation temporally and spatially, which contributes to the formation of different cell types, tissues, and organs. Gene regulation involves a complex network of players, including multiple DNA, RNA sequence elements and RNA and protein factors. These regulators interact with each other and carry out combinatorial regulatory functions. Our lab uses both computational and experimental approaches to study the biology of gene regulation from a systems point of view. Our current focus pertains to the regulation of gene expression at the RNA level via the process of pre-mRNA splicing and other post-transcriptional (or co-transcriptional) mechanisms. Splicing is a critical step enabling diversity in gene expression programs. More than 90% of all human genes undergo alternative splicing which allows multiple gene products with potentially different functions to be produced from a single gene locus. We are currently investigating splicing regulatory mechanisms using comparative genomics, high-throughput technologies, such as deep sequencing and microarrays, and systems level computational analysis, such as system identification and modeling approaches. A long-term goal of our research is to better understand the involvement of splicing in gene expression programs of different disease models.
Kaczor-Urbanowicz K, Kim Y, Li F, Galeev T, Kitchen RR, Koyano K, Elashoff D, Xiao X, Rozowsky J, Wong DTW, "Novel approaches for bioinformatic analysis of salivary RNA Sequencing data in the biomarker development process", Bioinformatics, 34 (1): 1-8 (2018) .
Brummer A, Yang Y, Chan TW, Xiao X, "Structure-mediated modulation of mRNA abundance by A-to-I editing", Nature Communications, 8 (1): 1-13 (2017) .
Touma M, Kang X, Gao F, Zhao Y, Cass AA, Biniwale R, Xiao X, Eghbali M, Coppola G, Reemtsen B, Wang Y, "Wnt11 signaling regulates chamber-specific cardiomyocyte proliferation in neonatal heart maturation and disease", JCI Insight, 2 (17): 1-11 (2017) .
Yang Y, Fan X, Mao M, Song X, Wu P, Zhang Y, Jin Y, Yang Y, Chen L, Wang Y,Wong CC, Xiao X, Wang Z., "Extensive translation of circular RNAs driven by N6-methyladenosine", Cell Research, 27 (5): 626-641 (2017) .
Hasin-Brumshtein Y, Khan AH, Hormozdiari F, Pan C, Parks B, Petyuk VA, Bruemmer A, Pellegrini M, Xiao X, Eskin E, Smith RD, Lusis AJ, Smith DJ, "Hypothalamic transcriptomes of 99 mouse strains reveal trans eQTL hotspots, splicing QTLs and novel non-coding genes", eLife, e15614 : 1-10 (2016) .
Touma M, Kang X, Zhao Y, Cass AA, Goa F, Biniwali R, Coppola G, Xiao X, Reemtsen B, Wang Y., "Decoding the long noncoding RNA in neonatal heart during perinatal circulatory transition: a roadmap for functional discovery", Circulation Cardiovascular Genetics, 9 (5): 395-407 (2016) .
Wang Z, Zhang XJ, Ji YX, Zhang P, Deng KQ, Gong J, Ren S, Wang X, Chen I, Wang H, Gao C, Yokota T, Ang YS, Li S, Cass A, Vondriska T, Li G, Deb A, Srivastava D, Yang HT, Xiao X, Li H, Wang Y, "A long non-coding RNA defines an epigenetic checkpoint for cardiac hypertrophy", Nature Medicine, 1-10 (2016) .
Meng Q, Ying Z, Noble E, Zhao Y, Agrawal R, Mikhail A, Zhuang Y, Tyagi E, Zhang Q, Lee JH, Morselli M, Orozco L, Guo W, Kilts TM, Zhu J, Zhang B, Pellegrini M, Xiao X, Young MF, Gomez-Pinilla F, Yang X, "Systems nutrigenomics reveals opposite actions of fructose and DHA on gene networks linking metabolism and brain function", eBiomedicine, 7 : 157-166 (2016) .
Sun H, Olson KC, Gao C, Prosdocimo DA, Zhou M, Wang Z, Jeyaraj D, Youn JY, Ren S, Liu Y, Rau CD, Shah S, Ilkayeva O, Gui WJ, Williams NS, Wynn RM, Newgard CB, Cai H, Xiao X, Chuang DT, Schulze PC, Lynch C, Jain MK, Wang Y, "Catabolic defect of branched-chain amino acids promotes heart failure", Circulation, 133 (21): 2038-2049 (2016) .
Fuxjager M, Lee JH, Chan TM, Bahn JH, Chew JG, Xiao X, Schlinger B, "Hormones, genes and athleticism: effect of androgens on the avian muscular transcriptome", Molecular Endocrinology, 30 (2): 254-271 (2016) .