Education and Training

Publications

1. Yamamoto R, Liu Z, Choudhury M, Xiao X. dsRID: in silico identification of dsRNA regions using long-read RNA-seq data.. Bioinformatics (Oxford, England), 2023.
2. Khan AH, Bagley JR, LaPierre N, Gonzalez-Figueroa C, Spencer TC, Choudhury M, Xiao X, Eskin E, Jentsch JD, Smith DJ. Genetic pathways regulating the longitudinal acquisition of cocaine self-administration in a panel of inbred and recombinant inbred mice.. Cell reports, 2023.
3. Liu Z, Quinones-Valdez G, Fu T, Huang E, Choudhury M, Reese F, Mortazavi A, Xiao X. L-GIREMI uncovers RNA editing sites in long-read RNA-seq.. Genome biology, 2023.
4. Yamamoto R, Liu Z, Choudhury M, Xiao X. dsRID: Editing-free in silico identification of dsRNA region using long-read RNA-seq data.. bioRxiv : the preprint server for biology, 2023.
5. Choudhury M, Fu T, Amoah K, Jun HI, Chan TW, Park S, Walker DW, Bahn JH, Xiao X. Widespread RNA hypoediting in schizophrenia and its relevance to mitochondrial function.. Science advances, 2023.
6. Chan TW, Dodson JP, Arbet J, Boutros PC, Xiao X. Single-Cell Analysis in Lung Adenocarcinoma Implicates RNA Editing in Cancer Innate Immunity and Patient Prognosis.. Cancer research, 2023.
7. Quinones-Valdez G, Fu T, Chan TW, Xiao X. scAllele: A versatile tool for the detection and analysis of variants in scRNA-seq.. Science advances, 2022.
8. He J, Fu T, Zhang L, Wanrong Gao L, Rensel M, Remage-Healey L, White SA, Gedman G, Whitelegge J, Xiao X, Schlinger BA. Improved zebra finch brain transcriptome identifies novel proteins with sex differences.. Gene, 2022.
9. Fu T, Chan TW, Bahn JH, Kim TH, Rowat AC, Xiao X. Multifaceted role of RNA editing in promoting loss-of-function of PODXL in cancer.. iScience, 2022.
10. Wang H, Chan TW, Vashisht AA, Drew BG, Calkin AC, Harris TE, Wohlschlegel JA, Xiao X, Reue K. Lipin 1 modulates mRNA splicing during fasting adaptation in liver.. JCI insight, 2021.
11. Guo L, Bloom J, Sykes S, Huang E, Kashif Z, Pham E, Ho K, Alcaraz A, Xiao XG, Duarte-Vogel S, Kruglyak L. Genetics of white color and iridophoroma in "Lemon Frost" leopard geckos.. PLoS genetics, 2021.
12. Gordon A, Yoon SJ, Tran SS, Makinson CD, Park JY, Andersen J, Valencia AM, Horvath S, Xiao X, Huguenard JR, Pa?ca SP, Geschwind DH. Long-term maturation of human cortical organoids matches key early postnatal transitions.. Nature neuroscience, 2021.
13. Amoah K, Hsiao YE, Bahn JH, Sun Y, Burghard C, Tan BX, Yang EW, Xiao X. Allele-specific alternative splicing and its functional genetic variants in human tissues.. Genome research, 2021.
14. Tavanasefat H, Li F, Koyano K, Gourtani BK, Marty V, Mulpuri Y, Lee SH, Shin KH, Wong DTW, Xiao X, Spigelman I, Kim Y. Molecular consequences of fetal alcohol exposure on amniotic exosomal miRNAs with functional implications for stem cell potency and differentiation.. PloS one, 2020.
15. Koyano K, Bahn JH, Xiao X. Extracellular microRNA 3' end modification across diverse body fluids.. Epigenetics, 2020.
16. Chan TW, Fu T, Bahn JH, Jun HI, Lee JH, Quinones-Valdez G, Cheng C, Xiao X. RNA editing in cancer impacts mRNA abundance in immune response pathways.. Genome biology, 2020.
17. Yokota T, Li J, Huang J, Xiong Z, Zhang Q, Chan T, Ding Y, Rau C, Sung K, Ren S, Kulkarni R, Hsiai T, Xiao X, Touma M, Minamisawa S, Wang Y. p38 Mitogen-activated protein kinase regulates chamber-specific perinatal growth in heart.. The Journal of clinical investigation, 2020.
18. Cass AA, Xiao X. mountainClimber Identifies Alternative Transcription Start and Polyadenylation Sites in RNA-Seq.. Cell systems, 2019.
19. 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.. Nature communications, 2019.
20. 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, 2019.
21. 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, 2018.
22. Chong 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, 2018.
23. 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.. Stem cell reports, 2018.
24. 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, 2018.
25. Kaczor-Urbanowicz KE, Kim Y, Li F, Galeev T, Kitchen RR, Gerstein M, Koyano K, Jeong SH, Wang X, Elashoff D, Kang SY, Kim SM, Kim K, Kim S, Chia D, Xiao X, Rozowsky J, Wong DTW. Novel approaches for bioinformatic analysis of salivary RNA sequencing data for development.. Bioinformatics (Oxford, England), 2018.
26. Xiao X, Garbutt CC, Hornicek F, Guo Z, Duan Z. Advances in chromosomal translocations and fusion genes in sarcomas and potential therapeutic applications.. Cancer treatment reviews, 2017.
27. Brümmer A, Yang Y, Chan TW, Xiao X. Structure-mediated modulation of mRNA abundance by A-to-I editing.. Nature communications, 2017.
28. Hasin-Brumshtein Y, Khan AH, Hormozdiari F, Pan C, Parks BW, Petyuk VA, Piehowski PD, Brümmer 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, 2016.
29. Touma M, Kang X, Zhao Y, Cass AA, Gao F, Biniwale R, Coppola G, Xiao X, Reemtsen B, Wang Y. Decoding the Long Noncoding RNA During Cardiac Maturation: A Roadmap for Functional Discovery.. Circulation. Cardiovascular genetics, 2016.
30. 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 Brain Gene Networks Linking Metabolic and Brain Disorders.. EBioMedicine, 2016.
31. 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, William 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, 2016.
32. Cass AA, Bahn JH, Lee JH, Greer C, Lin X, Kim Y, Hsiao YH, Xiao X. Global analyses of endonucleolytic cleavage in mammals reveal expanded repertoires of cleavage-inducing small RNAs and their targets.. Nucleic acids research, 2016.
33. Hsiao YH, Bahn JH, Lin X, Chan TM, Wang R, Xiao X. Alternative splicing modulated by genetic variants demonstrates accelerated evolution regulated by highly conserved proteins.. Genome research, 2016.
34. Fuxjager MJ, Lee JH, Chan TM, Bahn JH, Chew JG, Xiao X, Schlinger BA. Research Resource: Hormones, Genes, and Athleticism: Effect of Androgens on the Avian Muscular Transcriptome.. Molecular endocrinology (Baltimore, Md.), 2016.
35. Ahn J, Xiao X. RASER: reads aligner for SNPs and editing sites of RNA.. Bioinformatics (Oxford, England), 2015.
36. Lin X, Lo HC, Wong DT, Xiao X. Noncoding RNAs in human saliva as potential disease biomarkers.. Frontiers in genetics, 2015.
37. Zhang Q, Xiao X. Genome sequence-independent identification of RNA editing sites.. Nature methods, 2015.
38. Li Z, Yu J, Hosohama L, Nee K, Gkountela S, Chaudhari S, Cass AA, Xiao X, Clark AT. The Sm protein methyltransferase PRMT5 is not required for primordial germ cell specification in mice.. The EMBO journal, 2014.
39. Romay MC, Che N, Becker SN, Pouldar D, Hagopian R, Xiao X, Lusis AJ, Berliner JA, Civelek M. Regulation of NF-κB signaling by oxidized glycerophospholipid and IL-1β induced miRs-21-3p and -27a-5p in human aortic endothelial cells.. Journal of lipid research, 2014.
40. Xiao XG, Touma M, Wang Y. Decoding the noncoding transcripts in human heart failure.. Circulation, 2014.
41. Chan TM, Lo LY, Sze-To HY, Leung KS, Xiao X, Wong MH. Modeling associated protein-DNA pattern discovery with unified scores.. IEEE/ACM transactions on computational biology and bioinformatics, 2013.
42. Lee JH, Ang JK, Xiao X. Analysis and design of RNA sequencing experiments for identifying RNA editing and other single-nucleotide variants.. RNA (New York, N.Y.), 2013.
43. Bass B, Hundley H, Li JB, Peng Z, Pickrell J, Xiao XG, Yang L. The difficult calls in RNA editing. Interviewed by H Craig Mak.. Nature biotechnology, 2012.
44. Li G, Bahn JH, Lee JH, Peng G, Chen Z, Nelson SF, Xiao X. Identification of allele-specific alternative mRNA processing via transcriptome sequencing.. Nucleic acids research, 2012.
45. Anderson ES, Lin CH, Xiao X, Stoilov P, Burge CB, Black DL. The cardiotonic steroid digitoxin regulates alternative splicing through depletion of the splicing factors SRSF3 and TRA2B.. RNA (New York, N.Y.), 2012.
46. Gomez G, Lee JH, Veldman MB, Lu J, Xiao X, Lin S. Identification of vascular and hematopoietic genes downstream of etsrp by deep sequencing in zebrafish.. PloS one, 2012.
47. Lee JH, Gao C, Peng G, Greer C, Ren S, Wang Y, Xiao X. Analysis of transcriptome complexity through RNA sequencing in normal and failing murine hearts.. Circulation research, 2011.
48. Bahn JH, Lee JH, Li G, Greer C, Peng G, Xiao X. Accurate identification of A-to-I RNA editing in human by transcriptome sequencing.. Genome research, 2011.
49. Xiao X, Lee JH. Systems analysis of alternative splicing and its regulation.. Wiley interdisciplinary reviews. Systems biology and medicine, 2010.
50. Puppione DL, Ryan CM, Bassilian S, Souda P, Xiao X, Ryder OA, Whitelegge JP. Detection of two distinct forms of apoC-I in great apes.. Comparative biochemistry and physiology. Part D, Genomics & proteomics, 2010.