2022
scAllele: a versatile tool for the detection and analysis of variants in scRNA-seq
Quinones-Valdez G, Fu T, Chan TW, Xiao X.
BioRxiv, doi: https://doi.org/10.1101/2022.03.29.486330; Preprint.
L-GIREMI uncovers RNA editing sites in long-read RNA-seq
Liu Z, Quinones-Valdez G, Fu T, Choudhury M, Reese F, Mortazavi A, Xiao X.
BioRxiv, doi:https://doi.org/10.1101/2022.03.23.485515; Preprint.
2021
Lipin 1 modulates mRNA splicing during fasting adaptation in liver
Wang H, Chan TW, Vashisht AA, Drew BG, Calkin AC, Harris TE, Wohlschlegel JA, Xiao X, Reue K
JCI Insight. 2021 Sep 8;6(17):150114. doi: 10.1172/jci.insight.150114.
Fe(III) heme sets an activation threshold for processing distinct groups of pri-miRNAs in mammalian cells
Weitz SH, Quick-Cleveland J, Jacob JP, Barr I, Senturia R, Koyano K, Xiao X, Weiss S, Guo F.
BioRxiv, doi: https://doi.org/10.1101/2020.02.18.955294; Preprint.
Genetics of white color and iridophoroma in “Lemon Frost” leopard geckos
Guo L, Bloom J, Sykes S, Huang E, Kashif Z, Pham E, Ho K, Alcaraz A, Xiao X, Duarte-Vogel S, Kruglyak L.
PLoS Genetics, doi: https://doi.org/10.1371/journal.pgen.1009580
Long-term maturation of human cortical organoids matches key early postnatal transitions
Gordon A ,Yoon SJ, Tran SS, Makinson CD, Park JY, Andersen J, Valencia AM , Horvath S, Xiao X, Huguenard JR, Pașca SP, Geschwind DH
Nature Neuroscience, 2021 Feb 22. doi: 10.1038/s41593-021-00802-y.
Allele-specific alternative splicing and its functional genetic variants in human tissues
Amoah K, Hsiao YHE, Bahn JH, Sun Y, Burghard C, Tan BX, Yang EW, Xiao X.
Genome Research, Published in Advance January 15, 2021, doi:10.1101/gr.265637.120
2020
Molecular consequences of fetal alcohol exposure on amniotic exosomal miRNAs with functional implications for stem cell potency and differentiation
Tavanasefat H, Li F, Koyano K, Khalilian Gourtani B, Marty V, Mulpuri Y, Lee SH, Shin KH, Wong DTW, Xiao X, Spigelman I, Kim Y.
PLoS One. 2020 Nov 16;15(11):e0242276. doi: 10.1371/journal.pone.0242276.
Extracellular microRNA 3' end modification across diverse body fluids
Koyano K, Bahn JH, Xiao X.
Epigenetics. 2020 Nov 2:1-16. doi: 10.1080/15592294.2020.1834922.
RNA editing in cancer impacts mRNA abundance in immune response pathways
Chan T, Fu F, Bahn JH, Jun HI, Lee JH, Quinones-Valdez G, Cheng C, Xiao X.
Genome Biology 2020 Oct 26;21(1):268. doi: 10.1186/s13059-020-02171-4.
Expanded encyclopaedias of DNA elements in the human and mouse genomes
The ENCODE Project Consortium
Nature, 583, pages699–710(2020)
Perspectives on ENCODE.
The ENCODE Project Consortium
Nature. 2020 Jul;583(7818):693-698.
p38 mitogen-activated protein kinase regulates chamber specific perinatal growth in heart
Yokota T, Li J, Huang J, Xiong Z, Zhang Q, Chan T, Ding Y, Rau C, Sung K, Ren S, Kulkarni R, Hsiao T, Xiao X, Touma M, Minamisawa S, Wang Y
Journal of Clinical Investigation, In press, published online June 23, 2020.
Statistical inference of differential RNA editing sites from RNA-sequencing data by hierarchical modeling.
Tran SS, Zhou Q, Xiao X.
Bioinformatics, 2020 January, btaa066
2019
mountainClimber identifies alternative transcription start and polyadenylation sites in RNA-seq.
Cass AA, Xiao X.
Cell Systems, 2019 September 18; DOI:https://doi.org/10.1016/j.cels.2019.07.011
DeepPASTA: deep neural network based polyadenylation site analysis.
Arefeen A, Xiao X, Jiang T.
Bioinformatics. 2019 Apr 25;. doi: 10.1093/bioinformatics/btz283. [Epub ahead of print] PubMed PMID: 31081512.
Establishing Foundational Knowledge and Technologies for Extracellular RNA Research.
The Extracellular RNA Communication Consortium
Cell. 2019 Apr 4;177(2):231-242. doi: 10.1016/j.cell.2019.03.023. PubMed PMID: 30951667.
Allele-specific binding of RNA-binding proteins reveals functional genetic variants in the RNA.
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.
Nat Commun. 2019 Mar 22;10(1):1338. doi: 10.1038/s41467-019-09292-w. PubMed PMID: 30902979.
Regulation of RNA editing by RNA-binding proteins in human cells.
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.
Commun Biol. 2019;2:19. doi: 10.1038/s42003-018-0271-8. eCollection 2019. PubMed PMID: 30652130.
A Multiplexed Assay for Exon Recognition Reveals that an Unappreciated Fraction of Rare Genetic Variants Cause Large-Effect Splicing Disruptions.
Cheung R, Insigne KD, Yao D, Burghard CP, Wang J, Hsiao YE, Jones EM, Goodman DB, Xiao X, Kosuri S.
Mol Cell. 2019 Jan 3;73(1):183-194.e8. doi: 10.1016/j.molcel.2018.10.037. Epub 2018 Nov 29. PubMed PMID: 30503770.
Widespread RNA editing dysregulation in brains from autistic individuals.
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.
Nat Neurosci. 2019 Jan;22(1):25-36. doi: 10.1038/s41593-018-0287-x. Epub 2018 Dec 17. PubMed PMID: 30559470 .
2018
Human tRNA-Derived Small RNAs Modulate Host-Oral Microbial Interactions.
He X, Li F, Bor B, Koyano K, Cen L, Xiao X, Shi W, Wong DTW.
J Dent Res. 2018 Oct;97(11):1236-1243. doi: 10.1177/0022034518770605. Epub 2018 Apr 27. PubMed PMID: 29702004.
Coregulation of alternative splicing by hnRNPM and ESRP1 during EMT.
Harvey SE, Xu Y, Lin X, Gao XD, Qiu Y, Ahn J, Xiao X, Cheng C.
RNA. 2018 Oct;24(10):1326-1338. doi: 10.1261/rna.066712.118. Epub 2018 Jul 24. PubMed PMID: 30042172.
TAPAS: tool for alternative polyadenylation site analysis.
Arefeen A, Liu J, Xiao X, Jiang T.
Bioinformatics. 2018 Aug 1;34(15):2521-2529. doi: 10.1093/bioinformatics/bty110. PubMed PMID: 30052912.
Characterization of Human Salivary Extracellular RNA by Next-generation Sequencing.
Li F, Kaczor-Urbanowicz KE, Sun J, Majem B, Lo HC, Kim Y, Koyano K, Rao SL, Kang SY, Kim SM, Kim KM, Kim S, Chia D, Elashoff D, Grogan TR, Xiao X, Wong DTW.
Clin Chem. 2018 Jul;64(7):1085-1095. doi: 10.1373/clinchem.2017.285072. Epub 2018 Apr 23. PubMed PMID: 29685897.
RNA editing in nascent RNA affects pre-mRNA splicing.
Hsiao YE, Bahn JH, Yang Y, Lin X, Tran S, Yang EW, Quinones-Valdez G, Xiao X.
Genome Res. 2018 Jun;28(6):812-823. doi: 10.1101/gr.231209.117. Epub 2018 May 3. PubMed PMID: 29724793.
Loss of MECP2 Leads to Activation of P53 and Neuronal Senescence.
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.
Stem Cell Reports. 2018 May 8;10(5):1453-1463. doi: 10.1016/j.stemcr.2018.04.001. PubMed PMID: 29742391.
FoxP2 isoforms delineate spatiotemporal transcriptional networks for vocal learning in the zebra finch.
Burkett ZD, Day NF, Kimball TH, Aamodt CM, Heston JB, Hilliard AT, Xiao X, White SA.
Elife. 2018 Jan 23;7. doi: 10.7554/eLife.30649. PubMed PMID: 29360038.
2017
Novel approaches for bioinformatic analysis of salivary RNA sequencing data for development.
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.
Bioinformatics. 2018 Jan 1;34(1):1-8. doi: 10.1093/bioinformatics/btx504. PubMed PMID: 28961734.
Structure-mediated modulation of mRNA abundance by A-to-I editing.
Brümmer A, Yang Y, Chan TW, Xiao X.
Nat Commun. 2017 Nov 2;8(1):1255. doi: 10.1038/s41467-017-01459-7. PubMed PMID: 29093448.
Wnt11 regulates cardiac chamber development and disease during perinatal maturation.
Touma M, Kang X, Gao F, Zhao Y, Cass AA, Biniwale R, Xiao X, Eghbali M, Coppola G, Reemtsen B, Wang Y.
JCI Insight. 2017 Sep 7;2(17). doi: 10.1172/jci.insight.94904. eCollection 2017 Sep 7. PubMed PMID: 28878122.
Extensive translation of circular RNAs driven by N6-methyladenosine.
Yang Y, Fan X, Mao M, Song X, Wu P, Zhang Y, Jin Y, Yang Y, Chen LL, Wang Y, Wong CC, Xiao X, Wang Z.
Cell Res. 2017 May;27(5):626-641. doi: 10.1038/cr.2017.31. Epub 2017 Mar 10. PubMed PMID: 28281539.
2016
The long noncoding RNA Chaer defines an epigenetic checkpoint in cardiac hypertrophy.
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 TM, Li G, Deb A, Srivastava D, Yang HT, Xiao X, Li H, Wang Y.
Nat Med. 2016 Oct;22(10):1131-1139. doi: 10.1038/nm.4179. Epub 2016 Sep 12. PubMed PMID: 27618650.
Decoding the Long Noncoding RNA During Cardiac Maturation: A Roadmap for Functional Discovery.
Touma M, Kang X, Zhao Y, Cass AA, Gao F, Biniwale R, Coppola G, Xiao X, Reemtsen B, Wang Y.
Circ Cardiovasc Genet. 2016 Oct;9(5):395-407. doi: 10.1161/CIRCGENETICS.115.001363. Epub 2016 Sep 2. PubMed PMID: 27591185.
Hypothalamic transcriptomes of 99 mouse strains reveal trans eQTL hotspots, splicing QTLs and novel non-coding genes.
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.
Elife. 2016 Sep 13;5. doi: 10.7554/eLife.15614. PubMed PMID: 27623010.
Catabolic Defect of Branched-Chain Amino Acids Promotes Heart Failure.
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.
Circulation. 2016 May 24;133(21):2038-49. doi: 10.1161/CIRCULATIONAHA.115.020226. Epub 2016 Apr 8. PubMed PMID: 27059949.
Systems Nutrigenomics Reveals Brain Gene Networks Linking Metabolic and Brain Disorders.
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.
EBioMedicine. 2016 May;7:157-66. doi: 10.1016/j.ebiom.2016.04.008. Epub 2016 Apr 13. PubMed PMID: 27322469.
Global analyses of endonucleolytic cleavage in mammals reveal expanded repertoires of cleavage-inducing small RNAs and their targets.
Cass AA, Bahn JH, Lee JH, Greer C, Lin X, Kim Y, Hsiao YH, Xiao X.
Nucleic Acids Res. 2016 Apr 20;44(7):3253-63. doi: 10.1093/nar/gkw164. Epub 2016 Mar 14. PubMed PMID: 26975654.
Alternative splicing modulated by genetic variants demonstrates accelerated evolution regulated by highly conserved proteins.
Hsiao YH, Bahn JH, Lin X, Chan TM, Wang R, Xiao X.
Genome Res. 2016 Apr;26(4):440-50. doi: 10.1101/gr.193359.115. Epub 2016 Feb 17. PubMed PMID: 26888265.
Research Resource: Hormones, Genes, and Athleticism: Effect of Androgens on the Avian Muscular Transcriptome.
Fuxjager MJ, Lee JH, Chan TM, Bahn JH, Chew JG, Xiao X, Schlinger BA.
Mol Endocrinol. 2016 Feb;30(2):254-71. doi: 10.1210/me.2015-1270. Epub 2016 Jan 8. PubMed PMID: 26745669.
2015
RBFox1-mediated RNA splicing regulates cardiac hypertrophy and heart failure.
Gao C, Ren S, Lee JH, Qiu J, Chapski DJ, Rau CD, Zhou Y, Abdellatif M, Nakano A, Vondriska TM, Xiao X, Fu XD, Chen JN, Wang Y.
J Clin Invest. 2016 Jan;126(1):195-206. doi: 10.1172/JCI84015. Epub 2015 Nov 30. PubMed PMID: 26619120.
RASER: reads aligner for SNPs and editing sites of RNA.
Ahn J, Xiao X.
Bioinformatics. 2015 Dec 15;31(24):3906-13. doi: 10.1093/bioinformatics/btv505. Epub 2015 Aug 30. PubMed PMID: 26323713.
ESRP2 controls an adult splicing programme in hepatocytes to support postnatal liver maturation.
Bhate A, Parker DJ, Bebee TW, Ahn J, Arif W, Rashan EH, Chorghade S, Chau A, Lee JH, Anakk S, Carstens RP, Xiao X, Kalsotra A.
Nat Commun. 2015 Nov 4;6:8768. doi: 10.1038/ncomms9768. PubMed PMID: 26531099.
Noncoding RNAs in human saliva as potential disease biomarkers.
Lin X, Lo HC, Wong DT, Xiao X.
Front Genet. 2015;6:175. doi: 10.3389/fgene.2015.00175. eCollection 2015. PubMed PMID: 25999984.
Genome sequence-independent identification of RNA editing sites.
Zhang Q, Xiao X.
Nat Methods. 2015 Apr;12(4):347-50. doi: 10.1038/nmeth.3314. Epub 2015 Mar 2. PubMed PMID: 25730491.
The Sm protein methyltransferase PRMT5 is not required for primordial germ cell specification in mice.
Li Z, Yu J, Hosohama L, Nee K, Gkountela S, Chaudhari S, Cass AA, Xiao X, Clark AT.
EMBO J. 2015 Mar 12;34(6):748-58. doi: 10.15252/embj.201489319. Epub 2014 Dec 17. PubMed PMID: 25519955.
Genomic analysis of ADAR1 binding and its involvement in multiple RNA processing pathways.
Bahn JH, Ahn J, Lin X, Zhang Q, Lee JH, Civelek M, Xiao X.
Nat Commun. 2015 Mar 9;6:6355. doi: 10.1038/ncomms7355. PubMed PMID: 25751603.
The landscape of microRNA, Piwi-interacting RNA, and circular RNA in human saliva.
Bahn JH, Zhang Q, Li F, Chan TM, Lin X, Kim Y, Wong DT, Xiao X.
Clin Chem. 2015 Jan;61(1):221-30. doi: 10.1373/clinchem.2014.230433. Epub 2014 Nov 6. PubMed PMID: 25376581.
Global approaches to alternative splicing and its regulation: Recent advances and open questions. .
Hsiao Y, Cass AA, Bahn J, Lin X, Xiao X.
Chapter In: Translational Bioinformatics in Transcriptomics and Gene Regulation. Dordrecht: Springer; 2015.
2014
Regulation of NF-κB signaling by oxidized glycerophospholipid and IL-1β induced miRs-21-3p and -27a-5p in human aortic endothelial cells.
Romay MC, Che N, Becker SN, Pouldar D, Hagopian R, Xiao X, Lusis AJ, Berliner JA, Civelek M.
J Lipid Res. 2015 Jan;56(1):38-50. doi: 10.1194/jlr.M052670. Epub 2014 Oct 19. PubMed PMID: 25327529.
Cell type-restricted activity of hnRNPM promotes breast cancer metastasis via regulating alternative splicing.
Xu Y, Gao XD, Lee JH, Huang H, Tan H, Ahn J, Reinke LM, Peter ME, Feng Y, Gius D, Siziopikou KP, Peng J, Xiao X, Cheng C.
Genes Dev.2014 Jun 1;28(11):1191-203. doi: 10.1101/gad.241968.114. Epub 2014 May 19. PubMed PMID: 24840202.
Decoding the noncoding transcripts in human heart failure.
Xiao XG, Touma M, Wang Y.
Circulation. 2014 Mar 4;129(9):958-60. doi: 10.1161/CIRCULATIONAHA.114.007548. Epub 2014 Jan 15. PubMed PMID: 24429689.
2013
Analysis and design of RNA sequencing experiments for identifying RNA editing and other single-nucleotide variants.
Lee JH, Ang JK, Xiao X.
RNA. 2013 Jun;19(6):725-32. doi: 10.1261/rna.037903.112. Epub 2013 Apr 18. PubMed PMID: 23598527.
Modeling associated protein-DNA pattern discovery with unified scores.
Chan TM, Lo LY, Sze-To HY, Leung KS, Xiao X, Wong MH.
IEEE/ACM Trans Comput Biol Bioinform. 2013 May-Jun;10(3):696-707. doi: 10.1109/TCBB.2013.60. PubMed PMID: 24091402.
A complex network of factors with overlapping affinities represses splicing through intronic elements.
Wang Y, Xiao X, Zhang J, Choudhury R, Robertson A, Li K, Ma M, Burge CB, Wang Z.
Nat Struct Mol Biol. 2013 Jan;20(1):36-45. doi: 10.1038/nsmb.2459. Epub 2012 Dec 16. PubMed PMID: 23241926.
2012
The difficult calls in RNA editing. Interviewed by H Craig Mak.
Bass B, Hundley H, Li JB, Peng Z, Pickrell J, Xiao XG, Yang L.
Nat Biotechnol. 2012 Dec;30(12):1207-9. doi: 10.1038/nbt.2452. PubMed PMID: 23222792.
Intronic splicing enhancers, cognate splicing factors and context-dependent regulation rules.
Wang Y, Ma M, Xiao X, Wang Z.
Nat Struct Mol Biol. 2012 Oct;19(10):1044-52. doi: 10.1038/nsmb.2377. Epub 2012 Sep 16. PubMed PMID: 22983564.
Identification of allele-specific alternative mRNA processing via transcriptome sequencing.
Li G, Bahn JH, Lee JH, Peng G, Chen Z, Nelson SF, Xiao X.
Nucleic Acids Res. 2012 Jul;40(13):e104. doi: 10.1093/nar/gks280. Epub 2012 Mar 29. PubMed PMID: 22467206.
The cardiotonic steroid digitoxin regulates alternative splicing through depletion of the splicing factors SRSF3 and TRA2B.
Anderson ES, Lin CH, Xiao X, Stoilov P, Burge CB, Black DL.
RNA. 2012 May;18(5):1041-9. doi: 10.1261/rna.032912.112. Epub 2012 Mar 28. PubMed PMID: 22456266.
Identification of vascular and hematopoietic genes downstream of etsrp by deep sequencing in zebrafish.
Gomez G, Lee JH, Veldman MB, Lu J, Xiao X, Lin S.
PLoS One. 2012;7(3):e31658. doi: 10.1371/journal.pone.0031658. Epub 2012 Mar 16. PubMed PMID: 22438865.
2011
Accurate identification of A-to-I RNA editing in human by transcriptome sequencing.
Bahn JH, Lee JH, Li G, Greer C, Peng G, Xiao X.
Genome Res. 2012 Jan;22(1):142-50. doi: 10.1101/gr.124107.111. Epub 2011 Sep 29. PubMed PMID: 21960545.
Analysis of transcriptome complexity through RNA sequencing in normal and failing murine hearts.
Lee JH, Gao C, Peng G, Greer C, Ren S, Wang Y, Xiao X.
Circ Res. 2011 Dec 9;109(12):1332-41. doi: 10.1161/CIRCRESAHA.111.249433. Epub 2011 Oct 27. PubMed PMID: 22034492.
2010
Systems analysis of alternative splicing and its regulation.
Xiao X, Lee JH.
Wiley Interdiscip Rev Syst Biol Med. 2010 Sep-Oct;2(5):550-565. doi: 10.1002/wsbm.84. Review. PubMed PMID: 20836047.
Detection of two distinct forms of apoC-I in great apes.
Puppione DL, Ryan CM, Bassilian S, Souda P, Xiao X, Ryder OA, Whitelegge JP.
Comp Biochem Physiol Part D Genomics Proteomics. 2010 Mar;5(1):73-9. doi: 10.1016/j.cbd.2009.12.003. PubMed PMID: 20209111.
scAllele: a versatile tool for the detection and analysis of variants in scRNA-seq
Quinones-Valdez G, Fu T, Chan TW, Xiao X.
BioRxiv, doi: https://doi.org/10.1101/2022.03.29.486330; Preprint.
L-GIREMI uncovers RNA editing sites in long-read RNA-seq
Liu Z, Quinones-Valdez G, Fu T, Choudhury M, Reese F, Mortazavi A, Xiao X.
BioRxiv, doi:https://doi.org/10.1101/2022.03.23.485515; Preprint.
2021
Lipin 1 modulates mRNA splicing during fasting adaptation in liver
Wang H, Chan TW, Vashisht AA, Drew BG, Calkin AC, Harris TE, Wohlschlegel JA, Xiao X, Reue K
JCI Insight. 2021 Sep 8;6(17):150114. doi: 10.1172/jci.insight.150114.
Fe(III) heme sets an activation threshold for processing distinct groups of pri-miRNAs in mammalian cells
Weitz SH, Quick-Cleveland J, Jacob JP, Barr I, Senturia R, Koyano K, Xiao X, Weiss S, Guo F.
BioRxiv, doi: https://doi.org/10.1101/2020.02.18.955294; Preprint.
Genetics of white color and iridophoroma in “Lemon Frost” leopard geckos
Guo L, Bloom J, Sykes S, Huang E, Kashif Z, Pham E, Ho K, Alcaraz A, Xiao X, Duarte-Vogel S, Kruglyak L.
PLoS Genetics, doi: https://doi.org/10.1371/journal.pgen.1009580
Long-term maturation of human cortical organoids matches key early postnatal transitions
Gordon A ,Yoon SJ, Tran SS, Makinson CD, Park JY, Andersen J, Valencia AM , Horvath S, Xiao X, Huguenard JR, Pașca SP, Geschwind DH
Nature Neuroscience, 2021 Feb 22. doi: 10.1038/s41593-021-00802-y.
Allele-specific alternative splicing and its functional genetic variants in human tissues
Amoah K, Hsiao YHE, Bahn JH, Sun Y, Burghard C, Tan BX, Yang EW, Xiao X.
Genome Research, Published in Advance January 15, 2021, doi:10.1101/gr.265637.120
2020
Molecular consequences of fetal alcohol exposure on amniotic exosomal miRNAs with functional implications for stem cell potency and differentiation
Tavanasefat H, Li F, Koyano K, Khalilian Gourtani B, Marty V, Mulpuri Y, Lee SH, Shin KH, Wong DTW, Xiao X, Spigelman I, Kim Y.
PLoS One. 2020 Nov 16;15(11):e0242276. doi: 10.1371/journal.pone.0242276.
Extracellular microRNA 3' end modification across diverse body fluids
Koyano K, Bahn JH, Xiao X.
Epigenetics. 2020 Nov 2:1-16. doi: 10.1080/15592294.2020.1834922.
RNA editing in cancer impacts mRNA abundance in immune response pathways
Chan T, Fu F, Bahn JH, Jun HI, Lee JH, Quinones-Valdez G, Cheng C, Xiao X.
Genome Biology 2020 Oct 26;21(1):268. doi: 10.1186/s13059-020-02171-4.
Expanded encyclopaedias of DNA elements in the human and mouse genomes
The ENCODE Project Consortium
Nature, 583, pages699–710(2020)
Perspectives on ENCODE.
The ENCODE Project Consortium
Nature. 2020 Jul;583(7818):693-698.
p38 mitogen-activated protein kinase regulates chamber specific perinatal growth in heart
Yokota T, Li J, Huang J, Xiong Z, Zhang Q, Chan T, Ding Y, Rau C, Sung K, Ren S, Kulkarni R, Hsiao T, Xiao X, Touma M, Minamisawa S, Wang Y
Journal of Clinical Investigation, In press, published online June 23, 2020.
Statistical inference of differential RNA editing sites from RNA-sequencing data by hierarchical modeling.
Tran SS, Zhou Q, Xiao X.
Bioinformatics, 2020 January, btaa066
2019
mountainClimber identifies alternative transcription start and polyadenylation sites in RNA-seq.
Cass AA, Xiao X.
Cell Systems, 2019 September 18; DOI:https://doi.org/10.1016/j.cels.2019.07.011
DeepPASTA: deep neural network based polyadenylation site analysis.
Arefeen A, Xiao X, Jiang T.
Bioinformatics. 2019 Apr 25;. doi: 10.1093/bioinformatics/btz283. [Epub ahead of print] PubMed PMID: 31081512.
Establishing Foundational Knowledge and Technologies for Extracellular RNA Research.
The Extracellular RNA Communication Consortium
Cell. 2019 Apr 4;177(2):231-242. doi: 10.1016/j.cell.2019.03.023. PubMed PMID: 30951667.
Allele-specific binding of RNA-binding proteins reveals functional genetic variants in the RNA.
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.
Nat Commun. 2019 Mar 22;10(1):1338. doi: 10.1038/s41467-019-09292-w. PubMed PMID: 30902979.
Regulation of RNA editing by RNA-binding proteins in human cells.
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.
Commun Biol. 2019;2:19. doi: 10.1038/s42003-018-0271-8. eCollection 2019. PubMed PMID: 30652130.
A Multiplexed Assay for Exon Recognition Reveals that an Unappreciated Fraction of Rare Genetic Variants Cause Large-Effect Splicing Disruptions.
Cheung R, Insigne KD, Yao D, Burghard CP, Wang J, Hsiao YE, Jones EM, Goodman DB, Xiao X, Kosuri S.
Mol Cell. 2019 Jan 3;73(1):183-194.e8. doi: 10.1016/j.molcel.2018.10.037. Epub 2018 Nov 29. PubMed PMID: 30503770.
Widespread RNA editing dysregulation in brains from autistic individuals.
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.
Nat Neurosci. 2019 Jan;22(1):25-36. doi: 10.1038/s41593-018-0287-x. Epub 2018 Dec 17. PubMed PMID: 30559470 .
2018
Human tRNA-Derived Small RNAs Modulate Host-Oral Microbial Interactions.
He X, Li F, Bor B, Koyano K, Cen L, Xiao X, Shi W, Wong DTW.
J Dent Res. 2018 Oct;97(11):1236-1243. doi: 10.1177/0022034518770605. Epub 2018 Apr 27. PubMed PMID: 29702004.
Coregulation of alternative splicing by hnRNPM and ESRP1 during EMT.
Harvey SE, Xu Y, Lin X, Gao XD, Qiu Y, Ahn J, Xiao X, Cheng C.
RNA. 2018 Oct;24(10):1326-1338. doi: 10.1261/rna.066712.118. Epub 2018 Jul 24. PubMed PMID: 30042172.
TAPAS: tool for alternative polyadenylation site analysis.
Arefeen A, Liu J, Xiao X, Jiang T.
Bioinformatics. 2018 Aug 1;34(15):2521-2529. doi: 10.1093/bioinformatics/bty110. PubMed PMID: 30052912.
Characterization of Human Salivary Extracellular RNA by Next-generation Sequencing.
Li F, Kaczor-Urbanowicz KE, Sun J, Majem B, Lo HC, Kim Y, Koyano K, Rao SL, Kang SY, Kim SM, Kim KM, Kim S, Chia D, Elashoff D, Grogan TR, Xiao X, Wong DTW.
Clin Chem. 2018 Jul;64(7):1085-1095. doi: 10.1373/clinchem.2017.285072. Epub 2018 Apr 23. PubMed PMID: 29685897.
RNA editing in nascent RNA affects pre-mRNA splicing.
Hsiao YE, Bahn JH, Yang Y, Lin X, Tran S, Yang EW, Quinones-Valdez G, Xiao X.
Genome Res. 2018 Jun;28(6):812-823. doi: 10.1101/gr.231209.117. Epub 2018 May 3. PubMed PMID: 29724793.
Loss of MECP2 Leads to Activation of P53 and Neuronal Senescence.
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.
Stem Cell Reports. 2018 May 8;10(5):1453-1463. doi: 10.1016/j.stemcr.2018.04.001. PubMed PMID: 29742391.
FoxP2 isoforms delineate spatiotemporal transcriptional networks for vocal learning in the zebra finch.
Burkett ZD, Day NF, Kimball TH, Aamodt CM, Heston JB, Hilliard AT, Xiao X, White SA.
Elife. 2018 Jan 23;7. doi: 10.7554/eLife.30649. PubMed PMID: 29360038.
2017
Novel approaches for bioinformatic analysis of salivary RNA sequencing data for development.
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.
Bioinformatics. 2018 Jan 1;34(1):1-8. doi: 10.1093/bioinformatics/btx504. PubMed PMID: 28961734.
Structure-mediated modulation of mRNA abundance by A-to-I editing.
Brümmer A, Yang Y, Chan TW, Xiao X.
Nat Commun. 2017 Nov 2;8(1):1255. doi: 10.1038/s41467-017-01459-7. PubMed PMID: 29093448.
Wnt11 regulates cardiac chamber development and disease during perinatal maturation.
Touma M, Kang X, Gao F, Zhao Y, Cass AA, Biniwale R, Xiao X, Eghbali M, Coppola G, Reemtsen B, Wang Y.
JCI Insight. 2017 Sep 7;2(17). doi: 10.1172/jci.insight.94904. eCollection 2017 Sep 7. PubMed PMID: 28878122.
Extensive translation of circular RNAs driven by N6-methyladenosine.
Yang Y, Fan X, Mao M, Song X, Wu P, Zhang Y, Jin Y, Yang Y, Chen LL, Wang Y, Wong CC, Xiao X, Wang Z.
Cell Res. 2017 May;27(5):626-641. doi: 10.1038/cr.2017.31. Epub 2017 Mar 10. PubMed PMID: 28281539.
2016
The long noncoding RNA Chaer defines an epigenetic checkpoint in cardiac hypertrophy.
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 TM, Li G, Deb A, Srivastava D, Yang HT, Xiao X, Li H, Wang Y.
Nat Med. 2016 Oct;22(10):1131-1139. doi: 10.1038/nm.4179. Epub 2016 Sep 12. PubMed PMID: 27618650.
Decoding the Long Noncoding RNA During Cardiac Maturation: A Roadmap for Functional Discovery.
Touma M, Kang X, Zhao Y, Cass AA, Gao F, Biniwale R, Coppola G, Xiao X, Reemtsen B, Wang Y.
Circ Cardiovasc Genet. 2016 Oct;9(5):395-407. doi: 10.1161/CIRCGENETICS.115.001363. Epub 2016 Sep 2. PubMed PMID: 27591185.
Hypothalamic transcriptomes of 99 mouse strains reveal trans eQTL hotspots, splicing QTLs and novel non-coding genes.
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.
Elife. 2016 Sep 13;5. doi: 10.7554/eLife.15614. PubMed PMID: 27623010.
Catabolic Defect of Branched-Chain Amino Acids Promotes Heart Failure.
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.
Circulation. 2016 May 24;133(21):2038-49. doi: 10.1161/CIRCULATIONAHA.115.020226. Epub 2016 Apr 8. PubMed PMID: 27059949.
Systems Nutrigenomics Reveals Brain Gene Networks Linking Metabolic and Brain Disorders.
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.
EBioMedicine. 2016 May;7:157-66. doi: 10.1016/j.ebiom.2016.04.008. Epub 2016 Apr 13. PubMed PMID: 27322469.
Global analyses of endonucleolytic cleavage in mammals reveal expanded repertoires of cleavage-inducing small RNAs and their targets.
Cass AA, Bahn JH, Lee JH, Greer C, Lin X, Kim Y, Hsiao YH, Xiao X.
Nucleic Acids Res. 2016 Apr 20;44(7):3253-63. doi: 10.1093/nar/gkw164. Epub 2016 Mar 14. PubMed PMID: 26975654.
Alternative splicing modulated by genetic variants demonstrates accelerated evolution regulated by highly conserved proteins.
Hsiao YH, Bahn JH, Lin X, Chan TM, Wang R, Xiao X.
Genome Res. 2016 Apr;26(4):440-50. doi: 10.1101/gr.193359.115. Epub 2016 Feb 17. PubMed PMID: 26888265.
Research Resource: Hormones, Genes, and Athleticism: Effect of Androgens on the Avian Muscular Transcriptome.
Fuxjager MJ, Lee JH, Chan TM, Bahn JH, Chew JG, Xiao X, Schlinger BA.
Mol Endocrinol. 2016 Feb;30(2):254-71. doi: 10.1210/me.2015-1270. Epub 2016 Jan 8. PubMed PMID: 26745669.
2015
RBFox1-mediated RNA splicing regulates cardiac hypertrophy and heart failure.
Gao C, Ren S, Lee JH, Qiu J, Chapski DJ, Rau CD, Zhou Y, Abdellatif M, Nakano A, Vondriska TM, Xiao X, Fu XD, Chen JN, Wang Y.
J Clin Invest. 2016 Jan;126(1):195-206. doi: 10.1172/JCI84015. Epub 2015 Nov 30. PubMed PMID: 26619120.
RASER: reads aligner for SNPs and editing sites of RNA.
Ahn J, Xiao X.
Bioinformatics. 2015 Dec 15;31(24):3906-13. doi: 10.1093/bioinformatics/btv505. Epub 2015 Aug 30. PubMed PMID: 26323713.
ESRP2 controls an adult splicing programme in hepatocytes to support postnatal liver maturation.
Bhate A, Parker DJ, Bebee TW, Ahn J, Arif W, Rashan EH, Chorghade S, Chau A, Lee JH, Anakk S, Carstens RP, Xiao X, Kalsotra A.
Nat Commun. 2015 Nov 4;6:8768. doi: 10.1038/ncomms9768. PubMed PMID: 26531099.
Noncoding RNAs in human saliva as potential disease biomarkers.
Lin X, Lo HC, Wong DT, Xiao X.
Front Genet. 2015;6:175. doi: 10.3389/fgene.2015.00175. eCollection 2015. PubMed PMID: 25999984.
Genome sequence-independent identification of RNA editing sites.
Zhang Q, Xiao X.
Nat Methods. 2015 Apr;12(4):347-50. doi: 10.1038/nmeth.3314. Epub 2015 Mar 2. PubMed PMID: 25730491.
The Sm protein methyltransferase PRMT5 is not required for primordial germ cell specification in mice.
Li Z, Yu J, Hosohama L, Nee K, Gkountela S, Chaudhari S, Cass AA, Xiao X, Clark AT.
EMBO J. 2015 Mar 12;34(6):748-58. doi: 10.15252/embj.201489319. Epub 2014 Dec 17. PubMed PMID: 25519955.
Genomic analysis of ADAR1 binding and its involvement in multiple RNA processing pathways.
Bahn JH, Ahn J, Lin X, Zhang Q, Lee JH, Civelek M, Xiao X.
Nat Commun. 2015 Mar 9;6:6355. doi: 10.1038/ncomms7355. PubMed PMID: 25751603.
The landscape of microRNA, Piwi-interacting RNA, and circular RNA in human saliva.
Bahn JH, Zhang Q, Li F, Chan TM, Lin X, Kim Y, Wong DT, Xiao X.
Clin Chem. 2015 Jan;61(1):221-30. doi: 10.1373/clinchem.2014.230433. Epub 2014 Nov 6. PubMed PMID: 25376581.
Global approaches to alternative splicing and its regulation: Recent advances and open questions. .
Hsiao Y, Cass AA, Bahn J, Lin X, Xiao X.
Chapter In: Translational Bioinformatics in Transcriptomics and Gene Regulation. Dordrecht: Springer; 2015.
2014
Regulation of NF-κB signaling by oxidized glycerophospholipid and IL-1β induced miRs-21-3p and -27a-5p in human aortic endothelial cells.
Romay MC, Che N, Becker SN, Pouldar D, Hagopian R, Xiao X, Lusis AJ, Berliner JA, Civelek M.
J Lipid Res. 2015 Jan;56(1):38-50. doi: 10.1194/jlr.M052670. Epub 2014 Oct 19. PubMed PMID: 25327529.
Cell type-restricted activity of hnRNPM promotes breast cancer metastasis via regulating alternative splicing.
Xu Y, Gao XD, Lee JH, Huang H, Tan H, Ahn J, Reinke LM, Peter ME, Feng Y, Gius D, Siziopikou KP, Peng J, Xiao X, Cheng C.
Genes Dev.2014 Jun 1;28(11):1191-203. doi: 10.1101/gad.241968.114. Epub 2014 May 19. PubMed PMID: 24840202.
Decoding the noncoding transcripts in human heart failure.
Xiao XG, Touma M, Wang Y.
Circulation. 2014 Mar 4;129(9):958-60. doi: 10.1161/CIRCULATIONAHA.114.007548. Epub 2014 Jan 15. PubMed PMID: 24429689.
2013
Analysis and design of RNA sequencing experiments for identifying RNA editing and other single-nucleotide variants.
Lee JH, Ang JK, Xiao X.
RNA. 2013 Jun;19(6):725-32. doi: 10.1261/rna.037903.112. Epub 2013 Apr 18. PubMed PMID: 23598527.
Modeling associated protein-DNA pattern discovery with unified scores.
Chan TM, Lo LY, Sze-To HY, Leung KS, Xiao X, Wong MH.
IEEE/ACM Trans Comput Biol Bioinform. 2013 May-Jun;10(3):696-707. doi: 10.1109/TCBB.2013.60. PubMed PMID: 24091402.
A complex network of factors with overlapping affinities represses splicing through intronic elements.
Wang Y, Xiao X, Zhang J, Choudhury R, Robertson A, Li K, Ma M, Burge CB, Wang Z.
Nat Struct Mol Biol. 2013 Jan;20(1):36-45. doi: 10.1038/nsmb.2459. Epub 2012 Dec 16. PubMed PMID: 23241926.
2012
The difficult calls in RNA editing. Interviewed by H Craig Mak.
Bass B, Hundley H, Li JB, Peng Z, Pickrell J, Xiao XG, Yang L.
Nat Biotechnol. 2012 Dec;30(12):1207-9. doi: 10.1038/nbt.2452. PubMed PMID: 23222792.
Intronic splicing enhancers, cognate splicing factors and context-dependent regulation rules.
Wang Y, Ma M, Xiao X, Wang Z.
Nat Struct Mol Biol. 2012 Oct;19(10):1044-52. doi: 10.1038/nsmb.2377. Epub 2012 Sep 16. PubMed PMID: 22983564.
Identification of allele-specific alternative mRNA processing via transcriptome sequencing.
Li G, Bahn JH, Lee JH, Peng G, Chen Z, Nelson SF, Xiao X.
Nucleic Acids Res. 2012 Jul;40(13):e104. doi: 10.1093/nar/gks280. Epub 2012 Mar 29. PubMed PMID: 22467206.
The cardiotonic steroid digitoxin regulates alternative splicing through depletion of the splicing factors SRSF3 and TRA2B.
Anderson ES, Lin CH, Xiao X, Stoilov P, Burge CB, Black DL.
RNA. 2012 May;18(5):1041-9. doi: 10.1261/rna.032912.112. Epub 2012 Mar 28. PubMed PMID: 22456266.
Identification of vascular and hematopoietic genes downstream of etsrp by deep sequencing in zebrafish.
Gomez G, Lee JH, Veldman MB, Lu J, Xiao X, Lin S.
PLoS One. 2012;7(3):e31658. doi: 10.1371/journal.pone.0031658. Epub 2012 Mar 16. PubMed PMID: 22438865.
2011
Accurate identification of A-to-I RNA editing in human by transcriptome sequencing.
Bahn JH, Lee JH, Li G, Greer C, Peng G, Xiao X.
Genome Res. 2012 Jan;22(1):142-50. doi: 10.1101/gr.124107.111. Epub 2011 Sep 29. PubMed PMID: 21960545.
Analysis of transcriptome complexity through RNA sequencing in normal and failing murine hearts.
Lee JH, Gao C, Peng G, Greer C, Ren S, Wang Y, Xiao X.
Circ Res. 2011 Dec 9;109(12):1332-41. doi: 10.1161/CIRCRESAHA.111.249433. Epub 2011 Oct 27. PubMed PMID: 22034492.
2010
Systems analysis of alternative splicing and its regulation.
Xiao X, Lee JH.
Wiley Interdiscip Rev Syst Biol Med. 2010 Sep-Oct;2(5):550-565. doi: 10.1002/wsbm.84. Review. PubMed PMID: 20836047.
Detection of two distinct forms of apoC-I in great apes.
Puppione DL, Ryan CM, Bassilian S, Souda P, Xiao X, Ryder OA, Whitelegge JP.
Comp Biochem Physiol Part D Genomics Proteomics. 2010 Mar;5(1):73-9. doi: 10.1016/j.cbd.2009.12.003. PubMed PMID: 20209111.