Xinshu Xiao

Title(s)Professor, Integrative Biology And Physiology
SchoolCollege of Letters and Science
ORCID ORCID Icon0000-0002-9362-8029 Additional info
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    Massachusetts Institute of Technology, Cambridge, MAPhD2004Health Sciences and Technology

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    Regulation and function of dsRNAs derived from retrotransposable elements in AD
    NIH/NIA R01AG078950Sep 1, 2022 - May 31, 2027
    Role: Principal Investigator
    Exploiting public genomic and transcriptomic data to uncover cancer-RNA editing relationships
    NIH/NCI R01CA262686Jul 1, 2022 - Jun 30, 2027
    Role: Principal Investigator
    Systematic analysis of functional 3’ UTR genetic variants and their relevance to Alzheimer’s Disease
    NIH/NIA R01AG075206Feb 15, 2022 - Nov 30, 2026
    Role: Principal Investigator
    Systematic approaches to deciphering regulation and function of RNA editing in brain
    NIH R01MH123177Dec 1, 2020 - Oct 31, 2025
    Role: Principal Investigator
    Functional genetic variants in post-transcriptional regulation in Alzheimer?s Disease
    NIH R56AG064931Sep 15, 2019 - Aug 31, 2021
    Role: Principal Investigator
    Prioritization of splicing-altering genetic variants in Alzheimer's disease
    NIH R01AG056476Aug 1, 2017 - Apr 30, 2022
    Role: Principal Investigator
    Analysis of functional genetic variants in RNA processing and expression
    NIH U01HG009417Feb 1, 2017 - Jan 31, 2022
    Role: Principal Investigator
    Informatic tools for single-nucleotide analysis of cancer RNA-Seq
    NIH U01CA204695Apr 12, 2016 - Mar 31, 2020
    Role: Principal Investigator
    Analysis of causal genetic variants in pre-mRNA processing using ENCODE data
    NIH U01HG007013Sep 17, 2012 - Jun 30, 2017
    Role: Principal Investigator
    Functional genetic variations in splicing regulation
    NIH R01HG006264Apr 3, 2012 - Mar 31, 2019
    Role: Principal Investigator
    Functions of genetic variants in alternative splicing and biological networks
    NIH R21DA027039Sep 30, 2009 - Aug 31, 2011
    Role: Principal Investigator

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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. dsRID: in silico identification of dsRNA regions using long-read RNA-seq data. Bioinformatics. 2023 11 01; 39(11). Yamamoto R, Liu Z, Choudhury M, Xiao X. PMID: 37871161; PMCID: PMC10628436.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    2. Genetic pathways regulating the longitudinal acquisition of cocaine self-administration in a panel of inbred and recombinant inbred mice. Cell Rep. 2023 08 29; 42(8):112856. Khan AH, Bagley JR, LaPierre N, Gonzalez-Figueroa C, Spencer TC, Choudhury M, Xiao X, Eskin E, Jentsch JD, Smith DJ. PMID: 37481717; PMCID: PMC10530068.
      View in: PubMed   Mentions: 1     Fields:    Translation:Animals
    3. L-GIREMI uncovers RNA editing sites in long-read RNA-seq. Genome Biol. 2023 07 20; 24(1):171. Liu Z, Quinones-Valdez G, Fu T, Huang E, Choudhury M, Reese F, Mortazavi A, Xiao X. PMID: 37474948; PMCID: PMC10360234.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    4. dsRID: Editing-free in silico identification of dsRNA region using long-read RNA-seq data. bioRxiv. 2023 Jun 07. Yamamoto R, Liu Z, Choudhury M, Xiao X. PMID: 37333092; PMCID: PMC10274638.
      View in: PubMed   Mentions:
    5. Widespread RNA hypoediting in schizophrenia and its relevance to mitochondrial function. Sci Adv. 2023 04 07; 9(14):eade9997. Choudhury M, Fu T, Amoah K, Jun HI, Chan TW, Park S, Walker DW, Bahn JH, Xiao X. PMID: 37027465; PMCID: PMC10081846.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    6. Single-Cell Analysis in Lung Adenocarcinoma Implicates RNA Editing in Cancer Innate Immunity and Patient Prognosis. Cancer Res. 2023 02 03; 83(3):374-385. Chan TW, Dodson JP, Arbet J, Boutros PC, Xiao X. PMID: 36449563; PMCID: PMC9898195.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    7. scAllele: A versatile tool for the detection and analysis of variants in scRNA-seq. Sci Adv. 2022 Sep 02; 8(35):eabn6398. Quinones-Valdez G, Fu T, Chan TW, Xiao X. PMID: 36054357.
      View in: PubMed   Mentions: 2     Fields:    
    8. Improved zebra finch brain transcriptome identifies novel proteins with sex differences. Gene. 2022 Nov 15; 843:146803. He J, Fu T, Zhang L, Wanrong Gao L, Rensel M, Remage-Healey L, White SA, Gedman G, Whitelegge J, Xiao X, Schlinger BA. PMID: 35961439.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimalsCells
    9. Multifaceted role of RNA editing in promoting loss-of-function of PODXL in cancer. iScience. 2022 Aug 19; 25(8):104836. Fu T, Chan TW, Bahn JH, Kim TH, Rowat AC, Xiao X. PMID: 35992085; PMCID: PMC9382340.
      View in: PubMed   Mentions: 1  
    10. Lipin 1 modulates mRNA splicing during fasting adaptation in liver. JCI Insight. 2021 09 08; 6(17). Wang H, Chan TW, Vashisht AA, Drew BG, Calkin AC, Harris TE, Wohlschlegel JA, Xiao X, Reue K. PMID: 34494556; PMCID: PMC8492312.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansAnimalsCells
    11. Genetics of white color and iridophoroma in "Lemon Frost" leopard geckos. PLoS Genet. 2021 06; 17(6):e1009580. Guo L, Bloom J, Sykes S, Huang E, Kashif Z, Pham E, Ho K, Alcaraz A, Xiao XG, Duarte-Vogel S, Kruglyak L. PMID: 34166378; PMCID: PMC8224956.
      View in: PubMed   Mentions: 7     Fields:    Translation:Animals
    12. Long-term maturation of human cortical organoids matches key early postnatal transitions. Nat Neurosci. 2021 03; 24(3):331-342. 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. PMID: 33619405; PMCID: PMC8109149.
      View in: PubMed   Mentions: 110     Fields:    Translation:HumansCells
    13. Allele-specific alternative splicing and its functional genetic variants in human tissues. Genome Res. 2021 03; 31(3):359-371. Amoah K, Hsiao YE, Bahn JH, Sun Y, Burghard C, Tan BX, Yang EW, Xiao X. PMID: 33452016; PMCID: PMC7919445.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    14. Molecular consequences of fetal alcohol exposure on amniotic exosomal miRNAs with functional implications for stem cell potency and differentiation. PLoS One. 2020; 15(11):e0242276. Tavanasefat H, Li F, Koyano K, Gourtani BK, Marty V, Mulpuri Y, Lee SH, Shin KH, Wong DTW, Xiao X, Spigelman I, Kim Y. PMID: 33196678; PMCID: PMC7668603.
      View in: PubMed   Mentions: 8     Fields:    Translation:AnimalsCells
    15. Extracellular microRNA 3' end modification across diverse body fluids. Epigenetics. 2021 09; 16(9):1000-1015. Koyano K, Bahn JH, Xiao X. PMID: 33092484; PMCID: PMC8451466.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    16. RNA editing in cancer impacts mRNA abundance in immune response pathways. Genome Biol. 2020 10 26; 21(1):268. Chan TW, Fu T, Bahn JH, Jun HI, Lee JH, Quinones-Valdez G, Cheng C, Xiao X. PMID: 33106178; PMCID: PMC7586670.
      View in: PubMed   Mentions: 17     Fields:    Translation:HumansCells
    17. p38 Mitogen-activated protein kinase regulates chamber-specific perinatal growth in heart. J Clin Invest. 2020 10 01; 130(10):5287-5301. 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. PMID: 32573492; PMCID: PMC7524480.
      View in: PubMed   Mentions: 9     Fields:    Translation:AnimalsCells
    18. mountainClimber Identifies Alternative Transcription Start and Polyadenylation Sites in RNA-Seq. Cell Syst. 2019 10 23; 9(4):393-400.e6. Cass AA, Xiao X. PMID: 31542416; PMCID: PMC6813887.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansCells
    19. Allele-specific binding of RNA-binding proteins reveals functional genetic variants in the RNA. Nat Commun. 2019 03 22; 10(1):1338. 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. PMID: 30902979; PMCID: PMC6430814.
      View in: PubMed   Mentions: 25     Fields:    Translation:HumansCells
    20. Regulation of RNA editing by RNA-binding proteins in human cells. Commun Biol. 2019; 2:19. 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. PMID: 30652130; PMCID: PMC6331435.
      View in: PubMed   Mentions: 63  Translation:HumansCells
    21. Widespread RNA editing dysregulation in brains from autistic individuals. Nat Neurosci. 2019 01; 22(1):25-36. 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. PMID: 30559470; PMCID: PMC6375307.
      View in: PubMed   Mentions: 95     Fields:    Translation:HumansCells
    22. A Multiplexed Assay for Exon Recognition Reveals that an Unappreciated Fraction of Rare Genetic Variants Cause Large-Effect Splicing Disruptions. Mol Cell. 2019 01 03; 73(1):183-194.e8. Chong R, Insigne KD, Yao D, Burghard CP, Wang J, Hsiao YE, Jones EM, Goodman DB, Xiao X, Kosuri S. PMID: 30503770; PMCID: PMC6599603.
      View in: PubMed   Mentions: 47     Fields:    Translation:HumansCells
    23. Loss of MECP2 Leads to Activation of P53 and Neuronal Senescence. Stem Cell Reports. 2018 05 08; 10(5):1453-1463. 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. PMID: 29742391; PMCID: PMC5995366.
      View in: PubMed   Mentions: 34     Fields:    Translation:HumansCells
    24. FoxP2 isoforms delineate spatiotemporal transcriptional networks for vocal learning in the zebra finch. Elife. 2018 01 23; 7. Burkett ZD, Day NF, Kimball TH, Aamodt CM, Heston JB, Hilliard AT, Xiao X, White SA. PMID: 29360038; PMCID: PMC5826274.
      View in: PubMed   Mentions: 11     Fields:    Translation:Animals
    25. Novel approaches for bioinformatic analysis of salivary RNA sequencing data for development. Bioinformatics. 2018 01 01; 34(1):1-8. 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. PMID: 28961734; PMCID: PMC5859991.
      View in: PubMed   Mentions: 13     Fields:    Translation:Humans
    26. Advances in chromosomal translocations and fusion genes in sarcomas and potential therapeutic applications. Cancer Treat Rev. 2018 Feb; 63:61-70. Xiao X, Garbutt CC, Hornicek F, Guo Z, Duan Z. PMID: 29247978.
      View in: PubMed   Mentions: 17     Fields:    Translation:HumansAnimals
    27. Structure-mediated modulation of mRNA abundance by A-to-I editing. Nat Commun. 2017 11 02; 8(1):1255. Brümmer A, Yang Y, Chan TW, Xiao X. PMID: 29093448; PMCID: PMC5665907.
      View in: PubMed   Mentions: 40     Fields:    Translation:HumansCells
    28. Hypothalamic transcriptomes of 99 mouse strains reveal trans eQTL hotspots, splicing QTLs and novel non-coding genes. Elife. 2016 09 13; 5. 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. PMID: 27623010; PMCID: PMC5053804.
      View in: PubMed   Mentions: 23     Fields:    Translation:AnimalsCells
    29. Decoding the Long Noncoding RNA During Cardiac Maturation: A Roadmap for Functional Discovery. Circ Cardiovasc Genet. 2016 Oct; 9(5):395-407. Touma M, Kang X, Zhao Y, Cass AA, Gao F, Biniwale R, Coppola G, Xiao X, Reemtsen B, Wang Y. PMID: 27591185; PMCID: PMC5085833.
      View in: PubMed   Mentions: 26     Fields:    Translation:HumansAnimalsCells
    30. Systems Nutrigenomics Reveals Brain Gene Networks Linking Metabolic and Brain Disorders. EBioMedicine. 2016 May; 7:157-66. 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. PMID: 27322469; PMCID: PMC4909610.
      View in: PubMed   Mentions: 37     Fields:    Translation:HumansAnimals
    31. Catabolic Defect of Branched-Chain Amino Acids Promotes Heart Failure. Circulation. 2016 May 24; 133(21):2038-49. 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. PMID: 27059949; PMCID: PMC4879058.
      View in: PubMed   Mentions: 217     Fields:    Translation:HumansAnimalsCells
    32. Global analyses of endonucleolytic cleavage in mammals reveal expanded repertoires of cleavage-inducing small RNAs and their targets. Nucleic Acids Res. 2016 Apr 20; 44(7):3253-63. Cass AA, Bahn JH, Lee JH, Greer C, Lin X, Kim Y, Hsiao YH, Xiao X. PMID: 26975654; PMCID: PMC4838385.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansAnimalsCells
    33. Alternative splicing modulated by genetic variants demonstrates accelerated evolution regulated by highly conserved proteins. Genome Res. 2016 Apr; 26(4):440-50. Hsiao YH, Bahn JH, Lin X, Chan TM, Wang R, Xiao X. PMID: 26888265; PMCID: PMC4817768.
      View in: PubMed   Mentions: 24     Fields:    Translation:HumansAnimalsCells
    34. Research Resource: Hormones, Genes, and Athleticism: Effect of Androgens on the Avian Muscular Transcriptome. Mol Endocrinol. 2016 Feb; 30(2):254-71. Fuxjager MJ, Lee JH, Chan TM, Bahn JH, Chew JG, Xiao X, Schlinger BA. PMID: 26745669; PMCID: PMC4792231.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansAnimalsCells
    35. RASER: reads aligner for SNPs and editing sites of RNA. Bioinformatics. 2015 Dec 15; 31(24):3906-13. Ahn J, Xiao X. PMID: 26323713; PMCID: PMC4692970.
      View in: PubMed   Mentions: 14     Fields:    Translation:Cells
    36. Noncoding RNAs in human saliva as potential disease biomarkers. Front Genet. 2015; 6:175. Lin X, Lo HC, Wong DT, Xiao X. PMID: 25999984; PMCID: PMC4423433.
      View in: PubMed   Mentions: 21  
    37. Genome sequence-independent identification of RNA editing sites. Nat Methods. 2015 Apr; 12(4):347-50. Zhang Q, Xiao X. PMID: 25730491; PMCID: PMC4382388.
      View in: PubMed   Mentions: 63     Fields:    Translation:HumansCells
    38. The Sm protein methyltransferase PRMT5 is not required for primordial germ cell specification in mice. EMBO J. 2015 Mar 12; 34(6):748-58. Li Z, Yu J, Hosohama L, Nee K, Gkountela S, Chaudhari S, Cass AA, Xiao X, Clark AT. PMID: 25519955; PMCID: PMC4369312.
      View in: PubMed   Mentions: 20     Fields:    Translation:AnimalsCells
    39. Regulation of NF-κB signaling by oxidized glycerophospholipid and IL-1β induced miRs-21-3p and -27a-5p in human aortic endothelial cells. J Lipid Res. 2015 Jan; 56(1):38-50. Romay MC, Che N, Becker SN, Pouldar D, Hagopian R, Xiao X, Lusis AJ, Berliner JA, Civelek M. PMID: 25327529; PMCID: PMC4274069.
      View in: PubMed   Mentions: 24     Fields:    Translation:HumansCells
    40. Decoding the noncoding transcripts in human heart failure. Circulation. 2014 Mar 04; 129(9):958-60. Xiao XG, Touma M, Wang Y. PMID: 24429689; PMCID: PMC4046328.
      View in: PubMed   Mentions: 8     Fields:    Translation:Humans
    41. Modeling associated protein-DNA pattern discovery with unified scores. IEEE/ACM Trans Comput Biol Bioinform. 2013 May-Jun; 10(3):696-707. Chan TM, Lo LY, Sze-To HY, Leung KS, Xiao X, Wong MH. PMID: 24091402.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    42. Analysis and design of RNA sequencing experiments for identifying RNA editing and other single-nucleotide variants. RNA. 2013 Jun; 19(6):725-32. Lee JH, Ang JK, Xiao X. PMID: 23598527; PMCID: PMC3683905.
      View in: PubMed   Mentions: 42     Fields:    Translation:HumansCells
    43. The difficult calls in RNA editing. Interviewed by H Craig Mak. Nat Biotechnol. 2012 Dec; 30(12):1207-9. Bass B, Hundley H, Li JB, Peng Z, Pickrell J, Xiao XG, Yang L. PMID: 23222792.
      View in: PubMed   Mentions: 19     Fields:    Translation:HumansCells
    44. Identification of allele-specific alternative mRNA processing via transcriptome sequencing. Nucleic Acids Res. 2012 Jul; 40(13):e104. Li G, Bahn JH, Lee JH, Peng G, Chen Z, Nelson SF, Xiao X. PMID: 22467206; PMCID: PMC3401465.
      View in: PubMed   Mentions: 41     Fields:    Translation:HumansCells
    45. The cardiotonic steroid digitoxin regulates alternative splicing through depletion of the splicing factors SRSF3 and TRA2B. RNA. 2012 May; 18(5):1041-9. Anderson ES, Lin CH, Xiao X, Stoilov P, Burge CB, Black DL. PMID: 22456266; PMCID: PMC3334691.
      View in: PubMed   Mentions: 37     Fields:    Translation:HumansCells
    46. Identification of vascular and hematopoietic genes downstream of etsrp by deep sequencing in zebrafish. PLoS One. 2012; 7(3):e31658. Gomez G, Lee JH, Veldman MB, Lu J, Xiao X, Lin S. PMID: 22438865; PMCID: PMC3306315.
      View in: PubMed   Mentions: 16     Fields:    Translation:AnimalsCells
    47. Analysis of transcriptome complexity through RNA sequencing in normal and failing murine hearts. Circ Res. 2011 Dec 09; 109(12):1332-41. Lee JH, Gao C, Peng G, Greer C, Ren S, Wang Y, Xiao X. PMID: 22034492; PMCID: PMC3243366.
      View in: PubMed   Mentions: 116     Fields:    Translation:AnimalsCells
    48. Accurate identification of A-to-I RNA editing in human by transcriptome sequencing. Genome Res. 2012 Jan; 22(1):142-50. Bahn JH, Lee JH, Li G, Greer C, Peng G, Xiao X. PMID: 21960545; PMCID: PMC3246201.
      View in: PubMed   Mentions: 207     Fields:    Translation:HumansCells
    49. Systems analysis of alternative splicing and its regulation. Wiley Interdiscip Rev Syst Biol Med. 2010 Sep-Oct; 2(5):550-565. Xiao X, Lee JH. PMID: 20836047.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansAnimalsCells
    50. Detection of two distinct forms of apoC-I in great apes. Comp Biochem Physiol Part D Genomics Proteomics. 2010 Mar; 5(1):73-9. Puppione DL, Ryan CM, Bassilian S, Souda P, Xiao X, Ryder OA, Whitelegge JP. PMID: 20209111; PMCID: PMC2830554.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansAnimalsCells
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