Xing Laboratory Publications

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Below is a list of selected publications from the Xing Lab.

Xin R, Gao Y, Gao Y, Wang R, Kadash-Edmondson KE, Liu B, Wang Y, Lin L, Xing Y. isoCirc catalogs full-length circular RNA isoforms in human transcriptomes. Nat Commun. 2021 Jan; 12(1):266. doi: 10.1038/s41467-020-20459-8. PMID: 33436621; PMCID: PMC7803736
Demirdjian L, Xu Y, Bahrami-Samani E, Pan Y, Stein S, Xie Z, Park E, Wu YN, Xing Y. Detecting Allele-Specific Alternative Splicing From Population-Scale RNA-Seq Data. Am J Hum Genet. 2020 Sep; 107(3): 461-472. PubMed PMID 32781045
Zhang Y, Yang HT, Kadash-Edmondson K, Pan Y, Pan Z, Davidson BL, Xing Y. Regional Variation of Splicing QTLs in Human Brain. Am J Hum Genet. 2020 Aug; 107(2): 196-210. PubMed PMID 32589925
Phillips JW*, Pan Y*, Tsai BL, Xie Z, Demirdjian L, Xiao W, Yang HT, Zhang Y, Lin CH, Cheng D, Hu Q, Liu S, Black DL, Witte ON+, Xing Y+. Pathway-guided analysis identifies Myc-dependent alternative pre-mRNA splicing in aggressive prostate cancers. Proc Nat Acad Sci USA. 2020 Mar; 117(10): 5269-5279. PubMed PMID: 32086391. (+Joint corresponding authors; *Joint first authors)
Zhang Z*, Pan Z*, Ying Y, Xie Z, Adhikari S, Phillips J, Carstens RP, Black DL, Wu Y, Xing Y. Deep learning-augmented RNA-seq analysis of transcript splicing. Nat Methods. 2019 Jan; 16(4):307-310. PMID: 30923373 (*Joint first authors)
Park E, Pan Z, Zhang Z, Lin L, Xing Y. The expanding landscape of alternative splicing variation in human populations. Am J Hum Genet. 2018 Jan; 102(1): 11-26. PubMed PMID 29304370
Molinie B*, Wang J*, Lim KS, Hillebrand R, Lu ZX, Van Wittenberghe N, Howard BD, Daneshvar K, Mullen A, Dedon P, Xing Y+, Giallourakis CC.+. (m6A-LAIC-seq) reveals the census and complexity of the m6A epitranscriptome. Nat Methods. 2016 Aug; 13(8):692-698. PMID: 27376769 (+Joint corresponding authors; *Joint first authors)
Shen S*, Park JW*, Lu ZX, Lin L, Henry MD, Wu YN, Zhou Q, Xing Y. rMATS: robust and flexible detection of differential alternative splicing from replicate RNA-Seq data. Proc Natl Acad Sci USA. 2014 Dec; 111(51): E5593-5601. PubMed PMID 25480548. (*Joint first authors.)
Batista PJ, Molinie B , Wang J, Qu K, Zhang J, Li L, Bouley DM, Lujan E, Haddad B, Daneshvar K, Carter AC, Flynn RA, Zhou C, Lim KS, Dedon P, Wernig M, Mullen AC, Xing Y*, Giallourakis CC*, Chang HY.*. m(6)A RNA modification controls cell fate transition in mammalian embryonic stem cells. Cell Stem Cell. 2014 Oct; 15(6): 707-719. PubMed PMID 25456834. (*Joint corresponding authors.)
Xing Y, Lee C. Alternative splicing and RNA selection pressure--evolutionary consequences for eukaryotic genomes. Nat Rev Genet. 2006 Jul; 7(7): 499-509. PubMed PMID 16770337