| Year |
Citation |
Score |
| 2023 |
Yamamoto R, Liu Z, Choudhury M, Xiao X. dsRID: in silico identification of dsRNA regions using long-read RNA-seq data. Bioinformatics (Oxford, England). PMID 37871161 DOI: 10.1093/bioinformatics/btad649 |
0.301 |
|
| 2023 |
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. 24: 171. PMID 37474948 DOI: 10.1186/s13059-023-03012-w |
0.401 |
|
| 2023 |
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. PMID 37333092 DOI: 10.1101/2023.06.02.543466 |
0.384 |
|
| 2023 |
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. 9: eade9997. PMID 37027465 DOI: 10.1126/sciadv.ade9997 |
0.343 |
|
| 2023 |
Zheng R, Dunlap M, Lyu J, Gonzalez-Figueroa C, Bobkov G, Harvey SE, Chan TW, Quinones-Valdez G, Choudhury M, Vuong A, Flynn RA, Chang HY, Xiao X, Cheng C. LINE-associated cryptic splicing induces dsRNA-mediated interferon response and tumor immunity. Biorxiv : the Preprint Server For Biology. PMID 36865202 DOI: 10.1101/2023.02.23.529804 |
0.358 |
|
| 2022 |
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. PMID 36449563 DOI: 10.1158/0008-5472.CAN-22-1062 |
0.336 |
|
| 2022 |
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. 8: eabn6398. PMID 36054357 DOI: 10.1126/sciadv.abn6398 |
0.329 |
|
| 2022 |
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. 25: 104836. PMID 35992085 DOI: 10.1016/j.isci.2022.104836 |
0.425 |
|
| 2022 |
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. 146803. PMID 35961439 DOI: 10.1016/j.gene.2022.146803 |
0.316 |
|
| 2021 |
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. 6. PMID 34494556 DOI: 10.1172/jci.insight.150114 |
0.336 |
|
| 2021 |
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. PMID 33452016 DOI: 10.1101/gr.265637.120 |
0.312 |
|
| 2020 |
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. 21: 268. PMID 33106178 DOI: 10.1186/s13059-020-02171-4 |
0.426 |
|
| 2020 |
Tran SS, Zhou Q, Xiao X. Statistical inference of differential RNA editing sites from RNA-sequencing data by hierarchical modeling. Bioinformatics (Oxford, England). PMID 32003773 DOI: 10.1093/Bioinformatics/Btaa066 |
0.502 |
|
| 2019 |
Cass AA, Xiao X. mountainClimber Identifies Alternative Transcription Start and Polyadenylation Sites in RNA-Seq. Cell Systems. PMID 31542416 DOI: 10.1016/J.Cels.2019.07.011 |
0.547 |
|
| 2019 |
Arefeen A, Xiao X, Jiang T. DeepPASTA: deep neural network based polyadenylation site analysis. Bioinformatics (Oxford, England). PMID 31081512 DOI: 10.1093/Bioinformatics/Btz283 |
0.466 |
|
| 2019 |
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, ... ... Xiao X, et al. Allele-specific binding of RNA-binding proteins reveals functional genetic variants in the RNA. Nature Communications. 10: 1338. PMID 30902979 DOI: 10.1038/S41467-019-09292-W |
0.72 |
|
| 2019 |
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. 2: 19. PMID 30652130 DOI: 10.1038/s42003-018-0271-8 |
0.631 |
|
| 2019 |
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. 22: 25-36. PMID 30559470 DOI: 10.1038/S41593-018-0287-X |
0.581 |
|
| 2018 |
Cheung 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. PMID 30503770 DOI: 10.1016/J.Molcel.2018.10.037 |
0.388 |
|
| 2018 |
Arefeen A, Liu J, Xiao X, Jiang T. TAPAS: tool for alternative polyadenylation site analysis. Bioinformatics (Oxford, England). 34: 2521-2529. PMID 30052912 DOI: 10.1093/Bioinformatics/Bty110 |
0.442 |
|
| 2018 |
Harvey SE, Xu Y, Lin X, Gao XD, Qiu Y, Ahn J, Xiao X, Cheng C. Co-regulation of alternative splicing by hnRNPM and ESRP1 during EMT. Rna (New York, N.Y.). PMID 30042172 DOI: 10.1261/Rna.066712.118 |
0.451 |
|
| 2018 |
Hsiao YE, Bahn JH, Yang Y, Lin X, Tran S, Yang EW, Quinones-Valdez G, Xiao X. RNA editing in nascent RNA affects pre-mRNA splicing. Genome Research. PMID 29724793 DOI: 10.1101/Gr.231209.117 |
0.532 |
|
| 2018 |
He X, Li F, Bor B, Koyano K, Cen L, Xiao X, Shi W, Wong DTW. Human tRNA-Derived Small RNAs Modulate Host-Oral Microbial Interactions. Journal of Dental Research. 22034518770605. PMID 29702004 DOI: 10.1177/0022034518770605 |
0.404 |
|
| 2018 |
Li F, Kaczor-Urbanowicz KE, Sun J, Majem B, Lo HC, Kim Y, Koyano K, Liu Rao S, Young Kang S, Mi Kim S, Kim KM, Kim S, Chia D, Elashoff D, Grogan TR, ... Xiao X, et al. Characterization of Human Salivary Extracellular RNA by Next-generation Sequencing. Clinical Chemistry. PMID 29685897 DOI: 10.1373/Clinchem.2017.285072 |
0.494 |
|
| 2017 |
Brümmer A, Yang Y, Chan TW, Xiao X. Structure-mediated modulation of mRNA abundance by A-to-I editing. Nature Communications. 8: 1255. PMID 29093448 DOI: 10.1038/S41467-017-01459-7 |
0.524 |
|
| 2017 |
Kaczor-Urbanowicz KE, Kim Y, Li F, Galeev T, Kitchen RR, Koyano K, Jeong SH, Wang X, Elashoff D, Kang SY, Kim SM, Kim K, Kim S, Chia D, Xiao X, et al. Novel approaches for bioinformatic analysis of salivary RNA Sequencing data in the biomarker development process. Bioinformatics (Oxford, England). PMID 28961734 DOI: 10.1093/Bioinformatics/Btx504 |
0.457 |
|
| 2017 |
Touma M, Kang X, Gao F, Zhao Y, Cass AA, Biniwale R, Xiao X, Eghbali M, Coppola G, Reemtsen B, Wang Y. Wnt11 regulates cardiac chamber development and disease during perinatal maturation. Jci Insight. 2. PMID 28878122 DOI: 10.1172/Jci.Insight.94904 |
0.309 |
|
| 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 N(6)-methyladenosine. Cell Research. PMID 28281539 DOI: 10.1038/Cr.2017.31 |
0.627 |
|
| 2017 |
Gao C, Hu J, Wei C, Hsiao YE, Ren S, Xue Y, Zhou Y, Zhang J, Chen J, Xiao X, Fu X, Xing Y, Wang Y. Function Beyond RNA Splicing for RBFox Family Members in Heart Journal of Molecular and Cellular Cardiology. 112: 146-147. DOI: 10.1016/J.Yjmcc.2017.07.050 |
0.41 |
|
| 2016 |
Hasin-Brumshtein Y, Khan AH, Hormozdiari F, Pan C, Parks BW, Petyuk VA, Piehowski PD, 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. 5. PMID 27623010 DOI: 10.7554/Elife.15614 |
0.422 |
|
| 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, ... ... Xiao X, et al. The long noncoding RNA Chaer defines an epigenetic checkpoint in cardiac hypertrophy. Nature Medicine. PMID 27618650 DOI: 10.1038/Nm.4179 |
0.372 |
|
| 2016 |
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. PMID 27591185 DOI: 10.1161/Circgenetics.115.001363 |
0.401 |
|
| 2016 |
Cass AA, Bahn JH, Lee JH, Greer C, Lin X, Kim Y, Hsiao YE, Xiao X. Global analyses of endonucleolytic cleavage in mammals reveal expanded repertoires of cleavage-inducing small RNAs and their targets. Nucleic Acids Research. PMID 26975654 DOI: 10.1093/Nar/Gkw164 |
0.517 |
|
| 2016 |
Hsiao YE, 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. PMID 26888265 DOI: 10.1101/Gr.193359.115 |
0.489 |
|
| 2016 |
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.). me20151270. PMID 26745669 DOI: 10.1210/Me.2015-1270 |
0.31 |
|
| 2015 |
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. RBFox1-mediated RNA splicing regulates cardiac hypertrophy and heart failure. The Journal of Clinical Investigation. PMID 26619120 DOI: 10.1172/Jci84015 |
0.449 |
|
| 2015 |
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. ESRP2 controls an adult splicing programme in hepatocytes to support postnatal liver maturation. Nature Communications. 6: 8768. PMID 26531099 DOI: 10.1038/Ncomms9768 |
0.375 |
|
| 2015 |
Ahn J, Xiao X. RASER: reads aligner for SNPs and editing sites of RNA. Bioinformatics (Oxford, England). PMID 26323713 DOI: 10.1093/Bioinformatics/Btv505 |
0.402 |
|
| 2015 |
Bahn JH, Ahn J, Lin X, Zhang Q, Lee JH, Civelek M, Xiao X. Genomic analysis of ADAR1 binding and its involvement in multiple RNA processing pathways. Nature Communications. 6: 6355. PMID 25751603 DOI: 10.1038/Ncomms7355 |
0.471 |
|
| 2015 |
Zhang Q, Xiao X. Genome sequence-independent identification of RNA editing sites Nature Methods. 12: 347-350. PMID 25730491 DOI: 10.1038/Nmeth.3314 |
0.473 |
|
| 2015 |
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. 34: 748-58. PMID 25519955 DOI: 10.15252/Embj.201489319 |
0.371 |
|
| 2015 |
Bahn JH, Zhang Q, Li F, Chan TM, Lin X, Kim Y, Wong DT, Xiao X. The landscape of microRNA, Piwi-interacting RNA, and circular RNA in human saliva. Clinical Chemistry. 61: 221-30. PMID 25376581 DOI: 10.1373/Clinchem.2014.230433 |
0.437 |
|
| 2014 |
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. Cell type-restricted activity of hnRNPM promotes breast cancer metastasis via regulating alternative splicing. Genes & Development. 28: 1191-203. PMID 24840202 DOI: 10.1101/Gad.241968.114 |
0.363 |
|
| 2013 |
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 / Ieee, Acm. 10: 696-707. PMID 24091402 DOI: 10.1109/Tcbb.2013.60 |
0.352 |
|
| 2013 |
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.). 19: 725-32. PMID 23598527 DOI: 10.1261/Rna.037903.112 |
0.492 |
|
| 2013 |
Wang Y, Xiao X, Zhang J, Choudhury R, Robertson A, Li K, Ma M, Burge CB, Wang Z. A complex network of factors with overlapping affinities represses splicing through intronic elements Nature Structural and Molecular Biology. 20: 36-45. PMID 23241926 DOI: 10.1038/Nsmb.2459 |
0.724 |
|
| 2012 |
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. 30: 1207-9. PMID 23222792 DOI: 10.1038/Nbt.2452 |
0.363 |
|
| 2012 |
Wang Y, Ma M, Xiao X, Wang Z. Intronic splicing enhancers, cognate splicing factors and context-dependent regulation rules. Nature Structural & Molecular Biology. 19: 1044-52. PMID 22983564 DOI: 10.1038/Nsmb.2377 |
0.653 |
|
| 2012 |
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. 40: e104. PMID 22467206 DOI: 10.1093/Nar/Gks280 |
0.48 |
|
| 2012 |
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.). 18: 1041-9. PMID 22456266 DOI: 10.1261/Rna.032912.112 |
0.657 |
|
| 2012 |
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. 7: e31658. PMID 22438865 DOI: 10.1371/Journal.Pone.0031658 |
0.402 |
|
| 2012 |
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. 22: 142-50. PMID 21960545 DOI: 10.1101/Gr.124107.111 |
0.407 |
|
| 2011 |
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. 109: 1332-41. PMID 22034492 DOI: 10.1161/Circresaha.111.249433 |
0.365 |
|
| 2011 |
Xiao X, Lee JH. Systems analysis of alternative splicing and its regulation. Wiley Interdisciplinary Reviews. Systems Biology and Medicine. 2: 550-565. PMID 20836047 DOI: 10.1002/Wsbm.84 |
0.513 |
|
| 2009 |
Xiao X, Wang Z, Jang M, Nutiu R, Wang ET, Burge CB. Splice site strength-dependent activity and genetic buffering by poly-G runs Nature Structural and Molecular Biology. 16: 1094-1100. PMID 19749754 DOI: 10.1038/Nsmb.1661 |
0.745 |
|
| 2008 |
Kalsotra A, Xiao X, Ward AJ, Castle JC, Johnson JM, Burge CB, Cooper TA. A postnatal switch of CELF and MBNL proteins reprograms alternative splicing in the developing heart Proceedings of the National Academy of Sciences of the United States of America. 105: 20333-20338. PMID 19075228 DOI: 10.1073/Pnas.0809045105 |
0.609 |
|
| 2007 |
Xiao X, Wang Z, Jang M, Burge CB. Coevolutionary networks of splicing cis-regulatory elements Proceedings of the National Academy of Sciences of the United States of America. 104: 18583-18588. PMID 17998536 DOI: 10.1073/Pnas.0707349104 |
0.714 |
|
| 2007 |
Calarco JA, Xing Y, Cáceres M, Calarco JP, Xiao X, Pan Q, Lee C, Preuss TM, Blencowe BJ. Global analysis of alternative splicing differences between humans and chimpanzees. Genes & Development. 21: 2963-75. PMID 17978102 DOI: 10.1101/Gad.1606907 |
0.413 |
|
| 2007 |
Wang Z, Xiao X, Friedman B, Shomron N, Burge CB. Towards an RNA Splicing Code The Faseb Journal. 21. DOI: 10.1096/Fasebj.21.5.A147-B |
0.631 |
|
| 2006 |
Stadler MB, Shomron N, Yeo GW, Schneider A, Xiao X, Burge CB. Inference of splicing regulatory activities by sequence neighborhood analysis. Plos Genetics. 2: e191. PMID 17121466 DOI: 10.1371/Journal.Pgen.0020191 |
0.693 |
|
| 2006 |
Wang Z, Xiao X, Van Nostrand E, Burge CB. General and Specific Functions of Exonic Splicing Silencers in Splicing Control Molecular Cell. 23: 61-70. PMID 16797197 DOI: 10.1016/J.Molcel.2006.05.018 |
0.704 |
|
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