{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,20]],"date-time":"2026-06-20T07:10:21Z","timestamp":1781939421897,"version":"3.54.5"},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"12","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Fragmented RNA immunoprecipitation combined with RNA sequencing enabled the unbiased study of RNA epigenome at a near single-base resolution; however, unique features of this new type of data call for novel computational techniques.<\/jats:p>\n               <jats:p>Result: Through examining the connections of RNA epigenome sequencing data with two well-studied data types, ChIP-Seq and RNA-Seq, we unveiled the salient characteristics of this new data type. The computational strategies were discussed accordingly, and a novel data processing pipeline was proposed that combines several existing tools with a newly developed exome-based approach \u2018exomePeak\u2019 for detecting, representing and visualizing the post-transcriptional RNA modification sites on the transcriptome.<\/jats:p>\n               <jats:p>Availability: The MATLAB package \u2018exomePeak\u2019 and additional details are available at http:\/\/compgenomics.utsa.edu\/exomePeak\/.<\/jats:p>\n               <jats:p>Contact: \u00a0yufei.huang@utsa.edu or jmeng@mit.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt171","type":"journal-article","created":{"date-parts":[[2013,4,16]],"date-time":"2013-04-16T00:15:15Z","timestamp":1366071315000},"page":"1565-1567","source":"Crossref","is-referenced-by-count":176,"title":["Exome-based analysis for RNA epigenome sequencing data"],"prefix":"10.1093","volume":"29","author":[{"given":"Jia","family":"Meng","sequence":"first","affiliation":[{"name":"1 Picower Institute for Learning and Memory, 2Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, 3Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, MA 02139, 4Department of Electrical and Computer Engineering, University of Texas at San Antonio, San, Antonio, TX 78249, 5Department of Cellular & Structural Biology, 6Greehey Children\u2019s Cancer Research Institute and 7Department of Epidemiology and Biostatistics, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA"},{"name":"1 Picower Institute for Learning and Memory, 2Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, 3Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, MA 02139, 4Department of Electrical and Computer Engineering, University of Texas at San Antonio, San, Antonio, TX 78249, 5Department of Cellular & Structural Biology, 6Greehey Children\u2019s Cancer Research Institute and 7Department of Epidemiology and Biostatistics, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA"},{"name":"1 Picower Institute for Learning and Memory, 2Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, 3Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, MA 02139, 4Department of Electrical and Computer Engineering, University of Texas at San Antonio, San, Antonio, TX 78249, 5Department of Cellular & Structural Biology, 6Greehey Children\u2019s Cancer Research Institute and 7Department of Epidemiology and Biostatistics, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaodong","family":"Cui","sequence":"additional","affiliation":[{"name":"1 Picower Institute for Learning and Memory, 2Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, 3Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, MA 02139, 4Department of Electrical and Computer Engineering, University of Texas at San Antonio, San, Antonio, TX 78249, 5Department of Cellular & Structural Biology, 6Greehey Children\u2019s Cancer Research Institute and 7Department of Epidemiology and Biostatistics, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manjeet K.","family":"Rao","sequence":"additional","affiliation":[{"name":"1 Picower Institute for Learning and Memory, 2Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, 3Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, MA 02139, 4Department of Electrical and Computer Engineering, University of Texas at San Antonio, San, Antonio, TX 78249, 5Department of Cellular & Structural Biology, 6Greehey Children\u2019s Cancer Research Institute and 7Department of Epidemiology and Biostatistics, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA"},{"name":"1 Picower Institute for Learning and Memory, 2Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, 3Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, MA 02139, 4Department of Electrical and Computer Engineering, University of Texas at San Antonio, San, Antonio, TX 78249, 5Department of Cellular & Structural Biology, 6Greehey Children\u2019s Cancer Research Institute and 7Department of Epidemiology and Biostatistics, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yidong","family":"Chen","sequence":"additional","affiliation":[{"name":"1 Picower Institute for Learning and Memory, 2Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, 3Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, MA 02139, 4Department of Electrical and Computer Engineering, University of Texas at San Antonio, San, Antonio, TX 78249, 5Department of Cellular & Structural Biology, 6Greehey Children\u2019s Cancer Research Institute and 7Department of Epidemiology and Biostatistics, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA"},{"name":"1 Picower Institute for Learning and Memory, 2Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, 3Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, MA 02139, 4Department of Electrical and Computer Engineering, University of Texas at San Antonio, San, Antonio, TX 78249, 5Department of Cellular & Structural Biology, 6Greehey Children\u2019s Cancer Research Institute and 7Department of Epidemiology 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