{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,6,6]],"date-time":"2024-06-06T10:36:03Z","timestamp":1717670163214},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"24","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,12,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: The sequencing of personal genomes enabled analysis of variation in transcription factor (TF) binding, chromatin structure and gene expression and indicated how they contribute to phenotypic variation. It is hypothesized that using the reference genome for mapping ChIP-seq or RNA-seq reads may introduce errors, especially at polymorphic genomic regions.<\/jats:p>\n               <jats:p>Results: We developed a Personal Genome Editor (perEditor) that changes the reference human genome (NCBI36\/hg18) into an individual genome, taking into account single nucleotide polymorphisms (SNPs), insertions and deletions, copy number variation, and chromosomal rearrangements. perEditor outputs two alleles (maternal, paternal) of the individual genome that is ready for mapping ChIP-seq and RNA-seq reads, and enabling the analyses of allele specific binding, chromatin structure and gene expression.<\/jats:p>\n               <jats:p>Availability: perEditor is available at http:\/\/biocomp.bioen.uiuc.edu\/perEditor.<\/jats:p>\n               <jats:p>Contact: \u00a0szhong@illinois.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr578","type":"journal-article","created":{"date-parts":[[2011,10,18]],"date-time":"2011-10-18T04:27:59Z","timestamp":1318912079000},"page":"3427-3429","source":"Crossref","is-referenced-by-count":9,"title":["Mapping personal functional data to personal genomes"],"prefix":"10.1093","volume":"27","author":[{"given":"Marcelo","family":"Rivas-Astroza","sequence":"first","affiliation":[{"name":"1 Department of Bioengineering and 2Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA"}]},{"given":"Dan","family":"Xie","sequence":"additional","affiliation":[{"name":"1 Department of Bioengineering and 2Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA"}]},{"given":"Xiaoyi","family":"Cao","sequence":"additional","affiliation":[{"name":"1 Department of Bioengineering and 2Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA"}]},{"given":"Sheng","family":"Zhong","sequence":"additional","affiliation":[{"name":"1 Department of Bioengineering and 2Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA"},{"name":"1 Department of Bioengineering and 2Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA"}]}],"member":"286","published-online":{"date-parts":[[2011,10,17]]},"reference":[{"key":"2023012511294722300_B1","doi-asserted-by":"crossref","first-page":"232","DOI":"10.1126\/science.1183621","article-title":"Variation in transcription factor binding among humans","volume":"328","author":"Kasowski","year":"2010","journal-title":"Science"},{"key":"2023012511294722300_B2","doi-asserted-by":"crossref","first-page":"R25","DOI":"10.1186\/gb-2009-10-3-r25","article-title":"Ultrafast and memory-efficient alignment of short DNA sequences to the human genome","volume":"10","author":"Langmead","year":"2009","journal-title":"Genome Biol."},{"key":"2023012511294722300_B3","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1126\/science.1207018","article-title":"Widespread RNA and DNA sequence differences in the human transcriptome","volume":"333","author":"Li","year":"2011","journal-title":"Science"},{"key":"2023012511294722300_B4","doi-asserted-by":"crossref","first-page":"47","DOI":"10.31887\/DCNS.2010.12.1\/jlunshof","article-title":"Personal genomes in progress: from the human genome project to the personal genome project","volume":"12","author":"Lunshof","year":"2010","journal-title":"Dialog. 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Neurosci."},{"key":"2023012511294722300_B5","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1126\/science.1184655","article-title":"Heritable individual-specific and allele-specific chromatin signatures in humans","volume":"328","author":"McDaniell","year":"2010","journal-title":"Science"},{"key":"2023012511294722300_B6","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1038\/nature08658","article-title":"A comprehensive catalogue of somatic mutations from a human cancer genome","volume":"463","author":"Pleasance","year":"2009","journal-title":"Nature"},{"key":"2023012511294722300_B7","doi-asserted-by":"crossref","first-page":"184","DOI":"10.1038\/nature08629","article-title":"A small-cell lung cancer genome with complex signatures of tobacco exposure","volume":"463","author":"Pleasance","year":"2010","journal-title":"Nature"},{"key":"2023012511294722300_B8","doi-asserted-by":"crossref","first-page":"1061","DOI":"10.1038\/nature09534","article-title":"A map of human genome variation from population-scale sequencing","volume":"467","author":"The 1000 Genomes Project Consortium","year":"2010","journal-title":"Nature"},{"key":"2023012511294722300_B9","doi-asserted-by":"crossref","first-page":"e1001033","DOI":"10.1371\/journal.pgen.1001033","article-title":"Inter- and intra-individual variation in allele-specific dna methylation and gene expression in children conceived using assisted reproductive technology","volume":"6","author":"Turan","year":"2010","journal-title":"Plos Genet."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/24\/3427\/48861110\/bioinformatics_27_24_3427.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/24\/3427\/48861110\/bioinformatics_27_24_3427.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T11:30:06Z","timestamp":1674646206000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/27\/24\/3427\/306080"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,10,17]]},"references-count":9,"journal-issue":{"issue":"24","published-print":{"date-parts":[[2011,12,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btr578","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2011,12,15]]},"published":{"date-parts":[[2011,10,17]]}}}