{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:56Z","timestamp":1772138096684,"version":"3.50.1"},"reference-count":38,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2019,9,10]],"date-time":"2019-09-10T00:00:00Z","timestamp":1568073600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"National Institutes of Health of The United States","award":["5R01NS079715"],"award-info":[{"award-number":["5R01NS079715"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Functional genomics experiments generate genomewide signal profiles that are dense information sources for annotating the regulatory elements. These profiles measure epigenetic activity at the nucleotide resolution and they exhibit distinctive patterns as they fluctuate along the genome. Most notable of these patterns are the valley patterns that are prevalently observed in assays such as ChIP Sequencing and bisulfite sequencing. The genomic positions of valleys pinpoint locations of cis-regulatory elements such as enhancers and insulators. Systematic identification of the valleys provides novel information for delineating the annotation of regulatory elements. Nevertheless, the valleys are not reported by majority of the analysis pipelines.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We describe EpiSAFARI, a computational method for sensitive detection of valleys from diverse types of epigenetic profiles. EpiSAFARI employs a novel smoothing method for decreasing noise in signal profiles and accounts for technical factors such as sparse signals, mappability and nucleotide content. In performance comparisons, EpiSAFARI performs favorably in terms of accuracy. The histone modification valleys detected by EpiSAFARI exhibit high conservation, transcription factor binding and they are enriched in nascent transcription. In addition, the large clusters of histone valleys are found to be enriched at the promoters of the developmentally associated genes. Differential histone valleys exhibit concordance with differential DNase signal at cell line specific valleys. DNA methylation valleys exhibit elevated conservation and high transcription factor binding. Specifically, we observed enriched binding of transcription factors associated with chromatin structure around methyl-valleys.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>EpiSAFARI is publicly available at https:\/\/github.com\/harmancilab\/EpiSAFARI.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz702","type":"journal-article","created":{"date-parts":[[2019,9,5]],"date-time":"2019-09-05T15:27:43Z","timestamp":1567697263000},"page":"1014-1021","source":"Crossref","is-referenced-by-count":1,"title":["EpiSAFARI: sensitive detection of valleys in epigenetic signals for enhancing annotations of functional elements"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9696-1118","authenticated-orcid":false,"given":"Arif","family":"Harmanci","sequence":"first","affiliation":[{"name":"School of Biomedical Informatics, Center for Precision Health , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9696-1118","authenticated-orcid":false,"given":"Akdes Serin","family":"Harmanci","sequence":"additional","affiliation":[{"name":"School of Biomedical Informatics, Center for Systems Medicine, University of Texas Health Science Center , Houston, TX 77030, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jyothishmathi","family":"Swaminathan","sequence":"additional","affiliation":[{"name":"Department of Pediatrics , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vidya","family":"Gopalakrishnan","sequence":"additional","affiliation":[{"name":"Department of Pediatrics , USA"},{"name":"Department of Molecular and Cellular Oncology , USA"},{"name":"Brain Tumor Center , USA"},{"name":"Center for Cancer Epigenetics, University of Texas, M.D. Anderson Cancer Center , Houston, TX 77030, USA"},{"name":"M.D. Anderson UTHealth Graduate School of Biomedical Sciences , Houston, TX 77030, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,9,10]]},"reference":[{"key":"2023013110165150400_btz702-B1","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1038\/nprot.2012.145","article-title":"Multiscale analysis of genome-wide replication timing profiles using a wavelet-based signal-processing algorithm","volume":"8","author":"Audit","year":"2013","journal-title":"Nat. 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