{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,17]],"date-time":"2026-06-17T07:18:25Z","timestamp":1781680705763,"version":"3.54.5"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2016,10,12]],"date-time":"2016-10-12T00:00:00Z","timestamp":1476230400000},"content-version":"vor","delay-in-days":303,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: DNAshapeR predicts DNA shape features in an ultra-fast, high-throughput manner from genomic sequencing data. The package takes either nucleotide sequence or genomic coordinates as input and generates various graphical representations for visualization and further analysis. DNAshapeR further encodes DNA sequence and shape features as user-defined combinations of k-mer and DNA shape features. The resulting feature matrices can be readily used as input of various machine learning software packages for further modeling studies.<\/jats:p>\n               <jats:p>Availability and implementation: The DNAshapeR software package was implemented in the statistical programming language R and is freely available through the Bioconductor project at https:\/\/www.bioconductor.org\/packages\/devel\/bioc\/html\/DNAshapeR.html and at the GitHub developer site, http:\/\/tsupeichiu.github.io\/DNAshapeR\/.<\/jats:p>\n               <jats:p>Contact: \u00a0rohs@usc.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv735","type":"journal-article","created":{"date-parts":[[2015,12,15]],"date-time":"2015-12-15T02:54:41Z","timestamp":1450148081000},"page":"1211-1213","source":"Crossref","is-referenced-by-count":184,"title":["DNAshapeR: an R\/Bioconductor package for DNA shape prediction and feature encoding"],"prefix":"10.1093","volume":"32","author":[{"given":"Tsu-Pei","family":"Chiu","sequence":"first","affiliation":[{"name":"1 Molecular and Computational Biology Program, Departments of Biological Sciences, Chemistry, Physics, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA,"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Federico","family":"Comoglio","sequence":"additional","affiliation":[{"name":"2 Department of Biosystems Science and Engineering, ETH Z\u00fcrich, Mattenstrasse 26, 4058 Basel, Switzerland and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tianyin","family":"Zhou","sequence":"additional","affiliation":[{"name":"1 Molecular and Computational Biology Program, Departments of Biological Sciences, Chemistry, Physics, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA,"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lin","family":"Yang","sequence":"additional","affiliation":[{"name":"1 Molecular and Computational Biology Program, Departments of Biological Sciences, Chemistry, Physics, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA,"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Renato","family":"Paro","sequence":"additional","affiliation":[{"name":"2 Department of Biosystems Science and Engineering, ETH Z\u00fcrich, Mattenstrasse 26, 4058 Basel, Switzerland and"},{"name":"3 Faculty of Science, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Remo","family":"Rohs","sequence":"additional","affiliation":[{"name":"1 Molecular and Computational Biology Program, Departments of Biological Sciences, Chemistry, Physics, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA,"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2015,12,14]]},"reference":[{"key":"2023020112003337200_btv735-B1","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1016\/j.cell.2015.02.008","article-title":"Deconvolving the recognition of DNA shape from sequence","volume":"161","author":"Abe","year":"2015","journal-title":"Cell"},{"key":"2023020112003337200_btv735-B2","doi-asserted-by":"crossref","first-page":"D103","DOI":"10.1093\/nar\/gku977","article-title":"GBshape: a genome browser database for DNA shape annotations","volume":"43","author":"Chiu","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023020112003337200_btv735-B3","doi-asserted-by":"crossref","first-page":"821","DOI":"10.1016\/j.celrep.2015.03.070","article-title":"High-resolution profiling of Drosophila replication start sites reveals a DNA shape and chromatin signature of metazoan origins","volume":"11","author":"Comoglio","year":"2015","journal-title":"Cell Rep"},{"key":"2023020112003337200_btv735-B4","doi-asserted-by":"crossref","first-page":"395","DOI":"10.1038\/nbt.3121","article-title":"ChIP-nexus enables improved detection of in vivo transcription factor binding footprints","volume":"33","author":"He","year":"2015","journal-title":"Nat. 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