{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,25]],"date-time":"2026-01-25T11:45:39Z","timestamp":1769341539318,"version":"3.49.0"},"reference-count":69,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2018,1,10]],"date-time":"2018-01-10T00:00:00Z","timestamp":1515542400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,5,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Nucleosome positioning plays significant roles in proper genome packing and its accessibility to execute transcription regulation. Despite a multitude of nucleosome positioning resources available on line including experimental datasets of genome-wide nucleosome occupancy profiles and computational tools to the analysis on these data, the complex language of eukaryotic Nucleosome positioning remains incompletely understood.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, we address this challenge using an approach based on a state-of-the-art machine learning method. We present a novel convolutional neural network (CNN) to understand nucleosome positioning. We combined Inception-like networks with a gating mechanism for the response of multiple patterns and long term association in DNA sequences. We developed the open-source package LeNup based on the CNN to predict nucleosome positioning in Homo sapiens, Caenorhabditis elegans, Drosophila melanogaster as well as Saccharomyces cerevisiae genomes. We trained LeNup on four benchmark datasets. LeNup achieved greater predictive accuracy than previously published methods.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>LeNup is freely available as Python and Lua script source code under a BSD style license from https:\/\/github.com\/biomedBit\/LeNup.<\/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\/bty003","type":"journal-article","created":{"date-parts":[[2018,1,9]],"date-time":"2018-01-09T21:39:22Z","timestamp":1515533962000},"page":"1705-1712","source":"Crossref","is-referenced-by-count":41,"title":["LeNup: learning nucleosome positioning from DNA sequences with improved convolutional neural networks"],"prefix":"10.1093","volume":"34","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4231-8223","authenticated-orcid":false,"given":"Juhua","family":"Zhang","sequence":"first","affiliation":[{"name":"Department of Biomedical Engineering, Beijing Institute of Technology, Beijing, China"},{"name":"Key Laboratory of Convergence Medical Engineering System and Healthcare Technology of the Ministry of Industry and Information Technology, School of Life Science, Beijing Institute of Technology, Beijing, China"}]},{"given":"Wenbo","family":"Peng","sequence":"additional","affiliation":[{"name":"Department of Biomedical Engineering, Beijing Institute of Technology, Beijing, China"}]},{"given":"Lei","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Biomedical Engineering, Beijing Institute of Technology, Beijing, China"}]}],"member":"286","published-online":{"date-parts":[[2018,1,10]]},"reference":[{"key":"2023012713421253700_bty003-B1","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1093\/bioinformatics\/btw562","article-title":"Prediction of nucleosome positioning by the incorporation of frequencies and distributions of three different nucleotide segment lengths into a general pseudo k-tuple nucleotide composition","volume":"33","author":"Awazu","year":"2017","journal-title":"Bioinformatics"},{"key":"2023012713421253700_bty003-B2","doi-asserted-by":"crossref","first-page":"823","DOI":"10.1016\/j.cell.2007.05.009","article-title":"High-resolution profiling of histone methylations in the human genome","volume":"129","author":"Barski","year":"2007","journal-title":"Cell"},{"key":"2023012713421253700_bty003-B3","doi-asserted-by":"crossref","first-page":"554","DOI":"10.1038\/nrg3017","article-title":"Determinants and dynamics of genome accessibility","volume":"12","author":"Bell","year":"2011","journal-title":"Nat. Rev. Genet"},{"key":"2023012713421253700_bty003-B4","doi-asserted-by":"crossref","first-page":"1798","DOI":"10.1109\/TPAMI.2013.50","article-title":"Representation learning: a review and new perspectives","volume":"35","author":"Bengio","year":"2013","journal-title":"Pattern Anal. Mach. Intell. IEEE Trans"},{"key":"2023012713421253700_bty003-B5","doi-asserted-by":"crossref","first-page":"R62","DOI":"10.1186\/gb-2004-5-9-r62","article-title":"Global nucleosome occupancy in yeast","volume":"5","author":"Bernstein","year":"2004","journal-title":"Genome Biol"},{"key":"2023012713421253700_bty003-B6","doi-asserted-by":"crossref","first-page":"496","DOI":"10.1038\/nature11142","article-title":"A map of nucleosome positions in yeast at base-pair resolution","volume":"486","author":"Brogaard","year":"2012","journal-title":"Nature"},{"key":"2023012713421253700_bty003-B7","first-page":"e4784","article-title":"iNuc-PhysChem: a sequence-based predictor for identifying nucleosomes via physicochemical properties","volume":"7","author":"Chen","year":"2012","journal-title":"PLoS One"},{"key":"2023012713421253700_bty003-B8","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1016\/j.ygeno.2015.12.005","article-title":"Using deformation energy to analyze nucleosome positioning in genomes","volume":"107","author":"Chen","year":"2016","journal-title":"Genomics"},{"key":"2023012713421253700_bty003-B9","doi-asserted-by":"crossref","first-page":"246","DOI":"10.1002\/prot.1035","article-title":"Prediction of protein cellular attributes using pseudo-amino acid composition","volume":"43","author":"Chou","year":"2001","journal-title":"PROTEINS Struct. Funct. Genet"},{"key":"2023012713421253700_bty003-B10","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1093\/bioinformatics\/bth466","article-title":"Using amphiphilic pseudo amino acid composition to predict enzyme subfamily classes","volume":"21","author":"Chou","year":"2005","journal-title":"Bioinformatics"},{"key":"2023012713421253700_bty003-B11","first-page":"2493","article-title":"Natural language processing (almost) from scratch","volume":"12","author":"Collobert","year":"2011","journal-title":"J. Mach. Learn. Res"},{"key":"2023012713421253700_bty003-B12","author":"Dauphin","year":"2016"},{"key":"2023012713421253700_bty003-B13","doi-asserted-by":"crossref","first-page":"748","DOI":"10.1101\/gad.1913210","article-title":"Conserved nucleosome positioning defines replication origins","volume":"24","author":"Eaton","year":"2010","journal-title":"Genes Dev"},{"key":"2023012713421253700_bty003-B14","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1038\/nature21056","article-title":"Dermatologist classification of skin cancer with deep neural networks","volume":"542","author":"Esteva","year":"2017","journal-title":"Nature"},{"key":"2023012713421253700_bty003-B15","first-page":"1889","article-title":"Working set selection using second order information for training support vector machines","volume":"6","author":"Fan","year":"2005","journal-title":"J. Mach. Learn. Res"},{"key":"2023012713421253700_bty003-B16","doi-asserted-by":"crossref","first-page":"e1000216","DOI":"10.1371\/journal.pcbi.1000216","article-title":"Distinct modes of regulation by chromatin encoded through nucleosome positioning signals","volume":"4","author":"Field","year":"2008","journal-title":"PLoS Comput. Biol"},{"key":"2023012713421253700_bty003-B17","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1016\/j.gde.2012.11.008","article-title":"Mechanisms by which transcription factors gain access to target sequence elements in chromatin","volume":"23","author":"Guertin","year":"2013","journal-title":"Curr. Opin. Genet. Dev"},{"key":"2023012713421253700_bty003-B18","doi-asserted-by":"crossref","first-page":"1522","DOI":"10.1093\/bioinformatics\/btu083","article-title":"iNuc-PseKNC: a sequence-based predictor for predicting nucleosome positioning in genomes with pseudo k-tuple nucleotide composition","volume":"30","author":"Guo","year":"2014","journal-title":"Bioinformatics"},{"key":"2023012713421253700_bty003-B19","doi-asserted-by":"crossref","first-page":"e1000134","DOI":"10.1371\/journal.pcbi.1000134","article-title":"Predicting human nucleosome occupancy from primary sequence","volume":"4","author":"Gupta","year":"2008","journal-title":"PLoS Comput. Biol"},{"key":"2023012713421253700_bty003-B20","doi-asserted-by":"crossref","first-page":"1532","DOI":"10.1101\/gr.207241.116","article-title":"Nucleosomal signatures impose nucleosome positioning in coding and noncoding sequences in the genome","volume":"26","author":"Gonzalez","year":"2016","journal-title":"Genome Res"},{"key":"2023012713421253700_bty003-B21","doi-asserted-by":"crossref","first-page":"504","DOI":"10.1126\/science.1127647","article-title":"Reducing the dimensionality of data with neural networks","volume":"313","author":"Hinton","year":"2006","journal-title":"Science"},{"key":"2023012713421253700_bty003-B22","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1109\/MSP.2012.2205597","article-title":"Deep neural networks for acoustic modeling in speech recognition","volume":"29","author":"Hinton","year":"2012","journal-title":"IEEE Signal Process. Mag"},{"key":"2023012713421253700_bty003-B23","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1006\/jmbi.1996.0503","article-title":"Nucleosome DNA sequence pattern revealed by multiple alignment of experimentally mapped sequences","volume":"262","author":"Ioshikhes","year":"1996","journal-title":"J. Mol. Biol"},{"key":"2023012713421253700_bty003-B24","doi-asserted-by":"crossref","first-page":"1863","DOI":"10.1101\/gr.116228.110","article-title":"Variety of genomic DNA patterns for nucleosome positioning","volume":"21","author":"Ioshikhes","year":"2011","journal-title":"Genome Res"},{"key":"2023012713421253700_bty003-B25","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1038\/nrg2522","article-title":"Nucleosome positioning and gene regulation: advances through genomics","volume":"10","author":"Jiang","year":"2009","journal-title":"Nat. Rev. Genet"},{"key":"2023012713421253700_bty003-B26","doi-asserted-by":"crossref","first-page":"362","DOI":"10.1038\/nature07667","article-title":"The DNA-encoded nucleosome organization of a eukaryotic genome","volume":"458","author":"Kaplan","year":"2009","journal-title":"Nature"},{"key":"2023012713421253700_bty003-B27","doi-asserted-by":"crossref","first-page":"990","DOI":"10.1101\/gr.200535.115","article-title":"Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks","volume":"26","author":"Kelley","year":"2016","journal-title":"Genome Res"},{"key":"2023012713421253700_bty003-B28","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1016\/S0092-8674(00)81958-3","article-title":"Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome","volume":"98","author":"Kornberg","year":"1999","journal-title":"Cell"},{"key":"2023012713421253700_bty003-B29","first-page":"1090","article-title":"ImageNet classification with deep convolutional neural networks","volume":"25","author":"Krizhevsky","year":"2012","journal-title":"In Proc. Adv. Neural Information Process. Syst"},{"key":"2023012713421253700_bty003-B30","doi-asserted-by":"crossref","first-page":"436","DOI":"10.1038\/nature14539","article-title":"Deep learning","volume":"521","author":"LeCun","year":"2015","journal-title":"Nature"},{"key":"2023012713421253700_bty003-B31","doi-asserted-by":"crossref","first-page":"900","DOI":"10.1038\/ng1400","article-title":"Evidence for nucleosome depletion at active regulatory regions genome-wide","volume":"36","author":"Lee","year":"2004","journal-title":"Nat. Genetics"},{"key":"2023012713421253700_bty003-B32","doi-asserted-by":"crossref","first-page":"1235","DOI":"10.1038\/ng2117","article-title":"A high- resolution atlas of nucleosome occupancy in yeast","volume":"39","author":"Lee","year":"2007","journal-title":"Nat. Genet"},{"key":"2023012713421253700_bty003-B33","doi-asserted-by":"crossref","first-page":"i121","DOI":"10.1093\/bioinformatics\/btu277","article-title":"Deep learning of the tissue-regulated splicing code","volume":"30","author":"Leung","year":"2014","journal-title":"Bioinformatics"},{"key":"2023012713421253700_bty003-B34","doi-asserted-by":"crossref","first-page":"2411","DOI":"10.1093\/bioinformatics\/btw186","article-title":"iDHS-EL: identifying DNase I hypersensitive sites by fusing three different modes of pseudo nucleotide composition into an ensemble","volume":"32","author":"Liu","year":"2016","journal-title":"Bioinformatics"},{"key":"2023012713421253700_bty003-B35","doi-asserted-by":"crossref","first-page":"1182","DOI":"10.1101\/gr.188680.114","article-title":"Determinants of nucleosome positioning and their influence on plant gene expression","volume":"25","author":"Liu","year":"2015","journal-title":"Genome Res"},{"key":"2023012713421253700_bty003-B36","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1126\/science.aah4712","article-title":"RPA binds histone H3-H4 and functions in DNA replication-coupled nucleosome assembly","volume":"355","author":"Liu","year":"2017","journal-title":"Science"},{"key":"2023012713421253700_bty003-B37","doi-asserted-by":"crossref","first-page":"251","DOI":"10.1038\/38444","article-title":"Crystal structure of the nucleosome core particle at 2.8 \u00c5 resolution","volume":"389","author":"Luger","year":"1997","journal-title":"Nature"},{"key":"2023012713421253700_bty003-B38","doi-asserted-by":"crossref","first-page":"358","DOI":"10.1038\/nature06929","article-title":"Nucleosome organization in the Drosophila genome","volume":"453","author":"Mavrich","year":"2008","journal-title":"Nature"},{"key":"2023012713421253700_bty003-B39","doi-asserted-by":"crossref","first-page":"3746","DOI":"10.1093\/nar\/gkn262","article-title":"DNA physical properties determine nucleosome occupancy from yeast to fly","volume":"11","author":"Miele","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"2023012713421253700_bty003-B40","doi-asserted-by":"crossref","first-page":"6293","DOI":"10.1073\/pnas.1404475111","article-title":"Training-free atomistic prediction of nucleosome occupancy","volume":"111","author":"Minary","year":"2014","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023012713421253700_bty003-B41","doi-asserted-by":"crossref","first-page":"4707","DOI":"10.1093\/nar\/gkp475","article-title":"Using DNA mechanics to predict in vitro nucleosome positions and formation energies","volume":"37","author":"Morozov","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"2023012713421253700_bty003-B42","doi-asserted-by":"crossref","first-page":"E6427","DOI":"10.1073\/pnas.1605543113","article-title":"Regulated large-scale nucleosome density patterns and precise nucleosome positioning correlate with V(D)J recombination","volume":"113","author":"Pulivarthy","year":"2016","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023012713421253700_bty003-B43","doi-asserted-by":"crossref","first-page":"e1001274","DOI":"10.1371\/journal.pgen.1001274","article-title":"Transcription initiation patterns indicate divergent strategies for gene regulation at the chromatin level","volume":"7","author":"Rach","year":"2011","journal-title":"PLoS Genetics"},{"key":"2023012713421253700_bty003-B44","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1038\/nature01595","article-title":"The structure of DNA in the nucleosome core","volume":"423","author":"Richmond","year":"2003","journal-title":"Nature"},{"key":"2023012713421253700_bty003-B45","doi-asserted-by":"crossref","first-page":"659","DOI":"10.1016\/0022-2836(86)90452-3","article-title":"Sequence periodicities in chicken nucleosome core DNA","volume":"191","author":"Satchwell","year":"1986","journal-title":"J. Mol. Biol"},{"key":"2023012713421253700_bty003-B46","doi-asserted-by":"crossref","first-page":"887","DOI":"10.1016\/j.cell.2008.02.022","article-title":"Dynamic regulation of nucleosome positioning in the human genome","volume":"132","author":"Schones","year":"2008","journal-title":"Cell"},{"key":"2023012713421253700_bty003-B47","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1038\/nature04979","article-title":"A genomic code for nucleosome positioning","volume":"442","author":"Segal","year":"2006","journal-title":"Nature"},{"key":"2023012713421253700_bty003-B48","doi-asserted-by":"crossref","DOI":"10.1016\/j.tig.2009.06.002","article-title":"What controls nucleosome positions?","volume":"25","author":"Segal","year":"2009","journal-title":"Trends Genet"},{"key":"2023012713421253700_bty003-B49","doi-asserted-by":"crossref","first-page":"484","DOI":"10.1038\/nature16961","article-title":"Mastering the game of Go with deep neural networks and tree search","volume":"529","author":"Silver","year":"2016","journal-title":"Nature"},{"key":"2023012713421253700_bty003-B50","doi-asserted-by":"crossref","first-page":"375","DOI":"10.1038\/nature09869","article-title":"Genome-wide analysis reveals novel molecular features of mouse recombination hotspots","volume":"472","author":"Smagulova","year":"2011","journal-title":"Nature"},{"key":"2023012713421253700_bty003-B51","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1038\/nsmb.2506","article-title":"Determinants of nucleosome positioning","volume":"20","author":"Struhl","year":"2013","journal-title":"Nat. Struct. Mol. Biol"},{"key":"2023012713421253700_bty003-B52","author":"Szegedy","year":"2015"},{"key":"2023012713421253700_bty003-B53","author":"Szegedy","year":"2016"},{"key":"2023012713421253700_bty003-B54","doi-asserted-by":"crossref","first-page":"2587","DOI":"10.1039\/C6MB00221H","article-title":"iNuc-STNC: a sequence-based predictor for identification of nucleosome positioning in genomes by extending the concept of SAAC and Chous PseAAC","volume":"12","author":"Tahir","year":"2016","journal-title":"Mol. Biosyst"},{"key":"2023012713421253700_bty003-B55","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1038\/nsmb.1658","article-title":"Nucleosome positioning as a determinant of exon recognition","volume":"16","author":"Tilgner","year":"2009","journal-title":"Nat. Struct. Mol. Biol"},{"key":"2023012713421253700_bty003-B56","doi-asserted-by":"crossref","first-page":"1051","DOI":"10.1101\/gr.076463.108","article-title":"A high-resolution, nucleosome position map of C. elegans reveals lack of universal sequence-dictated positioning","volume":"18","author":"Valouev","year":"2008","journal-title":"Genome Res"},{"key":"2023012713421253700_bty003-B57","doi-asserted-by":"crossref","first-page":"516","DOI":"10.1038\/nature10002","article-title":"Determinants of nucleosome organization in primary human cells","volume":"474","author":"Valouev","year":"2011","journal-title":"Nature"},{"key":"2023012713421253700_bty003-B58","doi-asserted-by":"crossref","first-page":"E2514","DOI":"10.1073\/pnas.1205659109","article-title":"Sequence-based prediction of single nucleosome positioning and genome-wide nucleosome occupancy","volume":"109","author":"van der Heijden","year":"2012","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023012713421253700_bty003-B59","doi-asserted-by":"crossref","first-page":"2651","DOI":"10.1016\/j.celrep.2016.07.083","article-title":"Dynamics of nucleosome positioning maturation following genomic replication","volume":"16","author":"Vasseur","year":"2016","journal-title":"Cell Rep"},{"key":"2023012713421253700_bty003-B60","doi-asserted-by":"crossref","first-page":"889","DOI":"10.1007\/s10577-012-9328-6","article-title":"Calculation of nucleosomal DNA deformation energy: its implication for nucleosome positioning","volume":"20","author":"Wang","year":"2012","journal-title":"Chromosome Res"},{"key":"2023012713421253700_bty003-B61","first-page":"90","article-title":"High-resolution nucleosome mapping reveals transcription-dependent promoter packaging","volume":"2010","author":"Weiner","year":"2009","journal-title":"Genome Res"},{"key":"2023012713421253700_bty003-B62","doi-asserted-by":"crossref","first-page":"31847","DOI":"10.1074\/jbc.274.45.31847","article-title":"Nucleosome structural features and intrinsic properties of the TATAAACGCC repeat sequence","volume":"274","author":"Widlund","year":"1999","journal-title":"J. Biol. Chem"},{"key":"2023012713421253700_bty003-B63","doi-asserted-by":"crossref","first-page":"1031","DOI":"10.1038\/nature06391","article-title":"Chromatin remodelling at promoters suppresses antisense transcription","volume":"450","author":"Whitehouse","year":"2007","journal-title":"Nature"},{"key":"2023012713421253700_bty003-B64","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1471-2105-11-346","article-title":"Predicting nucleosome positioning using a duration Hidden Markov Model","volume":"11","author":"Xi","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2023012713421253700_bty003-B65","doi-asserted-by":"crossref","first-page":"1254806","DOI":"10.1126\/science.1254806","article-title":"The human splicing code reveals new insights into the genetic determinants of disease","volume":"347","author":"Xiong","year":"2015","journal-title":"Science"},{"key":"2023012713421253700_bty003-B66","doi-asserted-by":"crossref","first-page":"626","DOI":"10.1126\/science.1112178","article-title":"Genome-scale identification of nucleosome positions in S-cerevisiae","volume":"309","author":"Yuan","year":"2005","journal-title":"Science"},{"key":"2023012713421253700_bty003-B67","doi-asserted-by":"crossref","first-page":"e13","DOI":"10.1371\/journal.pcbi.0040013","article-title":"Genomic sequence is highly predictive of local nucleosome depletion","volume":"4","author":"Yuan","year":"2008","journal-title":"PLoS Computat. Biol"},{"key":"2023012713421253700_bty003-B68","doi-asserted-by":"crossref","first-page":"847","DOI":"10.1038\/nsmb.1636","article-title":"Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo","volume":"16","author":"Zhang","year":"2009","journal-title":"Nat. Struct. Mol. Biol"},{"key":"2023012713421253700_bty003-B69","doi-asserted-by":"crossref","first-page":"351","DOI":"10.1101\/gr.195602.115","article-title":"Mapping nucleosome positions using DNase-seq","volume":"26","author":"Zhong","year":"2016","journal-title":"Genome Res"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/10\/1705\/48935658\/bioinformatics_34_10_1705.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/10\/1705\/48935658\/bioinformatics_34_10_1705.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T14:24:19Z","timestamp":1674829459000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/10\/1705\/4796955"}},"subtitle":[],"editor":[{"given":"John","family":"Hancock","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2018,1,10]]},"references-count":69,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2018,5,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty003","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2018,5,15]]},"published":{"date-parts":[[2018,1,10]]}}}