{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,12]],"date-time":"2026-09-12T17:24:34Z","timestamp":1789233874411,"version":"build-2803163510"},"reference-count":23,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2019,3,6]],"date-time":"2019-03-06T00:00:00Z","timestamp":1551830400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100009432","name":"Government Council on Grants, Russian Federation","doi-asserted-by":"publisher","award":["14.W03.31.0012"],"award-info":[{"award-number":["14.W03.31.0012"]}],"id":[{"id":"10.13039\/501100009432","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002261","name":"Russian Foundation for Basic Research","doi-asserted-by":"publisher","award":["18-34-20024"],"award-info":[{"award-number":["18-34-20024"]}],"id":[{"id":"10.13039\/501100002261","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2019,12]]},"DOI":"10.1186\/s12859-019-2706-8","type":"journal-article","created":{"date-parts":[[2019,3,6]],"date-time":"2019-03-06T13:04:31Z","timestamp":1551877471000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":50,"title":["svist4get: a simple visualization tool for genomic tracks from sequencing experiments"],"prefix":"10.1186","volume":"20","author":[{"given":"Artyom A.","family":"Egorov","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ekaterina A.","family":"Sakharova","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aleksandra S.","family":"Anisimova","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sergey E.","family":"Dmitriev","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vadim N.","family":"Gladyshev","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6554-8128","authenticated-orcid":false,"given":"Ivan V.","family":"Kulakovskiy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2019,3,6]]},"reference":[{"key":"2706_CR1","doi-asserted-by":"publisher","unstructured":"Fujita PA, Rhead B, Zweig AS, Hinrichs AS, Karolchik D, Cline MS, et al. The UCSC genome browser database: update 2011. Nucleic Acids Res. 2011;39 Database issue:D876\u201382. https:\/\/doi.org\/10.1093\/nar\/gkq963 .","DOI":"10.1093\/nar\/gkq963"},{"key":"2706_CR2","doi-asserted-by":"publisher","first-page":"217","DOI":"10.1038\/nbt.2840","volume":"32","author":"J Severin","year":"2014","unstructured":"Severin J, Lizio M, Harshbarger J, Kawaji H, Daub CO, Hayashizaki Y, et al. Interactive visualization and analysis of large-scale sequencing datasets using ZENBU. Nat Biotechnol. 2014;32:217\u20139.","journal-title":"Nat Biotechnol"},{"key":"2706_CR3","doi-asserted-by":"publisher","first-page":"178","DOI":"10.1093\/bib\/bbs017","volume":"14","author":"H Thorvaldsd\u00f3ttir","year":"2013","unstructured":"Thorvaldsd\u00f3ttir H, Robinson JT, Mesirov JP. Integrative genomics viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform. 2013;14:178\u201392.","journal-title":"Brief Bioinform"},{"key":"2706_CR4","doi-asserted-by":"publisher","unstructured":"Freese NH, Norris DC, Loraine AE. Integrated genome browser: visual analytics platform for genomics. Bioinformatics. 2016;32:2089\u201395. https:\/\/doi.org\/10.1093\/bioinformatics\/btw069 .","DOI":"10.1093\/bioinformatics\/btw069"},{"key":"2706_CR5","doi-asserted-by":"crossref","first-page":"1568","DOI":"10.1093\/bioinformatics\/btx007","volume":"33","author":"D Beraldi","year":"2017","unstructured":"Beraldi D. ASCIIGenome: a command line genome browser for console terminals. Bioinformatics. 2017;33:1568\u20139.","journal-title":"Bioinformatics."},{"key":"2706_CR6","doi-asserted-by":"publisher","first-page":"e8","DOI":"10.12704\/vb\/e8","volume":"1","author":"T Valeev","year":"2013","unstructured":"Valeev T, Yevshin I, Kolpakov F. BioUML Genome Browser. Virtual Biol. 2013;1:e8.","journal-title":"Virtual Biol"},{"key":"2706_CR7","first-page":"335","volume-title":"Methods in molecular biology","author":"F Hahne","year":"2016","unstructured":"Hahne F, Ivanek R. Visualizing genomic data using Gviz and bioconductor. In: Methods in molecular biology; 2016. p. 335\u201351."},{"key":"2706_CR8","doi-asserted-by":"publisher","first-page":"R77","DOI":"10.1186\/gb-2012-13-8-r77","volume":"13","author":"T Yin","year":"2012","unstructured":"Yin T, Cook D, Lawrence M. Ggbio: an R package for extending the grammar of graphics for genomic data. Genome Biol. 2012;13:R77.","journal-title":"Genome Biol"},{"key":"2706_CR9","doi-asserted-by":"publisher","first-page":"e2209","DOI":"10.7717\/peerj.2209","volume":"4","author":"G Georgiou","year":"2016","unstructured":"Georgiou G, van Heeringen SJ. Fluff: exploratory analysis and visualization of high-throughput sequencing data. PeerJ. 2016;4:e2209.","journal-title":"PeerJ."},{"key":"2706_CR10","doi-asserted-by":"publisher","first-page":"284","DOI":"10.1186\/1471-2164-15-284","volume":"15","author":"L Shen","year":"2014","unstructured":"Shen L, Shao N, Liu X, Nestler E. Ngs.Plot: quick mining and visualization of next-generation sequencing data by integrating genomic databases. BMC Genomics. 2014;15:284.","journal-title":"BMC Genomics"},{"key":"2706_CR11","doi-asserted-by":"publisher","first-page":"1422","DOI":"10.1093\/bioinformatics\/btp163","volume":"25","author":"PJA Cock","year":"2009","unstructured":"Cock PJA, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, et al. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics. 2009;25:1422\u20133.","journal-title":"Bioinformatics."},{"key":"2706_CR12","doi-asserted-by":"publisher","first-page":"3423","DOI":"10.1093\/bioinformatics\/btr539","volume":"27","author":"RK Dale","year":"2011","unstructured":"Dale RK, Pedersen BS, Quinlan AR. Pybedtools: a flexible Python library for manipulating genomic datasets and annotations. Bioinformatics. 2011;27:3423\u20134.","journal-title":"Bioinformatics."},{"key":"2706_CR13","doi-asserted-by":"crossref","unstructured":"Ram\u00edrez F, D\u00fcndar F, Diehl S, Gr\u00fcning BA, Manke T. DeepTools: a flexible platform for exploring deep-sequencing data. Nucleic Acids Res. 2014:W187\u201391.","DOI":"10.1093\/nar\/gku365"},{"key":"2706_CR14","doi-asserted-by":"publisher","first-page":"11.12.1","DOI":"10.1002\/0471250953.bi1112s47","volume":"8","author":"AR Quinlan","year":"2014","unstructured":"Quinlan AR. BEDTools: the Swiss-Army tool for genome feature analysis. Curr Protoc Bioinforma. 2014;8:11.12.1\u201334.","journal-title":"Curr Protoc Bioinforma"},{"issue":"Database issue","key":"2706_CR15","first-page":"D64","volume":"41","author":"LR Meyer","year":"2013","unstructured":"Meyer LR, Zweig AS, Hinrichs AS, Karolchik D, Kuhn RM, Wong M, et al. The UCSC genome browser database: extensions and updates 2013. Nucleic Acids Res. 2013;41(Database issue):D64\u20139.","journal-title":"Nucleic Acids Res"},{"key":"2706_CR16","doi-asserted-by":"publisher","unstructured":"Makeeva DS, Lando AS, Anisimova AS, Egorov AA, Logacheva MD, Penin AA, et al. Translatome and transcriptome analysis of TMA20 (MCT-1) and TMA64 (eIF2D) knockout yeast strains: Data Br. 2019;23:103701. https:\/\/doi.org\/10.1016\/j.dib.2019.103701 .","DOI":"10.1016\/j.dib.2019.103701"},{"key":"2706_CR17","doi-asserted-by":"publisher","first-page":"e1004692","DOI":"10.1371\/journal.pgen.1004692","volume":"10","author":"FW Albert","year":"2014","unstructured":"Albert FW, Muzzey D, Weissman JS, Kruglyak L. Genetic influences on translation in yeast. PLoS Genet. 2014;10:e1004692.","journal-title":"PLoS Genet"},{"key":"2706_CR18","doi-asserted-by":"publisher","first-page":"D823","DOI":"10.1093\/nar\/gkx790","volume":"46","author":"AM Michel","year":"2018","unstructured":"Michel AM, Kiniry SJ, O\u2019Connor PBF, Mullan JP, Baranov PV. GWIPS-viz: 2018 update. Nucleic Acids Res. 2018;46:D823\u201330.","journal-title":"Nucleic Acids Res"},{"key":"2706_CR19","doi-asserted-by":"publisher","first-page":"D754","DOI":"10.1093\/nar\/gkx1098","volume":"46","author":"DR Zerbino","year":"2018","unstructured":"Zerbino DR, Achuthan P, Akanni W, Amode MR, Barrell D, Bhai J, et al. Ensembl 2018. Nucleic Acids Res. 2018;46:D754\u201361.","journal-title":"Nucleic Acids Res"},{"key":"2706_CR20","doi-asserted-by":"publisher","first-page":"116","DOI":"10.1186\/s13059-017-1222-2","volume":"18","author":"V Castelo-Szekely","year":"2017","unstructured":"Castelo-Szekely V, Arpat AB, Janich P, Gatfield D. Translational contributions to tissue specificity in rhythmic and constitutive gene expression. Genome Biol. 2017;18:116.","journal-title":"Genome Biol"},{"key":"2706_CR21","doi-asserted-by":"publisher","first-page":"1848","DOI":"10.1101\/gr.195404.115","volume":"25","author":"P Janich","year":"2015","unstructured":"Janich P, Arpat AB, Castelo-Szekely V, Lopes M, Gatfield D. Ribosome profiling reveals the rhythmic liver translatome and circadian clock regulation by upstream open reading frames. Genome Res. 2015;25:1848\u201359.","journal-title":"Genome Res"},{"key":"2706_CR22","doi-asserted-by":"crossref","unstructured":"Michel AM, Fox G, M. Kiran A, De Bo C, O\u2019Connor PBF, Heaphy SM, et al. GWIPS-viz: development of a ribo-seq genome browser. Nucleic Acids Res 2014;42:D859-D864.","DOI":"10.1093\/nar\/gkt1035"},{"key":"2706_CR23","doi-asserted-by":"publisher","first-page":"1760","DOI":"10.1101\/gr.135350.111","volume":"22","author":"J Harrow","year":"2012","unstructured":"Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, et al. GENCODE: the reference human genome annotation for the ENCODE project. Genome Res. 2012;22:1760\u201374.","journal-title":"Genome Res"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-019-2706-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12859-019-2706-8\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-019-2706-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,14]],"date-time":"2023-09-14T05:33:16Z","timestamp":1694669596000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-019-2706-8"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,3,6]]},"references-count":23,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2019,12]]}},"alternative-id":["2706"],"URL":"https:\/\/doi.org\/10.1186\/s12859-019-2706-8","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,3,6]]},"assertion":[{"value":"24 October 2018","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"27 February 2019","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"6 March 2019","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Not applicable.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}},{"value":"Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Publisher\u2019s Note"}}],"article-number":"113"}}