{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,30]],"date-time":"2025-10-30T22:36:04Z","timestamp":1761863764559,"version":"3.37.3"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2017,7,11]],"date-time":"2017-07-11T00:00:00Z","timestamp":1499731200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Irys Extract is a software tool for generating genomic information from data collected by the BioNano Genomics Irys platform. The tool allows the user easy access to the raw data in the form of cropped images and genetically aligned intensity profiles. The latter are also made compatible with the BED format for using with popular genomic browsers such as the UCSC Genome Browser.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Irys Extract has been developed in Matlab R2015a, it was tested to work with IrysView 2.4.0.15879 and AutoDetect 2.1.4.9159, and it currently runs under Microsoft Windows operating systems (7-10). Irys Extract can be downloaded alongside its manual and a demo dataset at http:\/\/www.nanobiophotonix.com and https:\/\/sites.google.com\/site\/raniarielly\/.<\/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\/btx437","type":"journal-article","created":{"date-parts":[[2017,7,4]],"date-time":"2017-07-04T11:09:43Z","timestamp":1499166583000},"page":"134-136","source":"Crossref","is-referenced-by-count":7,"title":["Irys Extract"],"prefix":"10.1093","volume":"34","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6666-4091","authenticated-orcid":false,"given":"Rani","family":"Arielly","sequence":"first","affiliation":[{"name":"School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel"}]},{"given":"Yuval","family":"Ebenstein","sequence":"additional","affiliation":[{"name":"School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel"}]}],"member":"286","published-online":{"date-parts":[[2017,7,11]]},"reference":[{"year":"2014","author":"Amini","key":"2023020208403377100_btx437-B1"},{"key":"2023020208403377100_btx437-B2","doi-asserted-by":"crossref","DOI":"10.1557\/opl.2011.866","article-title":"Single-molecule rapid imaging of linear genomes in nanochannel array","volume":"1346","author":"Austin","year":"2011","journal-title":"MRS Proc"},{"key":"2023020208403377100_btx437-B3","doi-asserted-by":"crossref","first-page":"e177.","DOI":"10.1093\/nar\/gkq673","article-title":"Single molecule linear analysis of DNA in nano-channel labeled with sequence specific fluorescent probes","volume":"38","author":"Das","year":"2010","journal-title":"Nucleic Acids Res"},{"key":"2023020208403377100_btx437-B4","doi-asserted-by":"crossref","first-page":"e117.","DOI":"10.1093\/nar\/gkv563","article-title":"Bacteriophage strain typing by rapid single molecule analysis","volume":"43","author":"Grunwald","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023020208403377100_btx437-B5","doi-asserted-by":"crossref","first-page":"pdb.top093211.","DOI":"10.1101\/pdb.top093211","article-title":"Data formats in bioinformatics","volume":"2016","author":"Hung","year":"2016","journal-title":"Cold Spring Harb. Protoc"},{"key":"2023020208403377100_btx437-B6","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1101\/gr.229102","article-title":"The human genome browser at UCSC","volume":"12","author":"Kent","year":"2002","journal-title":"Genome Res"},{"key":"2023020208403377100_btx437-B7","doi-asserted-by":"crossref","first-page":"771","DOI":"10.1038\/nbt.2303","article-title":"Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly","volume":"30","author":"Lam","year":"2012","journal-title":"Nat. Biotechnol"},{"key":"2023020208403377100_btx437-B8","doi-asserted-by":"crossref","first-page":"8599.","DOI":"10.1039\/c3cc42543f","article-title":"Optical detection of epigenetic marks: sensitive quantification and direct imaging of individual hydroxymethylcytosine bases","volume":"49","author":"Michaeli","year":"2013","journal-title":"Chem. Commun"},{"key":"2023020208403377100_btx437-B9","doi-asserted-by":"crossref","first-page":"1857","DOI":"10.1002\/cbic.201500329","article-title":"One-pot chemoenzymatic cascade for labeling of the epigenetic marker 5-hydroxymethylcytosine","volume":"16","author":"Nifker","year":"2015","journal-title":"ChemBioChem"},{"year":"2017","author":"Pang","key":"2023020208403377100_btx437-B10"},{"key":"2023020208403377100_btx437-B11","doi-asserted-by":"crossref","first-page":"44003.","DOI":"10.1088\/2050-6120\/4\/4\/044003","article-title":"Simple and cost-effective fluorescent labeling of 5-hydroxymethylcytosine","volume":"4","author":"Shahal","year":"2016","journal-title":"Methods Appl. Fluoresc"},{"key":"2023020208403377100_btx437-B12","doi-asserted-by":"crossref","first-page":"7771","DOI":"10.1021\/ja503677n","article-title":"Lighting Up Individual DNA Damage Sites by In Vitro Repair Synthesis","volume":"136","author":"Zirkin","year":"2014","journal-title":"J. Am. Chem. Soc"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/1\/134\/49043444\/bioinformatics_34_1_134.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/1\/134\/49043444\/bioinformatics_34_1_134.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T08:47:01Z","timestamp":1675327621000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/1\/134\/3952671"}},"subtitle":[],"editor":[{"given":"Robert","family":"Murphy","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2017,7,11]]},"references-count":12,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2018,1,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btx437","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2018,1,1]]},"published":{"date-parts":[[2017,7,11]]}}}