{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,28]],"date-time":"2026-08-28T21:08:01Z","timestamp":1787951281844,"version":"build-2784847793"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2018,7,24]],"date-time":"2018-07-24T00:00:00Z","timestamp":1532390400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The number of genomes (including meta-genomes) is increasing at an accelerating pace. In the near future, we may need to estimate pairwise distances between millions of genomes. Even with the use of cloud computing, very few softwares can perform such estimation.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>The multi-threaded software BinDash can perform such estimation using only a typical personal laptop. BinDash implemented b-bit one-permutation rolling MinHash with optimal densification, an existing data-mining technique. BinDash empirically outperforms the state-of-the-art software in terms of precision, compression ratio, memory usage and runtime according to our evaluation. Our evaluation is performed with a Dell Inspiron 157\u00a0559 Notebook on all bacterial genomes in RefSeq.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>BinDash is released under the Apache 2.0 license at https:\/\/github.com\/zhaoxiaofei\/BinDash.<\/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\/bty651","type":"journal-article","created":{"date-parts":[[2018,7,19]],"date-time":"2018-07-19T22:46:32Z","timestamp":1532040392000},"page":"671-673","source":"Crossref","is-referenced-by-count":68,"title":["BinDash, software for fast genome distance estimation on a typical personal laptop"],"prefix":"10.1093","volume":"35","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1665-2498","authenticated-orcid":false,"given":"XiaoFei","family":"Zhao","sequence":"first","affiliation":[{"name":"Independent researcher, Waterloo, ON, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2018,7,24]]},"reference":[{"key":"2023051511012481400_bty651-B1","author":"Broder","year":"1997"},{"key":"2023051511012481400_bty651-B2","doi-asserted-by":"crossref","first-page":"D73","DOI":"10.1093\/nar\/gkv1226","article-title":"Assembly: a resource for assembled genomes at NCBI","volume":"44","author":"Kitts","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023051511012481400_bty651-B3","volume-title":"Proceedings of the 19th International Conference on World Wide Web","author":"Li","year":"2010"},{"key":"2023051511012481400_bty651-B4","volume-title":"Advances in Neural Information Processing Systems","author":"Li","year":"2012"},{"key":"2023051511012481400_bty651-B5","volume-title":"2014 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","author":"Maillet","year":"2014"},{"key":"2023051511012481400_bty651-B6","doi-asserted-by":"crossref","first-page":"132.","DOI":"10.1186\/s13059-016-0997-x","article-title":"Mash: fast genome and metagenome distance estimation using minhash","volume":"17","author":"Ondov","year":"2016","journal-title":"Genome Biol"},{"key":"2023051511012481400_bty651-B7","doi-asserted-by":"crossref","first-page":"D61","DOI":"10.1093\/nar\/gkl842","article-title":"NCBI reference sequences (refseq): a curated non-redundant sequence database of genomes, transcripts and proteins","volume":"35","author":"Pruitt","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"2023051511012481400_bty651-B8","volume-title":"International Conference on Machine Learning","author":"Shrivastava","year":"2017"},{"key":"2023051511012481400_bty651-B9","volume-title":"International Conference on Machine Learning","author":"Shrivastava","year":"2014"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/4\/671\/50320256\/bioinformatics_35_4_671.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/4\/671\/50320256\/bioinformatics_35_4_671.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,15]],"date-time":"2023-05-15T11:01:47Z","timestamp":1684148507000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/35\/4\/671\/5058094"}},"subtitle":[],"editor":[{"given":"John","family":"Hancock","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2018,7,24]]},"references-count":9,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2019,2,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty651","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019,2,15]]},"published":{"date-parts":[[2018,7,24]]}}}