{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T03:53:16Z","timestamp":1772077996326,"version":"3.50.1"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"17","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: The number of human genomes that have been sequenced completely for different individuals has increased rapidly in recent years. Storing and transferring complete genomes between computers for the purpose of applying various applications and analysis tools will soon become a major hurdle, hindering the analysis phase. Therefore, there is a growing need to compress these data efficiently. Here, we describe a technique to compress human genomes based on entropy coding, using a reference genome and known Single Nucleotide Polymorphisms (SNPs). Furthermore, we explore several intrinsic features of genomes and information in other genomic databases to further improve the compression attained. Using these methods, we compress James Watson\u2019s genome to 2.5 megabytes (MB), improving on recent work by 37%. Similar compression is obtained for most genomes available from the 1000 Genomes Project. Our biologically inspired techniques promise even greater gains for genomes of lower organisms and for human genomes as more genomic data become available.<\/jats:p>\n               <jats:p>Availability: Code is available at sourceforge.net\/projects\/genomezip\/<\/jats:p>\n               <jats:p>Contact: \u00a0golan.yona@stanford.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt362","type":"journal-article","created":{"date-parts":[[2013,6,23]],"date-time":"2013-06-23T00:20:14Z","timestamp":1371946814000},"page":"2199-2202","source":"Crossref","is-referenced-by-count":29,"title":["The human genome contracts again"],"prefix":"10.1093","volume":"29","author":[{"given":"Dmitri S.","family":"Pavlichin","sequence":"first","affiliation":[{"name":"1 Department of Physics and 2Department of Electrical Engineering, Stanford University, CA 94305, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tsachy","family":"Weissman","sequence":"additional","affiliation":[{"name":"1 Department of Physics and 2Department of Electrical Engineering, Stanford University, CA 94305, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Golan","family":"Yona","sequence":"additional","affiliation":[{"name":"1 Department of Physics and 2Department of Electrical Engineering, Stanford University, CA 94305, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2013,6,22]]},"reference":[{"key":"2023012810463003600_btt362-B1","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1038\/nature11632","article-title":"An integrated map of genetic variation from 1,092 human genomes","volume":"491","author":"1000 Genomes Project Consortium et al.","year":"2012","journal-title":"Nature"},{"key":"2023012810463003600_btt362-B2","doi-asserted-by":"crossref","first-page":"274","DOI":"10.1093\/bioinformatics\/btn582","article-title":"Human genomes as email attachments","volume":"25","author":"Christley","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012810463003600_btt362-B3","doi-asserted-by":"crossref","first-page":"R116","DOI":"10.1186\/gb-2007-8-6-r116","article-title":"GC- and AT-rich chromatin domains differ in conformation and histone modification status and are differentially modulated by Rpd3p","volume":"8","author":"Dekker","year":"2007","journal-title":"Genome Biol."},{"key":"2023012810463003600_btt362-B4","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":"2023012810463003600_btt362-B5","doi-asserted-by":"crossref","first-page":"663","DOI":"10.1038\/ng1816","article-title":"Evaluating and improving power in whole-genome association studies using fixed marker sets","volume":"38","author":"Pe\u2019er","year":"2006","journal-title":"Nat. Genet."},{"key":"2023012810463003600_btt362-B6","doi-asserted-by":"crossref","first-page":"308","DOI":"10.1093\/nar\/29.1.308","article-title":"dbSNP: the NCBI database of genetic variation","volume":"29","author":"Sherry","year":"2001","journal-title":"Nucleic Acid Res."},{"key":"2023012810463003600_btt362-B7","doi-asserted-by":"crossref","first-page":"851","DOI":"10.1038\/nature06258","article-title":"A second generation human haplotype map of over 3.1 million SNPs","volume":"449","author":"The International HapMap Consortium et al.","year":"2007","journal-title":"Nature"},{"key":"2023012810463003600_btt362-B8","doi-asserted-by":"crossref","first-page":"872","DOI":"10.1038\/nature06884","article-title":"The complete genome of an individual by massively parallel DNA sequencing","volume":"452","author":"Wheeler","year":"2008","journal-title":"Nature"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/17\/2199\/48891064\/bioinformatics_29_17_2199.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/17\/2199\/48891064\/bioinformatics_29_17_2199.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,28]],"date-time":"2023-01-28T10:46:45Z","timestamp":1674902805000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/29\/17\/2199\/242283"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,6,22]]},"references-count":8,"journal-issue":{"issue":"17","published-print":{"date-parts":[[2013,9,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btt362","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2013,9,1]]},"published":{"date-parts":[[2013,6,22]]}}}