{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,19]],"date-time":"2026-06-19T08:20:50Z","timestamp":1781857250943,"version":"3.54.5"},"reference-count":22,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2019,8,10]],"date-time":"2019-08-10T00:00:00Z","timestamp":1565395200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Wellcome Sanger core funding","award":["WT206194"],"award-info":[{"award-number":["WT206194"]}]},{"DOI":"10.13039\/100010269","name":"Wellcome","doi-asserted-by":"publisher","award":["211276\/Z\/18\/Z"],"award-info":[{"award-number":["211276\/Z\/18\/Z"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"name":"EMBO Long-Term Fellowship"},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["108437\/Z\/15\/Z"],"award-info":[{"award-number":["108437\/Z\/15\/Z"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Increasing numbers of large scale single cell RNA-Seq projects are leading to a data explosion, which can only be fully exploited through data integration. A number of methods have been developed to combine diverse datasets by removing technical batch effects, but most are computationally intensive. To overcome the challenge of enormous datasets, we have developed BBKNN, an extremely fast graph-based data integration algorithm. We illustrate the power of BBKNN on large scale mouse atlasing data, and favourably benchmark its run time against a number of competing methods.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>BBKNN is available at https:\/\/github.com\/Teichlab\/bbknn, along with documentation and multiple example notebooks, and can be installed from pip.<\/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\/btz625","type":"journal-article","created":{"date-parts":[[2019,8,8]],"date-time":"2019-08-08T07:35:30Z","timestamp":1565249730000},"page":"964-965","source":"Crossref","is-referenced-by-count":881,"title":["BBKNN: fast batch alignment of single cell transcriptomes"],"prefix":"10.1093","volume":"36","author":[{"given":"Krzysztof","family":"Pola\u0144ski","sequence":"first","affiliation":[{"name":"Cellular Genetics, Wellcome Sanger Institute , Hinxton, Cambridge CB10 1SA, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew D","family":"Young","sequence":"additional","affiliation":[{"name":"Cellular Genetics, Wellcome Sanger Institute , Hinxton, Cambridge CB10 1SA, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhichao","family":"Miao","sequence":"additional","affiliation":[{"name":"Cellular Genetics, Wellcome Sanger Institute , Hinxton, Cambridge CB10 1SA, UK"},{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute , Hinxton, Cambridge CB10 1SD, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kerstin B","family":"Meyer","sequence":"additional","affiliation":[{"name":"Cellular Genetics, Wellcome Sanger Institute , Hinxton, Cambridge CB10 1SA, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sarah A","family":"Teichmann","sequence":"additional","affiliation":[{"name":"Cellular Genetics, Wellcome Sanger Institute , Hinxton, Cambridge CB10 1SA, UK"},{"name":"Theory of Condensed Matter Group, Cavendish Laboratory\/Department of Physics, University of Cambridge , Cambridge CB3 0HE, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jong-Eun","family":"Park","sequence":"additional","affiliation":[{"name":"Cellular Genetics, Wellcome Sanger Institute , Hinxton, Cambridge CB10 1SA, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2019,8,10]]},"reference":[{"key":"2023013110091049500_btz625-B1","author":"Barkas","year":"2018"},{"key":"2023013110091049500_btz625-B2","doi-asserted-by":"crossref","first-page":"411.","DOI":"10.1038\/nbt.4096","article-title":"Integrating single-cell transcriptomic data across different conditions, technologies, and species","volume":"36","author":"Butler","year":"2018","journal-title":"Nat. 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