{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T21:20:22Z","timestamp":1790025622460,"version":"4.0.1"},"reference-count":39,"publisher":"Oxford University Press (OUP)","issue":"19","license":[{"start":{"date-parts":[[2022,8,16]],"date-time":"2022-08-16T00:00:00Z","timestamp":1660608000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100008398","name":"VILLUM FONDEN","doi-asserted-by":"publisher","award":["34299"],"award-info":[{"award-number":["34299"]}],"id":[{"id":"10.13039\/100008398","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100008398","name":"VILLUM FONDEN","doi-asserted-by":"publisher","award":["15510"],"award-info":[{"award-number":["15510"]}],"id":[{"id":"10.13039\/100008398","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100018870","name":"Poul Due Jensen Foundation","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100018870","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,9,30]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Despite recent advancements in sequencing technologies and assembly methods, obtaining high-quality microbial genomes from metagenomic samples is still not a trivial task. Current metagenomic binners do not take full advantage of assembly graphs and are not optimized for long-read assemblies. Deep graph learning algorithms have been proposed in other fields to deal with complex graph data structures. The graph structure generated during the assembly process could be integrated with contig features to obtain better bins with deep learning.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We propose GraphMB, which uses graph neural networks to incorporate the assembly graph into the binning process. We test GraphMB on long-read datasets of different complexities, and compare the performance with other binners in terms of the number of High Quality (HQ) genome bins obtained. With our approach, we were able to obtain unique bins on all real datasets, and obtain more bins on most datasets. In particular, we obtained on average 17.5% more HQ bins when compared with state-of-the-art binners and 13.7% when aggregating the results of our binner with the others. These results indicate that a deep learning model can integrate contig-specific and graph-structure information to improve metagenomic binning.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>GraphMB is available from https:\/\/github.com\/MicrobialDarkMatter\/GraphMB.<\/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\/btac557","type":"journal-article","created":{"date-parts":[[2022,8,16]],"date-time":"2022-08-16T09:57:52Z","timestamp":1660643872000},"page":"4481-4487","source":"Crossref","is-referenced-by-count":62,"title":["Metagenomic binning with assembly graph embeddings"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7965-6536","authenticated-orcid":false,"given":"Andre","family":"Lamurias","sequence":"first","affiliation":[{"name":"Department of Computer Science, Aalborg University , 9000 Aalborg, Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mantas","family":"Sereika","sequence":"additional","affiliation":[{"name":"Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University , 9000 Aalborg, Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6151-190X","authenticated-orcid":false,"given":"Mads","family":"Albertsen","sequence":"additional","affiliation":[{"name":"Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University , 9000 Aalborg, Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katja","family":"Hose","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Aalborg University , 9000 Aalborg, Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas Dyhre","family":"Nielsen","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Aalborg University , 9000 Aalborg, Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,8,16]]},"reference":[{"key":"2023041408231916200_","doi-asserted-by":"crossref","first-page":"533","DOI":"10.1038\/nbt.2579","article-title":"Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes","volume":"31","author":"Albertsen","year":"2013","journal-title":"Nat. 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