{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:33:33Z","timestamp":1772138013204,"version":"3.50.1"},"reference-count":57,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2021,8,28]],"date-time":"2021-08-28T00:00:00Z","timestamp":1630108800000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Luxembourg National Research Fund","award":["PRIDE17\/11823097"],"award-info":[{"award-number":["PRIDE17\/11823097"]}]},{"name":"Luxembourg National Research Fund","award":["C19\/BM\/13684739"],"award-info":[{"award-number":["C19\/BM\/13684739"]}]},{"name":"Luxembourg National Research Fund","award":["C17\/SR\/11687962"],"award-info":[{"award-number":["C17\/SR\/11687962"]}]},{"DOI":"10.13039\/501100001711","name":"Swiss National Science Foundation","doi-asserted-by":"publisher","award":["CRSII5_180241"],"award-info":[{"award-number":["CRSII5_180241"]}],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000781","name":"European Research Council","doi-asserted-by":"publisher","award":["ERC-CoG 863664"],"award-info":[{"award-number":["ERC-CoG 863664"]}],"id":[{"id":"10.13039\/501100000781","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,11,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Real-world evaluations of metagenomic reconstructions are challenged by distinguishing reconstruction artifacts from genes and proteins present in situ. Here, we evaluate short-read-only, long-read-only and hybrid assembly approaches on four different metagenomic samples of varying complexity. We demonstrate how different assembly approaches affect gene and protein inference, which is particularly relevant for downstream functional analyses. For a human gut microbiome sample, we use complementary metatranscriptomic and metaproteomic data to assess the metagenomic data-based protein predictions. Our findings pave the way for critical assessments of metagenomic reconstructions. We propose a reference-independent solution, which exploits the synergistic effects of multi-omic data integration for the in situ study of microbiomes using long-read sequencing data.<\/jats:p>","DOI":"10.1093\/bib\/bbab330","type":"journal-article","created":{"date-parts":[[2021,8,2]],"date-time":"2021-08-02T15:12:51Z","timestamp":1627917171000},"source":"Crossref","is-referenced-by-count":10,"title":["Functional meta-omics provide critical insights into long- and short-read assemblies"],"prefix":"10.1093","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4541-427X","authenticated-orcid":false,"given":"Valentina","family":"Galata","sequence":"first","affiliation":[{"name":"Luxembourg Centre for Systems Biomedicine, 7, avenue des Hauts-Fourneaux, Esch-sur-Alzette L-4362, Luxembourg"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7559-3400","authenticated-orcid":false,"given":"Susheel Bhanu","family":"Busi","sequence":"additional","affiliation":[{"name":"Luxembourg Centre for Systems Biomedicine, 7, avenue des Hauts-Fourneaux, Esch-sur-Alzette L-4362, Luxembourg"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3356-8562","authenticated-orcid":false,"given":"Beno\u00eet Josef","family":"Kunath","sequence":"additional","affiliation":[{"name":"Luxembourg Centre for Systems Biomedicine, 7, avenue des Hauts-Fourneaux, Esch-sur-Alzette L-4362, Luxembourg"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6483-7489","authenticated-orcid":false,"given":"Laura","family":"de Nies","sequence":"additional","affiliation":[{"name":"Luxembourg Centre for Systems Biomedicine, 7, avenue des Hauts-Fourneaux, Esch-sur-Alzette L-4362, Luxembourg"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2270-2217","authenticated-orcid":false,"given":"Magdalena","family":"Calusinska","sequence":"additional","affiliation":[{"name":"BioSystems and Bioprocessing Engineering, Luxembourg Institute of Science and Technology, Rue du Brill 41, Belvaux L-4422, Luxembourg"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1402-1254","authenticated-orcid":false,"given":"Rashi","family":"Halder","sequence":"additional","affiliation":[{"name":"Luxembourg Centre for Systems Biomedicine, 7, avenue des Hauts-Fourneaux, Esch-sur-Alzette L-4362, Luxembourg"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8698-3770","authenticated-orcid":false,"given":"Patrick","family":"May","sequence":"additional","affiliation":[{"name":"Luxembourg Centre for Systems Biomedicine, 7, avenue des Hauts-Fourneaux, Esch-sur-Alzette L-4362, Luxembourg"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6478-2924","authenticated-orcid":false,"given":"Paul","family":"Wilmes","sequence":"additional","affiliation":[{"name":"Luxembourg Centre for Systems Biomedicine, 7, avenue des Hauts-Fourneaux, Esch-sur-Alzette L-4362, Luxembourg"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1100-1282","authenticated-orcid":false,"given":"C\u00e9dric Christian","family":"Laczny","sequence":"additional","affiliation":[{"name":"Luxembourg Centre for Systems Biomedicine, 7, avenue des Hauts-Fourneaux, Esch-sur-Alzette L-4362, Luxembourg"}]}],"member":"286","published-online":{"date-parts":[[2021,8,27]]},"reference":[{"key":"2021110815090928400_ref1","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1038\/nrg.2018.5","article-title":"Genomics: next regeneration sequencing for reference genomes","volume":"19","author":"Burgess","year":"2018","journal-title":"Nat Rev Genet"},{"key":"2021110815090928400_ref2","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1186\/s13059-020-1935-5","article-title":"Opportunities and challenges in long-read sequencing data analysis","volume":"21","author":"Amarasinghe","year":"2020","journal-title":"Genome Biol"},{"key":"2021110815090928400_ref3","doi-asserted-by":"crossref","DOI":"10.1093\/gigascience\/giz043","article-title":"Ultra-deep, long-read nanopore sequencing of mock microbial 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