{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,17]],"date-time":"2025-10-17T13:49:08Z","timestamp":1760708948783,"version":"3.37.3"},"reference-count":38,"publisher":"Oxford University Press (OUP)","issue":"6","funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01 GM108501","2T32GM008715-16"],"award-info":[{"award-number":["R01 GM108501","2T32GM008715-16"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Most microbes on Earth have never been grown in a laboratory, and can only be studied through DNA sequences. Environmental DNA sequence samples are complex mixtures of fragments from many different species, often unknown. There is a pressing need for methods that can reliably reconstruct genomes from complex metagenomic samples in order to address questions in ecology, bioremediation, and human health.<\/jats:p>\n               <jats:p>Results: We present the SOrting by NEtwork Completion (SONEC) approach for assigning reactions to incomplete metabolic networks based on a metabolite connectivity score. We successfully demonstrate proof of concept in a set of 100 genome-scale metabolic network reconstructions, and delineate the variables that impact reaction assignment accuracy. We further demonstrate the integration of SONEC with existing approaches (such as cross-sample scaffold abundance profile clustering) on a set of 94 metagenomic samples from the Human Microbiome Project. We show that not only does SONEC aid in reconstructing species-level genomes, but it also improves functional predictions made with the resulting metabolic networks.<\/jats:p>\n               <jats:p>Availability and implementation: The datasets and code presented in this work are available at: https:\/\/bitbucket.org\/mattbiggs\/sorting_by_network_completion\/.<\/jats:p>\n               <jats:p>Contact: \u00a0papin@virginia.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv671","type":"journal-article","created":{"date-parts":[[2015,11,15]],"date-time":"2015-11-15T01:38:21Z","timestamp":1447551501000},"page":"867-874","source":"Crossref","is-referenced-by-count":7,"title":["Metabolic network-guided binning of metagenomic sequence fragments"],"prefix":"10.1093","volume":"32","author":[{"given":"Matthew B.","family":"Biggs","sequence":"first","affiliation":[{"name":"Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, 22903 USA"}]},{"given":"Jason A.","family":"Papin","sequence":"additional","affiliation":[{"name":"Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, 22903 USA"}]}],"member":"286","published-online":{"date-parts":[[2015,11,14]]},"reference":[{"key":"2023020111565245300_btv671-B1","doi-asserted-by":"crossref","first-page":"e1002358","DOI":"10.1371\/journal.pcbi.1002358","article-title":"Metabolic reconstruction for metagenomic data and its application to the human microbiome","volume":"8","author":"Abubucker","year":"2012","journal-title":"PLoS Comput. 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