{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,29]],"date-time":"2026-05-29T09:18:06Z","timestamp":1780046286830,"version":"3.53.1"},"reference-count":157,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2024,7,31]],"date-time":"2024-07-31T00:00:00Z","timestamp":1722384000000},"content-version":"vor","delay-in-days":6,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000062","name":"National Institute of Diabetes and Digestive and Kidney Diseases","doi-asserted-by":"publisher","award":["RC2DK116713"],"award-info":[{"award-number":["RC2DK116713"]}],"id":[{"id":"10.13039\/100000062","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000923","name":"Australian Research Council","doi-asserted-by":"publisher","award":["DP220102915"],"award-info":[{"award-number":["DP220102915"]}],"id":[{"id":"10.13039\/501100000923","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,7,25]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Metagenomics involves the study of genetic material obtained directly from communities of microorganisms living in natural environments. The field of metagenomics has provided valuable insights into the structure, diversity and ecology of microbial communities. Once an environmental sample is sequenced and processed, metagenomic binning clusters the sequences into bins representing different taxonomic groups such as species, genera, or higher levels. Several computational tools have been developed to automate the process of metagenomic binning. These tools have enabled the recovery of novel draft genomes of microorganisms allowing us to study their behaviors and functions within microbial communities. This review classifies and analyzes different approaches of metagenomic binning and different refinement, visualization, and evaluation techniques used by these methods. Furthermore, the review highlights the current challenges and areas of improvement present within the field of research.<\/jats:p>","DOI":"10.1093\/bib\/bbae372","type":"journal-article","created":{"date-parts":[[2024,8,1]],"date-time":"2024-08-01T01:54:09Z","timestamp":1722477249000},"source":"Crossref","is-referenced-by-count":18,"title":["Solving genomic puzzles: computational methods for metagenomic binning"],"prefix":"10.1093","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2651-8719","authenticated-orcid":false,"given":"Vijini","family":"Mallawaarachchi","sequence":"first","affiliation":[{"name":"Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University , Adelaide, SA 5042, 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abundance-based algorithm for binning metagenomic sequences using l-tuples","volume":"18","author":"Wu","year":"2011","journal-title":"J Comput Biol"},{"key":"2024080705380978200_ref53","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1186\/s12859-015-0473-8","article-title":"MBBC: an efficient approach for metagenomic binning based on clustering","volume":"16","author":"Wang","year":"2015","journal-title":"BMC Bioinformatics"},{"key":"2024080705380978200_ref54","doi-asserted-by":"crossref","first-page":"822","DOI":"10.1038\/nbt.2939","article-title":"Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes","volume":"32","author":"Nielsen","year":"2014","journal-title":"Nat Biotechnol"},{"key":"2024080705380978200_ref55","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1016\/0888-7543(88)90007-9","article-title":"Genomic mapping by fingerprinting random clones: a mathematical 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nucleotide composition of microbial genomes indicates differential patterns of selection on core and accessory genomes","volume":"18","author":"Bohlin","year":"2017","journal-title":"BMC Genomics"},{"key":"2024080705380978200_ref140","doi-asserted-by":"crossref","first-page":"464","DOI":"10.1186\/1471-2164-11-464","article-title":"Analysis of intra-genomic GC content homogeneity within prokaryotes","volume":"11","author":"Bohlin","year":"2010","journal-title":"BMC Genomics"},{"key":"2024080705380978200_ref141","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1000057","article-title":"Investigations of oligonucleotide usage variance within and between prokaryotes","volume":"4","author":"Bohlin","year":"2008","journal-title":"PLoS Comput Biol"},{"key":"2024080705380978200_ref142","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1111\/j.1601-5223.1998.00173.x","article-title":"Nitrogen-fixing aerobic bacteria have higher genomic GC content than non-fixing species within the same genus","volume":"128","author":"McEwan","year":"1998","journal-title":"Hereditas"},{"key":"2024080705380978200_ref143","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1016\/j.bbrc.2006.12.008","article-title":"GC content and genome length in Chargaff compliant genomes","volume":"353","author":"Mitchell","year":"2007","journal-title":"Biochem Biophys Res Commun"},{"key":"2024080705380978200_ref144","doi-asserted-by":"crossref","first-page":"260","DOI":"10.1007\/s00239-002-2323-3","article-title":"Aerobiosis increases the genomic guanine plus cytosine content (GC%) in prokaryotes","volume":"55","author":"Naya","year":"2002","journal-title":"J Mol Evol"},{"key":"2024080705380978200_ref145","doi-asserted-by":"crossref","first-page":"800","DOI":"10.1093\/molbev\/msp281","article-title":"Modal codon usage: assessing the typical codon usage of a genome","volume":"27","author":"Davis","year":"2010","journal-title":"Mol Biol 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