{"entity": "researcher", "timestamp": "2026-09-28T23:04:38.956Z", "family": "Quince", "given": "Christopher", "initials": "C", "orcid": "0000-0003-1884-8440", "affiliations": ["Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK. c.quince@warwick.ac.uk."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/b448f09b33fd4ef49fc7d4d769178aeb.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/b448f09b33fd4ef49fc7d4d769178aeb"}}, "publications": [{"entity": "publication", "iuid": "0f888e662e884e7290b58c2f5b3702b9", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0f888e662e884e7290b58c2f5b3702b9.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0f888e662e884e7290b58c2f5b3702b9"}}, "title": "DESMAN: a new tool for de novo extraction of strains from metagenomes.", "authors": [{"family": "Quince", "given": "Christopher", "initials": "C", "orcid": "0000-0003-1884-8440", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b448f09b33fd4ef49fc7d4d769178aeb.json"}}, {"family": "Delmont", "given": "Tom O", "initials": "TO"}, {"family": "Raguideau", "given": "S\u00e9bastien", "initials": "S"}, {"family": "Alneberg", "given": "Johannes", "initials": "J"}, {"family": "Darling", "given": "Aaron E", "initials": "AE"}, {"family": "Collins", "given": "Gavin", "initials": "G"}, {"family": "Eren", "given": "A Murat", "initials": "AM"}], "type": "journal article", "published": "2017-09-21", "journal": {"title": "Genome Biol.", "issn": "1474-760X", "volume": "18", "issue": "1", "pages": "181", "issn-l": "1474-7596"}, "abstract": "We introduce DESMAN for De novo Extraction of Strains from Metagenomes. Large multi-sample metagenomes are being generated but strain variation results in fragmentary co-assemblies. Current algorithms can bin contigs into metagenome-assembled genomes but are unable to resolve strain-level variation. DESMAN identifies variants in core genes and uses co-occurrence across samples to link variants into haplotypes and abundance profiles. These are then searched for against non-core genes to determine the accessory genome of each strain. We validated DESMAN on a complex 50-species 210-genome 96-sample synthetic mock data set and then applied it to the Tara Oceans microbiome.", "doi": "10.1186/s13059-017-1309-9", "pmid": "28934976", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC5607848"}, {"db": "pii", "key": "10.1186/s13059-017-1309-9"}], "notes": [], "created": "2018-12-05T11:25:22.835Z", "modified": "2026-09-23T06:43:21.030Z"}]}