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Article: MetaMarker: a pipeline for de novo discovery of novel metagenomic biomarkers

TitleMetaMarker: a pipeline for de novo discovery of novel metagenomic biomarkers
Authors
Koohi-Moghadam, MBorad, MJTran, NLSwanson, KRBoardman, LASun, HWang, JW
Issue Date2019
PublisherOxford University Press (OUP): Policy B - Oxford Open Option B. The Journal's web site is located at http://bioinformatics.oxfordjournals.org/
Citation
Bioinformatics, 2019, v. 35 n. 19, p. 3812-3814 How to Cite?
DOI: http://dx.doi.org/10.1093/bioinformatics/btz123
AbstractWe present MetaMarker, a pipeline for discovering metagenomic biomarkers from whole-metagenome sequencing samples. Different from existing methods, MetaMarker is based on a de novo approach that does not require mapping raw reads to a reference database. We applied MetaMarker on whole-metagenome sequencing of colorectal cancer (CRC) stool samples from France to discover CRC specific metagenomic biomarkers. We showed robustness of the discovered biomarkers by validating in independent samples from Hong Kong, Austria, Germany and Denmark. We further demonstrated these biomarkers could be used to build a machine learning classifier for CRC prediction.
Persistent Identifierhttp://hdl.handle.net/10722/270070
ISSN
1367-4803
2021 Impact Factor: 6.931
2020 SCImago Journal Rankings: 3.599
PubMed Central ID
PMC6761932
ISI Accession Number ID
WOS:000499322300033

 

DC FieldValueLanguage
dc.contributor.authorKoohi-Moghadam, M-
dc.contributor.authorBorad, MJ-
dc.contributor.authorTran, NL-
dc.contributor.authorSwanson, KR-
dc.contributor.authorBoardman, LA-
dc.contributor.authorSun, H-
dc.contributor.authorWang, JW-
dc.date.accessioned2019-05-20T05:08:54Z-
dc.date.available2019-05-20T05:08:54Z-
dc.date.issued2019-
dc.identifier.citationBioinformatics, 2019, v. 35 n. 19, p. 3812-3814-
dc.identifier.issn1367-4803-
dc.identifier.urihttp://hdl.handle.net/10722/270070-
dc.description.abstractWe present MetaMarker, a pipeline for discovering metagenomic biomarkers from whole-metagenome sequencing samples. Different from existing methods, MetaMarker is based on a de novo approach that does not require mapping raw reads to a reference database. We applied MetaMarker on whole-metagenome sequencing of colorectal cancer (CRC) stool samples from France to discover CRC specific metagenomic biomarkers. We showed robustness of the discovered biomarkers by validating in independent samples from Hong Kong, Austria, Germany and Denmark. We further demonstrated these biomarkers could be used to build a machine learning classifier for CRC prediction.-
dc.languageeng-
dc.publisherOxford University Press (OUP): Policy B - Oxford Open Option B. The Journal's web site is located at http://bioinformatics.oxfordjournals.org/-
dc.relation.ispartofBioinformatics-
dc.titleMetaMarker: a pipeline for de novo discovery of novel metagenomic biomarkers-
dc.typeArticle-
dc.identifier.emailKoohi-Moghadam, M: koohi@hku.hk-
dc.identifier.emailSun, H: hsun@hku.hk-
dc.identifier.authorityKoohi-Moghadam, M=rp02665-
dc.identifier.authoritySun, H=rp00777-
dc.description.naturelink_to_subscribed_fulltext-
dc.identifier.doi10.1093/bioinformatics/btz123-
dc.identifier.pmid30825371-
dc.identifier.pmcidPMC6761932-
dc.identifier.scopuseid_2-s2.0-85072717584-
dc.identifier.hkuros297867-
dc.identifier.volume35-
dc.identifier.issue19-
dc.identifier.spage3812-
dc.identifier.epage3814-
dc.identifier.isiWOS:000499322300033-
dc.publisher.placeUnited Kingdom-
dc.identifier.issnl1367-4803-

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