File Download

There are no files associated with this item.

  Links for fulltext
     (May Require Subscription)
Supplementary

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

TitleMetaMarker: a pipeline for de novo discovery of novel metagenomic biomarkers
Authors
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?
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
2017 Impact Factor: 5.481
2015 SCImago Journal Rankings: 4.643
PubMed Central ID
ISI Accession Number ID

 

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-

Export via OAI-PMH Interface in XML Formats


OR


Export to Other Non-XML Formats