MersV1, PubMed, Checkpoint, bibRecord, 001652

ARK: Aggregation of Reads by K-Means for Estimation of Bacterial Community Composition.

Identifieur interne : 001652 ( PubMed/Checkpoint ); précédent : 001651; suivant : 001653

ARK: Aggregation of Reads by K-Means for Estimation of Bacterial Community Composition.

Auteurs : David Koslicki [États-Unis] ; Saikat Chatterjee [Suède] ; Damon Shahrivar [Suède] ; Alan W. Walker [Royaume-Uni] ; Suzanna C. Francis [Royaume-Uni] ; Louise J. Fraser [Royaume-Uni] ; Mikko Vehkaper [Royaume-Uni] ; Yueheng Lan [République populaire de Chine] ; Jukka Corander [Finlande]

Source :

PloS one [ 1932-6203 ] ; 2015.

RBID : pubmed:26496191

Descripteurs français

KwdFr :
- ADN bactérien (), ADN bactérien (génétique), ARN ribosomique 16S (génétique), Algorithmes, Analyse de regroupements, Analyse de séquence d'ADN, Bactéries (), Bactéries (génétique), Fèces (microbiologie), Humains, Internet, Microbiote (génétique), Métagénomique (), Reproductibilité des résultats, Réaction de polymérisation en chaîne.
MESH :
- génétique : ADN bactérien, ARN ribosomique 16S, Bactéries, Microbiote.
- microbiologie : Fèces.
- ADN bactérien, Algorithmes, Analyse de regroupements, Analyse de séquence d'ADN, Bactéries, Humains, Internet, Métagénomique, Reproductibilité des résultats, Réaction de polymérisation en chaîne.

English descriptors

KwdEn :
- Algorithms, Bacteria (classification), Bacteria (genetics), Cluster Analysis, DNA, Bacterial (chemistry), DNA, Bacterial (genetics), Feces (microbiology), Humans, Internet, Metagenomics (methods), Microbiota (genetics), Polymerase Chain Reaction, RNA, Ribosomal, 16S (genetics), Reproducibility of Results, Sequence Analysis, DNA.
MESH :
- chemical , chemistry : DNA, Bacterial.
- classification : Bacteria.
- genetics : Bacteria, DNA, Bacterial, Microbiota, RNA, Ribosomal, 16S.
- methods : Metagenomics.
- microbiology : Feces.
- Algorithms, Cluster Analysis, Humans, Internet, Polymerase Chain Reaction, Reproducibility of Results, Sequence Analysis, DNA.

Abstract

Estimation of bacterial community composition from high-throughput sequenced 16S rRNA gene amplicons is a key task in microbial ecology. Since the sequence data from each sample typically consist of a large number of reads and are adversely impacted by different levels of biological and technical noise, accurate analysis of such large datasets is challenging.

DOI: 10.1371/journal.pone.0140644
PubMed: 26496191

Affiliations:

Links toward previous steps (curation, corpus...)

to stream PubMed, to step Corpus: 001415
to stream PubMed, to step Curation: 001415

Links to Exploration step

pubmed:26496191

Le document en format XML

<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">ARK: Aggregation of Reads by K-Means for Estimation of Bacterial Community Composition.</title>
<author><name sortKey="Koslicki, David" sort="Koslicki, David" uniqKey="Koslicki D" first="David" last="Koslicki">David Koslicki</name>
<affiliation wicri:level="1"><nlm:affiliation>Dept of Mathematics, Oregon State University, Corvallis, United States of America.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Dept of Mathematics, Oregon State University, Corvallis</wicri:regionArea>
<wicri:noRegion>Corvallis</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Chatterjee, Saikat" sort="Chatterjee, Saikat" uniqKey="Chatterjee S" first="Saikat" last="Chatterjee">Saikat Chatterjee</name>
<affiliation wicri:level="3"><nlm:affiliation>Dept of Communication Theory, KTH Royal Institute of Technology, Stockholm, Sweden.</nlm:affiliation>
<country xml:lang="fr">Suède</country>
<wicri:regionArea>Dept of Communication Theory, KTH Royal Institute of Technology, Stockholm</wicri:regionArea>
<placeName><settlement type="city">Stockholm</settlement>
<region nuts="2">Svealand</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Shahrivar, Damon" sort="Shahrivar, Damon" uniqKey="Shahrivar D" first="Damon" last="Shahrivar">Damon Shahrivar</name>
<affiliation wicri:level="3"><nlm:affiliation>Dept of Communication Theory, KTH Royal Institute of Technology, Stockholm, Sweden.</nlm:affiliation>
<country xml:lang="fr">Suède</country>
<wicri:regionArea>Dept of Communication Theory, KTH Royal Institute of Technology, Stockholm</wicri:regionArea>
<placeName><settlement type="city">Stockholm</settlement>
<region nuts="2">Svealand</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Walker, Alan W" sort="Walker, Alan W" uniqKey="Walker A" first="Alan W" last="Walker">Alan W. Walker</name>
<affiliation wicri:level="1"><nlm:affiliation>Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom.</nlm:affiliation>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen</wicri:regionArea>
<wicri:noRegion>Aberdeen</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Francis, Suzanna C" sort="Francis, Suzanna C" uniqKey="Francis S" first="Suzanna C" last="Francis">Suzanna C. Francis</name>
<affiliation wicri:level="3"><nlm:affiliation>MRC Tropical Epidemiology Group, London School of Hygiene and Tropical Medicine, London, United Kingdom.</nlm:affiliation>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>MRC Tropical Epidemiology Group, London School of Hygiene and Tropical Medicine, London</wicri:regionArea>
<placeName><settlement type="city">Londres</settlement>
<region type="country">Angleterre</region>
<region type="région" nuts="1">Grand Londres</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Fraser, Louise J" sort="Fraser, Louise J" uniqKey="Fraser L" first="Louise J" last="Fraser">Louise J. Fraser</name>
<affiliation wicri:level="1"><nlm:affiliation>Illumina Cambridge Ltd., Chesterford Research Park, Essex, United Kingdom.</nlm:affiliation>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Illumina Cambridge Ltd., Chesterford Research Park, Essex</wicri:regionArea>
<wicri:noRegion>Essex</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Vehkaper, Mikko" sort="Vehkaper, Mikko" uniqKey="Vehkaper M" first="Mikko" last="Vehkaper">Mikko Vehkaper</name>
<affiliation wicri:level="1"><nlm:affiliation>Dept of Electronic and Electrical Engineering, University of Sheffield, Sheffield, United Kingdom.</nlm:affiliation>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Dept of Electronic and Electrical Engineering, University of Sheffield, Sheffield</wicri:regionArea>
<wicri:noRegion>Sheffield</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Lan, Yueheng" sort="Lan, Yueheng" uniqKey="Lan Y" first="Yueheng" last="Lan">Yueheng Lan</name>
<affiliation wicri:level="3"><nlm:affiliation>Dept of Physics, Tsinghua University, Beijing, China.</nlm:affiliation>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>Dept of Physics, Tsinghua University, Beijing</wicri:regionArea>
<placeName><settlement type="city">Pékin</settlement>
</placeName>
</affiliation>
</author>
<author><name sortKey="Corander, Jukka" sort="Corander, Jukka" uniqKey="Corander J" first="Jukka" last="Corander">Jukka Corander</name>
<affiliation wicri:level="4"><nlm:affiliation>Dept of Mathematics and Statistics, University of Helsinki, Helsinki, Finland.</nlm:affiliation>
<country xml:lang="fr">Finlande</country>
<wicri:regionArea>Dept of Mathematics and Statistics, University of Helsinki, Helsinki</wicri:regionArea>
<orgName type="university">Université d'Helsinki</orgName>
<placeName><settlement type="city">Helsinki</settlement>
<region type="région" nuts="2">Uusimaa</region>
</placeName>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PubMed</idno>
<date when="2015">2015</date>
<idno type="RBID">pubmed:26496191</idno>
<idno type="pmid">26496191</idno>
<idno type="doi">10.1371/journal.pone.0140644</idno>
<idno type="wicri:Area/PubMed/Corpus">001415</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001415</idno>
<idno type="wicri:Area/PubMed/Curation">001415</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">001415</idno>
<idno type="wicri:Area/PubMed/Checkpoint">001652</idno>
<idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">001652</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en">ARK: Aggregation of Reads by K-Means for Estimation of Bacterial Community Composition.</title>
<author><name sortKey="Koslicki, David" sort="Koslicki, David" uniqKey="Koslicki D" first="David" last="Koslicki">David Koslicki</name>
<affiliation wicri:level="1"><nlm:affiliation>Dept of Mathematics, Oregon State University, Corvallis, United States of America.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Dept of Mathematics, Oregon State University, Corvallis</wicri:regionArea>
<wicri:noRegion>Corvallis</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Chatterjee, Saikat" sort="Chatterjee, Saikat" uniqKey="Chatterjee S" first="Saikat" last="Chatterjee">Saikat Chatterjee</name>
<affiliation wicri:level="3"><nlm:affiliation>Dept of Communication Theory, KTH Royal Institute of Technology, Stockholm, Sweden.</nlm:affiliation>
<country xml:lang="fr">Suède</country>
<wicri:regionArea>Dept of Communication Theory, KTH Royal Institute of Technology, Stockholm</wicri:regionArea>
<placeName><settlement type="city">Stockholm</settlement>
<region nuts="2">Svealand</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Shahrivar, Damon" sort="Shahrivar, Damon" uniqKey="Shahrivar D" first="Damon" last="Shahrivar">Damon Shahrivar</name>
<affiliation wicri:level="3"><nlm:affiliation>Dept of Communication Theory, KTH Royal Institute of Technology, Stockholm, Sweden.</nlm:affiliation>
<country xml:lang="fr">Suède</country>
<wicri:regionArea>Dept of Communication Theory, KTH Royal Institute of Technology, Stockholm</wicri:regionArea>
<placeName><settlement type="city">Stockholm</settlement>
<region nuts="2">Svealand</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Walker, Alan W" sort="Walker, Alan W" uniqKey="Walker A" first="Alan W" last="Walker">Alan W. Walker</name>
<affiliation wicri:level="1"><nlm:affiliation>Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom.</nlm:affiliation>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen</wicri:regionArea>
<wicri:noRegion>Aberdeen</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Francis, Suzanna C" sort="Francis, Suzanna C" uniqKey="Francis S" first="Suzanna C" last="Francis">Suzanna C. Francis</name>
<affiliation wicri:level="3"><nlm:affiliation>MRC Tropical Epidemiology Group, London School of Hygiene and Tropical Medicine, London, United Kingdom.</nlm:affiliation>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>MRC Tropical Epidemiology Group, London School of Hygiene and Tropical Medicine, London</wicri:regionArea>
<placeName><settlement type="city">Londres</settlement>
<region type="country">Angleterre</region>
<region type="région" nuts="1">Grand Londres</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Fraser, Louise J" sort="Fraser, Louise J" uniqKey="Fraser L" first="Louise J" last="Fraser">Louise J. Fraser</name>
<affiliation wicri:level="1"><nlm:affiliation>Illumina Cambridge Ltd., Chesterford Research Park, Essex, United Kingdom.</nlm:affiliation>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Illumina Cambridge Ltd., Chesterford Research Park, Essex</wicri:regionArea>
<wicri:noRegion>Essex</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Vehkaper, Mikko" sort="Vehkaper, Mikko" uniqKey="Vehkaper M" first="Mikko" last="Vehkaper">Mikko Vehkaper</name>
<affiliation wicri:level="1"><nlm:affiliation>Dept of Electronic and Electrical Engineering, University of Sheffield, Sheffield, United Kingdom.</nlm:affiliation>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Dept of Electronic and Electrical Engineering, University of Sheffield, Sheffield</wicri:regionArea>
<wicri:noRegion>Sheffield</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Lan, Yueheng" sort="Lan, Yueheng" uniqKey="Lan Y" first="Yueheng" last="Lan">Yueheng Lan</name>
<affiliation wicri:level="3"><nlm:affiliation>Dept of Physics, Tsinghua University, Beijing, China.</nlm:affiliation>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>Dept of Physics, Tsinghua University, Beijing</wicri:regionArea>
<placeName><settlement type="city">Pékin</settlement>
</placeName>
</affiliation>
</author>
<author><name sortKey="Corander, Jukka" sort="Corander, Jukka" uniqKey="Corander J" first="Jukka" last="Corander">Jukka Corander</name>
<affiliation wicri:level="4"><nlm:affiliation>Dept of Mathematics and Statistics, University of Helsinki, Helsinki, Finland.</nlm:affiliation>
<country xml:lang="fr">Finlande</country>
<wicri:regionArea>Dept of Mathematics and Statistics, University of Helsinki, Helsinki</wicri:regionArea>
<orgName type="university">Université d'Helsinki</orgName>
<placeName><settlement type="city">Helsinki</settlement>
<region type="région" nuts="2">Uusimaa</region>
</placeName>
</affiliation>
</author>
</analytic>
<series><title level="j">PloS one</title>
<idno type="eISSN">1932-6203</idno>
<imprint><date when="2015" type="published">2015</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term>
<term>Bacteria (classification)</term>
<term>Bacteria (genetics)</term>
<term>Cluster Analysis</term>
<term>DNA, Bacterial (chemistry)</term>
<term>DNA, Bacterial (genetics)</term>
<term>Feces (microbiology)</term>
<term>Humans</term>
<term>Internet</term>
<term>Metagenomics (methods)</term>
<term>Microbiota (genetics)</term>
<term>Polymerase Chain Reaction</term>
<term>RNA, Ribosomal, 16S (genetics)</term>
<term>Reproducibility of Results</term>
<term>Sequence Analysis, DNA</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>ADN bactérien ()</term>
<term>ADN bactérien (génétique)</term>
<term>ARN ribosomique 16S (génétique)</term>
<term>Algorithmes</term>
<term>Analyse de regroupements</term>
<term>Analyse de séquence d'ADN</term>
<term>Bactéries ()</term>
<term>Bactéries (génétique)</term>
<term>Fèces (microbiologie)</term>
<term>Humains</term>
<term>Internet</term>
<term>Microbiote (génétique)</term>
<term>Métagénomique ()</term>
<term>Reproductibilité des résultats</term>
<term>Réaction de polymérisation en chaîne</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>DNA, Bacterial</term>
</keywords>
<keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Bacteria</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Bacteria</term>
<term>DNA, Bacterial</term>
<term>Microbiota</term>
<term>RNA, Ribosomal, 16S</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN bactérien</term>
<term>ARN ribosomique 16S</term>
<term>Bactéries</term>
<term>Microbiote</term>
</keywords>
<keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Metagenomics</term>
</keywords>
<keywords scheme="MESH" qualifier="microbiologie" xml:lang="fr"><term>Fèces</term>
</keywords>
<keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Feces</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Algorithms</term>
<term>Cluster Analysis</term>
<term>Humans</term>
<term>Internet</term>
<term>Polymerase Chain Reaction</term>
<term>Reproducibility of Results</term>
<term>Sequence Analysis, DNA</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>ADN bactérien</term>
<term>Algorithmes</term>
<term>Analyse de regroupements</term>
<term>Analyse de séquence d'ADN</term>
<term>Bactéries</term>
<term>Humains</term>
<term>Internet</term>
<term>Métagénomique</term>
<term>Reproductibilité des résultats</term>
<term>Réaction de polymérisation en chaîne</term>
</keywords>
</textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en">Estimation of bacterial community composition from high-throughput sequenced 16S rRNA gene amplicons is a key task in microbial ecology. Since the sequence data from each sample typically consist of a large number of reads and are adversely impacted by different levels of biological and technical noise, accurate analysis of such large datasets is challenging.</div>
</front>
</TEI>
<pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">26496191</PMID>
<DateCompleted><Year>2016</Year>
<Month>06</Month>
<Day>15</Day>
</DateCompleted>
<DateRevised><Year>2018</Year>
<Month>11</Month>
<Day>13</Day>
</DateRevised>
<Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Electronic">1932-6203</ISSN>
<JournalIssue CitedMedium="Internet"><Volume>10</Volume>
<Issue>10</Issue>
<PubDate><Year>2015</Year>
</PubDate>
</JournalIssue>
<Title>PloS one</Title>
<ISOAbbreviation>PLoS ONE</ISOAbbreviation>
</Journal>
<ArticleTitle>ARK: Aggregation of Reads by K-Means for Estimation of Bacterial Community Composition.</ArticleTitle>
<Pagination><MedlinePgn>e0140644</MedlinePgn>
</Pagination>
<ELocationID EIdType="doi" ValidYN="Y">10.1371/journal.pone.0140644</ELocationID>
<Abstract><AbstractText Label="MOTIVATION" NlmCategory="BACKGROUND">Estimation of bacterial community composition from high-throughput sequenced 16S rRNA gene amplicons is a key task in microbial ecology. Since the sequence data from each sample typically consist of a large number of reads and are adversely impacted by different levels of biological and technical noise, accurate analysis of such large datasets is challenging.</AbstractText>
<AbstractText Label="RESULTS" NlmCategory="RESULTS">There has been a recent surge of interest in using compressed sensing inspired and convex-optimization based methods to solve the estimation problem for bacterial community composition. These methods typically rely on summarizing the sequence data by frequencies of low-order k-mers and matching this information statistically with a taxonomically structured database. Here we show that the accuracy of the resulting community composition estimates can be substantially improved by aggregating the reads from a sample with an unsupervised machine learning approach prior to the estimation phase. The aggregation of reads is a pre-processing approach where we use a standard K-means clustering algorithm that partitions a large set of reads into subsets with reasonable computational cost to provide several vectors of first order statistics instead of only single statistical summarization in terms of k-mer frequencies. The output of the clustering is then processed further to obtain the final estimate for each sample. The resulting method is called Aggregation of Reads by K-means (ARK), and it is based on a statistical argument via mixture density formulation. ARK is found to improve the fidelity and robustness of several recently introduced methods, with only a modest increase in computational complexity.</AbstractText>
<AbstractText Label="AVAILABILITY" NlmCategory="BACKGROUND">An open source, platform-independent implementation of the method in the Julia programming language is freely available at https://github.com/dkoslicki/ARK. A Matlab implementation is available at http://www.ee.kth.se/ctsoftware.</AbstractText>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Koslicki</LastName>
<ForeName>David</ForeName>
<Initials>D</Initials>
<AffiliationInfo><Affiliation>Dept of Mathematics, Oregon State University, Corvallis, United States of America.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Chatterjee</LastName>
<ForeName>Saikat</ForeName>
<Initials>S</Initials>
<AffiliationInfo><Affiliation>Dept of Communication Theory, KTH Royal Institute of Technology, Stockholm, Sweden.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Shahrivar</LastName>
<ForeName>Damon</ForeName>
<Initials>D</Initials>
<AffiliationInfo><Affiliation>Dept of Communication Theory, KTH Royal Institute of Technology, Stockholm, Sweden.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Walker</LastName>
<ForeName>Alan W</ForeName>
<Initials>AW</Initials>
<AffiliationInfo><Affiliation>Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Francis</LastName>
<ForeName>Suzanna C</ForeName>
<Initials>SC</Initials>
<AffiliationInfo><Affiliation>MRC Tropical Epidemiology Group, London School of Hygiene and Tropical Medicine, London, United Kingdom.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Fraser</LastName>
<ForeName>Louise J</ForeName>
<Initials>LJ</Initials>
<AffiliationInfo><Affiliation>Illumina Cambridge Ltd., Chesterford Research Park, Essex, United Kingdom.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Vehkaperä</LastName>
<ForeName>Mikko</ForeName>
<Initials>M</Initials>
<AffiliationInfo><Affiliation>Dept of Electronic and Electrical Engineering, University of Sheffield, Sheffield, United Kingdom.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Lan</LastName>
<ForeName>Yueheng</ForeName>
<Initials>Y</Initials>
<AffiliationInfo><Affiliation>Dept of Physics, Tsinghua University, Beijing, China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Corander</LastName>
<ForeName>Jukka</ForeName>
<Initials>J</Initials>
<AffiliationInfo><Affiliation>Dept of Mathematics and Statistics, University of Helsinki, Helsinki, Finland.</Affiliation>
</AffiliationInfo>
</Author>
</AuthorList>
<Language>eng</Language>
<GrantList CompleteYN="Y"><Grant><Agency>Wellcome Trust</Agency>
<Country>United Kingdom</Country>
</Grant>
<Grant><GrantID>G0701039</GrantID>
<Agency>Medical Research Council</Agency>
<Country>United Kingdom</Country>
</Grant>
<Grant><GrantID>MR/K012126/1</GrantID>
<Agency>Medical Research Council</Agency>
<Country>United Kingdom</Country>
</Grant>
<Grant><GrantID>G1002369</GrantID>
<Agency>Medical Research Council</Agency>
<Country>United Kingdom</Country>
</Grant>
</GrantList>
<PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType>
<PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType>
</PublicationTypeList>
<ArticleDate DateType="Electronic"><Year>2015</Year>
<Month>10</Month>
<Day>23</Day>
</ArticleDate>
</Article>
<MedlineJournalInfo><Country>United States</Country>
<MedlineTA>PLoS One</MedlineTA>
<NlmUniqueID>101285081</NlmUniqueID>
<ISSNLinking>1932-6203</ISSNLinking>
</MedlineJournalInfo>
<ChemicalList><Chemical><RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="D004269">DNA, Bacterial</NameOfSubstance>
</Chemical>
<Chemical><RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="D012336">RNA, Ribosomal, 16S</NameOfSubstance>
</Chemical>
</ChemicalList>
<CitationSubset>IM</CitationSubset>
<MeshHeadingList><MeshHeading><DescriptorName UI="D000465" MajorTopicYN="Y">Algorithms</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D001419" MajorTopicYN="N">Bacteria</DescriptorName>
<QualifierName UI="Q000145" MajorTopicYN="N">classification</QualifierName>
<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D016000" MajorTopicYN="N">Cluster Analysis</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D004269" MajorTopicYN="N">DNA, Bacterial</DescriptorName>
<QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D005243" MajorTopicYN="N">Feces</DescriptorName>
<QualifierName UI="Q000382" MajorTopicYN="N">microbiology</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D020407" MajorTopicYN="N">Internet</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D056186" MajorTopicYN="N">Metagenomics</DescriptorName>
<QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D064307" MajorTopicYN="N">Microbiota</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D016133" MajorTopicYN="N">Polymerase Chain Reaction</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D012336" MajorTopicYN="N">RNA, Ribosomal, 16S</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D015203" MajorTopicYN="N">Reproducibility of Results</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName>
</MeshHeading>
</MeshHeadingList>
</MedlineCitation>
<PubmedData><History><PubMedPubDate PubStatus="received"><Year>2015</Year>
<Month>04</Month>
<Day>20</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="accepted"><Year>2015</Year>
<Month>09</Month>
<Day>28</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="entrez"><Year>2015</Year>
<Month>10</Month>
<Day>27</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="pubmed"><Year>2015</Year>
<Month>10</Month>
<Day>27</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="medline"><Year>2016</Year>
<Month>6</Month>
<Day>16</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
</History>
<PublicationStatus>epublish</PublicationStatus>
<ArticleIdList><ArticleId IdType="pubmed">26496191</ArticleId>
<ArticleId IdType="doi">10.1371/journal.pone.0140644</ArticleId>
<ArticleId IdType="pii">PONE-D-15-15487</ArticleId>
<ArticleId IdType="pmc">PMC4619776</ArticleId>
</ArticleIdList>
<ReferenceList><Reference><Citation>Bioinformatics. 2003 Jan;19(1):22-9</Citation>
<ArticleIdList><ArticleId IdType="pubmed">12499289</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Nucleic Acids Res. 2011 Aug;39(14):e95</Citation>
<ArticleIdList><ArticleId IdType="pubmed">21596775</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Science. 2007 Feb 23;315(5815):1126-30</Citation>
<ArticleIdList><ArticleId IdType="pubmed">17272687</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Bioinformatics. 2011 Jan 1;27(1):127-9</Citation>
<ArticleIdList><ArticleId IdType="pubmed">21062764</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Nucleic Acids Res. 2010 Dec;38(22):e200</Citation>
<ArticleIdList><ArticleId IdType="pubmed">20880993</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Bioinformatics. 2010 Sep 15;26(18):i420-5</Citation>
<ArticleIdList><ArticleId IdType="pubmed">20823302</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Appl Environ Microbiol. 2007 Aug;73(16):5261-7</Citation>
<ArticleIdList><ArticleId IdType="pubmed">17586664</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Bioinformatics. 2013 Sep 1;29(17):2096-102</Citation>
<ArticleIdList><ArticleId IdType="pubmed">23786768</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Genome Res. 2007 Mar;17(3):377-86</Citation>
<ArticleIdList><ArticleId IdType="pubmed">17255551</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Adv Bioinformatics. 2008;2008:205969</Citation>
<ArticleIdList><ArticleId IdType="pubmed">19956701</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Bioinformatics. 2015 Mar 15;31(6):817-24</Citation>
<ArticleIdList><ArticleId IdType="pubmed">25388150</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>PLoS One. 2014;9(3):e91784</Citation>
<ArticleIdList><ArticleId IdType="pubmed">24626336</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>PLoS One. 2013;8(4):e60811</Citation>
<ArticleIdList><ArticleId IdType="pubmed">23579286</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Bioinformatics. 2011 Jun 15;27(12):1618-24</Citation>
<ArticleIdList><ArticleId IdType="pubmed">21546400</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Bioinformatics. 2010 Oct 1;26(19):2460-1</Citation>
<ArticleIdList><ArticleId IdType="pubmed">20709691</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Nucleic Acids Res. 2012 Jul;40(12):5240-9</Citation>
<ArticleIdList><ArticleId IdType="pubmed">22406836</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Bioinformatics. 2014 Sep 1;30(17):2423-31</Citation>
<ArticleIdList><ArticleId IdType="pubmed">24812337</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Nucleic Acids Res. 2012 Jul;40(12):e94</Citation>
<ArticleIdList><ArticleId IdType="pubmed">22434876</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>BMC Genomics. 2011 Nov 30;12 Suppl 3:S17</Citation>
<ArticleIdList><ArticleId IdType="pubmed">22369513</ArticleId>
</ArticleIdList>
</Reference>
</ReferenceList>
</PubmedData>
</pubmed>
<affiliations><list><country><li>Finlande</li>
<li>Royaume-Uni</li>
<li>République populaire de Chine</li>
<li>Suède</li>
<li>États-Unis</li>
</country>
<region><li>Angleterre</li>
<li>Grand Londres</li>
<li>Svealand</li>
<li>Uusimaa</li>
</region>
<settlement><li>Helsinki</li>
<li>Londres</li>
<li>Pékin</li>
<li>Stockholm</li>
</settlement>
<orgName><li>Université d'Helsinki</li>
</orgName>
</list>
<tree><country name="États-Unis"><noRegion><name sortKey="Koslicki, David" sort="Koslicki, David" uniqKey="Koslicki D" first="David" last="Koslicki">David Koslicki</name>
</noRegion>
</country>
<country name="Suède"><region name="Svealand"><name sortKey="Chatterjee, Saikat" sort="Chatterjee, Saikat" uniqKey="Chatterjee S" first="Saikat" last="Chatterjee">Saikat Chatterjee</name>
</region>
<name sortKey="Shahrivar, Damon" sort="Shahrivar, Damon" uniqKey="Shahrivar D" first="Damon" last="Shahrivar">Damon Shahrivar</name>
</country>
<country name="Royaume-Uni"><noRegion><name sortKey="Walker, Alan W" sort="Walker, Alan W" uniqKey="Walker A" first="Alan W" last="Walker">Alan W. Walker</name>
</noRegion>
<name sortKey="Francis, Suzanna C" sort="Francis, Suzanna C" uniqKey="Francis S" first="Suzanna C" last="Francis">Suzanna C. Francis</name>
<name sortKey="Fraser, Louise J" sort="Fraser, Louise J" uniqKey="Fraser L" first="Louise J" last="Fraser">Louise J. Fraser</name>
<name sortKey="Vehkaper, Mikko" sort="Vehkaper, Mikko" uniqKey="Vehkaper M" first="Mikko" last="Vehkaper">Mikko Vehkaper</name>
</country>
<country name="République populaire de Chine"><noRegion><name sortKey="Lan, Yueheng" sort="Lan, Yueheng" uniqKey="Lan Y" first="Yueheng" last="Lan">Yueheng Lan</name>
</noRegion>
</country>
<country name="Finlande"><region name="Uusimaa"><name sortKey="Corander, Jukka" sort="Corander, Jukka" uniqKey="Corander J" first="Jukka" last="Corander">Jukka Corander</name>
</region>
</country>
</tree>
</affiliations>
</record>

Pour manipuler ce document sous Unix (Dilib)

EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/PubMed/Checkpoint

HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 001652 | SxmlIndent | more

HfdSelect -h $EXPLOR_AREA/Data/PubMed/Checkpoint/biblio.hfd -nk 001652 | SxmlIndent | more

Pour mettre un lien sur cette page dans le réseau Wicri

{{Explor lien
   |wiki=    Sante
   |area=    MersV1
   |flux=    PubMed
   |étape=   Checkpoint
   |type=    RBID
   |clé=     pubmed:26496191
   |texte=   ARK: Aggregation of Reads by K-Means for Estimation of Bacterial Community Composition.
}}

Pour générer des pages wiki

HfdIndexSelect -h $EXPLOR_AREA/Data/PubMed/Checkpoint/RBID.i   -Sk "pubmed:26496191" \
       | HfdSelect -Kh $EXPLOR_AREA/Data/PubMed/Checkpoint/biblio.hfd   \
       | NlmPubMed2Wicri -a MersV1

This area was generated with Dilib version V0.6.33.
Data generation: Mon Apr 20 23:26:43 2020. Site generation: Sat Mar 27 09:06:09 2021

	Serveur d'exploration MERS
	Attention, ce site est en cours de développement ! Attention, site généré par des moyens informatiques à partir de corpus bruts. Les informations ne sont donc pas validées.

Serveur d'exploration MERS

ARK: Aggregation of Reads by K-Means for Estimation of Bacterial Community Composition.

ARK: Aggregation of Reads by K-Means for Estimation of Bacterial Community Composition.

Source :

Descripteurs français

English descriptors

Abstract

Links toward previous steps (curation, corpus...)

Links to Exploration step

Le document en format XML

Pour manipuler ce document sous Unix (Dilib)

Pour mettre un lien sur cette page dans le réseau Wicri

Pour générer des pages wiki