{"id":"https://openalex.org/W2125708453","doi":"https://doi.org/10.1371/journal.pone.0140644","title":"ARK: Aggregation of Reads by K-Means for Estimation of Bacterial Community Composition","display_name":"ARK: Aggregation of Reads by K-Means for Estimation of Bacterial Community Composition","publication_year":2015,"publication_date":"2015-10-23","ids":{"openalex":"https://openalex.org/W2125708453","doi":"https://doi.org/10.1371/journal.pone.0140644","mag":"2125708453","pmid":"https://pubmed.ncbi.nlm.nih.gov/26496191","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/4619776"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pone.0140644","doi":"https://doi.org/10.1371/journal.pone.0140644","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pone.0140644","pdf_url":"https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0140644&type=printable","source":{"id":"https://openalex.org/S202381698","display_name":"PLoS ONE","issn_l":"1932-6203","issn":["1932-6203"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","cwts-core","doaj","dongbi-c","doyens","erih-plus","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS ONE","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0140644&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5002668669","display_name":"David Koslicki","orcid":"https://orcid.org/0000-0002-0640-954X","observed_orcids":["https://orcid.org/0000-0002-0640-954X"]},"institutions":[{"id":"https://openalex.org/I131249849","display_name":"Oregon State University","ror":"https://ror.org/00ysfqy60","country_code":"US","type":"education","lineage":["https://openalex.org/I131249849"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David Koslicki","raw_affiliation_strings":["Dept of Mathematics, Oregon State University, Corvallis, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dept of Mathematics, Oregon State University, Corvallis, United States of America","institution_ids":["https://openalex.org/I131249849"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077666857","display_name":"S. Chatterjee","orcid":"https://orcid.org/0000-0003-3509-7300","observed_orcids":["https://orcid.org/0000-0003-3509-7300"]},"institutions":[{"id":"https://openalex.org/I86987016","display_name":"KTH Royal Institute of Technology","ror":"https://ror.org/026vcq606","country_code":"SE","type":"education","lineage":["https://openalex.org/I86987016"]}],"countries":["SE"],"is_corresponding":true,"raw_author_name":"Saikat Chatterjee","raw_affiliation_strings":["Dept of Communication Theory, KTH Royal Institute of Technology, Stockholm, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dept of Communication Theory, KTH Royal Institute of Technology, Stockholm, Sweden","institution_ids":["https://openalex.org/I86987016"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037278658","display_name":"Damon Shahrivar","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I86987016","display_name":"KTH Royal Institute of Technology","ror":"https://ror.org/026vcq606","country_code":"SE","type":"education","lineage":["https://openalex.org/I86987016"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Damon Shahrivar","raw_affiliation_strings":["Dept of Communication Theory, KTH Royal Institute of Technology, Stockholm, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dept of Communication Theory, KTH Royal Institute of Technology, Stockholm, Sweden","institution_ids":["https://openalex.org/I86987016"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087071913","display_name":"Alan W. Walker","orcid":"https://orcid.org/0000-0001-5099-8495","observed_orcids":["https://orcid.org/0000-0001-5099-8495"]},"institutions":[{"id":"https://openalex.org/I195460627","display_name":"University of Aberdeen","ror":"https://ror.org/016476m91","country_code":"GB","type":"education","lineage":["https://openalex.org/I195460627"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Alan W. Walker","raw_affiliation_strings":["Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom","institution_ids":["https://openalex.org/I195460627"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063683644","display_name":"Suzanna C. Francis","orcid":"https://orcid.org/0000-0002-3724-4813","observed_orcids":["https://orcid.org/0000-0002-3724-4813"]},"institutions":[{"id":"https://openalex.org/I4210089966","display_name":"London School of Hygiene & Tropical Medicine","ror":"https://ror.org/00a0jsq62","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I4210089966"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Suzanna C. Francis","raw_affiliation_strings":["MRC Tropical Epidemiology Group, London School of Hygiene and Tropical Medicine, London, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"MRC Tropical Epidemiology Group, London School of Hygiene and Tropical Medicine, London, United Kingdom","institution_ids":["https://openalex.org/I4210089966"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042717446","display_name":"Louise J. Fraser","orcid":"https://orcid.org/0000-0001-9709-6827","observed_orcids":["https://orcid.org/0000-0001-9709-6827"]},"institutions":[{"id":"https://openalex.org/I4210113899","display_name":"Illumina (United Kingdom)","ror":"https://ror.org/027c2yv63","country_code":"GB","type":"company","lineage":["https://openalex.org/I178645029","https://openalex.org/I4210113899"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Louise J. Fraser","raw_affiliation_strings":["Illumina Cambridge Ltd., Chesterford Research Park, Essex, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Illumina Cambridge Ltd., Chesterford Research Park, Essex, United Kingdom","institution_ids":["https://openalex.org/I4210113899"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058197462","display_name":"Mikko Vehkaper\u00e4","orcid":"https://orcid.org/0000-0002-3085-538X","observed_orcids":["https://orcid.org/0000-0002-3085-538X"]},"institutions":[{"id":"https://openalex.org/I91136226","display_name":"University of Sheffield","ror":"https://ror.org/05krs5044","country_code":"GB","type":"education","lineage":["https://openalex.org/I91136226"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Mikko Vehkaper\u00e4","raw_affiliation_strings":["Dept of Electronic and Electrical Engineering, University of Sheffield, Sheffield, United Kingdom","Department of Electronic and Electrical Engineering, University of Sheffield, Sheffield, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dept of Electronic and Electrical Engineering, University of Sheffield, Sheffield, United Kingdom","institution_ids":["https://openalex.org/I91136226"]},{"raw_affiliation_string":"Department of Electronic and Electrical Engineering, University of Sheffield, Sheffield, United Kingdom","institution_ids":["https://openalex.org/I91136226"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048205117","display_name":"Yueheng Lan","orcid":"https://orcid.org/0000-0002-2950-8022","observed_orcids":["https://orcid.org/0000-0002-2950-8022"]},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yueheng Lan","raw_affiliation_strings":["Dept of Physics, Tsinghua University, Beijing, China","Department of Physics Tsinghua University Beijing China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dept of Physics, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]},{"raw_affiliation_string":"Department of Physics Tsinghua University Beijing China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5013196979","display_name":"Jukka Corander","orcid":"https://orcid.org/0000-0002-7752-1942","observed_orcids":["https://orcid.org/0000-0002-7752-1942"]},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Jukka Corander","raw_affiliation_strings":["Dept of Mathematics and Statistics, University of Helsinki, Helsinki, Finland","Department of Mathematics and Statistics, University of Helsinki Helsinki, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dept of Mathematics and Statistics, University of Helsinki, Helsinki, Finland","institution_ids":["https://openalex.org/I133731052"]},{"raw_affiliation_string":"Department of Mathematics and Statistics, University of Helsinki Helsinki, Finland","institution_ids":["https://openalex.org/I133731052"]}]}],"institutions":[],"countries_distinct_count":5,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5077666857"],"corresponding_institution_ids":["https://openalex.org/I86987016"],"apc_list":{"value":2382,"currency":"USD","value_usd":2382},"apc_paid":{"value":1383,"currency":"EUR","value_usd":1491},"fwci":0.3538,"has_fulltext":true,"cited_by_count":8,"citation_normalized_percentile":{"value":0.55995966,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":95},"biblio":{"volume":"10","issue":"10","first_page":"e0140644","last_page":"e0140644"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.8140000104904175,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.8140000104904175,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11791","display_name":"Microbial Community Ecology and Physiology","score":0.15109999477863312,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10066","display_name":"Gut microbiota and health","score":0.007899999618530273,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/bacterial-community-composition","display_name":"bacterial community composition","score":0.9020000100135803},{"id":"https://openalex.org/keywords/16s-rrna-gene-amplicons","display_name":"16S rRNA gene amplicons","score":0.984000027179718},{"id":"https://openalex.org/keywords/k-means-clustering","display_name":"K-means clustering","score":0.9160000085830688},{"id":"https://openalex.org/keywords/mixture-density-models","display_name":"mixture density models","score":0.4819999933242798},{"id":"https://openalex.org/keywords/compressed-sensing","display_name":"compressed sensing","score":0.7269999980926514},{"id":"https://openalex.org/keywords/convex-optimization","display_name":"convex optimization","score":0.7749999761581421},{"id":"https://openalex.org/keywords/k-mer-frequency","display_name":"k-mer frequency","score":0.7540000081062317},{"id":"https://openalex.org/keywords/next-generation-sequencing","display_name":"next-generation sequencing","score":0.6050000190734863},{"id":"https://openalex.org/keywords/microbial-ecology","display_name":"microbial ecology","score":0.5139999985694885}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6667752265930176},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.6070115566253662},{"id":"https://openalex.org/C170858558","wikidata":"https://www.wikidata.org/wiki/Q1394144","display_name":"Automatic summarization","level":2,"score":0.5024416446685791},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.44172734022140503},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.4393693506717682},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3726980686187744},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.36205482482910156},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3411135673522949},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2143876850605011},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D004269","descriptor_name":"DNA, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004269","descriptor_name":"DNA, Bacterial","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D005243","descriptor_name":"Feces","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012336","descriptor_name":"RNA, Ribosomal, 16S","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016133","descriptor_name":"Polymerase Chain Reaction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":11,"locations":[{"id":"doi:10.1371/journal.pone.0140644","doi":"https://doi.org/10.1371/journal.pone.0140644","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pone.0140644","pdf_url":"https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0140644&type=printable","source":{"id":"https://openalex.org/S202381698","display_name":"PLoS ONE","issn_l":"1932-6203","issn":["1932-6203"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","cwts-core","doaj","dongbi-c","doyens","erih-plus","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS ONE","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:4619776","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4619776","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS One","raw_type":"Text"},{"id":"pmid:26496191","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26496191","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PloS one","raw_type":"Journal Article"},{"id":"pmh:oai:eprints.whiterose.ac.uk:91765","doi":null,"is_oa":false,"landing_page_url":"http://eprints.whiterose.ac.uk/91765/1/ARK%3A%20Aggregation%20of%20Reads%20by%20K-Means%20for%20Estimation%20of%20Bacterial%20Community%20Composition..pdf","pdf_url":"http://eprints.whiterose.ac.uk/91765/1/ARK%3A%20Aggregation%20of%20Reads%20by%20K-Means%20for%20Estimation%20of%20Bacterial%20Community%20Composition..pdf","source":{"id":"https://openalex.org/S4306400854","display_name":"White Rose Research Online (University of Leeds, The University of Sheffield, University of York)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2800616092","host_organization_name":"White Rose University Consortium","host_organization_lineage":["https://openalex.org/I2800616092"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"","raw_type":"Article"},{"id":"pmh:oai:researchonline.lshtm.ac.uk:2338123","doi":null,"is_oa":false,"landing_page_url":"https://researchonline.lshtm.ac.uk/view/creators/eidesfra.html>;","pdf_url":null,"source":{"id":"https://openalex.org/S4306402527","display_name":"LSHTM Research Online (London School of Hygiene and Tropical Medicine)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4210089966","host_organization_name":"London School of Hygiene & Tropical Medicine","host_organization_lineage":["https://openalex.org/I4210089966"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"Article"},{"id":"pmh:oai:aaltodoc.aalto.fi:123456789/103494","doi":null,"is_oa":true,"landing_page_url":"https://research.aalto.fi/en/publications/de5b2c23-648d-466d-a299-5200708d86e2","pdf_url":"https://research.aalto.fi/files/61233318/pone.0140644.pdf","source":{"id":"https://openalex.org/S4306401662","display_name":"Aaltodoc (Aalto University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I9927081","host_organization_name":"Aalto University","host_organization_lineage":["https://openalex.org/I9927081"],"host_organization_lineage_names":[],"type":"repository"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.802.8273","doi":null,"is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.802.8273","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/94/2a/pone.0140644.PMC4619776.pdf","raw_type":"text"},{"id":"pmh:oai:RePEc:plo:pone00:0140644","doi":null,"is_oa":false,"landing_page_url":"https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0140644","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:aura.abdn.ac.uk:2164/5145","doi":null,"is_oa":false,"landing_page_url":"http://hdl.handle.net/2164/5145","pdf_url":null,"source":{"id":"https://openalex.org/S4306400966","display_name":"Aberdeen University Research Archive (Aberdeen University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I195460627","host_organization_name":"University of Aberdeen","host_organization_lineage":["https://openalex.org/I195460627"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Journal article"},{"id":"pmh:oai:doaj.org/article:d0e8caa4c0b744dfbd0a80f1b1ed8ade","doi":null,"is_oa":true,"landing_page_url":"https://doaj.org/article/d0e8caa4c0b744dfbd0a80f1b1ed8ade","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS ONE, Vol 10, Iss 10, p e0140644 (2015)","raw_type":"article"},{"id":"pmh:oai:helda.helsinki.fi:10138/160555","doi":null,"is_oa":true,"landing_page_url":"http://hdl.handle.net/10138/160555","pdf_url":null,"source":{"id":"https://openalex.org/S4210213322","display_name":"Ty\u00f6v\u00e4entutkimus Vuosikirja","issn_l":"0784-1272","issn":["0784-1272","1459-7780"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":["ddh","jufo-1"],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Article"}],"best_oa_location":{"id":"doi:10.1371/journal.pone.0140644","doi":"https://doi.org/10.1371/journal.pone.0140644","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pone.0140644","pdf_url":"https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0140644&type=printable","source":{"id":"https://openalex.org/S202381698","display_name":"PLoS ONE","issn_l":"1932-6203","issn":["1932-6203"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","cwts-core","doaj","dongbi-c","doyens","erih-plus","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS ONE","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G1635254334","display_name":null,"funder_award_id":"G1002369","funder_id":"https://openalex.org/F4320334626","funder_display_name":"Medical Research Council"},{"id":"https://openalex.org/G1990557893","display_name":"Epidemiological and statistical research on health problems of developing countries: MRC Tropical Epidemiology Group","funder_award_id":"MR/K012126/1","funder_id":"https://openalex.org/F4320334626","funder_display_name":"Medical Research Council"},{"id":"https://openalex.org/G8073091741","display_name":"Intelligent Stochastic Computation Methods for Complex Statistical Model Learning","funder_award_id":"239784","funder_id":"https://openalex.org/F4320338352","funder_display_name":"FP7 Ideas: European Research Council"}],"funders":[{"id":"https://openalex.org/F4320311904","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08"},{"id":"https://openalex.org/F4320312695","display_name":"Rural and Environment Science and Analytical Services Division","ror":"https://ror.org/02hrqhj53"},{"id":"https://openalex.org/F4320313269","display_name":"Scottish Government","ror":"https://ror.org/04v2xmd71"},{"id":"https://openalex.org/F4320321108","display_name":"Academy of Finland","ror":"https://ror.org/05k73zm37"},{"id":"https://openalex.org/F4320322581","display_name":"Vetenskapsr\u00e5det","ror":"https://ror.org/03zttf063"},{"id":"https://openalex.org/F4320334626","display_name":"Medical Research Council","ror":"https://ror.org/03x94j517"},{"id":"https://openalex.org/F4320338352","display_name":"FP7 Ideas: European Research Council","ror":"https://ror.org/0472cxd90"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2125708453.pdf","grobid_xml":"https://content.openalex.org/works/W2125708453.grobid-xml"},"referenced_works_count":26,"referenced_works":["https://openalex.org/W104576831","https://openalex.org/W2026414340","https://openalex.org/W2033956230","https://openalex.org/W2039326100","https://openalex.org/W2062842656","https://openalex.org/W2063310369","https://openalex.org/W2078689689","https://openalex.org/W2095132285","https://openalex.org/W2097493826","https://openalex.org/W2100561213","https://openalex.org/W2101305949","https://openalex.org/W2116895571","https://openalex.org/W2123009189","https://openalex.org/W2124351063","https://openalex.org/W2128124531","https://openalex.org/W2134383396","https://openalex.org/W2136777606","https://openalex.org/W2140638310","https://openalex.org/W2145567333","https://openalex.org/W2152885278","https://openalex.org/W2153138305","https://openalex.org/W2153993827","https://openalex.org/W2157571621","https://openalex.org/W2799061466","https://openalex.org/W2799148064","https://openalex.org/W7014191107"],"related_works":["https://openalex.org/W7099611967","https://openalex.org/W2136777606","https://openalex.org/W2124069500","https://openalex.org/W2062842656","https://openalex.org/W2097493826","https://openalex.org/W7095936061","https://openalex.org/W2034153329","https://openalex.org/W3005658675","https://openalex.org/W2903417164","https://openalex.org/W2998646257"],"abstract_inverted_index":{"MOTIVATION:":[0],"Estimation":[1],"of":[2,29,33,42,49,62,93,112,142,161,173,178,185,190,211,237,256],"bacterial":[3,79],"community":[4,80,115],"composition":[5,116],"from":[6,24,126],"high-throughput":[7],"sequenced":[8],"16S":[9],"rRNA":[10],"gene":[11],"amplicons":[12],"is":[13,53,144,193,208,218,229,264,272],"a":[14,30,59,102,127,145,151,158,221,244],"key":[15],"task":[16],"in":[17,64,183,247,259],"microbial":[18],"ecology.":[19],"Since":[20],"the":[21,75,88,110,113,124,137,191,199,233,257,260],"sequence":[22,89],"data":[23,90],"each":[25,203],"sample":[26,128],"typically":[27,84],"consist":[28],"large":[31,51,159],"number":[32],"reads":[34,125,143,162],"and":[35,44,69,96,216,235],"are":[36],"adversely":[37],"impacted":[38],"by":[39,91,122,213],"different":[40],"levels":[41],"biological":[43],"technical":[45],"noise,":[46],"accurate":[47],"analysis":[48],"such":[50],"datasets":[52],"challenging.":[54],"RESULTS:":[55],"There":[56],"has":[57],"been":[58],"recent":[60],"surge":[61],"interest":[63],"using":[65],"compressed":[66],"sensing":[67],"inspired":[68],"convex-optimization":[70],"based":[71,219],"methods":[72,83],"to":[73,136,169,197,231],"solve":[74],"estimation":[76,138],"problem":[77],"for":[78,202],"composition.":[81],"These":[82],"rely":[85],"on":[86,220],"summarizing":[87],"frequencies":[92],"low-order":[94],"k-mers":[95],"matching":[97],"this":[98],"information":[99],"statistically":[100],"with":[101,129,165,242],"taxonomically":[103],"structured":[104],"database.":[105],"Here":[106],"we":[107,149],"show":[108],"that":[109,156],"accuracy":[111],"resulting":[114,206],"estimates":[117],"can":[118],"be":[119],"substantially":[120],"improved":[121],"aggregating":[123],"an":[130],"unsupervised":[131],"machine":[132],"learning":[133],"approach":[134,147],"prior":[135],"phase.":[139],"The":[140,188,205],"aggregation":[141],"pre-processing":[146],"where":[148],"use":[150],"standard":[152],"K-means":[153,214],"clustering":[154,192],"algorithm":[155],"partitions":[157],"set":[160],"into":[163],"subsets":[164],"reasonable":[166],"computational":[167,248],"cost":[168],"provide":[170],"several":[171,238],"vectors":[172],"first":[174],"order":[175],"statistics":[176],"instead":[177],"only":[179,243],"single":[180],"statistical":[181,222],"summarization":[182],"terms":[184],"k-mer":[186],"frequencies.":[187],"output":[189],"then":[194],"processed":[195],"further":[196],"obtain":[198],"final":[200],"estimate":[201],"sample.":[204],"method":[207,258],"called":[209],"Aggregation":[210],"Reads":[212],"(ARK),":[215],"it":[217],"argument":[223],"via":[224],"mixture":[225],"density":[226],"formulation.":[227],"ARK":[228],"found":[230],"improve":[232],"fidelity":[234],"robustness":[236],"recently":[239],"introduced":[240],"methods,":[241],"modest":[245],"increase":[246],"complexity.":[249],"AVAILABILITY:":[250],"An":[251],"open":[252],"source,":[253],"platform-independent":[254],"implementation":[255,271],"Julia":[261],"programming":[262],"language":[263],"freely":[265],"available":[266,273],"at":[267,274],"https://github.com/dkoslicki/ARK.":[268],"A":[269],"Matlab":[270],"http://www.ee.kth.se/ctsoftware.":[275]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1}],"updated_date":"2026-11-06T12:05:46.655746","created_date":"2016-06-24T00:00:00"}
