{"id":"https://openalex.org/W4367600964","doi":"https://doi.org/10.1371/journal.pcbi.1011001","title":"ResMiCo: Increasing the quality of metagenome-assembled genomes with deep learning","display_name":"ResMiCo: Increasing the quality of metagenome-assembled genomes with deep learning","publication_year":2023,"publication_date":"2023-05-01","ids":{"openalex":"https://openalex.org/W4367600964","doi":"https://doi.org/10.1371/journal.pcbi.1011001","pmid":"https://pubmed.ncbi.nlm.nih.gov/37126495"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1011001","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011001","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1371/journal.pcbi.1011001","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5072028497","display_name":"Olga Mineeva","orcid":null},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]},{"id":"https://openalex.org/I4210135521","display_name":"Max Planck Institute for Intelligent Systems","ror":"https://ror.org/04fq9j139","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210135521"]}],"countries":["CH","DE"],"is_corresponding":true,"raw_author_name":"Olga Mineeva","raw_affiliation_strings":["Department of Computer Science, ETH Z\u00fcrich, Z\u00fcrich, Switzerland","Department of Empirical Inference, Max Planck Institute for Intelligent Systems, T\u00fcbingen, Germany","Swiss Institute for Bioinformatics, Lausanne, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, ETH Z\u00fcrich, Z\u00fcrich, Switzerland","institution_ids":["https://openalex.org/I35440088"]},{"raw_affiliation_string":"Department of Empirical Inference, Max Planck Institute for Intelligent Systems, T\u00fcbingen, Germany","institution_ids":["https://openalex.org/I4210135521"]},{"raw_affiliation_string":"Swiss Institute for Bioinformatics, Lausanne, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071749437","display_name":"Daniel Danciu","orcid":"https://orcid.org/0000-0002-6175-3642"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Daniel Danciu","raw_affiliation_strings":["Department of Computer Science, ETH Z\u00fcrich, Z\u00fcrich, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, ETH Z\u00fcrich, Z\u00fcrich, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044005697","display_name":"Bernhard Sch\u00f6lkopf","orcid":"https://orcid.org/0000-0002-8177-0925"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]},{"id":"https://openalex.org/I4210135521","display_name":"Max Planck Institute for Intelligent Systems","ror":"https://ror.org/04fq9j139","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210135521"]}],"countries":["CH","DE"],"is_corresponding":true,"raw_author_name":"Bernhard Sch\u00f6lkopf","raw_affiliation_strings":["Department of Computer Science, ETH Z\u00fcrich, Z\u00fcrich, Switzerland","Department of Empirical Inference, Max Planck Institute for Intelligent Systems, T\u00fcbingen, Germany","ETH AI center, ETH Z\u00fcrich, Z\u00fcrich, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, ETH Z\u00fcrich, Z\u00fcrich, Switzerland","institution_ids":["https://openalex.org/I35440088"]},{"raw_affiliation_string":"Department of Empirical Inference, Max Planck Institute for Intelligent Systems, T\u00fcbingen, Germany","institution_ids":["https://openalex.org/I4210135521"]},{"raw_affiliation_string":"ETH AI center, ETH Z\u00fcrich, Z\u00fcrich, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066589732","display_name":"Ruth E. Ley","orcid":"https://orcid.org/0000-0002-9087-1672"},"institutions":[{"id":"https://openalex.org/I4210165766","display_name":"Max Planck Institute for Biology","ror":"https://ror.org/0243gzr89","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210165766"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Ruth E. Ley","raw_affiliation_strings":["Department of Microbiome Science, Max Planck Institute for Biology, T\u00fcbingen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Microbiome Science, Max Planck Institute for Biology, T\u00fcbingen, Germany","institution_ids":["https://openalex.org/I4210165766"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035416263","display_name":"Gunnar R\u00e4tsch","orcid":"https://orcid.org/0000-0001-5486-8532"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]},{"id":"https://openalex.org/I4210100468","display_name":"University Hospital of Zurich","ror":"https://ror.org/01462r250","country_code":"CH","type":"funder","lineage":["https://openalex.org/I4210100468"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Gunnar R\u00e4tsch","raw_affiliation_strings":["Department of Biology, ETH Z\u00fcrich, Z\u00fcrich, Switzerland","Department of Computer Science, ETH Z\u00fcrich, Z\u00fcrich, Switzerland","ETH AI center, ETH Z\u00fcrich, Z\u00fcrich, Switzerland","Medical Informatics Unit, Z\u00fcrich University Hospital, Z\u00fcrich, Switzerland","Swiss Institute for Bioinformatics, Lausanne, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, ETH Z\u00fcrich, Z\u00fcrich, Switzerland","institution_ids":["https://openalex.org/I35440088"]},{"raw_affiliation_string":"Department of Computer Science, ETH Z\u00fcrich, Z\u00fcrich, Switzerland","institution_ids":["https://openalex.org/I35440088"]},{"raw_affiliation_string":"ETH AI center, ETH Z\u00fcrich, Z\u00fcrich, Switzerland","institution_ids":["https://openalex.org/I35440088"]},{"raw_affiliation_string":"Medical Informatics Unit, Z\u00fcrich University Hospital, Z\u00fcrich, Switzerland","institution_ids":["https://openalex.org/I4210100468"]},{"raw_affiliation_string":"Swiss Institute for Bioinformatics, Lausanne, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5035541714","display_name":"Nicholas D. Youngblut","orcid":"https://orcid.org/0000-0002-7424-5276"},"institutions":[{"id":"https://openalex.org/I4210165766","display_name":"Max Planck Institute for Biology","ror":"https://ror.org/0243gzr89","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210165766"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Nicholas D. Youngblut","raw_affiliation_strings":["Department of Microbiome Science, Max Planck Institute for Biology, T\u00fcbingen, Germany"],"raw_orcid":"https://orcid.org/0000-0002-7424-5276","affiliations":[{"raw_affiliation_string":"Department of Microbiome Science, Max Planck Institute for Biology, T\u00fcbingen, Germany","institution_ids":["https://openalex.org/I4210165766"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5035416263","https://openalex.org/A5035541714","https://openalex.org/A5044005697","https://openalex.org/A5066589732","https://openalex.org/A5071749437","https://openalex.org/A5072028497"],"corresponding_institution_ids":["https://openalex.org/I12708293","https://openalex.org/I35440088","https://openalex.org/I4210100468","https://openalex.org/I4210135521","https://openalex.org/I4210165766"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":1.4537,"has_fulltext":true,"cited_by_count":10,"citation_normalized_percentile":{"value":0.81636484,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"19","issue":"5","first_page":"e1011001","last_page":"e1011001"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":1.0,"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":1.0,"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/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.9948999881744385,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9876000285148621,"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/metagenomics","display_name":"Metagenomics","score":0.8658883571624756},{"id":"https://openalex.org/keywords/contig","display_name":"Contig","score":0.7065081000328064},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6839742660522461},{"id":"https://openalex.org/keywords/hyperparameter","display_name":"Hyperparameter","score":0.5523003339767456},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5390858054161072},{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.523255467414856},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5179383158683777},{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.5054805278778076},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.48525333404541016},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.47873684763908386},{"id":"https://openalex.org/keywords/preprocessor","display_name":"Preprocessor","score":0.4725722372531891},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4097728729248047},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.36325353384017944},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.275049090385437},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.24636545777320862},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.09479013085365295},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.08772978186607361}],"concepts":[{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.8658883571624756},{"id":"https://openalex.org/C59582021","wikidata":"https://www.wikidata.org/wiki/Q1128751","display_name":"Contig","level":4,"score":0.7065081000328064},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6839742660522461},{"id":"https://openalex.org/C8642999","wikidata":"https://www.wikidata.org/wiki/Q4171168","display_name":"Hyperparameter","level":2,"score":0.5523003339767456},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5390858054161072},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.523255467414856},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5179383158683777},{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.5054805278778076},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.48525333404541016},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.47873684763908386},{"id":"https://openalex.org/C34736171","wikidata":"https://www.wikidata.org/wiki/Q918333","display_name":"Preprocessor","level":2,"score":0.4725722372531891},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4097728729248047},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.36325353384017944},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.275049090385437},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.24636545777320862},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.09479013085365295},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.08772978186607361},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1011001","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011001","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:37126495","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37126495","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,"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 computational biology","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10174551","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10174551","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10174551/pdf/pcbi.1011001.pdf","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,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:oai:RePEc:plo:pcbi00:1011001","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011001","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,"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:doaj.org/article:3da1308b99c642dfbd9b7c8030f366a2","is_oa":true,"landing_page_url":"https://doaj.org/article/3da1308b99c642dfbd9b7c8030f366a2","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,"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 Computational Biology, Vol 19, Iss 5, p e1011001 (2023)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1011001","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011001","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320318144","display_name":"Max-Planck-F\u00f6rderstiftung","ror":null},{"id":"https://openalex.org/F4320321652","display_name":"Eidgen\u00f6ssische Technische Hochschule Z\u00fcrich","ror":"https://ror.org/05a28rw58"},{"id":"https://openalex.org/F4320331705","display_name":"Max Planck ETH Center for Learning Systems","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":63,"referenced_works":["https://openalex.org/W1522301498","https://openalex.org/W1836465849","https://openalex.org/W1982579644","https://openalex.org/W2056833498","https://openalex.org/W2098531465","https://openalex.org/W2110417468","https://openalex.org/W2113679889","https://openalex.org/W2125826054","https://openalex.org/W2131953535","https://openalex.org/W2157539385","https://openalex.org/W2160734881","https://openalex.org/W2170551349","https://openalex.org/W2175526948","https://openalex.org/W2194775991","https://openalex.org/W2197368019","https://openalex.org/W2308359027","https://openalex.org/W2432815617","https://openalex.org/W2490420619","https://openalex.org/W2525711135","https://openalex.org/W2599417231","https://openalex.org/W2605409611","https://openalex.org/W2612690371","https://openalex.org/W2758005814","https://openalex.org/W2767733991","https://openalex.org/W2773939681","https://openalex.org/W2786672974","https://openalex.org/W2807007689","https://openalex.org/W2883386984","https://openalex.org/W2889019390","https://openalex.org/W2909194804","https://openalex.org/W2910615673","https://openalex.org/W2913972921","https://openalex.org/W2918965813","https://openalex.org/W2921815890","https://openalex.org/W2951076599","https://openalex.org/W2952204926","https://openalex.org/W2955133522","https://openalex.org/W2980110280","https://openalex.org/W2988411281","https://openalex.org/W2991113705","https://openalex.org/W2996904338","https://openalex.org/W3007623812","https://openalex.org/W3008812673","https://openalex.org/W3037492894","https://openalex.org/W3042305844","https://openalex.org/W3097720621","https://openalex.org/W3128596093","https://openalex.org/W3135997498","https://openalex.org/W3169976301","https://openalex.org/W3170803369","https://openalex.org/W3182475814","https://openalex.org/W3186451577","https://openalex.org/W3199470543","https://openalex.org/W3205017888","https://openalex.org/W4205280965","https://openalex.org/W4287073474","https://openalex.org/W4287728573","https://openalex.org/W4307542026","https://openalex.org/W4308999955","https://openalex.org/W4309326290","https://openalex.org/W6679554340","https://openalex.org/W6753575212","https://openalex.org/W6780233385"],"related_works":["https://openalex.org/W4238897586","https://openalex.org/W2330186985","https://openalex.org/W2950447380","https://openalex.org/W2055448750","https://openalex.org/W2345730070","https://openalex.org/W2107854630","https://openalex.org/W4319294554","https://openalex.org/W3134563641","https://openalex.org/W1986608492","https://openalex.org/W4394186879"],"abstract_inverted_index":{"The":[0,190],"number":[1],"of":[2,46,53,65,99,111,142,185,195,205],"published":[3],"metagenome":[4,164,178,206],"assemblies":[5,207],"is":[6,69,135,148],"rapidly":[7],"growing":[8],"due":[9],"to":[10,32,77,150,176,181],"advances":[11],"in":[12,56,125],"sequencing":[13,16],"technologies.":[14],"However,":[15],"errors,":[17],"variable":[18],"coverage,":[19],"repetitive":[20],"genomic":[21,37],"regions,":[22],"and":[23,67,114,123,145,154,193,208],"other":[24],"factors":[25],"can":[26,41,117,173],"produce":[27],"misassemblies,":[28],"which":[29],"are":[30],"challenging":[31],"detect":[33],"for":[34,50,87,96,120,188,201],"taxonomically":[35],"novel":[36,151],"data.":[38,79],"Assembly":[39],"errors":[40],"affect":[42],"all":[43],"downstream":[44],"analyses":[45],"the":[47,51,54,83,126,140,143,146,198],"assemblies.":[48],"Accuracy":[49],"state":[52,141],"art":[55],"reference-free":[57,97],"misassembly":[58],"prediction":[59],"does":[60],"not":[61,70],"exceed":[62],"an":[63],"AUPRC":[64],"0.57,":[66],"it":[68],"clear":[71],"how":[72,171],"well":[73],"these":[74],"models":[75],"generalize":[76],"real-world":[78,167],"Here,":[80],"we":[81,105,131],"present":[82],"Residual":[84],"neural":[85],"network":[86],"Misassembled":[88],"Contig":[89],"identification":[90,98],"(ResMiCo),":[91],"a":[92,108],"deep":[93],"learning":[94],"approach":[95],"misassembled":[100,161],"contigs.":[101],"To":[102],"develop":[103],"ResMiCo,":[104],"first":[106],"generated":[107],"training":[109],"dataset":[110],"unprecedented":[112],"size":[113],"complexity":[115],"that":[116,133],"be":[118,174],"used":[119,175],"further":[121],"benchmarking":[122],"developments":[124],"field.":[127],"Through":[128],"rigorous":[129],"validation,":[130],"show":[132],"ResMiCo":[134,158,172,196],"substantially":[136],"more":[137],"accurate":[138],"than":[139],"art,":[144],"model":[147],"robust":[149],"taxonomic":[152],"diversity":[153],"varying":[155],"assembly":[156,179,209],"methods.":[157],"estimated":[159],"7%":[160],"contigs":[162],"per":[163],"across":[165],"multiple":[166],"datasets.":[168],"We":[169],"demonstrate":[170],"optimize":[177],"hyperparameters":[180],"improve":[182],"accuracy,":[183,191],"instead":[184],"optimizing":[186],"solely":[187],"contiguity.":[189],"robustness,":[192],"ease-of-use":[194],"make":[197],"tool":[199],"suitable":[200],"general":[202],"quality":[203],"control":[204],"methodology":[210],"optimization.":[211]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":4}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}