{"id":"https://openalex.org/W4367315258","doi":"https://doi.org/10.1093/bib/bbad162","title":"A survey on computational strategies for genome-resolved gut metagenomics","display_name":"A survey on computational strategies for genome-resolved gut metagenomics","publication_year":2023,"publication_date":"2023-04-27","ids":{"openalex":"https://openalex.org/W4367315258","doi":"https://doi.org/10.1093/bib/bbad162","pmid":"https://pubmed.ncbi.nlm.nih.gov/37114640"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbad162","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad162","pdf_url":"https://academic.oup.com/bib/article-pdf/24/3/bbad162/50411073/bbad162.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bib/article-pdf/24/3/bbad162/50411073/bbad162.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5021764064","display_name":"Longhao Jia","orcid":"https://orcid.org/0000-0002-3490-840X"},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]},{"id":"https://openalex.org/I4210085920","display_name":"Shanghai Institute for Science of Science","ror":"https://ror.org/004srxn73","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210085920"]},{"id":"https://openalex.org/I4210164150","display_name":"Shanghai Center for Brain Science and Brain-Inspired Technology","ror":"https://ror.org/0551a0y31","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210164150"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Longhao Jia","raw_affiliation_strings":["Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University , Shanghai 200433, China"],"affiliations":[{"raw_affiliation_string":"Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University , Shanghai 200433, China","institution_ids":["https://openalex.org/I4210164150","https://openalex.org/I4210085920","https://openalex.org/I24943067"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064247976","display_name":"Yingjian Wu","orcid":"https://orcid.org/0000-0002-9720-6712"},"institutions":[{"id":"https://openalex.org/I47720641","display_name":"Huazhong University of Science and Technology","ror":"https://ror.org/00p991c53","country_code":"CN","type":"education","lineage":["https://openalex.org/I47720641"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yingjian Wu","raw_affiliation_strings":["Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology , Wuhan 430074, Hubei, China"],"affiliations":[{"raw_affiliation_string":"Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology , Wuhan 430074, Hubei, China","institution_ids":["https://openalex.org/I47720641"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046944569","display_name":"Yanqi Dong","orcid":"https://orcid.org/0009-0005-2900-5467"},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]},{"id":"https://openalex.org/I4210085920","display_name":"Shanghai Institute for Science of Science","ror":"https://ror.org/004srxn73","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210085920"]},{"id":"https://openalex.org/I4210164150","display_name":"Shanghai Center for Brain Science and Brain-Inspired Technology","ror":"https://ror.org/0551a0y31","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210164150"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yanqi Dong","raw_affiliation_strings":["Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University , Shanghai 200433, China"],"affiliations":[{"raw_affiliation_string":"Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University , Shanghai 200433, China","institution_ids":["https://openalex.org/I4210164150","https://openalex.org/I4210085920","https://openalex.org/I24943067"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101422631","display_name":"Jingchao Chen","orcid":"https://orcid.org/0000-0002-6978-497X"},"institutions":[{"id":"https://openalex.org/I47720641","display_name":"Huazhong University of Science and Technology","ror":"https://ror.org/00p991c53","country_code":"CN","type":"education","lineage":["https://openalex.org/I47720641"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jingchao Chen","raw_affiliation_strings":["Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology , Wuhan 430074, Hubei, China"],"affiliations":[{"raw_affiliation_string":"Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology , Wuhan 430074, Hubei, China","institution_ids":["https://openalex.org/I47720641"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100625505","display_name":"Wei\u2010Hua Chen","orcid":"https://orcid.org/0000-0001-5160-4398"},"institutions":[{"id":"https://openalex.org/I134841294","display_name":"Binzhou Medical University","ror":"https://ror.org/008w1vb37","country_code":"CN","type":"education","lineage":["https://openalex.org/I134841294"]},{"id":"https://openalex.org/I151013683","display_name":"Binzhou University","ror":"https://ror.org/05frpfj73","country_code":"CN","type":"education","lineage":["https://openalex.org/I151013683"]},{"id":"https://openalex.org/I47720641","display_name":"Huazhong University of Science and Technology","ror":"https://ror.org/00p991c53","country_code":"CN","type":"education","lineage":["https://openalex.org/I47720641"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Wei-Hua Chen","raw_affiliation_strings":["Institution of Medical Artificial Intelligence, Binzhou Medical University , Yantai 264003, China","Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology , Wuhan 430074, Hubei, China"],"affiliations":[{"raw_affiliation_string":"Institution of Medical Artificial Intelligence, Binzhou Medical University , Yantai 264003, China","institution_ids":["https://openalex.org/I151013683","https://openalex.org/I134841294"]},{"raw_affiliation_string":"Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology , Wuhan 430074, Hubei, China","institution_ids":["https://openalex.org/I47720641"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5049435754","display_name":"Xing\u2010Ming Zhao","orcid":"https://orcid.org/0000-0002-4531-3970"},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]},{"id":"https://openalex.org/I4210085920","display_name":"Shanghai Institute for Science of Science","ror":"https://ror.org/004srxn73","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210085920"]},{"id":"https://openalex.org/I4210164150","display_name":"Shanghai Center for Brain Science and Brain-Inspired Technology","ror":"https://ror.org/0551a0y31","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210164150"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xing-Ming Zhao","raw_affiliation_strings":["Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University , Shanghai 200433, China","Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Ministry of Education, Ministry of Education , Shanghai 200433, China","MOE Frontiers Center for Brain Science, Fudan University , Shanghai 200433, China","State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, Fudan University , Shanghai, China"],"affiliations":[{"raw_affiliation_string":"Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University , Shanghai 200433, China","institution_ids":["https://openalex.org/I4210164150","https://openalex.org/I4210085920","https://openalex.org/I24943067"]},{"raw_affiliation_string":"Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Ministry of Education, Ministry of Education , Shanghai 200433, China","institution_ids":[]},{"raw_affiliation_string":"MOE Frontiers Center for Brain Science, Fudan University , Shanghai 200433, China","institution_ids":["https://openalex.org/I24943067"]},{"raw_affiliation_string":"State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, Fudan University , Shanghai, China","institution_ids":["https://openalex.org/I24943067"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5049435754","https://openalex.org/A5100625505"],"corresponding_institution_ids":["https://openalex.org/I134841294","https://openalex.org/I151013683","https://openalex.org/I24943067","https://openalex.org/I4210085920","https://openalex.org/I4210164150","https://openalex.org/I47720641"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":2.5589,"has_fulltext":true,"cited_by_count":17,"citation_normalized_percentile":{"value":0.89543226,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"24","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9955999851226807,"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":0.9955999851226807,"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/T10066","display_name":"Gut microbiota and health","score":0.993399977684021,"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/T10141","display_name":"Probiotics and Fermented Foods","score":0.9739000201225281,"subfield":{"id":"https://openalex.org/subfields/1106","display_name":"Food Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.9232792854309082},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.6929490566253662},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6398035287857056},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.5233063697814941},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.49678972363471985},{"id":"https://openalex.org/keywords/sequence-assembly","display_name":"Sequence assembly","score":0.43453770875930786},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4178016781806946},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2930137515068054},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.264931857585907}],"concepts":[{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.9232792854309082},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6929490566253662},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6398035287857056},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.5233063697814941},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.49678972363471985},{"id":"https://openalex.org/C18949551","wikidata":"https://www.wikidata.org/wiki/Q740578","display_name":"Sequence assembly","level":5,"score":0.43453770875930786},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4178016781806946},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2930137515068054},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.264931857585907},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":"D017422","descriptor_name":"Sequence Analysis, DNA","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":"D041981","descriptor_name":"Gastrointestinal Tract","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D041981","descriptor_name":"Gastrointestinal Tract","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D041981","descriptor_name":"Gastrointestinal Tract","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbad162","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad162","pdf_url":"https://academic.oup.com/bib/article-pdf/24/3/bbad162/50411073/bbad162.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37114640","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37114640","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":"Briefings in bioinformatics","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bib/bbad162","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad162","pdf_url":"https://academic.oup.com/bib/article-pdf/24/3/bbad162/50411073/bbad162.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1100817172","display_name":null,"funder_award_id":"619320","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G1307575636","display_name":null,"funder_award_id":"61932008","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7537086629","display_name":null,"funder_award_id":"6193200","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8573963713","display_name":null,"funder_award_id":"2020YFA0712403","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8776634001","display_name":null,"funder_award_id":"2020YFA0712403","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G8899475930","display_name":null,"funder_award_id":"2018SHZDZX01","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8903503482","display_name":null,"funder_award_id":"T2225015","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4367315258.pdf","grobid_xml":"https://content.openalex.org/works/W4367315258.grobid-xml"},"referenced_works_count":96,"referenced_works":["https://openalex.org/W1878521557","https://openalex.org/W1939004772","https://openalex.org/W1969761972","https://openalex.org/W1996053875","https://openalex.org/W2032230795","https://openalex.org/W2054385769","https://openalex.org/W2055043387","https://openalex.org/W2080229897","https://openalex.org/W2096093282","https://openalex.org/W2097124003","https://openalex.org/W2098531465","https://openalex.org/W2102619694","https://openalex.org/W2103441770","https://openalex.org/W2103901746","https://openalex.org/W2112364185","https://openalex.org/W2113679889","https://openalex.org/W2118688136","https://openalex.org/W2141920662","https://openalex.org/W2143196592","https://openalex.org/W2158804744","https://openalex.org/W2175526948","https://openalex.org/W2179507357","https://openalex.org/W2296761881","https://openalex.org/W2345813655","https://openalex.org/W2531570974","https://openalex.org/W2599417231","https://openalex.org/W2736920791","https://openalex.org/W2742647527","https://openalex.org/W2745006471","https://openalex.org/W2767898240","https://openalex.org/W2773939681","https://openalex.org/W2784788330","https://openalex.org/W2789843538","https://openalex.org/W2896481903","https://openalex.org/W2910615673","https://openalex.org/W2913972921","https://openalex.org/W2921815890","https://openalex.org/W2927453907","https://openalex.org/W2932049125","https://openalex.org/W2938828179","https://openalex.org/W2938868597","https://openalex.org/W2950354111","https://openalex.org/W2950464960","https://openalex.org/W2950513687","https://openalex.org/W2950550329","https://openalex.org/W2950682748","https://openalex.org/W2950785362","https://openalex.org/W2960432853","https://openalex.org/W2965025968","https://openalex.org/W2966669703","https://openalex.org/W2970367351","https://openalex.org/W2992976869","https://openalex.org/W3005528502","https://openalex.org/W3008812673","https://openalex.org/W3011678041","https://openalex.org/W3019706413","https://openalex.org/W3034548692","https://openalex.org/W3042305844","https://openalex.org/W3046109898","https://openalex.org/W3090089243","https://openalex.org/W3091506611","https://openalex.org/W3093512139","https://openalex.org/W3097807397","https://openalex.org/W3118048495","https://openalex.org/W3120084484","https://openalex.org/W3125972683","https://openalex.org/W3127656915","https://openalex.org/W3131055609","https://openalex.org/W3132565579","https://openalex.org/W3134271022","https://openalex.org/W3135822094","https://openalex.org/W3193653929","https://openalex.org/W3205855923","https://openalex.org/W3213893926","https://openalex.org/W4205677193","https://openalex.org/W4206971319","https://openalex.org/W4221079230","https://openalex.org/W4225007447","https://openalex.org/W4225083538","https://openalex.org/W4225258284","https://openalex.org/W4283809266","https://openalex.org/W4286263931","https://openalex.org/W4286510420","https://openalex.org/W4292178604","https://openalex.org/W4304943053","https://openalex.org/W4308527139","https://openalex.org/W4308999955","https://openalex.org/W4313648386","https://openalex.org/W4313892413","https://openalex.org/W4399585236","https://openalex.org/W6745491619","https://openalex.org/W6771742792","https://openalex.org/W6783756656","https://openalex.org/W6811410568","https://openalex.org/W6847867908","https://openalex.org/W6869058137"],"related_works":["https://openalex.org/W2210738511","https://openalex.org/W2055448750","https://openalex.org/W2474302342","https://openalex.org/W1910109602","https://openalex.org/W4297131566","https://openalex.org/W2017364432","https://openalex.org/W2080583581","https://openalex.org/W3037682416","https://openalex.org/W3195915274","https://openalex.org/W3134563641"],"abstract_inverted_index":{"Recovering":[0],"high-quality":[1],"metagenome-assembled":[2],"genomes":[3,143],"(HQ-MAGs)":[4],"is":[5],"critical":[6],"for":[7,21,30,72],"exploring":[8],"microbial":[9],"compositions":[10],"and":[11,18,27,46,57,64,79,81,104,113,120,127,134],"microbe-phenotype":[12],"associations.":[13],"However,":[14],"multiple":[15],"sequencing":[16,47,59,93],"platforms":[17,48],"computational":[19,44],"tools":[20,45,71],"this":[22],"purpose":[23],"may":[24],"confuse":[25],"researchers":[26],"thus":[28],"call":[29],"extensive":[31],"evaluation.":[32],"Here,":[33],"we":[34],"systematically":[35],"evaluated":[36],"a":[37],"total":[38],"of":[39,42,91,100,138,151],"40":[40],"combinations":[41,82],"popular":[43],"(i.e.":[49],"strategies),":[50],"involving":[51],"eight":[52,54],"assemblers,":[53],"metagenomic":[55],"binners":[56],"four":[58],"technologies,":[60],"including":[61],"short-,":[62],"long-read":[63,114,119],"metaHiC":[65,121],"sequencing.":[66],"We":[67,95],"identified":[68],"the":[69,73,77,89,92,98,101,111,136,157],"best":[70],"individual":[74],"tasks":[75],"(e.g.":[76,83],"assembly":[78],"binning)":[80],"generating":[84],"more":[85,124],"HQ-MAGs)":[86],"depending":[87],"on":[88],"availability":[90],"data.":[94],"found":[96],"that":[97,148],"combination":[99],"hybrid":[102,112],"assemblies":[103],"metaHiC-based":[105],"binning":[106],"performed":[107],"best,":[108],"followed":[109],"by":[110],"assemblies.":[115],"More":[116],"importantly,":[117],"both":[118],"sequencings":[122],"link":[123],"mobile":[125],"elements":[126],"antibiotic":[128],"resistance":[129],"genes":[130],"to":[131],"bacterial":[132],"hosts":[133],"improve":[135],"quality":[137,153],"public":[139],"human":[140],"gut":[141],"reference":[142],"with":[144],"32%":[145],"(34/105)":[146],"HQ-MAGs":[147],"were":[149],"either":[150],"better":[152],"than":[154],"those":[155],"in":[156],"Unified":[158],"Human":[159],"Gastrointestinal":[160],"Genome":[161],"catalog":[162],"version":[163],"2":[164],"or":[165],"novel.":[166]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":2}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
