{"id":"https://openalex.org/W2884258548","doi":"https://doi.org/10.1093/bioinformatics/bty617","title":"A parallel computational framework for ultra-large-scale sequence clustering analysis","display_name":"A parallel computational framework for ultra-large-scale sequence clustering analysis","publication_year":2018,"publication_date":"2018-07-13","ids":{"openalex":"https://openalex.org/W2884258548","doi":"https://doi.org/10.1093/bioinformatics/bty617","mag":"2884258548","pmid":"https://pubmed.ncbi.nlm.nih.gov/30010718"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty617","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty617","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/3/380/48964796/bioinformatics_35_3_380.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"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/bioinformatics/article-pdf/35/3/380/48964796/bioinformatics_35_3_380.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100763402","display_name":"Wei Zheng","orcid":"https://orcid.org/0000-0002-5471-7328"},"institutions":[{"id":"https://openalex.org/I63190737","display_name":"University at Buffalo, State University of New York","ror":"https://ror.org/01y64my43","country_code":"US","type":"education","lineage":["https://openalex.org/I63190737"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wei Zheng","raw_affiliation_strings":["Department of Computer Science and Engineering, The State University of New York, NY, Buffalo, NY, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, The State University of New York, NY, Buffalo, NY, USA","institution_ids":["https://openalex.org/I63190737"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003590207","display_name":"Qi Mao","orcid":"https://orcid.org/0000-0002-6337-1568"},"institutions":[{"id":"https://openalex.org/I63190737","display_name":"University at Buffalo, State University of New York","ror":"https://ror.org/01y64my43","country_code":"US","type":"education","lineage":["https://openalex.org/I63190737"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Qi Mao","raw_affiliation_strings":["Department of Microbiology and Immunology, The State University of New York, NY, Buffalo, NY, USA"],"affiliations":[{"raw_affiliation_string":"Department of Microbiology and Immunology, The State University of New York, NY, Buffalo, NY, USA","institution_ids":["https://openalex.org/I63190737"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019676251","display_name":"Robert J. Genco","orcid":"https://orcid.org/0000-0001-7604-506X"},"institutions":[{"id":"https://openalex.org/I63190737","display_name":"University at Buffalo, State University of New York","ror":"https://ror.org/01y64my43","country_code":"US","type":"education","lineage":["https://openalex.org/I63190737"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Robert J Genco","raw_affiliation_strings":["Department of Oral Biology, The State University of New York, NY, Buffalo, NY, USA"],"affiliations":[{"raw_affiliation_string":"Department of Oral Biology, The State University of New York, NY, Buffalo, NY, USA","institution_ids":["https://openalex.org/I63190737"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016111941","display_name":"Jean Wactawski\u2010Wende","orcid":"https://orcid.org/0000-0003-3096-9595"},"institutions":[{"id":"https://openalex.org/I63190737","display_name":"University at Buffalo, State University of New York","ror":"https://ror.org/01y64my43","country_code":"US","type":"education","lineage":["https://openalex.org/I63190737"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jean Wactawski-Wende","raw_affiliation_strings":["Department of Epidemiology and Environmental Health, The State University of New York, NY, Buffalo, NY, USA"],"affiliations":[{"raw_affiliation_string":"Department of Epidemiology and Environmental Health, The State University of New York, NY, Buffalo, NY, USA","institution_ids":["https://openalex.org/I63190737"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042060228","display_name":"Michael Buck","orcid":"https://orcid.org/0000-0001-5320-3678"},"institutions":[{"id":"https://openalex.org/I63190737","display_name":"University at Buffalo, State University of New York","ror":"https://ror.org/01y64my43","country_code":"US","type":"education","lineage":["https://openalex.org/I63190737"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael Buck","raw_affiliation_strings":["Department of Biochemistry, University at Buffalo, The State University of New York, NY, Buffalo, NY, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, University at Buffalo, The State University of New York, NY, Buffalo, NY, USA","institution_ids":["https://openalex.org/I63190737"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090194899","display_name":"Yunpeng Cai","orcid":"https://orcid.org/0000-0001-8797-4243"},"institutions":[{"id":"https://openalex.org/I4210145761","display_name":"Shenzhen Institutes of Advanced Technology","ror":"https://ror.org/04gh4er46","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210145761"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yunpeng Cai","raw_affiliation_strings":["Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China"],"affiliations":[{"raw_affiliation_string":"Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China","institution_ids":["https://openalex.org/I4210145761"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5039662308","display_name":"Yijun Sun","orcid":"https://orcid.org/0000-0003-0610-6132"},"institutions":[{"id":"https://openalex.org/I63190737","display_name":"University at Buffalo, State University of New York","ror":"https://ror.org/01y64my43","country_code":"US","type":"education","lineage":["https://openalex.org/I63190737"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yijun Sun","raw_affiliation_strings":["Department of Computer Science and Engineering, The State University of New York, NY, Buffalo, NY, USA","Department of Microbiology and Immunology, The State University of New York, NY, Buffalo, NY, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, The State University of New York, NY, Buffalo, NY, USA","institution_ids":["https://openalex.org/I63190737"]},{"raw_affiliation_string":"Department of Microbiology and Immunology, The State University of New York, NY, Buffalo, NY, USA","institution_ids":["https://openalex.org/I63190737"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5039662308"],"corresponding_institution_ids":["https://openalex.org/I63190737"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.7416,"has_fulltext":true,"cited_by_count":11,"citation_normalized_percentile":{"value":0.70466737,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"35","issue":"3","first_page":"380","last_page":"388"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9993000030517578,"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":0.9993000030517578,"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":0.9902999997138977,"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":0.9868999719619751,"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/computer-science","display_name":"Computer science","score":0.8212763071060181},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.7876134514808655},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.7089173793792725},{"id":"https://openalex.org/keywords/spark","display_name":"SPARK (programming language)","score":0.6548888683319092},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5387926697731018},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5222171545028687},{"id":"https://openalex.org/keywords/scale","display_name":"Scale (ratio)","score":0.4957343339920044},{"id":"https://openalex.org/keywords/supercomputer","display_name":"Supercomputer","score":0.48523545265197754},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.2699568271636963},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.20377901196479797},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.12130361795425415}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8212763071060181},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.7876134514808655},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.7089173793792725},{"id":"https://openalex.org/C2781215313","wikidata":"https://www.wikidata.org/wiki/Q3493345","display_name":"SPARK (programming language)","level":2,"score":0.6548888683319092},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5387926697731018},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5222171545028687},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.4957343339920044},{"id":"https://openalex.org/C83283714","wikidata":"https://www.wikidata.org/wiki/Q121117","display_name":"Supercomputer","level":2,"score":0.48523545265197754},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.2699568271636963},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.20377901196479797},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.12130361795425415},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":true},{"descriptor_ui":"D012984","descriptor_name":"Software","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":true},{"descriptor_ui":"D012984","descriptor_name":"Software","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":true},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bty617","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty617","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/3/380/48964796/bioinformatics_35_3_380.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30010718","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30010718","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:6931356","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6931356","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty617","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty617","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/3/380/48964796/bioinformatics_35_3_380.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","score":0.4699999988079071,"display_name":"Industry, innovation and infrastructure"}],"awards":[{"id":"https://openalex.org/G2087396116","display_name":null,"funder_award_id":"China","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3317480652","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5039185795","display_name":null,"funder_award_id":"1R01DE024523","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6831756757","display_name":null,"funder_award_id":"11471313","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6999309555","display_name":null,"funder_award_id":"1R01AI125982","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7845554335","display_name":null,"funder_award_id":"# 11471313","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G848032724","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2884258548.pdf","grobid_xml":"https://content.openalex.org/works/W2884258548.grobid-xml"},"referenced_works_count":31,"referenced_works":["https://openalex.org/W410850256","https://openalex.org/W2006735776","https://openalex.org/W2020498246","https://openalex.org/W2045716015","https://openalex.org/W2055631148","https://openalex.org/W2072970694","https://openalex.org/W2073548709","https://openalex.org/W2078958937","https://openalex.org/W2097979671","https://openalex.org/W2106399600","https://openalex.org/W2115605863","https://openalex.org/W2115699469","https://openalex.org/W2124351063","https://openalex.org/W2130208436","https://openalex.org/W2132914434","https://openalex.org/W2134751812","https://openalex.org/W2136993578","https://openalex.org/W2140638310","https://openalex.org/W2154026962","https://openalex.org/W2156125289","https://openalex.org/W2156619206","https://openalex.org/W2162315106","https://openalex.org/W2163681976","https://openalex.org/W2171901261","https://openalex.org/W2564293829","https://openalex.org/W2610066872","https://openalex.org/W2963288913","https://openalex.org/W4246875694","https://openalex.org/W4285719527","https://openalex.org/W6614148910","https://openalex.org/W6674672532"],"related_works":["https://openalex.org/W2384867379","https://openalex.org/W2329539859","https://openalex.org/W3191490922","https://openalex.org/W2227905990","https://openalex.org/W2765823764","https://openalex.org/W3214280620","https://openalex.org/W4308507533","https://openalex.org/W2407107767","https://openalex.org/W2901787049","https://openalex.org/W2792181990"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1}],"updated_date":"2026-03-18T14:38:29.013473","created_date":"2025-10-10T00:00:00"}
