{"id":"https://openalex.org/W2002771682","doi":"https://doi.org/10.1109/tcbb.2015.2407574","title":"Efficient and Accurate OTU Clustering with GPU-Based Sequence Alignment and Dynamic Dendrogram Cutting","display_name":"Efficient and Accurate OTU Clustering with GPU-Based Sequence Alignment and Dynamic Dendrogram Cutting","publication_year":2015,"publication_date":"2015-02-26","ids":{"openalex":"https://openalex.org/W2002771682","doi":"https://doi.org/10.1109/tcbb.2015.2407574","mag":"2002771682","pmid":"https://pubmed.ncbi.nlm.nih.gov/26451819"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2015.2407574","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2015.2407574","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5063614815","display_name":"Thuy-Diem Nguyen","orcid":null},"institutions":[{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Thuy-Diem Nguyen","raw_affiliation_strings":["School of Computer Engineering, Nanyang Technological University, Singapore","School of Computer Engineering, Nanyang Technological University,,Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Engineering, Nanyang Technological University, Singapore","institution_ids":["https://openalex.org/I172675005"]},{"raw_affiliation_string":"School of Computer Engineering, Nanyang Technological University,,Singapore","institution_ids":["https://openalex.org/I172675005"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020388832","display_name":"Bertil Schmidt","orcid":"https://orcid.org/0000-0003-2597-8331"},"institutions":[{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Bertil Schmidt","raw_affiliation_strings":["Institut f\u00fcr Informatik, Johannes Gutenberg University, Mainz, Germany","Institut f\u00fcr Informatik, Johannes Gutenberg University Mainz, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institut f\u00fcr Informatik, Johannes Gutenberg University, Mainz, Germany","institution_ids":["https://openalex.org/I197323543"]},{"raw_affiliation_string":"Institut f\u00fcr Informatik, Johannes Gutenberg University Mainz, Germany","institution_ids":["https://openalex.org/I197323543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003837657","display_name":"Zejun Zheng","orcid":"https://orcid.org/0000-0002-0369-5667"},"institutions":[{"id":"https://openalex.org/I115228651","display_name":"Agency for Science, Technology and Research","ror":"https://ror.org/036wvzt09","country_code":"SG","type":"government","lineage":["https://openalex.org/I115228651"]},{"id":"https://openalex.org/I4210148498","display_name":"Bioinformatics Institute","ror":"https://ror.org/044w3nw43","country_code":"SG","type":"facility","lineage":["https://openalex.org/I115228651","https://openalex.org/I2801752549","https://openalex.org/I4210148498"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Zejun Zheng","raw_affiliation_strings":["Bioinformatics Institute, A*STAR, Singapore","Bioinformatics Institute (A-STAR), Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Institute, A*STAR, Singapore","institution_ids":["https://openalex.org/I115228651","https://openalex.org/I4210148498"]},{"raw_affiliation_string":"Bioinformatics Institute (A-STAR), Singapore","institution_ids":["https://openalex.org/I4210148498"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5112553040","display_name":"Chee-Keong Kwoh","orcid":null},"institutions":[{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Chee-Keong Kwoh","raw_affiliation_strings":["School of Computer Engineering, Nanyang Technological University, Singapore","School of Computer Engineering, Nanyang Technological University,,Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Engineering, Nanyang Technological University, Singapore","institution_ids":["https://openalex.org/I172675005"]},{"raw_affiliation_string":"School of Computer Engineering, Nanyang Technological University,,Singapore","institution_ids":["https://openalex.org/I172675005"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.5511,"has_fulltext":false,"cited_by_count":8,"citation_normalized_percentile":{"value":0.65997779,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"12","issue":"5","first_page":"1060","last_page":"1073"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9991000294685364,"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":0.9991000294685364,"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":0.9962999820709229,"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":0.9955999851226807,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/dendrogram","display_name":"Dendrogram","score":0.7767941355705261},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.7554879784584045},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6466267108917236},{"id":"https://openalex.org/keywords/hierarchical-clustering","display_name":"Hierarchical clustering","score":0.6314600110054016},{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.5048542618751526},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.4716179668903351},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.4453132748603821},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4193142354488373},{"id":"https://openalex.org/keywords/distance-matrix","display_name":"Distance matrix","score":0.41926777362823486},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3811759352684021},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.20186716318130493}],"concepts":[{"id":"https://openalex.org/C172312944","wikidata":"https://www.wikidata.org/wiki/Q1957903","display_name":"Dendrogram","level":4,"score":0.7767941355705261},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.7554879784584045},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6466267108917236},{"id":"https://openalex.org/C92835128","wikidata":"https://www.wikidata.org/wiki/Q1277447","display_name":"Hierarchical clustering","level":3,"score":0.6314600110054016},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.5048542618751526},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.4716179668903351},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.4453132748603821},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4193142354488373},{"id":"https://openalex.org/C111208986","wikidata":"https://www.wikidata.org/wiki/Q901698","display_name":"Distance matrix","level":2,"score":0.41926777362823486},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3811759352684021},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.20186716318130493},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0},{"id":"https://openalex.org/C81977670","wikidata":"https://www.wikidata.org/wiki/Q585259","display_name":"Genetic diversity","level":3,"score":0.0},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.0},{"id":"https://openalex.org/C149923435","wikidata":"https://www.wikidata.org/wiki/Q37732","display_name":"Demography","level":1,"score":0.0},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"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":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":"Q000295","qualifier_name":"instrumentation","is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":"Q000295","qualifier_name":"instrumentation","is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":"Q000295","qualifier_name":"instrumentation","is_major_topic":false},{"descriptor_ui":"D004867","descriptor_name":"Equipment Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004867","descriptor_name":"Equipment Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004867","descriptor_name":"Equipment Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D012329","descriptor_name":"RNA, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012329","descriptor_name":"RNA, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012329","descriptor_name":"RNA, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012336","descriptor_name":"RNA, Ribosomal, 16S","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012336","descriptor_name":"RNA, Ribosomal, 16S","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012336","descriptor_name":"RNA, Ribosomal, 16S","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012815","descriptor_name":"Signal Processing, Computer-Assisted","qualifier_ui":"Q000295","qualifier_name":"instrumentation","is_major_topic":false},{"descriptor_ui":"D012815","descriptor_name":"Signal Processing, Computer-Assisted","qualifier_ui":"Q000295","qualifier_name":"instrumentation","is_major_topic":false},{"descriptor_ui":"D012815","descriptor_name":"Signal Processing, Computer-Assisted","qualifier_ui":"Q000295","qualifier_name":"instrumentation","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000295","qualifier_name":"instrumentation","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000295","qualifier_name":"instrumentation","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000295","qualifier_name":"instrumentation","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019544","descriptor_name":"Equipment Failure Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019544","descriptor_name":"Equipment Failure Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019544","descriptor_name":"Equipment Failure Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000295","qualifier_name":"instrumentation","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000295","qualifier_name":"instrumentation","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000295","qualifier_name":"instrumentation","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2015.2407574","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2015.2407574","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:26451819","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26451819","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":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure","score":0.41999998688697815}],"awards":[],"funders":[{"id":"https://openalex.org/F4320320766","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302"},{"id":"https://openalex.org/F4320320965","display_name":"University of New South Wales","ror":"https://ror.org/03r8z3t63"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":48,"referenced_works":["https://openalex.org/W117094473","https://openalex.org/W938539187","https://openalex.org/W1532325895","https://openalex.org/W1975684011","https://openalex.org/W1979813476","https://openalex.org/W1988925586","https://openalex.org/W1990061958","https://openalex.org/W2000072710","https://openalex.org/W2001991386","https://openalex.org/W2006290495","https://openalex.org/W2030782070","https://openalex.org/W2033403400","https://openalex.org/W2051322058","https://openalex.org/W2072970694","https://openalex.org/W2073548709","https://openalex.org/W2074231493","https://openalex.org/W2082464084","https://openalex.org/W2087671769","https://openalex.org/W2088833470","https://openalex.org/W2099751670","https://openalex.org/W2103809637","https://openalex.org/W2106308757","https://openalex.org/W2108718991","https://openalex.org/W2123009189","https://openalex.org/W2124351063","https://openalex.org/W2130077037","https://openalex.org/W2130208436","https://openalex.org/W2132373491","https://openalex.org/W2132926880","https://openalex.org/W2136552678","https://openalex.org/W2136879569","https://openalex.org/W2140264006","https://openalex.org/W2140638310","https://openalex.org/W2141245797","https://openalex.org/W2149573313","https://openalex.org/W2150914285","https://openalex.org/W2153993827","https://openalex.org/W2156125289","https://openalex.org/W2156858199","https://openalex.org/W2162833336","https://openalex.org/W2167519901","https://openalex.org/W2610179052","https://openalex.org/W4213009331","https://openalex.org/W4233096244","https://openalex.org/W4244030505","https://openalex.org/W4293586268","https://openalex.org/W6684050148","https://openalex.org/W6764471787"],"related_works":["https://openalex.org/W2402452210","https://openalex.org/W328064821","https://openalex.org/W4387161531","https://openalex.org/W3200462660","https://openalex.org/W2072104876","https://openalex.org/W2273431480","https://openalex.org/W2062059194","https://openalex.org/W2503748124","https://openalex.org/W4324107405","https://openalex.org/W2365460378"],"abstract_inverted_index":{"De":[0],"novo":[1],"clustering":[2,35,47,80,107,171,195],"is":[3,49,110,184],"a":[4,12,31,59,95,113,157,168],"popular":[5],"technique":[6,56,83],"to":[7,45,57,142,186],"perform":[8],"taxonomic":[9,23],"profiling":[10],"of":[11,52,64,70,94],"microbial":[13],"community":[14],"by":[15,85,123,150],"grouping":[16],"16S":[17],"rRNA":[18],"amplicon":[19],"reads":[20,140],"into":[21],"operational":[22],"units":[24],"(OTUs).":[25],"In":[26],"this":[27,148],"work,":[28],"we":[29],"introduce":[30],"new":[32],"dendrogram-based":[33,130],"OTU":[34,79,105,190,194],"pipeline":[36],"called":[37],"CRiSPy.":[38],"The":[39],"key":[40],"idea":[41],"used":[42],"in":[43,76,90],"CRiSPy":[44,102,183],"improve":[46],"accuracy":[48],"the":[50,66,91,99,104],"application":[51],"an":[53,87,119],"anomaly":[54],"detection":[55],"obtain":[58],"dynamic":[60],"distance":[61,115,164],"cutoff":[62],"instead":[63],"using":[65],"de":[67],"facto":[68],"value":[69],"97":[71],"percent":[72],"sequence":[73,125],"similarity":[74],"as":[75],"most":[77,128,193],"existing":[78,129],"pipelines.":[81],"This":[82],"works":[84],"detecting":[86],"abrupt":[88],"change":[89],"merging":[92],"heights":[93],"dendrogram.":[96],"To":[97],"produce":[98,187],"output":[100],"dendrograms,":[101],"employs":[103],"hierarchical":[106,170],"approach":[108],"that":[109,182],"computed":[111],"on":[112,175],"genetic":[114],"matrix":[116,165],"derived":[117],"from":[118],"all-against-all":[120],"read":[121],"comparison":[122],"pairwise":[124,163],"alignment.":[126],"However,":[127],"tools":[131],"have":[132],"difficulty":[133,149],"processing":[134],"datasets":[135,177],"larger":[136],"than":[137,192],"10,000":[138],"unique":[139],"due":[141],"high":[143],"computational":[144],"complexity.":[145],"We":[146],"address":[147],"developing":[151],"two":[152],"efficient":[153],"algorithms":[154],"for":[155,162],"CRiSPy:":[156],"compute-efficient":[158],"GPU-accelerated":[159],"parallel":[160],"algorithm":[161],"computation":[166],"and":[167],"memory-efficient":[169],"algorithm.":[172],"Our":[173],"experiments":[174],"various":[176],"with":[178],"distinct":[179],"attributes":[180],"show":[181],"able":[185],"more":[188],"accurate":[189],"groupings":[191],"applications.":[196]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":2}],"updated_date":"2026-07-28T07:46:37.118299","created_date":"2025-10-10T00:00:00"}