{"id":"https://openalex.org/W4200113290","doi":"https://doi.org/10.1109/tcbb.2021.3132534","title":"Finding Overlapping Rmaps via Clustering","display_name":"Finding Overlapping Rmaps via Clustering","publication_year":2021,"publication_date":"2021-12-10","ids":{"openalex":"https://openalex.org/W4200113290","doi":"https://doi.org/10.1109/tcbb.2021.3132534","pmid":"https://pubmed.ncbi.nlm.nih.gov/34890332"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2021.3132534","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2021.3132534","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":null,"display_name":"Kingshuk Mukherjee","orcid":"https://orcid.org/0000-0002-1647-8741"},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kingshuk Mukherjee","raw_affiliation_strings":["Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL, USA"],"raw_orcid":"https://orcid.org/0000-0002-1647-8741","affiliations":[{"raw_affiliation_string":"Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL, USA","institution_ids":["https://openalex.org/I33213144"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Daniel Dole-Muinos","orcid":null},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Daniel Dole-Muinos","raw_affiliation_strings":["Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL, USA","institution_ids":["https://openalex.org/I33213144"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Massimiliano Rossi","orcid":"https://orcid.org/0000-0002-3012-1394"},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Massimiliano Rossi","raw_affiliation_strings":["Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL, USA"],"raw_orcid":"https://orcid.org/0000-0002-3012-1394","affiliations":[{"raw_affiliation_string":"Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL, USA","institution_ids":["https://openalex.org/I33213144"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Ayomide Ajayi","orcid":null},"institutions":[{"id":"https://openalex.org/I83909951","display_name":"Morgan State University","ror":"https://ror.org/017d8gk22","country_code":"US","type":"education","lineage":["https://openalex.org/I83909951"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ayomide Ajayi","raw_affiliation_strings":["Department of Computer Science, Morgan State University, Baltimore, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Morgan State University, Baltimore, MD, USA","institution_ids":["https://openalex.org/I83909951"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Mattia Prosperi","orcid":"https://orcid.org/0000-0002-9021-5595"},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mattia Prosperi","raw_affiliation_strings":["Department of Epidemiology, University of Florida, Gainesville, FL, USA"],"raw_orcid":"https://orcid.org/0000-0002-9021-5595","affiliations":[{"raw_affiliation_string":"Department of Epidemiology, University of Florida, Gainesville, FL, USA","institution_ids":["https://openalex.org/I33213144"]}]},{"author_position":"last","author":{"id":null,"display_name":"Christina Boucher","orcid":"https://orcid.org/0000-0001-9509-9725"},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Christina Boucher","raw_affiliation_strings":["Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL, USA"],"raw_orcid":"https://orcid.org/0000-0001-9509-9725","affiliations":[{"raw_affiliation_string":"Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL, USA","institution_ids":["https://openalex.org/I33213144"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.10636963,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"19","issue":"6","first_page":"3114","last_page":"3123"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.3009999990463257,"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":0.3009999990463257,"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/T13664","display_name":"Genome Rearrangement Algorithms","score":0.1460999995470047,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.13729999959468842,"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/cluster-analysis","display_name":"Cluster analysis","score":0.6171000003814697},{"id":"https://openalex.org/keywords/heuristics","display_name":"Heuristics","score":0.605400025844574},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4997999966144562},{"id":"https://openalex.org/keywords/orientation","display_name":"Orientation (vector space)","score":0.49540001153945923},{"id":"https://openalex.org/keywords/quantization","display_name":"Quantization (signal processing)","score":0.484499990940094},{"id":"https://openalex.org/keywords/gaussian","display_name":"Gaussian","score":0.41769999265670776},{"id":"https://openalex.org/keywords/vector-quantization","display_name":"Vector quantization","score":0.328000009059906},{"id":"https://openalex.org/keywords/resolution","display_name":"Resolution (logic)","score":0.3262999951839447}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7170000076293945},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.6171000003814697},{"id":"https://openalex.org/C127705205","wikidata":"https://www.wikidata.org/wiki/Q5748245","display_name":"Heuristics","level":2,"score":0.605400025844574},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4997999966144562},{"id":"https://openalex.org/C16345878","wikidata":"https://www.wikidata.org/wiki/Q107472979","display_name":"Orientation (vector space)","level":2,"score":0.49540001153945923},{"id":"https://openalex.org/C28855332","wikidata":"https://www.wikidata.org/wiki/Q198099","display_name":"Quantization (signal processing)","level":2,"score":0.484499990940094},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.42669999599456787},{"id":"https://openalex.org/C163716315","wikidata":"https://www.wikidata.org/wiki/Q901177","display_name":"Gaussian","level":2,"score":0.41769999265670776},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.38420000672340393},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.36890000104904175},{"id":"https://openalex.org/C199833920","wikidata":"https://www.wikidata.org/wiki/Q612536","display_name":"Vector quantization","level":2,"score":0.328000009059906},{"id":"https://openalex.org/C138268822","wikidata":"https://www.wikidata.org/wiki/Q1051925","display_name":"Resolution (logic)","level":2,"score":0.3262999951839447},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3249000012874603},{"id":"https://openalex.org/C103088060","wikidata":"https://www.wikidata.org/wiki/Q1062839","display_name":"Error detection and correction","level":2,"score":0.3052999973297119},{"id":"https://openalex.org/C61224824","wikidata":"https://www.wikidata.org/wiki/Q2260434","display_name":"Mixture model","level":2,"score":0.2930999994277954},{"id":"https://openalex.org/C58103923","wikidata":"https://www.wikidata.org/wiki/Q2286025","display_name":"Silhouette","level":2,"score":0.29269999265670776},{"id":"https://openalex.org/C61326573","wikidata":"https://www.wikidata.org/wiki/Q1496376","display_name":"Gaussian process","level":3,"score":0.29089999198913574},{"id":"https://openalex.org/C81669768","wikidata":"https://www.wikidata.org/wiki/Q2359161","display_name":"Precision and recall","level":2,"score":0.28299999237060547},{"id":"https://openalex.org/C49154492","wikidata":"https://www.wikidata.org/wiki/Q5300","display_name":"Central processing unit","level":2,"score":0.2827000021934509},{"id":"https://openalex.org/C8880873","wikidata":"https://www.wikidata.org/wiki/Q187787","display_name":"Genetic algorithm","level":2,"score":0.27709999680519104},{"id":"https://openalex.org/C32653426","wikidata":"https://www.wikidata.org/wiki/Q3813641","display_name":"Background subtraction","level":3,"score":0.2547000050544739}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"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":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2021.3132534","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2021.3132534","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:34890332","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34890332","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":[],"awards":[{"id":"https://openalex.org/G1562572150","display_name":null,"funder_award_id":"2013998","funder_id":"https://openalex.org/F4320335353","funder_display_name":"National Science Foundation of Sri Lanka"},{"id":"https://openalex.org/G8425121650","display_name":null,"funder_award_id":"1618814","funder_id":"https://openalex.org/F4320335353","funder_display_name":"National Science Foundation of Sri Lanka"}],"funders":[{"id":"https://openalex.org/F4320335353","display_name":"National Science Foundation of Sri Lanka","ror":"https://ror.org/010xaa060"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":31,"referenced_works":["https://openalex.org/W95267802","https://openalex.org/W1999660860","https://openalex.org/W2000597943","https://openalex.org/W2012012446","https://openalex.org/W2047555270","https://openalex.org/W2049633694","https://openalex.org/W2063287758","https://openalex.org/W2063985242","https://openalex.org/W2087064593","https://openalex.org/W2116902306","https://openalex.org/W2117383593","https://openalex.org/W2131852975","https://openalex.org/W2153689534","https://openalex.org/W2285299833","https://openalex.org/W2525022860","https://openalex.org/W2602637791","https://openalex.org/W2610754078","https://openalex.org/W2765429478","https://openalex.org/W2886603117","https://openalex.org/W2898039965","https://openalex.org/W2914149839","https://openalex.org/W2918574728","https://openalex.org/W2949860250","https://openalex.org/W2950079684","https://openalex.org/W2971458848","https://openalex.org/W2994746706","https://openalex.org/W3039515866","https://openalex.org/W3165081484","https://openalex.org/W6732138705","https://openalex.org/W6754870501","https://openalex.org/W6782777992"],"related_works":[],"abstract_inverted_index":{"Optical":[0,15],"mapping":[1,16],"is":[2,47,58,215,220],"a":[3,96,106],"method":[4],"for":[5,81],"creating":[6],"high":[7],"resolution":[8],"restriction":[9,26],"maps":[10],"of":[11,44,55,64,90,175],"an":[12],"entire":[13],"genome.":[14],"has":[17],"been":[18],"largely":[19],"automated,":[20],"and":[21,42,71,128,153,166,204,219],"first":[22,50],"produces":[23],"single":[24],"molecule":[25],"maps,":[27],"called":[28],"Rmaps,":[29,61,203],"which":[30,93,113],"are":[31],"assembled":[32],"to":[33,95,116,141,168,184,196,200],"generate":[34],"genome":[35],"wide":[36],"optical":[37],"maps.":[38],"Since":[39],"the":[40,49,53,68,91,99,137,144,161,170,173,206],"location":[41],"orientation":[43,70],"each":[45],"Rmap":[46,187],"unknown,":[48],"problem":[51],"in":[52,75,98,172,217],"analysis":[54],"this":[56,102],"data":[57,92,188],"finding":[59],"related":[60,83],"i.e.,":[62],"pairs":[63],"Rmaps":[65,84,122],"that":[66,119,133],"share":[67],"same":[69],"have":[72],"significant":[73],"overlap":[74],"their":[76],"genomic":[77],"location.":[78],"Although":[79],"heuristics":[80],"identifying":[82],"exist,":[85],"they":[86],"all":[87],"require":[88],"quantization":[89],"leads":[94],"loss":[97],"precision.":[100],"In":[101],"paper,":[103],"we":[104,114,131,157],"propose":[105],"Gaussian":[107],"mixture":[108],"modelling":[109],"clustering":[110],"based":[111],"method,":[112],"refer":[115],"as":[117],"OMclust,":[118],"finds":[120],"overlapping":[121],"without":[123],"quantization.":[124],"Using":[125],"both":[126],"simulated":[127],"real":[129],"datasets,":[130],"show":[132],"OMclust":[134,159,179],"substantially":[135],"improves":[136],"precision":[138],"(from":[139],"48.3%":[140],"73.3%)":[142],"over":[143],"state-of-the":[145],"art":[146],"methods":[147,164],"while":[148],"also":[149],"reducing":[150],"CPU":[151,207],"time":[152,208],"memory":[154],"consumption.":[155],"Further,":[156],"integrated":[158],"into":[160],"error":[162,185,197],"correction":[163],"(Elmeri":[165],"cOMet)":[167],"demonstrate":[169],"increase":[171],"performance":[174],"these":[176],"methods.":[177],"When":[178],"was":[180,194],"combined":[181],"with":[182],"cOMet":[183],"correct":[186,198],"generated":[189],"from":[190],"human":[191],"DNA,":[192],"it":[193],"able":[195],"close":[199],"3x":[201],"more":[202,210],"reduced":[205],"by":[209],"than":[211],"35x.":[212],"Our":[213],"software":[214],"written":[216],"C++":[218],"publicly":[221],"available":[222],"under":[223],"GNU":[224],"General":[225],"Public":[226],"License":[227],"at":[228],"https://github.com/kingufl/OMclust.":[229]},"counts_by_year":[],"updated_date":"2026-07-28T07:46:37.118299","created_date":"2021-12-31T00:00:00"}
