{"id":"https://openalex.org/W4220948515","doi":"https://doi.org/10.1186/s12859-022-04633-x","title":"Single cell lineage reconstruction using distance-based algorithms and the R package, DCLEAR","display_name":"Single cell lineage reconstruction using distance-based algorithms and the R package, DCLEAR","publication_year":2022,"publication_date":"2022-03-24","ids":{"openalex":"https://openalex.org/W4220948515","doi":"https://doi.org/10.1186/s12859-022-04633-x","pmid":"https://pubmed.ncbi.nlm.nih.gov/35331133"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-022-04633-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-022-04633-x","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-022-04633-x","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-022-04633-x","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5066838536","display_name":"Wuming Gong","orcid":"https://orcid.org/0000-0002-3147-4028"},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]},{"id":"https://openalex.org/I4210134111","display_name":"Minneapolis Heart Institute Foundation","ror":"https://ror.org/03mhcky17","country_code":"US","type":"funder","lineage":["https://openalex.org/I4210134111"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wuming Gong","raw_affiliation_strings":["Lillehei Heart Institute, University of Minnesota, Minneapolis, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Lillehei Heart Institute, University of Minnesota, Minneapolis, USA","institution_ids":["https://openalex.org/I130238516","https://openalex.org/I4210134111"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084814930","display_name":"Hyunwoo J. Kim","orcid":"https://orcid.org/0000-0002-2181-9264"},"institutions":[{"id":"https://openalex.org/I197347611","display_name":"Korea University","ror":"https://ror.org/047dqcg40","country_code":"KR","type":"education","lineage":["https://openalex.org/I197347611"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Hyunwoo J. Kim","raw_affiliation_strings":["Department of Computer Science and Engineering, Korea University, Seoul, Republic of Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Korea University, Seoul, Republic of Korea","institution_ids":["https://openalex.org/I197347611"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036817888","display_name":"Daniel J. Garry","orcid":"https://orcid.org/0000-0002-8970-7365"},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]},{"id":"https://openalex.org/I4210134111","display_name":"Minneapolis Heart Institute Foundation","ror":"https://ror.org/03mhcky17","country_code":"US","type":"funder","lineage":["https://openalex.org/I4210134111"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Daniel J. Garry","raw_affiliation_strings":["Lillehei Heart Institute, University of Minnesota, Minneapolis, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Lillehei Heart Institute, University of Minnesota, Minneapolis, USA","institution_ids":["https://openalex.org/I130238516","https://openalex.org/I4210134111"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5014457836","display_name":"Il\u2010Youp Kwak","orcid":"https://orcid.org/0000-0002-7117-7669"},"institutions":[{"id":"https://openalex.org/I67900169","display_name":"Chung-Ang University","ror":"https://ror.org/01r024a98","country_code":"KR","type":"education","lineage":["https://openalex.org/I67900169"]}],"countries":["KR"],"is_corresponding":true,"raw_author_name":"Il-Youp Kwak","raw_affiliation_strings":["Department of Applied Statistics, Chung-Ang University, Seoul, Republic of Korea. ikwak2@cau.ac.kr","Department of Applied Statistics, Chung-Ang University, Seoul, Republic of Korea"],"raw_orcid":"https://orcid.org/0000-0002-7117-7669","affiliations":[{"raw_affiliation_string":"Department of Applied Statistics, Chung-Ang University, Seoul, Republic of Korea. ikwak2@cau.ac.kr","institution_ids":["https://openalex.org/I67900169"]},{"raw_affiliation_string":"Department of Applied Statistics, Chung-Ang University, Seoul, Republic of Korea","institution_ids":["https://openalex.org/I67900169"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5014457836"],"corresponding_institution_ids":["https://openalex.org/I67900169"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":1.5669,"has_fulltext":true,"cited_by_count":24,"citation_normalized_percentile":{"value":0.82724577,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"23","issue":"1","first_page":"103","last_page":"103"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9739000201225281,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9739000201225281,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.013100000098347664,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/T10885","display_name":"Gene expression and cancer classification","score":0.0007999999797903001,"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":0.683082640171051},{"id":"https://openalex.org/keywords/lineage","display_name":"Lineage (genetic)","score":0.6214845776557922},{"id":"https://openalex.org/keywords/hamming-distance","display_name":"Hamming distance","score":0.5398778915405273},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5048306584358215},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.4911184012889862},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.4517010748386383},{"id":"https://openalex.org/keywords/distance-matrix","display_name":"Distance matrix","score":0.4197178781032562},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.33520781993865967},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.24259111285209656},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.20243045687675476},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.13093462586402893},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.13092908263206482},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.10462954640388489},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.10062411427497864}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.683082640171051},{"id":"https://openalex.org/C2776817793","wikidata":"https://www.wikidata.org/wiki/Q6553369","display_name":"Lineage (genetic)","level":3,"score":0.6214845776557922},{"id":"https://openalex.org/C193319292","wikidata":"https://www.wikidata.org/wiki/Q272172","display_name":"Hamming distance","level":2,"score":0.5398778915405273},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5048306584358215},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.4911184012889862},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.4517010748386383},{"id":"https://openalex.org/C111208986","wikidata":"https://www.wikidata.org/wiki/Q901698","display_name":"Distance matrix","level":2,"score":0.4197178781032562},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.33520781993865967},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.24259111285209656},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.20243045687675476},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.13093462586402893},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.13092908263206482},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.10462954640388489},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.10062411427497864}],"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":"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":"D019070","descriptor_name":"Cell Lineage","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019070","descriptor_name":"Cell Lineage","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019070","descriptor_name":"Cell Lineage","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-022-04633-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-022-04633-x","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-022-04633-x","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:35331133","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35331133","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:689f5a5067d742eb825770955795380d","is_oa":false,"landing_page_url":"https://doaj.org/article/689f5a5067d742eb825770955795380d","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 23, Iss 1, Pp 1-14 (2022)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8944039","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8944039","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-022-04633-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-022-04633-x","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-022-04633-x","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Partnerships for the goals","score":0.44999998807907104,"id":"https://metadata.un.org/sdg/17"}],"awards":[{"id":"https://openalex.org/G3346572468","display_name":null,"funder_award_id":"2020R1C1C1A01013020","funder_id":"https://openalex.org/F4320322120","funder_display_name":"National Research Foundation of Korea"},{"id":"https://openalex.org/G636969104","display_name":null,"funder_award_id":"2020R1C1C1A01013020","funder_id":"https://openalex.org/F4320322030","funder_display_name":"Ministry of Science, ICT and Future Planning"}],"funders":[{"id":"https://openalex.org/F4320320671","display_name":"National Research Foundation","ror":"https://ror.org/05s0g1g46"},{"id":"https://openalex.org/F4320322030","display_name":"Ministry of Science, ICT and Future Planning","ror":"https://ror.org/032e49973"},{"id":"https://openalex.org/F4320322120","display_name":"National Research Foundation of Korea","ror":"https://ror.org/013aysd81"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":14,"referenced_works":["https://openalex.org/W2060425093","https://openalex.org/W2097706568","https://openalex.org/W2120819924","https://openalex.org/W2151409320","https://openalex.org/W2229908198","https://openalex.org/W2260913036","https://openalex.org/W2406991867","https://openalex.org/W2557069473","https://openalex.org/W2794478094","https://openalex.org/W2795331645","https://openalex.org/W3015748341","https://openalex.org/W3171133702","https://openalex.org/W4399584518","https://openalex.org/W4399637265"],"related_works":["https://openalex.org/W2506149209","https://openalex.org/W2352153050","https://openalex.org/W2578129866","https://openalex.org/W4287777066","https://openalex.org/W4286977480","https://openalex.org/W1949367941","https://openalex.org/W3026153476","https://openalex.org/W2180288160","https://openalex.org/W240043582","https://openalex.org/W4387363394"],"abstract_inverted_index":{"BACKGROUND:":[0],"DCLEAR":[1,89,137,166,187],"is":[2,167,188],"an":[3],"R":[4,93,174],"package":[5,90],"used":[6],"for":[7,129,192],"single":[8,193],"cell":[9,24,43,194],"lineage":[10,25,44,195],"reconstruction.":[11,196],"The":[12,88],"advances":[13],"of":[14,23,38,42,108,146,157],"CRISPR-based":[15],"gene":[16],"editing":[17],"technologies":[18],"have":[19],"enabled":[20],"the":[21,36,56,60,74,84,92,117,121,136,147,161,179],"prediction":[22],"trees":[26,45],"based":[27],"on":[28],"observed":[29],"edited":[30],"barcodes":[31],"from":[32,72,120,173,177],"each":[33],"cell.":[34],"However,":[35],"performance":[37,158],"existing":[39],"reconstruction":[40,119],"methods":[41,128,151],"was":[46,96],"not":[47],"accessed":[48],"until":[49],"recently.":[50],"In":[51],"response":[52,99],"to":[53,68,100,160],"this":[54],"problem,":[55],"Allen":[57],"Institute":[58],"hosted":[59],"Cell":[61],"Lineage":[62],"Reconstruction":[63],"Dream":[64],"Challenge":[65],"in":[66,83,98,135],"2020":[67],"crowdsource":[69],"relevant":[70],"knowledge":[71],"across":[73],"world.":[75],"Our":[76,105],"team":[77],"won":[78],"sub-challenges":[79,101],"2":[80,102],"and":[81,103,115,170,176],"3":[82],"challenge":[85],"competition.":[86],"RESULTS:":[87],"contained":[91],"codes,":[94],"which":[95],"submitted":[97],"3.":[104,185],"method":[106],"consists":[107],"two":[109,126,145],"steps:":[110],"(1)":[111],"distance":[112,122,130,150,164],"matrix":[113,131],"estimation":[114,132],"(2)":[116],"tree":[118],"matrix.":[123],"We":[124],"proposed":[125],"novel":[127],"as":[133],"outlined":[134],"package.":[138],"Using":[139],"our":[140],"method,":[141],"we":[142],"find":[143],"that":[144],"more":[148],"sophisticated":[149],"display":[152],"a":[153,189],"substantially":[154],"improved":[155],"level":[156],"compared":[159],"traditional":[162],"Hamming":[163],"method.":[165],"open":[168],"source":[169],"freely":[171],"available":[172],"CRAN":[175],"under":[178],"GNU":[180],"General":[181],"Public":[182],"License,":[183],"version":[184],"CONCLUSIONS:":[186],"powerful":[190],"resource":[191]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":1}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
