{"id":"https://openalex.org/W4415655683","doi":"https://doi.org/10.1177/15578666251386082","title":"StarCDP: Dynamic Programming Algorithms for Fast and Accurate Cell Lineage Tree Reconstruction from CRISPR-Based Lineage Tracing Data","display_name":"StarCDP: Dynamic Programming Algorithms for Fast and Accurate Cell Lineage Tree Reconstruction from CRISPR-Based Lineage Tracing Data","publication_year":2025,"publication_date":"2025-10-29","ids":{"openalex":"https://openalex.org/W4415655683","doi":"https://doi.org/10.1177/15578666251386082","pmid":"https://pubmed.ncbi.nlm.nih.gov/41173524"},"language":"en","primary_location":{"id":"doi:10.1177/15578666251386082","is_oa":false,"landing_page_url":"https://doi.org/10.1177/15578666251386082","pdf_url":null,"source":{"id":"https://openalex.org/S78571599","display_name":"Journal of Computational Biology","issn_l":"1066-5277","issn":["1066-5277","1557-8666"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320443","host_organization_name":"Mary Ann Liebert, Inc.","host_organization_lineage":["https://openalex.org/P4310320443"],"host_organization_lineage_names":["Mary Ann Liebert, Inc."],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Biology","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/A5100308559","display_name":"J. P. Dai","orcid":"https://orcid.org/0009-0009-5699-2196"},"institutions":[{"id":"https://openalex.org/I66946132","display_name":"University of Maryland, College Park","ror":"https://ror.org/047s2c258","country_code":"US","type":"education","lineage":["https://openalex.org/I66946132"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Junyan Dai","raw_affiliation_strings":["Department of Computer Science, University of Maryland, College Park, Maryland, USA","University of Maryland Institute for Advanced Computer Studies, University of Maryland, College Park, Maryland, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Maryland, College Park, Maryland, USA","institution_ids":["https://openalex.org/I66946132"]},{"raw_affiliation_string":"University of Maryland Institute for Advanced Computer Studies, University of Maryland, College Park, Maryland, USA","institution_ids":["https://openalex.org/I66946132"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5045334836","display_name":"Erin K. Molloy","orcid":"https://orcid.org/0000-0001-5553-3312"},"institutions":[{"id":"https://openalex.org/I66946132","display_name":"University of Maryland, College Park","ror":"https://ror.org/047s2c258","country_code":"US","type":"education","lineage":["https://openalex.org/I66946132"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Erin K. Molloy","raw_affiliation_strings":["Department of Computer Science, University of Maryland, College Park, Maryland, USA","University of Maryland Institute for Advanced Computer Studies, University of Maryland, College Park, Maryland, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Maryland, College Park, Maryland, USA","institution_ids":["https://openalex.org/I66946132"]},{"raw_affiliation_string":"University of Maryland Institute for Advanced Computer Studies, University of Maryland, College Park, Maryland, USA","institution_ids":["https://openalex.org/I66946132"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5045334836"],"corresponding_institution_ids":["https://openalex.org/I66946132"],"apc_list":null,"apc_paid":null,"fwci":1.2656,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.82234032,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":98},"biblio":{"volume":"33","issue":"1","first_page":"48","last_page":"66"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9847999811172485,"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":0.9847999811172485,"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.00570000009611249,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.0010999999940395355,"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/scalability","display_name":"Scalability","score":0.7229999899864197},{"id":"https://openalex.org/keywords/lineage","display_name":"Lineage (genetic)","score":0.6669999957084656},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.6535999774932861},{"id":"https://openalex.org/keywords/tracing","display_name":"Tracing","score":0.6265000104904175},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.5945000052452087},{"id":"https://openalex.org/keywords/dynamic-programming","display_name":"Dynamic programming","score":0.5401999950408936},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.5231999754905701},{"id":"https://openalex.org/keywords/clade","display_name":"Clade","score":0.4717999994754791}],"concepts":[{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.7229999899864197},{"id":"https://openalex.org/C2776817793","wikidata":"https://www.wikidata.org/wiki/Q6553369","display_name":"Lineage (genetic)","level":3,"score":0.6669999957084656},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.6535999774932861},{"id":"https://openalex.org/C138673069","wikidata":"https://www.wikidata.org/wiki/Q322229","display_name":"Tracing","level":2,"score":0.6265000104904175},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6025999784469604},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.5945000052452087},{"id":"https://openalex.org/C37404715","wikidata":"https://www.wikidata.org/wiki/Q380679","display_name":"Dynamic programming","level":2,"score":0.5401999950408936},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5339000225067139},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.5231999754905701},{"id":"https://openalex.org/C44465124","wikidata":"https://www.wikidata.org/wiki/Q713623","display_name":"Clade","level":4,"score":0.4717999994754791},{"id":"https://openalex.org/C311688","wikidata":"https://www.wikidata.org/wiki/Q2393193","display_name":"Time complexity","level":2,"score":0.3887999951839447},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3880999982357025},{"id":"https://openalex.org/C22799545","wikidata":"https://www.wikidata.org/wiki/Q1805805","display_name":"Maximum parsimony","level":5,"score":0.34779998660087585},{"id":"https://openalex.org/C2780801425","wikidata":"https://www.wikidata.org/wiki/Q5164392","display_name":"Construct (python library)","level":2,"score":0.3443000018596649},{"id":"https://openalex.org/C2780897414","wikidata":"https://www.wikidata.org/wiki/Q7600592","display_name":"Star (game theory)","level":2,"score":0.3398999869823456},{"id":"https://openalex.org/C90119067","wikidata":"https://www.wikidata.org/wiki/Q43260","display_name":"Polynomial","level":2,"score":0.32760000228881836},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.32109999656677246},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3208000063896179},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3059999942779541},{"id":"https://openalex.org/C2777620950","wikidata":"https://www.wikidata.org/wiki/Q189105","display_name":"Cell lineage","level":4,"score":0.29019999504089355},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.2865999937057495},{"id":"https://openalex.org/C2834757","wikidata":"https://www.wikidata.org/wiki/Q4925424","display_name":"Monotone polygon","level":2,"score":0.27869999408721924},{"id":"https://openalex.org/C26619641","wikidata":"https://www.wikidata.org/wiki/Q3142246","display_name":"Phylogenetic network","level":4,"score":0.26759999990463257},{"id":"https://openalex.org/C62611344","wikidata":"https://www.wikidata.org/wiki/Q1062658","display_name":"Node (physics)","level":2,"score":0.26260000467300415},{"id":"https://openalex.org/C162319229","wikidata":"https://www.wikidata.org/wiki/Q175263","display_name":"Data structure","level":2,"score":0.2572000026702881},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.25099998712539673}],"mesh":[{"descriptor_ui":"D000098433","descriptor_name":"Dynamic Programming","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":true},{"descriptor_ui":"D000818","descriptor_name":"Animals","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":"D008175","descriptor_name":"Lung Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008175","descriptor_name":"Lung Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019070","descriptor_name":"Cell Lineage","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D064112","descriptor_name":"Clustered Regularly Interspaced Short Palindromic Repeats","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D064113","descriptor_name":"CRISPR-Cas Systems","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1177/15578666251386082","is_oa":false,"landing_page_url":"https://doi.org/10.1177/15578666251386082","pdf_url":null,"source":{"id":"https://openalex.org/S78571599","display_name":"Journal of Computational Biology","issn_l":"1066-5277","issn":["1066-5277","1557-8666"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320443","host_organization_name":"Mary Ann Liebert, Inc.","host_organization_lineage":["https://openalex.org/P4310320443"],"host_organization_lineage_names":["Mary Ann Liebert, Inc."],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Biology","raw_type":"journal-article"},{"id":"pmid:41173524","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41173524","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":"Journal of computational biology : a journal of computational molecular cell biology","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":36,"referenced_works":["https://openalex.org/W1889423108","https://openalex.org/W1967304777","https://openalex.org/W1972390207","https://openalex.org/W1984709097","https://openalex.org/W2060425093","https://openalex.org/W2084289491","https://openalex.org/W2095523744","https://openalex.org/W2145562754","https://openalex.org/W2146604274","https://openalex.org/W2521268904","https://openalex.org/W2587498643","https://openalex.org/W2787155168","https://openalex.org/W2794478094","https://openalex.org/W2795331645","https://openalex.org/W2796538159","https://openalex.org/W2801361050","https://openalex.org/W2802415313","https://openalex.org/W2803055706","https://openalex.org/W2896203075","https://openalex.org/W2952814943","https://openalex.org/W2954255127","https://openalex.org/W3015748341","https://openalex.org/W3042259581","https://openalex.org/W3171133702","https://openalex.org/W3173127629","https://openalex.org/W4229016240","https://openalex.org/W4231579661","https://openalex.org/W4310074701","https://openalex.org/W4379053919","https://openalex.org/W4385415871","https://openalex.org/W4389992940","https://openalex.org/W4390675502","https://openalex.org/W4405530888","https://openalex.org/W4409739068","https://openalex.org/W4409739446","https://openalex.org/W4411924941"],"related_works":[],"abstract_inverted_index":{"CRISPR-based":[0],"lineage":[1,26,194],"tracing,":[2],"coupled":[3],"with":[4,54,171],"single-cell":[5],"RNA":[6],"sequencing,":[7],"has":[8,30],"emerged":[9],"as":[10],"a":[11,84,106,117,198,231],"promising":[12],"approach":[13],"for":[14,151,248],"studying":[15],"development":[16],"and":[17,97,212,223],"disease":[18],"progression":[19],"at":[20],"the":[21,38,47,55,148,159,167,172,179,186,208,242],"cellular":[22],"level.":[23],"Thus,":[24],"cell":[25],"tree":[27],"(CLT)":[28],"reconstruction":[29,62],"attracted":[31],"significant":[32],"attention":[33],"in":[34,70,133,175],"recent":[35],"years,":[36],"including":[37],"introduction":[39],"of":[40,50,58,86,113,141,189,201,215],"Star":[41],"Homoplasy":[42],"Parsimony":[43],"(SHP)":[44],"to":[45,64,93,103,127,138,166,185,191,219],"model":[46,200],"unique":[48],"properties":[49],"CRISPR-induced":[51],"mutations,":[52],"along":[53],"Startle":[56],"family":[57],"methods.":[59],"However,":[60],"CLT":[61],"continues":[63],"be":[65],"challenged":[66],"by":[67,111],"technological":[68],"limitations":[69],"producing":[71],"consistent":[72],"phylogenetic":[73,180],"signals":[74],"across":[75],"CLTs.":[76],"To":[77],"address":[78],"these":[79],"issues,":[80],"we":[81],"present":[82],"Star-CDP,":[83],"collection":[85],"dynamic":[87],"programming":[88],"algorithms":[89],"that":[90,241],"enable":[91],"researchers":[92],"seek,":[94],"count,":[95],"sample,":[96],"build":[98],"consensus":[99,157,206,222],"trees":[100],"from":[101,115,197],"solutions":[102],"SHP":[104,210],"within":[105],"constrained":[107],"search":[108],"space,":[109],"defined":[110],"subsets":[112],"cells":[114,142,190],"which":[116],"solution":[118],"must":[119],"draw":[120],"its":[121],"clades.":[122],"When":[123],"using":[124],"our":[125,237],"procedure":[126],"construct":[128],"clade":[129],"constraints,":[130],"Star-CDP":[131,250],"runs":[132],"polynomial":[134],"time,":[135],"enabling":[136],"scalability":[137],"larger":[139],"numbers":[140,214],"than":[143],"Startle-ILP":[144],"(integer":[145],"linear":[146],"programming),":[147],"leading":[149,168],"method":[150],"SHP.":[152],"In":[153],"simulations,":[154],"Star-CDP's":[155,204],"strict":[156,205,221],"achieved":[158,207],"same":[160],"or":[161],"higher":[162],"accuracy":[163,176],"(f1-score)":[164],"compared":[165,218],"parsimony":[169],"methods,":[170],"greatest":[173],"gains":[174],"occurring":[177],"when":[178],"signal":[181],"was":[182],"limited":[183],"due":[184],"high":[187],"ratio":[188],"mutations.":[192],"On":[193],"tracing":[195],"data":[196,233],"mouse":[199],"lung":[202],"adenocarcinoma,":[203],"lowest":[209],"score":[211],"comparable":[213],"metastatic":[216],"reseedings":[217],"PAUP*'s":[220],"Startle-NNI":[224],"(nearest":[225],"neighbor":[226],"interchange),":[227],"all":[228],"benchmarked":[229],"on":[230,253],"standard":[232],"processing":[234],"pipeline":[235,243],"(although":[236],"study":[238],"also":[239],"revealed":[240],"can":[244],"impact":[245],"relative":[246],"performance":[247],"migrations/reseedings).":[249],"is":[251],"available":[252],"GitHub:":[254],"https://github.com/molloy-lab/Star-CDP.":[255]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1}],"updated_date":"2026-05-21T09:19:25.381259","created_date":"2025-10-29T00:00:00"}