{"id":"https://openalex.org/W2326872503","doi":"https://doi.org/10.1109/tcbb.2016.2537319","title":"DTL-RnB: Algorithms and Tools for Summarizing the Space of DTL Reconciliations","display_name":"DTL-RnB: Algorithms and Tools for Summarizing the Space of DTL Reconciliations","publication_year":2016,"publication_date":"2016-03-02","ids":{"openalex":"https://openalex.org/W2326872503","doi":"https://doi.org/10.1109/tcbb.2016.2537319","mag":"2326872503","pmid":"https://pubmed.ncbi.nlm.nih.gov/26955051"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2016.2537319","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2016.2537319","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"],"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/A5019319098","display_name":"Weishuo Ma","orcid":"https://orcid.org/0000-0001-9277-860X"},"institutions":[{"id":"https://openalex.org/I133543626","display_name":"Harvey Mudd College","ror":"https://ror.org/025ecfn45","country_code":"US","type":"education","lineage":["https://openalex.org/I133543626"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"W. Ma","raw_affiliation_strings":["Harvey Mudd College"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Harvey Mudd College","institution_ids":["https://openalex.org/I133543626"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086064947","display_name":"Dmitriy Smirnov","orcid":"https://orcid.org/0000-0002-6508-0705"},"institutions":[{"id":"https://openalex.org/I177881444","display_name":"Pomona College","ror":"https://ror.org/0074grg94","country_code":"US","type":"education","lineage":["https://openalex.org/I177881444"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"D. Smirnov","raw_affiliation_strings":["Pomona College"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Pomona College","institution_ids":["https://openalex.org/I177881444"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112557359","display_name":"J Forman","orcid":null},"institutions":[{"id":"https://openalex.org/I133543626","display_name":"Harvey Mudd College","ror":"https://ror.org/025ecfn45","country_code":"US","type":"education","lineage":["https://openalex.org/I133543626"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"J. Forman","raw_affiliation_strings":["Harvey Mudd College"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Harvey Mudd College","institution_ids":["https://openalex.org/I133543626"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053542267","display_name":"A. Schweickart","orcid":null},"institutions":[{"id":"https://openalex.org/I133543626","display_name":"Harvey Mudd College","ror":"https://ror.org/025ecfn45","country_code":"US","type":"education","lineage":["https://openalex.org/I133543626"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"A. Schweickart","raw_affiliation_strings":["Harvey Mudd College"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Harvey Mudd College","institution_ids":["https://openalex.org/I133543626"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108121624","display_name":"Christine Slocum","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"C. Slocum","raw_affiliation_strings":["California Polytechnic University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"California Polytechnic University","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059451002","display_name":"Sudharshan Srinivasan","orcid":"https://orcid.org/0000-0003-2103-7825"},"institutions":[{"id":"https://openalex.org/I133543626","display_name":"Harvey Mudd College","ror":"https://ror.org/025ecfn45","country_code":"US","type":"education","lineage":["https://openalex.org/I133543626"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"S. Srinivasan","raw_affiliation_strings":["Harvey Mudd College"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Harvey Mudd College","institution_ids":["https://openalex.org/I133543626"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5081839833","display_name":"Ran Libeskind-Hadas","orcid":"https://orcid.org/0000-0001-9120-1948"},"institutions":[{"id":"https://openalex.org/I133543626","display_name":"Harvey Mudd College","ror":"https://ror.org/025ecfn45","country_code":"US","type":"education","lineage":["https://openalex.org/I133543626"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"R. Libeskind-Hadas","raw_affiliation_strings":["Harvey Mudd College"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Harvey Mudd College","institution_ids":["https://openalex.org/I133543626"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":1.567,"has_fulltext":false,"cited_by_count":14,"citation_normalized_percentile":{"value":0.83177961,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"15","issue":"2","first_page":"411","last_page":"421"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9994000196456909,"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":0.9994000196456909,"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/T10012","display_name":"Genetic diversity and population structure","score":0.9642000198364258,"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/T11354","display_name":"Evolution and Paleontology Studies","score":0.9592999815940857,"subfield":{"id":"https://openalex.org/subfields/1911","display_name":"Paleontology"},"field":{"id":"https://openalex.org/fields/19","display_name":"Earth and Planetary Sciences"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6655101180076599},{"id":"https://openalex.org/keywords/space","display_name":"Space (punctuation)","score":0.6397426128387451},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.567805290222168},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.5602808594703674},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5381177067756653},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.42594239115715027},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.4248271882534027},{"id":"https://openalex.org/keywords/maximum-parsimony","display_name":"Maximum parsimony","score":0.41217195987701416},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.30756595730781555},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.26226261258125305},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.10244441032409668},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.09159284830093384},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.08183154463768005},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.0635739266872406}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6655101180076599},{"id":"https://openalex.org/C2778572836","wikidata":"https://www.wikidata.org/wiki/Q380933","display_name":"Space (punctuation)","level":2,"score":0.6397426128387451},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.567805290222168},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.5602808594703674},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5381177067756653},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.42594239115715027},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4248271882534027},{"id":"https://openalex.org/C22799545","wikidata":"https://www.wikidata.org/wiki/Q1805805","display_name":"Maximum parsimony","level":5,"score":0.41217195987701416},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.30756595730781555},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.26226261258125305},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.10244441032409668},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09159284830093384},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.08183154463768005},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0635739266872406},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C44465124","wikidata":"https://www.wikidata.org/wiki/Q713623","display_name":"Clade","level":4,"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":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2016.2537319","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2016.2537319","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"],"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:26955051","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26955051","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/10","score":0.4300000071525574,"display_name":"Reduced inequalities"}],"awards":[{"id":"https://openalex.org/G6418997412","display_name":null,"funder_award_id":"IIS-1419739","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"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":20,"referenced_works":["https://openalex.org/W157609093","https://openalex.org/W1970909551","https://openalex.org/W1974757757","https://openalex.org/W2011039300","https://openalex.org/W2026560157","https://openalex.org/W2100091570","https://openalex.org/W2110014387","https://openalex.org/W2112755610","https://openalex.org/W2117000771","https://openalex.org/W2123305821","https://openalex.org/W2132318428","https://openalex.org/W2132553324","https://openalex.org/W2135894797","https://openalex.org/W2138882560","https://openalex.org/W2144454528","https://openalex.org/W2147428165","https://openalex.org/W2148231054","https://openalex.org/W2162282699","https://openalex.org/W6606317737","https://openalex.org/W6676264541"],"related_works":["https://openalex.org/W2520823390","https://openalex.org/W4300265711","https://openalex.org/W2963820820","https://openalex.org/W2963207658","https://openalex.org/W2362218761","https://openalex.org/W2375151634","https://openalex.org/W2062354928","https://openalex.org/W2090308851","https://openalex.org/W2113708670","https://openalex.org/W3146310663"],"abstract_inverted_index":{"Phylogenetic":[0],"tree":[1],"reconciliation":[2],"is":[3,21,83],"an":[4],"important":[5],"technique":[6],"for":[7],"reconstructing":[8],"the":[9,30,39,42,49,67,73,80,97,108],"evolutionary":[10],"histories":[11],"of":[12,32,41,59,110],"species":[13],"and":[14,16,29,96],"genes":[15],"other":[17],"dependent":[18],"entities.":[19],"Reconciliation":[20],"typically":[22],"performed":[23],"in":[24,72],"a":[25,56,87],"maximum":[26],"parsimony":[27],"framework":[28],"number":[31,58],"optimal":[33,111],"reconciliations":[34,60,112],"can":[35,61],"grow":[36],"exponentially":[37],"with":[38],"size":[40],"trees,":[43],"making":[44],"it":[45],"difficult":[46],"to":[47,106],"understand":[48],"solution":[50,74],"space.":[51,75],"This":[52],"paper":[53],"demonstrates":[54],"how":[55],"small":[57],"be":[62],"found":[63],"that":[64,79,92,102],"collectively":[65],"contain":[66],"most":[68],"highly":[69],"supported":[70],"events":[71],"While":[76],"we":[77,85],"show":[78],"formal":[81],"problem":[82],"NP-complete,":[84],"give":[86],"approximation":[88],"algorithm,":[89],"experimental":[90],"results":[91],"indicate":[93],"its":[94],"effectiveness,":[95],"new":[98],"DTL-RnB":[99],"software":[100],"tool":[101],"uses":[103],"our":[104],"algorithms":[105],"summarize":[107],"space":[109],"(www.cs.hmc.edu/dtlrnb).":[113]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":2},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":3}],"updated_date":"2026-06-24T13:16:06.693445","created_date":"2025-10-10T00:00:00"}