{"id":"https://openalex.org/W1968393646","doi":"https://doi.org/10.1145/2147805.2147824","title":"Inference of tumor phylogenies from genomic assays on heterogeneous samples","display_name":"Inference of tumor phylogenies from genomic assays on heterogeneous samples","publication_year":2011,"publication_date":"2011-08-01","ids":{"openalex":"https://openalex.org/W1968393646","doi":"https://doi.org/10.1145/2147805.2147824","mag":"1968393646"},"language":"en","primary_location":{"id":"doi:10.1145/2147805.2147824","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2147805.2147824","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":null,"any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5031387460","display_name":"Ayshwarya Subramanian","orcid":"https://orcid.org/0000-0002-4134-7612"},"institutions":[{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ayshwarya Subramanian","raw_affiliation_strings":["Carnegie Mellon University, Pittsburgh PA","Carnegie-Mellon University, Pittsburgh, PA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Carnegie Mellon University, Pittsburgh PA","institution_ids":["https://openalex.org/I74973139"]},{"raw_affiliation_string":"Carnegie-Mellon University, Pittsburgh, PA","institution_ids":["https://openalex.org/I74973139"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027859218","display_name":"Stanley E. Shackney","orcid":null},"institutions":[{"id":"https://openalex.org/I4210111451","display_name":"Oncotherapeutics (United States)","ror":"https://ror.org/01s33dn56","country_code":"US","type":"company","lineage":["https://openalex.org/I4210111451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Stanley Shackney","raw_affiliation_strings":["Intelligent Oncotherapeutics, Pittsburgh PA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Intelligent Oncotherapeutics, Pittsburgh PA","institution_ids":["https://openalex.org/I4210111451"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5051953313","display_name":"Russell Schwartz","orcid":"https://orcid.org/0000-0002-4970-2252"},"institutions":[{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Russell Schwartz","raw_affiliation_strings":["Carnegie Mellon University, Pittsburgh PA","Carnegie-Mellon University, Pittsburgh, PA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Carnegie Mellon University, Pittsburgh PA","institution_ids":["https://openalex.org/I74973139"]},{"raw_affiliation_string":"Carnegie-Mellon University, Pittsburgh, PA","institution_ids":["https://openalex.org/I74973139"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"172","last_page":"181"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9998999834060669,"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"}},"topics":[{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9998999834060669,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9950000047683716,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9944000244140625,"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/inference","display_name":"Inference","score":0.6298826336860657},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6105362176895142},{"id":"https://openalex.org/keywords/tumor-progression","display_name":"Tumor progression","score":0.5915771722793579},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5892952084541321},{"id":"https://openalex.org/keywords/carcinogenesis","display_name":"Carcinogenesis","score":0.5870230197906494},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.4965727925300598},{"id":"https://openalex.org/keywords/tumor-heterogeneity","display_name":"Tumor heterogeneity","score":0.4135028123855591},{"id":"https://openalex.org/keywords/cancer","display_name":"Cancer","score":0.39180582761764526},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3309191167354584},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.3235349655151367},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.31871163845062256},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.30834847688674927},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.28247523307800293},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.17263242602348328}],"concepts":[{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6298826336860657},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6105362176895142},{"id":"https://openalex.org/C2779256057","wikidata":"https://www.wikidata.org/wiki/Q16909647","display_name":"Tumor progression","level":3,"score":0.5915771722793579},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5892952084541321},{"id":"https://openalex.org/C555283112","wikidata":"https://www.wikidata.org/wiki/Q1637543","display_name":"Carcinogenesis","level":3,"score":0.5870230197906494},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.4965727925300598},{"id":"https://openalex.org/C3018028425","wikidata":"https://www.wikidata.org/wiki/Q15917291","display_name":"Tumor heterogeneity","level":3,"score":0.4135028123855591},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.39180582761764526},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3309191167354584},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.3235349655151367},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.31871163845062256},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.30834847688674927},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.28247523307800293},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.17263242602348328}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1145/2147805.2147824","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2147805.2147824","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine","raw_type":"proceedings-article"},{"id":"pmh:doi:10.1184/r1/6099662","is_oa":true,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4406922384","display_name":"Open MIND","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Journal contribution"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.1016.2806","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.1016.2806","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://repository.cmu.edu/cgi/viewcontent.cgi?article%3D1433%26context%3Dbiology","raw_type":"text"},{"id":"pmh:oai:figshare.com:article/6099662","is_oa":true,"landing_page_url":"https://figshare.com/articles/journal_contribution/Inference_of_tumor_phylogenies_from_genomic_assays_on_heterogeneous_samples_/6099662","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"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":"","raw_type":"Text"},{"id":"doi:10.1184/r1/6099662.v1","is_oa":true,"landing_page_url":"https://doi.org/10.1184/r1/6099662.v1","pdf_url":null,"source":{"id":"https://openalex.org/S7407050927","display_name":"KiltHub Repository","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"JournalArticle"}],"best_oa_location":{"id":"pmh:doi:10.1184/r1/6099662","is_oa":true,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4406922384","display_name":"Open MIND","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Journal contribution"},"sustainable_development_goals":[{"score":0.5199999809265137,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"awards":[{"id":"https://openalex.org/G3565131345","display_name":"Generalizing Haplotype Models for Phylogenetics","funder_award_id":"0612099","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5018101021","display_name":null,"funder_award_id":"1R01AI076318","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6130491037","display_name":null,"funder_award_id":"612099","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6273398171","display_name":null,"funder_award_id":"1R01CA140214","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":53,"referenced_works":["https://openalex.org/W45999627","https://openalex.org/W188996788","https://openalex.org/W1525325364","https://openalex.org/W1591237700","https://openalex.org/W1600834905","https://openalex.org/W1746872022","https://openalex.org/W1842847600","https://openalex.org/W1902027874","https://openalex.org/W1964154017","https://openalex.org/W1964370455","https://openalex.org/W1966937303","https://openalex.org/W1984000380","https://openalex.org/W1989076816","https://openalex.org/W1999463736","https://openalex.org/W2000111986","https://openalex.org/W2009218955","https://openalex.org/W2011031878","https://openalex.org/W2014451495","https://openalex.org/W2030430397","https://openalex.org/W2032388424","https://openalex.org/W2032518018","https://openalex.org/W2042536531","https://openalex.org/W2044144566","https://openalex.org/W2051255001","https://openalex.org/W2061050600","https://openalex.org/W2064223130","https://openalex.org/W2067419109","https://openalex.org/W2077379519","https://openalex.org/W2091870725","https://openalex.org/W2093573907","https://openalex.org/W2097255042","https://openalex.org/W2100083515","https://openalex.org/W2109363337","https://openalex.org/W2112641584","https://openalex.org/W2115162083","https://openalex.org/W2124810156","https://openalex.org/W2126903025","https://openalex.org/W2128016314","https://openalex.org/W2131658210","https://openalex.org/W2131994307","https://openalex.org/W2134327202","https://openalex.org/W2151054251","https://openalex.org/W2153933760","https://openalex.org/W2154264025","https://openalex.org/W2154361640","https://openalex.org/W2159973767","https://openalex.org/W2161428561","https://openalex.org/W2171693612","https://openalex.org/W2233306219","https://openalex.org/W4229857027","https://openalex.org/W4231060015","https://openalex.org/W4255699138","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W4312203868","https://openalex.org/W2069013776","https://openalex.org/W2038264393","https://openalex.org/W2059637021","https://openalex.org/W2378282666","https://openalex.org/W4210644918","https://openalex.org/W1967821671","https://openalex.org/W2243442814","https://openalex.org/W4288032625","https://openalex.org/W4327586990"],"abstract_inverted_index":{"Motivation:":[0],"Tumorigenesis":[1],"can":[2,41],"in":[3],"principle":[4],"result":[5],"from":[6,56],"many":[7],"combinations":[8],"of":[9,18,72,95,106],"mutations,":[10,19],"but":[11],"only":[12],"a":[13,75],"few":[14],"roughly":[15],"equivalent":[16],"sequences":[17],"or":[20],"\"progression":[21],"pathways\",":[22],"seem":[23],"to":[24,51,78,102],"account":[25],"for":[26],"most":[27],"human":[28],"tumors.":[29,84],"There":[30],"is":[31],"hope":[32],"that":[33,67],"by":[34],"cataloguing":[35],"the":[36,65,92],"common":[37],"progression":[38],"pathways,":[39],"we":[40],"identify":[42,79,103],"broadly":[43],"useful":[44],"therapeutic":[45],"targets":[46],"and":[47],"reliable":[48],"diagnostic":[49],"tests":[50],"determine":[52],"who":[53],"will":[54],"benefit":[55],"any":[57],"given":[58],"treatment.":[59],"Phylogenetic":[60],"approaches,":[61],"which":[62,98],"rely":[63],"on":[64],"observation":[66],"tumors":[68],"are":[69],"evolving":[70],"populations":[71],"cells,":[73],"provide":[74],"promising":[76],"way":[77],"robust":[80],"evolutionary":[81],"features":[82],"across":[83],"They":[85],"face":[86],"their":[87],"own":[88],"challenges,":[89],"though,":[90],"including":[91],"high":[93],"heterogeneity":[94],"individual":[96],"tumors,":[97],"makes":[99],"it":[100],"difficult":[101],"specific":[104],"steps":[105],"progression.":[107]},"counts_by_year":[{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":1}],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}
