{"id":"https://openalex.org/W2806004564","doi":"https://doi.org/10.1093/bioinformatics/bty469","title":"Predicting clone genotypes from tumor bulk sequencing of multiple samples","display_name":"Predicting clone genotypes from tumor bulk sequencing of multiple samples","publication_year":2018,"publication_date":"2018-06-12","ids":{"openalex":"https://openalex.org/W2806004564","doi":"https://doi.org/10.1093/bioinformatics/bty469","mag":"2806004564","pmid":"https://pubmed.ncbi.nlm.nih.gov/29931046"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty469","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty469","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/23/4017/26676662/bty469.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/34/23/4017/26676662/bty469.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5062480014","display_name":"Sayaka Miura","orcid":"https://orcid.org/0000-0001-9881-2848"},"institutions":[{"id":"https://openalex.org/I84392919","display_name":"Temple University","ror":"https://ror.org/00kx1jb78","country_code":"US","type":"education","lineage":["https://openalex.org/I84392919"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sayaka Miura","raw_affiliation_strings":["Department of Biology, Temple University, Philadelphia, PA, USA","Institute for Genomics and Evolutionary Medicine"],"affiliations":[{"raw_affiliation_string":"Department of Biology, Temple University, Philadelphia, PA, USA","institution_ids":["https://openalex.org/I84392919"]},{"raw_affiliation_string":"Institute for Genomics and Evolutionary Medicine","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111725172","display_name":"Karen Gomez","orcid":null},"institutions":[{"id":"https://openalex.org/I84392919","display_name":"Temple University","ror":"https://ror.org/00kx1jb78","country_code":"US","type":"education","lineage":["https://openalex.org/I84392919"]},{"id":"https://openalex.org/I78577930","display_name":"Columbia University","ror":"https://ror.org/00hj8s172","country_code":"US","type":"education","lineage":["https://openalex.org/I78577930"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Karen Gomez","raw_affiliation_strings":["College of Physicians and Surgeons, Columbia University, New York, NY, USA","Department of Biology, Temple University, Philadelphia, PA, USA","Institute for Genomics and Evolutionary Medicine"],"affiliations":[{"raw_affiliation_string":"College of Physicians and Surgeons, Columbia University, New York, NY, USA","institution_ids":["https://openalex.org/I78577930"]},{"raw_affiliation_string":"Department of Biology, Temple University, Philadelphia, PA, USA","institution_ids":["https://openalex.org/I84392919"]},{"raw_affiliation_string":"Institute for Genomics and Evolutionary Medicine","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101553389","display_name":"Oscar Murillo","orcid":"https://orcid.org/0000-0003-1938-3905"},"institutions":[{"id":"https://openalex.org/I181547552","display_name":"Baylor College of Medicine","ror":"https://ror.org/02pttbw34","country_code":"US","type":"education","lineage":["https://openalex.org/I181547552","https://openalex.org/I2801539370"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Oscar Murillo","raw_affiliation_strings":["Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA","Institute for Genomics and Evolutionary Medicine"],"affiliations":[{"raw_affiliation_string":"Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA","institution_ids":["https://openalex.org/I181547552"]},{"raw_affiliation_string":"Institute for Genomics and Evolutionary Medicine","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005665859","display_name":"Louise A. Huuki-Myers","orcid":"https://orcid.org/0000-0001-5148-3602"},"institutions":[{"id":"https://openalex.org/I84392919","display_name":"Temple University","ror":"https://ror.org/00kx1jb78","country_code":"US","type":"education","lineage":["https://openalex.org/I84392919"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Louise A Huuki","raw_affiliation_strings":["Department of Biology, Temple University, Philadelphia, PA, USA","Institute for Genomics and Evolutionary Medicine"],"affiliations":[{"raw_affiliation_string":"Department of Biology, Temple University, Philadelphia, PA, USA","institution_ids":["https://openalex.org/I84392919"]},{"raw_affiliation_string":"Institute for Genomics and Evolutionary Medicine","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112447770","display_name":"Tracy Vu","orcid":null},"institutions":[{"id":"https://openalex.org/I84392919","display_name":"Temple University","ror":"https://ror.org/00kx1jb78","country_code":"US","type":"education","lineage":["https://openalex.org/I84392919"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tracy Vu","raw_affiliation_strings":["Department of Biology, Temple University, Philadelphia, PA, USA","Institute for Genomics and Evolutionary Medicine"],"affiliations":[{"raw_affiliation_string":"Department of Biology, Temple University, Philadelphia, PA, USA","institution_ids":["https://openalex.org/I84392919"]},{"raw_affiliation_string":"Institute for Genomics and Evolutionary Medicine","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037431525","display_name":"Tiffany Buturla","orcid":null},"institutions":[{"id":"https://openalex.org/I84392919","display_name":"Temple University","ror":"https://ror.org/00kx1jb78","country_code":"US","type":"education","lineage":["https://openalex.org/I84392919"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tiffany Buturla","raw_affiliation_strings":["Department of Biology, Temple University, Philadelphia, PA, USA","Institute for Genomics and Evolutionary Medicine"],"affiliations":[{"raw_affiliation_string":"Department of Biology, Temple University, Philadelphia, PA, USA","institution_ids":["https://openalex.org/I84392919"]},{"raw_affiliation_string":"Institute for Genomics and Evolutionary Medicine","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100680948","display_name":"Sudhir Kumar","orcid":"https://orcid.org/0000-0002-9918-8212"},"institutions":[{"id":"https://openalex.org/I84392919","display_name":"Temple University","ror":"https://ror.org/00kx1jb78","country_code":"US","type":"education","lineage":["https://openalex.org/I84392919"]},{"id":"https://openalex.org/I185163786","display_name":"King Abdulaziz University","ror":"https://ror.org/02ma4wv74","country_code":"SA","type":"education","lineage":["https://openalex.org/I185163786"]}],"countries":["SA","US"],"is_corresponding":true,"raw_author_name":"Sudhir Kumar","raw_affiliation_strings":["Center for Excellence in Genome Medicine and Research, King Abdulaziz University, Jeddah, Saudi Arabia","Department of Biology, Temple University, Philadelphia, PA, USA","Institute for Genomics and Evolutionary Medicine"],"affiliations":[{"raw_affiliation_string":"Center for Excellence in Genome Medicine and Research, King Abdulaziz University, Jeddah, Saudi Arabia","institution_ids":["https://openalex.org/I185163786"]},{"raw_affiliation_string":"Department of Biology, Temple University, Philadelphia, PA, USA","institution_ids":["https://openalex.org/I84392919"]},{"raw_affiliation_string":"Institute for Genomics and Evolutionary Medicine","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5100680948"],"corresponding_institution_ids":["https://openalex.org/I185163786","https://openalex.org/I84392919"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.8355,"has_fulltext":true,"cited_by_count":36,"citation_normalized_percentile":{"value":0.84185535,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"34","issue":"23","first_page":"4017","last_page":"4026"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":1.0,"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":1.0,"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/T10231","display_name":"Pancreatic and Hepatic Oncology Research","score":0.9916999936103821,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10417","display_name":"Lung Cancer Treatments and Mutations","score":0.988099992275238,"subfield":{"id":"https://openalex.org/subfields/2740","display_name":"Pulmonary and Respiratory Medicine"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/clone","display_name":"clone (Java method)","score":0.7808084487915039},{"id":"https://openalex.org/keywords/genotype","display_name":"Genotype","score":0.6638262271881104},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5297057628631592},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4962363839149475},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.42858532071113586},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.42195767164230347},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1857554018497467}],"concepts":[{"id":"https://openalex.org/C81089528","wikidata":"https://www.wikidata.org/wiki/Q5134986","display_name":"clone (Java method)","level":3,"score":0.7808084487915039},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.6638262271881104},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5297057628631592},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4962363839149475},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.42858532071113586},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.42195767164230347},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1857554018497467}],"mesh":[{"descriptor_ui":"D002999","descriptor_name":"Clone Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002999","descriptor_name":"Clone Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002999","descriptor_name":"Clone Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"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":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"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":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bty469","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty469","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/23/4017/26676662/bty469.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:29931046","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29931046","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:europepmc.org:5839775","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6247940","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty469","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty469","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/23/4017/26676662/bty469.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2804744938","display_name":null,"funder_award_id":"LM012487","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6804534272","display_name":null,"funder_award_id":"LM012758","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2806004564.pdf","grobid_xml":"https://content.openalex.org/works/W2806004564.grobid-xml"},"referenced_works_count":45,"referenced_works":["https://openalex.org/W1487781539","https://openalex.org/W1563750692","https://openalex.org/W1772151993","https://openalex.org/W1895753987","https://openalex.org/W1965151932","https://openalex.org/W1968657935","https://openalex.org/W1985405863","https://openalex.org/W2002295829","https://openalex.org/W2010873488","https://openalex.org/W2019863483","https://openalex.org/W2027246028","https://openalex.org/W2050146329","https://openalex.org/W2058166031","https://openalex.org/W2067817997","https://openalex.org/W2088580309","https://openalex.org/W2097455931","https://openalex.org/W2106963053","https://openalex.org/W2108371618","https://openalex.org/W2109991075","https://openalex.org/W2111187843","https://openalex.org/W2111762123","https://openalex.org/W2111874706","https://openalex.org/W2114095872","https://openalex.org/W2122392334","https://openalex.org/W2124600009","https://openalex.org/W2144847592","https://openalex.org/W2150575159","https://openalex.org/W2153938747","https://openalex.org/W2269040222","https://openalex.org/W2284361446","https://openalex.org/W2402730620","https://openalex.org/W2515462796","https://openalex.org/W2556080288","https://openalex.org/W2570401594","https://openalex.org/W2579382924","https://openalex.org/W2585248318","https://openalex.org/W2593152615","https://openalex.org/W2626355241","https://openalex.org/W2735315721","https://openalex.org/W2764126103","https://openalex.org/W2798766386","https://openalex.org/W4396738453","https://openalex.org/W6664676434","https://openalex.org/W6667573396","https://openalex.org/W6734158204"],"related_works":["https://openalex.org/W2899084033","https://openalex.org/W4391375266","https://openalex.org/W2377327490","https://openalex.org/W2560253012","https://openalex.org/W1524590520","https://openalex.org/W2412288087","https://openalex.org/W2371792548","https://openalex.org/W1697705604","https://openalex.org/W2419862115","https://openalex.org/W2017092658"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":4},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":9},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":8}],"updated_date":"2026-03-06T13:50:29.536080","created_date":"2025-10-10T00:00:00"}