{"id":"https://openalex.org/W2207661154","doi":"https://doi.org/10.1093/bioinformatics/btw035","title":"TRONCO: an R package for the inference of cancer progression models from heterogeneous genomic data","display_name":"TRONCO: an R package for the inference of cancer progression models from heterogeneous genomic data","publication_year":2016,"publication_date":"2016-02-09","ids":{"openalex":"https://openalex.org/W2207661154","doi":"https://doi.org/10.1093/bioinformatics/btw035","mag":"2207661154","pmid":"https://pubmed.ncbi.nlm.nih.gov/26861821"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btw035","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw035","pdf_url":null,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["arxiv","crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.research.ed.ac.uk/en/publications/4ec23af9-45ef-4b05-bcbf-eb676541d2a5","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Luca De Sano","orcid":null},"institutions":[{"id":"https://openalex.org/I66752286","display_name":"University of Milano-Bicocca","ror":"https://ror.org/01ynf4891","country_code":"IT","type":"education","lineage":["https://openalex.org/I66752286"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Luca De Sano","raw_affiliation_strings":["1 Department of Informatics, Systems and Communication, University of Milano-Bicocca,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Informatics, Systems and Communication, University of Milano-Bicocca,","institution_ids":["https://openalex.org/I66752286"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033643165","display_name":"Giulio Caravagna","orcid":"https://orcid.org/0000-0003-4240-3265"},"institutions":[{"id":"https://openalex.org/I66752286","display_name":"University of Milano-Bicocca","ror":"https://ror.org/01ynf4891","country_code":"IT","type":"education","lineage":["https://openalex.org/I66752286"]},{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]}],"countries":["GB","IT"],"is_corresponding":false,"raw_author_name":"Giulio Caravagna","raw_affiliation_strings":["1 Department of Informatics, Systems and Communication, University of Milano-Bicocca,","2 School of Informatics, University of Edinburgh, Edinburgh, UK,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Informatics, Systems and Communication, University of Milano-Bicocca,","institution_ids":["https://openalex.org/I66752286"]},{"raw_affiliation_string":"2 School of Informatics, University of Edinburgh, Edinburgh, UK,","institution_ids":["https://openalex.org/I98677209"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022687646","display_name":"Daniele Ramazzotti","orcid":"https://orcid.org/0000-0002-6087-2666"},"institutions":[{"id":"https://openalex.org/I66752286","display_name":"University of Milano-Bicocca","ror":"https://ror.org/01ynf4891","country_code":"IT","type":"education","lineage":["https://openalex.org/I66752286"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Daniele Ramazzotti","raw_affiliation_strings":["1 Department of Informatics, Systems and Communication, University of Milano-Bicocca,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Informatics, Systems and Communication, University of Milano-Bicocca,","institution_ids":["https://openalex.org/I66752286"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055916343","display_name":"Alex Graudenzi","orcid":"https://orcid.org/0000-0001-5452-1918"},"institutions":[{"id":"https://openalex.org/I4210095629","display_name":"Institute of Molecular Bioimaging and Physiology","ror":"https://ror.org/00s2j5046","country_code":"IT","type":"facility","lineage":["https://openalex.org/I4210095629","https://openalex.org/I4210155236"]},{"id":"https://openalex.org/I4210155236","display_name":"National Research Council","ror":"https://ror.org/04zaypm56","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I4210155236"]},{"id":"https://openalex.org/I66752286","display_name":"University of Milano-Bicocca","ror":"https://ror.org/01ynf4891","country_code":"IT","type":"education","lineage":["https://openalex.org/I66752286"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Alex Graudenzi","raw_affiliation_strings":["1 Department of Informatics, Systems and Communication, University of Milano-Bicocca,","3 Institute of Molecular Bioimaging and Physiology of the Italian National Research Council (IBFM-CNR), Milan, Italy,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Informatics, Systems and Communication, University of Milano-Bicocca,","institution_ids":["https://openalex.org/I66752286"]},{"raw_affiliation_string":"3 Institute of Molecular Bioimaging and Physiology of the Italian National Research Council (IBFM-CNR), Milan, Italy,","institution_ids":["https://openalex.org/I4210095629","https://openalex.org/I4210155236"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073163964","display_name":"Giancarlo Mauri","orcid":"https://orcid.org/0000-0003-3520-4022"},"institutions":[{"id":"https://openalex.org/I66752286","display_name":"University of Milano-Bicocca","ror":"https://ror.org/01ynf4891","country_code":"IT","type":"education","lineage":["https://openalex.org/I66752286"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Giancarlo Mauri","raw_affiliation_strings":["1 Department of Informatics, Systems and Communication, University of Milano-Bicocca,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Informatics, Systems and Communication, University of Milano-Bicocca,","institution_ids":["https://openalex.org/I66752286"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053379558","display_name":"Bud Mishra","orcid":null},"institutions":[{"id":"https://openalex.org/I36672615","display_name":"Courant Institute of Mathematical Sciences","ror":"https://ror.org/037tm7f56","country_code":"US","type":"education","lineage":["https://openalex.org/I36672615","https://openalex.org/I57206974"]},{"id":"https://openalex.org/I57206974","display_name":"New York University","ror":"https://ror.org/0190ak572","country_code":"US","type":"education","lineage":["https://openalex.org/I57206974"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bud Mishra","raw_affiliation_strings":["4 Courant Institute of Mathematical Sciences, New York University, New York, NY, USA and"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"4 Courant Institute of Mathematical Sciences, New York University, New York, NY, USA and","institution_ids":["https://openalex.org/I36672615","https://openalex.org/I57206974"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5037919963","display_name":"Marco Antoniotti","orcid":"https://orcid.org/0000-0002-2823-6838"},"institutions":[{"id":"https://openalex.org/I66752286","display_name":"University of Milano-Bicocca","ror":"https://ror.org/01ynf4891","country_code":"IT","type":"education","lineage":["https://openalex.org/I66752286"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Marco Antoniotti","raw_affiliation_strings":["1 Department of Informatics, Systems and Communication, University of Milano-Bicocca,","5 Milan Center for Neuroscience, University of Milan-Bicocca, Milan, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Informatics, Systems and Communication, University of Milano-Bicocca,","institution_ids":["https://openalex.org/I66752286"]},{"raw_affiliation_string":"5 Milan Center for Neuroscience, University of Milan-Bicocca, Milan, Italy","institution_ids":["https://openalex.org/I66752286"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5037919963"],"corresponding_institution_ids":["https://openalex.org/I66752286"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.9923,"has_fulltext":false,"cited_by_count":45,"citation_normalized_percentile":{"value":0.84429812,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"32","issue":"12","first_page":"1911","last_page":"1913"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.95660001039505,"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":0.95660001039505,"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/T11369","display_name":"Genetic factors in colorectal cancer","score":0.006000000052154064,"subfield":{"id":"https://openalex.org/subfields/2734","display_name":"Pathology and Forensic Medicine"},"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/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.00559999980032444,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/bioconductor","display_name":"Bioconductor","score":0.8559819459915161},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.7008960247039795},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.6617608666419983},{"id":"https://openalex.org/keywords/personalized-medicine","display_name":"Personalized medicine","score":0.5649352073669434},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4935649633407593},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.48528000712394714},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.45915690064430237},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.45716750621795654},{"id":"https://openalex.org/keywords/cancer","display_name":"Cancer","score":0.4474426209926605},{"id":"https://openalex.org/keywords/precision-medicine","display_name":"Precision medicine","score":0.44548454880714417},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.42426732182502747},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4108465313911438},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.368619441986084},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3672545552253723},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2427874207496643},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.21101295948028564},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.2107502818107605},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.19033262133598328},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.16048523783683777},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.08826828002929688}],"concepts":[{"id":"https://openalex.org/C2779694297","wikidata":"https://www.wikidata.org/wiki/Q2888953","display_name":"Bioconductor","level":3,"score":0.8559819459915161},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.7008960247039795},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6617608666419983},{"id":"https://openalex.org/C32220436","wikidata":"https://www.wikidata.org/wiki/Q2072214","display_name":"Personalized medicine","level":2,"score":0.5649352073669434},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4935649633407593},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.48528000712394714},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.45915690064430237},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.45716750621795654},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.4474426209926605},{"id":"https://openalex.org/C163763905","wikidata":"https://www.wikidata.org/wiki/Q17075943","display_name":"Precision medicine","level":2,"score":0.44548454880714417},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.42426732182502747},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4108465313911438},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.368619441986084},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3672545552253723},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2427874207496643},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.21101295948028564},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.2107502818107605},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.19033262133598328},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.16048523783683777},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.08826828002929688},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0},{"id":"https://openalex.org/C99454951","wikidata":"https://www.wikidata.org/wiki/Q932068","display_name":"Environmental health","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018450","descriptor_name":"Disease Progression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018450","descriptor_name":"Disease Progression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018450","descriptor_name":"Disease Progression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D044127","descriptor_name":"Epigenesis, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D044127","descriptor_name":"Epigenesis, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D044127","descriptor_name":"Epigenesis, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":9,"locations":[{"id":"doi:10.1093/bioinformatics/btw035","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw035","pdf_url":null,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:26861821","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26861821","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:pure.ed.ac.uk:openaire/4ec23af9-45ef-4b05-bcbf-eb676541d2a5","is_oa":true,"landing_page_url":"https://www.research.ed.ac.uk/en/publications/4ec23af9-45ef-4b05-bcbf-eb676541d2a5","pdf_url":null,"source":{"id":"https://openalex.org/S4406922455","display_name":"Edinburgh Research Explorer","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"De Sano, L, Caravagna, G, Ramazzotti, D, Graudenzi, A, Mauri, G, Mishra, B & Antoniotti, M 2016, 'TRONCO: an R package for the inference of cancer progression models from heterogeneous genomic data', Bioinformatics, vol. 32, no. 12, pp. 1911-1913. https://doi.org/10.1093/bioinformatics/btw035","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:arXiv.org:1509.07304","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1509.07304","pdf_url":"https://arxiv.org/pdf/1509.07304","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"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"},{"id":"pmh:oai:arts.units.it:11368/2956293","is_oa":false,"landing_page_url":"http://hdl.handle.net/11368/2956293","pdf_url":null,"source":{"id":"https://openalex.org/S4306402362","display_name":"ArTS Archivio della ricerca di Trieste (University of Trieste https://www.units.it/)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I142444530","host_organization_name":"University of Trieste","host_organization_lineage":["https://openalex.org/I142444530"],"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":"info:eu-repo/semantics/article"},{"id":"pmh:oai:boa.unimib.it:10281/100189","is_oa":false,"landing_page_url":"http://hdl.handle.net/10281/100189","pdf_url":null,"source":{"id":"https://openalex.org/S4306401259","display_name":"BOA (University of Milano-Bicocca)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I66752286","host_organization_name":"University of Milano-Bicocca","host_organization_lineage":["https://openalex.org/I66752286"],"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":"info:eu-repo/semantics/article"},{"id":"pmh:oai:europepmc.org:5255532","is_oa":false,"landing_page_url":"http://europepmc.org/pmc/articles/PMC6280783","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":"","raw_type":"Text"},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:32/12/1911","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/32/12/1911","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","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":"","raw_type":"TEXT"},{"id":"pmh:oai:pubmedcentral.nih.gov:6280783","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6280783","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pure.ed.ac.uk:openaire/4ec23af9-45ef-4b05-bcbf-eb676541d2a5","is_oa":true,"landing_page_url":"https://www.research.ed.ac.uk/en/publications/4ec23af9-45ef-4b05-bcbf-eb676541d2a5","pdf_url":null,"source":{"id":"https://openalex.org/S4406922455","display_name":"Edinburgh Research Explorer","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"De Sano, L, Caravagna, G, Ramazzotti, D, Graudenzi, A, Mauri, G, Mishra, B & Antoniotti, M 2016, 'TRONCO: an R package for the inference of cancer progression models from heterogeneous genomic data', Bioinformatics, vol. 32, no. 12, pp. 1911-1913. https://doi.org/10.1093/bioinformatics/btw035","raw_type":"info:eu-repo/semantics/publishedVersion"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":14,"referenced_works":["https://openalex.org/W1881305409","https://openalex.org/W1966331733","https://openalex.org/W1967304777","https://openalex.org/W2084829134","https://openalex.org/W2141811925","https://openalex.org/W2149441684","https://openalex.org/W2154598603","https://openalex.org/W2159675211","https://openalex.org/W2209688796","https://openalex.org/W2233432342","https://openalex.org/W2253465175","https://openalex.org/W3100320483","https://openalex.org/W4230962320","https://openalex.org/W4252595574"],"related_works":["https://openalex.org/W2728564446","https://openalex.org/W3045904767","https://openalex.org/W2161868542","https://openalex.org/W3082935376","https://openalex.org/W3156537409","https://openalex.org/W2140163842","https://openalex.org/W2747931568","https://openalex.org/W2921090651","https://openalex.org/W2133055377","https://openalex.org/W2287365612"],"abstract_inverted_index":{"MOTIVATION:":[0],"We":[1],"introduce":[2],"TRanslational":[3],"ONCOlogy":[4],"(TRONCO),":[5],"an":[6],"open-source":[7],"R":[8],"package":[9],"that":[10,56],"implements":[11],"the":[12,16,35,58,87,106],"state-of-the-art":[13],"algorithms":[14],"for":[15,85,93],"inference":[17],"of":[18,37,39,44,90],"cancer":[19,64],"progression":[20],"models":[21,33,55,80],"from":[22,49],"(epi)genomic":[23],"mutational":[24],"profiles.":[25],"TRONCO":[26,102],"can":[27,81],"be":[28],"used":[29],"to":[30],"extract":[31],"population-level":[32],"describing":[34],"trends":[36],"accumulation":[38],"alterations":[40],"in":[41,62],"a":[42],"cohort":[43],"cross-sectional":[45],"samples,":[46,68],"e.g.":[47,69],"retrieved":[48],"publicly":[50],"available":[51,127],"databases,":[52],"and":[53,115],"individual-level":[54],"reveal":[57],"clonal":[59],"evolutionary":[60,88],"history":[61],"single":[63],"patients,":[65],"when":[66],"multiple":[67,70],"biopsies":[71],"or":[72,96],"single-cell":[73],"sequencing":[74],"data,":[75],"are":[76,126],"available.":[77],"The":[78],"resulting":[79],"provide":[82],"key":[83],"hints":[84],"uncovering":[86],"trajectories":[89],"cancer,":[91],"especially":[92],"precision":[94],"medicine":[95],"personalized":[97],"therapy.":[98],"AVAILABILITY":[99],"AND":[100],"IMPLEMENTATION:":[101],"is":[103,109],"released":[104],"under":[105],"GPL":[107],"license,":[108],"hosted":[110],"at":[111,118,128],"http://bimib.disco.unimib.it/":[112],"(Software":[113],"section)":[114],"archived":[116],"also":[117],"bioconductor.org.":[119],"CONTACT:":[120],"tronco@disco.unimib.it":[121],"SUPPLEMENTARY":[122],"INFORMATION:":[123],"Supplementary":[124],"data":[125],"Bioinformatics":[129],"online.":[130]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":13},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":6},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":2}],"updated_date":"2026-04-29T09:16:38.111599","created_date":"2025-10-10T00:00:00"}
