{"id":"https://openalex.org/W3113285045","doi":"https://doi.org/10.1186/s12859-020-03736-7","title":"gpps: an ILP-based approach for inferring cancer progression with mutation losses from single cell data","display_name":"gpps: an ILP-based approach for inferring cancer progression with mutation losses from single cell data","publication_year":2020,"publication_date":"2020-12-01","ids":{"openalex":"https://openalex.org/W3113285045","doi":"https://doi.org/10.1186/s12859-020-03736-7","mag":"3113285045","pmid":"https://pubmed.ncbi.nlm.nih.gov/33297943"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-020-03736-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-03736-7","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-03736-7","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-03736-7","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5048411377","display_name":"Simone Ciccolella","orcid":"https://orcid.org/0000-0002-6469-4887"},"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":"Simone Ciccolella","raw_affiliation_strings":["Department of Informatics, Systems, and Communication, University of Milano - Bicocca, Milan, Italy. simone.ciccolella@unimib.it","Department of Informatics, Systems, and Communication, University of Milano - Bicocca, Milan, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Informatics, Systems, and Communication, University of Milano - Bicocca, Milan, Italy. simone.ciccolella@unimib.it","institution_ids":["https://openalex.org/I66752286"]},{"raw_affiliation_string":"Department of Informatics, Systems, and Communication, University of Milano - Bicocca, Milan, Italy","institution_ids":["https://openalex.org/I66752286"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044649325","display_name":"Mauricio Soto","orcid":"https://orcid.org/0000-0001-5977-9467"},"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":"Mauricio Soto Gomez","raw_affiliation_strings":["Department of Informatics, Systems, and Communication, University of Milano - Bicocca, Milan, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Informatics, Systems, and Communication, University of Milano - Bicocca, Milan, Italy","institution_ids":["https://openalex.org/I66752286"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026228482","display_name":"Murray Patterson","orcid":"https://orcid.org/0000-0002-4329-0234"},"institutions":[{"id":"https://openalex.org/I181565077","display_name":"Georgia State University","ror":"https://ror.org/03qt6ba18","country_code":"US","type":"education","lineage":["https://openalex.org/I181565077"]},{"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","US"],"is_corresponding":false,"raw_author_name":"Murray D. Patterson","raw_affiliation_strings":["Department of Informatics, Systems, and Communication, University of Milano - Bicocca, Milan, Italy","Georgia State University, Atlanta, GA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Informatics, Systems, and Communication, University of Milano - Bicocca, Milan, Italy","institution_ids":["https://openalex.org/I66752286"]},{"raw_affiliation_string":"Georgia State University, Atlanta, GA, USA","institution_ids":["https://openalex.org/I181565077"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059679442","display_name":"Gianluca Della Vedova","orcid":"https://orcid.org/0000-0001-5584-3089"},"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":"Gianluca Della Vedova","raw_affiliation_strings":["Department of Informatics, Systems, and Communication, University of Milano - Bicocca, Milan, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Informatics, Systems, and Communication, University of Milano - Bicocca, Milan, Italy","institution_ids":["https://openalex.org/I66752286"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068064308","display_name":"Iman Hajirasouliha","orcid":"https://orcid.org/0000-0002-0600-3371"},"institutions":[{"id":"https://openalex.org/I205783295","display_name":"Cornell University","ror":"https://ror.org/05bnh6r87","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295"]},{"id":"https://openalex.org/I4387153466","display_name":"Weill Cornell Medicine","ror":"https://ror.org/02r109517","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295","https://openalex.org/I4387153466"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Iman Hajirasouliha","raw_affiliation_strings":["Department of Physiology and Biophysics, Weill Cornell Medicine of Cornell University, NewYork City, 10021, NY, USA","Institute for Computational Biomedicine, Weill Cornell Medicine, New York City, NY, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Physiology and Biophysics, Weill Cornell Medicine of Cornell University, NewYork City, 10021, NY, USA","institution_ids":["https://openalex.org/I205783295"]},{"raw_affiliation_string":"Institute for Computational Biomedicine, Weill Cornell Medicine, New York City, NY, USA","institution_ids":["https://openalex.org/I205783295","https://openalex.org/I4387153466"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5038691764","display_name":"Paola Bonizzoni","orcid":"https://orcid.org/0000-0001-7289-4988"},"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":"Paola Bonizzoni","raw_affiliation_strings":["Department of Informatics, Systems, and Communication, University of Milano - Bicocca, Milan, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Informatics, Systems, and Communication, University of Milano - Bicocca, Milan, Italy","institution_ids":["https://openalex.org/I66752286"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5048411377"],"corresponding_institution_ids":["https://openalex.org/I66752286"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":1385,"currency":"EUR","value_usd":1493},"fwci":0.9898,"has_fulltext":true,"cited_by_count":19,"citation_normalized_percentile":{"value":0.72717359,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"21","issue":"S1","first_page":"413","last_page":"413"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.7242000102996826,"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":0.7242000102996826,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.21490000188350677,"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/T10158","display_name":"Cancer Immunotherapy and Biomarkers","score":0.009499999694526196,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.6593006253242493},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.6291475296020508},{"id":"https://openalex.org/keywords/single-cell-sequencing","display_name":"Single cell sequencing","score":0.5580570101737976},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5235438346862793},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5034002661705017},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.48901113867759705},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.45077913999557495},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4318733811378479},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2664855122566223},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.22469940781593323},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.14467531442642212},{"id":"https://openalex.org/keywords/exome-sequencing","display_name":"Exome sequencing","score":0.12959441542625427},{"id":"https://openalex.org/keywords/paleontology","display_name":"Paleontology","score":0.12130361795425415}],"concepts":[{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.6593006253242493},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.6291475296020508},{"id":"https://openalex.org/C174749747","wikidata":"https://www.wikidata.org/wiki/Q15917269","display_name":"Single cell sequencing","level":5,"score":0.5580570101737976},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5235438346862793},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5034002661705017},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.48901113867759705},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.45077913999557495},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4318733811378479},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2664855122566223},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.22469940781593323},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.14467531442642212},{"id":"https://openalex.org/C16671776","wikidata":"https://www.wikidata.org/wiki/Q5420592","display_name":"Exome sequencing","level":4,"score":0.12959441542625427},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.12130361795425415}],"mesh":[{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004252","descriptor_name":"DNA Mutational Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004252","descriptor_name":"DNA Mutational Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004252","descriptor_name":"DNA Mutational Analysis","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":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009154","descriptor_name":"Mutation","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":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"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":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","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":true},{"descriptor_ui":"D018450","descriptor_name":"Disease Progression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018450","descriptor_name":"Disease Progression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"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},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":7,"locations":[{"id":"doi:10.1186/s12859-020-03736-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-03736-7","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-03736-7","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:33297943","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33297943","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:boa.unimib.it:10281/327429","is_oa":true,"landing_page_url":"http://hdl.handle.net/10281/327429","pdf_url":"https://boa.unimib.it/bitstream/10281/327429/2/10281-327429_VoR.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:air.unimi.it:2434/961445","is_oa":true,"landing_page_url":"https://hdl.handle.net/2434/961445","pdf_url":null,"source":{"id":"https://openalex.org/S4306400516","display_name":"Archivio Istituzionale della Ricerca (Universita Degli Studi Di Milano)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I189158943","host_organization_name":"University of Milan","host_organization_lineage":["https://openalex.org/I189158943"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:doaj.org/article:68413e30146248ea8a28ed9354eb204a","is_oa":true,"landing_page_url":"https://doaj.org/article/68413e30146248ea8a28ed9354eb204a","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 21, Iss S1, Pp 1-16 (2020)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:7725124","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7725124","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:re.public.polimi.it:11311/1200834","is_oa":false,"landing_page_url":"http://hdl.handle.net/11311/1200834","pdf_url":null,"source":{"id":"https://openalex.org/S4306400312","display_name":"Virtual Community of Pathological Anatomy (University of Castilla La Mancha)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I79189158","host_organization_name":"University of Castilla-La Mancha","host_organization_lineage":["https://openalex.org/I79189158"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1186/s12859-020-03736-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-03736-7","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-03736-7","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.49000000953674316,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"awards":[{"id":"https://openalex.org/G4279947611","display_name":null,"funder_award_id":"IIS-1840275","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G434337789","display_name":null,"funder_award_id":"HORIZON2020","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G6305941982","display_name":"EAGER: Novel Computational Models and Algorithms for Mapping Link-Read Sequencing Data","funder_award_id":"1840275","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6697205189","display_name":"Pan-genome Graph Algorithms and Data Integration","funder_award_id":"872539","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G8411802876","display_name":"Modulation of anti-cancer immune response by regulatory non-coding RNAs","funder_award_id":"2013-0955","funder_id":"https://openalex.org/F4320321499","funder_display_name":"Fondazione Cariplo"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320321499","display_name":"Fondazione Cariplo","ror":"https://ror.org/01gb56c55"},{"id":"https://openalex.org/F4320332513","display_name":"Weill Cornell Medical College","ror":"https://ror.org/02r109517"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3113285045.pdf","grobid_xml":"https://content.openalex.org/works/W3113285045.grobid-xml"},"referenced_works_count":51,"referenced_works":["https://openalex.org/W938539187","https://openalex.org/W1534962401","https://openalex.org/W1539105590","https://openalex.org/W1596689408","https://openalex.org/W1967304777","https://openalex.org/W1982901388","https://openalex.org/W1986888627","https://openalex.org/W1990061958","https://openalex.org/W2002295829","https://openalex.org/W2004232113","https://openalex.org/W2032861672","https://openalex.org/W2034629821","https://openalex.org/W2063295224","https://openalex.org/W2071734901","https://openalex.org/W2072719910","https://openalex.org/W2074507113","https://openalex.org/W2076755063","https://openalex.org/W2084289491","https://openalex.org/W2114095872","https://openalex.org/W2117797567","https://openalex.org/W2129288227","https://openalex.org/W2138211150","https://openalex.org/W2144847592","https://openalex.org/W2147476214","https://openalex.org/W2156411023","https://openalex.org/W2157751858","https://openalex.org/W2166815431","https://openalex.org/W2338663666","https://openalex.org/W2340974016","https://openalex.org/W2346273585","https://openalex.org/W2477042637","https://openalex.org/W2482614962","https://openalex.org/W2514535054","https://openalex.org/W2592257068","https://openalex.org/W2606812723","https://openalex.org/W2612150380","https://openalex.org/W2734435792","https://openalex.org/W2747046901","https://openalex.org/W2754025713","https://openalex.org/W2762185802","https://openalex.org/W2890035501","https://openalex.org/W2922899473","https://openalex.org/W2949688529","https://openalex.org/W2952030916","https://openalex.org/W2956081200","https://openalex.org/W2970840218","https://openalex.org/W2980515223","https://openalex.org/W2994805414","https://openalex.org/W3075371075","https://openalex.org/W3102697518","https://openalex.org/W3103162178"],"related_works":["https://openalex.org/W3087547719","https://openalex.org/W2359210733","https://openalex.org/W2223496461","https://openalex.org/W2372203775","https://openalex.org/W2230825067","https://openalex.org/W4320709878","https://openalex.org/W1596598103","https://openalex.org/W4313342334","https://openalex.org/W2619166255","https://openalex.org/W2805859037"],"abstract_inverted_index":{"BACKGROUND:":[0],"Cancer":[1],"progression":[2,140],"reconstruction":[3,17,148],"is":[4,74,117],"an":[5],"important":[6],"development":[7],"stemming":[8],"from":[9,90,112],"the":[10,16,19,22,32,37,131,143],"phylogenetics":[11],"field.":[12],"In":[13],"this":[14,72],"context,":[15],"of":[18,67,106,133,145],"phylogeny":[20,89,147],"representing":[21],"evolutionary":[23],"history":[24],"presents":[25],"some":[26,64],"peculiar":[27],"aspects":[28],"that":[29,85],"depend":[30],"on":[31,149],"technology":[33],"used":[34],"to":[35,39,98,130,142],"obtain":[36],"data":[38,45],"analyze:":[40],"Single":[41,91,113,150],"Cell":[42,92,151],"DNA":[43],"Sequencing":[44,93],"have":[46],"great":[47],"specificity,":[48],"but":[49],"are":[50],"affected":[51],"by":[52,136],"moderate":[53],"false":[54],"negative":[55],"and":[56,120],"missing":[57],"value":[58],"rates.":[59],"Moreover,":[60],"there":[61],"has":[62],"been":[63],"recent":[65],"evidence":[66],"back":[68],"mutations":[69],"in":[70],"cancer:":[71],"phenomenon":[73],"currently":[75],"widely":[76],"ignored.":[77],"RESULTS:":[78],"We":[79],"present":[80],"a":[81,87,103,138],"new":[82,128,139],"tool,":[83],"gpps,":[84],"reconstructs":[86],"tumor":[88],"data,":[94],"allowing":[95],"each":[96],"mutation":[97],"be":[99],"lost":[100],"at":[101,122],"most":[102],"fixed":[104],"number":[105],"times.":[107],"The":[108],"General":[109],"Parsimony":[110],"Phylogeny":[111],"cell":[114],"(gpps)":[115],"tool":[116],"open":[118],"source":[119],"available":[121],"https://github.com/AlgoLab/gpps":[123],".":[124],"CONCLUSIONS:":[125],"gpps":[126],"provides":[127],"insights":[129],"analysis":[132],"intra-tumor":[134],"heterogeneity":[135],"proposing":[137],"model":[141],"field":[144],"cancer":[146],"data.":[152]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":8}],"updated_date":"2026-08-04T08:18:43.703281","created_date":"2025-10-10T00:00:00"}