{"id":"https://openalex.org/W2953163519","doi":"https://doi.org/10.1109/iccabs.2018.8542058","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":2018,"publication_date":"2018-10-01","ids":{"openalex":"https://openalex.org/W2953163519","doi":"https://doi.org/10.1109/iccabs.2018.8542058","mag":"2953163519"},"language":"en","primary_location":{"id":"doi:10.1109/iccabs.2018.8542058","is_oa":false,"landing_page_url":"https://doi.org/10.1109/iccabs.2018.8542058","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2018 IEEE 8th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/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 Computer Systems and Communication, University of Milano-Bicocca, Milan, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Computer 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 Computer Systems and Communication, University of Milano-Bicocca, Milan, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Computer 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/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":"Murray Patterson","raw_affiliation_strings":["Department of Computer Systems and Communication, University of Milano-Bicocca, Milan, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Computer Systems and Communication, University of Milano-Bicocca, Milan, Italy","institution_ids":["https://openalex.org/I66752286"]}]},{"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 Computer Systems and Communication, University of Milano-Bicocca, Milan, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Computer 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"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Iman Hajirasouliha","raw_affiliation_strings":["Institute for Computational Biomedicine, Weill Cornell, Medicine of Cornell University, NY, USA"],"affiliations":[{"raw_affiliation_string":"Institute for Computational Biomedicine, Weill Cornell, Medicine of Cornell University, NY, USA","institution_ids":["https://openalex.org/I205783295"]}]},{"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 Computer Systems and Communication, University of Milano-Bicocca, Milan, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Computer Systems and Communication, University of Milano-Bicocca, Milan, Italy","institution_ids":["https://openalex.org/I66752286"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5048411377"],"corresponding_institution_ids":["https://openalex.org/I66752286"],"apc_list":null,"apc_paid":null,"fwci":0.3173,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.54496751,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"1"},"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9980999827384949,"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/T11369","display_name":"Genetic factors in colorectal cancer","score":0.9850999712944031,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6553073525428772},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.5583834052085876},{"id":"https://openalex.org/keywords/cancer","display_name":"Cancer","score":0.4830682575702667},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3901243209838867},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.19407513737678528},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.18830430507659912},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1469341516494751}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6553073525428772},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.5583834052085876},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.4830682575702667},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3901243209838867},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.19407513737678528},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.18830430507659912},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1469341516494751}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/iccabs.2018.8542058","is_oa":false,"landing_page_url":"https://doi.org/10.1109/iccabs.2018.8542058","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2018 IEEE 8th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS)","raw_type":"proceedings-article"},{"id":"pmh:oai:boa.unimib.it:10281/218897","is_oa":false,"landing_page_url":"http://hdl.handle.net/10281/218897","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/conferenceObject"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.46000000834465027,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2350741829","https://openalex.org/W2530322880","https://openalex.org/W1596801655","https://openalex.org/W2359140296"],"abstract_inverted_index":{"Background":[0],"Cancer":[1],"progression":[2],"reconstruction":[3],"is":[4,16,60,65,96,101],"an":[5,74,115],"important":[6],"development":[7],"stemming":[8],"from":[9,45,133],"the":[10,14,19,55,86,143,176,203,241,245],"phylogenetics":[11],"field,":[12],"where":[13,48],"goal":[15],"to":[17,137,149,183,222],"infer":[18],"mutational":[20],"history":[21,44,64],"of":[22,25,54,85,88,157,179,202,233,244],"a":[23,43,51,57,63,79,93,105,124,130,138,154,224],"set":[24],"tumor":[26,131,185],"cells":[27],"carrying":[28],"these":[29,110],"cancerous":[30],"mutations.":[31,162],"Many":[32],"methods":[33],"have":[34,219],"been":[35,220],"developed":[36],"in":[37,62,91],"recent":[38],"years":[39],"for":[40,128],"inferring":[41],"such":[42],"bulk-sequencing":[46],"data,":[47],"they":[49],"construct":[50],"perfect":[52,106,144],"phylogeny":[53,132,186],"mutations:":[56],"mutation":[58,148,214],"which":[59,77,95,117,174,208],"gained":[61],"never":[66],"lost.":[67],"Single":[68],"Cell":[69],"Sequencing":[70],"(SCS)":[71],"technologies":[72],"are":[73],"emerging":[75],"alternative":[76],"offers":[78],"much":[80],"higher":[81],"resolution,":[82],"providing":[83],"evidence":[84],"existence":[87],"back":[89,161],"mutations":[90,236,243],"cancer:":[92],"phenomenon":[94],"currently":[97],"widely":[98],"ignored,":[99],"and":[100],"not":[102,210],"modeled":[103],"by":[104],"phylogeny.":[107],"Results":[108],"For":[109],"reasons":[111],"we":[112,190,218],"present":[113],"gpps,":[114],"approach":[116,127],"combines":[118],"Integer":[119],"Linear":[120],"Programming":[121],"(ILP)":[122],"with":[123],"Hill":[125],"Climbing":[126],"reconstructing":[129],"SCS":[134,180],"data":[135,168,173],"according":[136],"more":[139],"general":[140],"model":[141],"than":[142,200],"phylogeny:":[145],"allowing":[146],"each":[147],"be":[150],"lost":[151],"at":[152],"most":[153],"fixed":[155],"number":[156],"times,":[158],"thus":[159],"modeling":[160],"We":[163],"test":[164],"gpps":[165,193],"on":[166,206],"real":[167],"as":[169,171,195,197],"well":[170,196],"synthetic":[172],"simulates":[175],"error":[177],"rates":[178],"technologies,":[181],"comparing":[182],"state-of-the-art":[184],"inference":[187],"methods.":[188],"Here":[189],"reveal":[191],"that":[192],"performs":[194],"or":[198],"better":[199],"any":[201],"tools,":[204],"even":[205],"measures":[207],"do":[209],"take":[211],"into":[212],"account":[213],"losses.":[215],"Most":[216],"notably,":[217],"able":[221],"analyze":[223],"ER":[225],"<sup":[226],"xmlns:mml=\"http://www.w3.org/1998/Math/MathML\"":[227],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">+</sup>":[228],"breast":[229],"cancer":[230],"dataset":[231],"consisting":[232],"40":[234],"somatic":[235],"over":[237],"47":[238],"cells,":[239],"confirming":[240],"driver":[242],"original":[246],"study.":[247]},"counts_by_year":[{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
