{"id":"https://openalex.org/W1505396042","doi":"https://doi.org/10.5220/0004799401420148","title":"A Novel Pipeline for Identification and Prioritization of Gene Fusions in Patient-derived Xenografts of Metastatic Colorectal Cancer","display_name":"A Novel Pipeline for Identification and Prioritization of Gene Fusions in Patient-derived Xenografts of Metastatic Colorectal Cancer","publication_year":2014,"publication_date":"2014-01-01","ids":{"openalex":"https://openalex.org/W1505396042","doi":"https://doi.org/10.5220/0004799401420148","mag":"1505396042"},"language":"en","primary_location":{"id":"doi:10.5220/0004799401420148","is_oa":true,"landing_page_url":"https://doi.org/10.5220/0004799401420148","pdf_url":null,"source":null,"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.5220/0004799401420148","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5075195788","display_name":"Giulia Paciello","orcid":null},"institutions":[{"id":"https://openalex.org/I177477856","display_name":"Polytechnic University of Turin","ror":"https://ror.org/00bgk9508","country_code":"IT","type":"education","lineage":["https://openalex.org/I177477856"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Paciello Giulia","raw_affiliation_strings":["Polit\u00e9cnico di Torino"],"affiliations":[{"raw_affiliation_string":"Polit\u00e9cnico di Torino","institution_ids":["https://openalex.org/I177477856"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031653904","display_name":"Andrea Acquaviva","orcid":"https://orcid.org/0000-0002-7323-759X"},"institutions":[{"id":"https://openalex.org/I177477856","display_name":"Polytechnic University of Turin","ror":"https://ror.org/00bgk9508","country_code":"IT","type":"education","lineage":["https://openalex.org/I177477856"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Andrea Acquaviva","raw_affiliation_strings":["Polit\u00e9cnico di Torino"],"affiliations":[{"raw_affiliation_string":"Polit\u00e9cnico di Torino","institution_ids":["https://openalex.org/I177477856"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056598174","display_name":"Consalvo Petti","orcid":"https://orcid.org/0000-0002-3509-3142"},"institutions":[{"id":"https://openalex.org/I4210151091","display_name":"Candiolo Cancer Institute","ror":"https://ror.org/04wadq306","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I4210151091","https://openalex.org/I4210153126","https://openalex.org/I4210167100"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Consalvo Petti","raw_affiliation_strings":["Istituto Oncologico Candiolo"],"affiliations":[{"raw_affiliation_string":"Istituto Oncologico Candiolo","institution_ids":["https://openalex.org/I4210151091"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080555744","display_name":"Claudio Isella","orcid":"https://orcid.org/0000-0003-0679-4756"},"institutions":[{"id":"https://openalex.org/I4210151091","display_name":"Candiolo Cancer Institute","ror":"https://ror.org/04wadq306","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I4210151091","https://openalex.org/I4210153126","https://openalex.org/I4210167100"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Claudio Isella","raw_affiliation_strings":["Istituto Oncologico Candiolo"],"affiliations":[{"raw_affiliation_string":"Istituto Oncologico Candiolo","institution_ids":["https://openalex.org/I4210151091"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056194390","display_name":"Enzo M\u00e9dico","orcid":"https://orcid.org/0000-0002-3917-2438"},"institutions":[{"id":"https://openalex.org/I4210151091","display_name":"Candiolo Cancer Institute","ror":"https://ror.org/04wadq306","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I4210151091","https://openalex.org/I4210153126","https://openalex.org/I4210167100"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Enzo Medico","raw_affiliation_strings":["Istituto Oncologico Candiolo"],"affiliations":[{"raw_affiliation_string":"Istituto Oncologico Candiolo","institution_ids":["https://openalex.org/I4210151091"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5068452817","display_name":"Elisa Ficarra","orcid":"https://orcid.org/0000-0002-8061-2124"},"institutions":[{"id":"https://openalex.org/I177477856","display_name":"Polytechnic University of Turin","ror":"https://ror.org/00bgk9508","country_code":"IT","type":"education","lineage":["https://openalex.org/I177477856"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Elisa Ficarra","raw_affiliation_strings":["Polit\u00e9cnico di Torino"],"affiliations":[{"raw_affiliation_string":"Polit\u00e9cnico di Torino","institution_ids":["https://openalex.org/I177477856"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5075195788"],"corresponding_institution_ids":["https://openalex.org/I177477856"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.0579198,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"142","last_page":"148"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12996","display_name":"Cancer Research and Treatments","score":0.9768999814987183,"subfield":{"id":"https://openalex.org/subfields/1305","display_name":"Biotechnology"},"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/T12996","display_name":"Cancer Research and Treatments","score":0.9768999814987183,"subfield":{"id":"https://openalex.org/subfields/1305","display_name":"Biotechnology"},"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/T10878","display_name":"CRISPR and Genetic Engineering","score":0.9757999777793884,"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/T10336","display_name":"Cancer Cells and Metastasis","score":0.9592000246047974,"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/fusion-gene","display_name":"Fusion gene","score":0.6058470606803894},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5842012166976929},{"id":"https://openalex.org/keywords/colorectal-cancer","display_name":"Colorectal cancer","score":0.5275466442108154},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5230361223220825},{"id":"https://openalex.org/keywords/cancer","display_name":"Cancer","score":0.5169103145599365},{"id":"https://openalex.org/keywords/prioritization","display_name":"Prioritization","score":0.5072423815727234},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.5057559013366699},{"id":"https://openalex.org/keywords/cancer-research","display_name":"Cancer research","score":0.4610667824745178},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.452247679233551},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.4483713209629059},{"id":"https://openalex.org/keywords/stroma","display_name":"Stroma","score":0.4281185269355774},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.42369669675827026},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3701484799385071},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.35889995098114014},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.3063730001449585},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.29573437571525574},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.26964646577835083},{"id":"https://openalex.org/keywords/internal-medicine","display_name":"Internal medicine","score":0.16025713086128235},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.13617467880249023},{"id":"https://openalex.org/keywords/immunohistochemistry","display_name":"Immunohistochemistry","score":0.07570689916610718}],"concepts":[{"id":"https://openalex.org/C111829193","wikidata":"https://www.wikidata.org/wiki/Q1108970","display_name":"Fusion gene","level":3,"score":0.6058470606803894},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5842012166976929},{"id":"https://openalex.org/C526805850","wikidata":"https://www.wikidata.org/wiki/Q188874","display_name":"Colorectal cancer","level":3,"score":0.5275466442108154},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5230361223220825},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.5169103145599365},{"id":"https://openalex.org/C2777615720","wikidata":"https://www.wikidata.org/wiki/Q11888847","display_name":"Prioritization","level":2,"score":0.5072423815727234},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.5057559013366699},{"id":"https://openalex.org/C502942594","wikidata":"https://www.wikidata.org/wiki/Q3421914","display_name":"Cancer research","level":1,"score":0.4610667824745178},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.452247679233551},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.4483713209629059},{"id":"https://openalex.org/C52124034","wikidata":"https://www.wikidata.org/wiki/Q557179","display_name":"Stroma","level":3,"score":0.4281185269355774},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.42369669675827026},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3701484799385071},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.35889995098114014},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.3063730001449585},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.29573437571525574},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.26964646577835083},{"id":"https://openalex.org/C126322002","wikidata":"https://www.wikidata.org/wiki/Q11180","display_name":"Internal medicine","level":1,"score":0.16025713086128235},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.13617467880249023},{"id":"https://openalex.org/C204232928","wikidata":"https://www.wikidata.org/wiki/Q899285","display_name":"Immunohistochemistry","level":2,"score":0.07570689916610718},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C539667460","wikidata":"https://www.wikidata.org/wiki/Q2414942","display_name":"Management science","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.5220/0004799401420148","is_oa":true,"landing_page_url":"https://doi.org/10.5220/0004799401420148","pdf_url":null,"source":null,"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms","raw_type":"proceedings-article"},{"id":"pmh:oai:iris.unimore.it:11380/1240331","is_oa":true,"landing_page_url":"http://hdl.handle.net/11380/1240331","pdf_url":null,"source":{"id":"https://openalex.org/S4306400718","display_name":"IRIS UNIMORE (University of Modena and Reggio Emilia)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I122346577","host_organization_name":"University of Modena and Reggio Emilia","host_organization_lineage":["https://openalex.org/I122346577"],"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/conferenceObject"}],"best_oa_location":{"id":"doi:10.5220/0004799401420148","is_oa":true,"landing_page_url":"https://doi.org/10.5220/0004799401420148","pdf_url":null,"source":null,"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms","raw_type":"proceedings-article"},"sustainable_development_goals":[{"score":0.5099999904632568,"id":"https://metadata.un.org/sdg/10","display_name":"Reduced inequalities"},{"score":0.47999998927116394,"id":"https://metadata.un.org/sdg/16","display_name":"Peace, Justice and strong institutions"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W4394932387","https://openalex.org/W2506292322","https://openalex.org/W1955580232","https://openalex.org/W4283209547","https://openalex.org/W2417404793","https://openalex.org/W2399513595","https://openalex.org/W2066577782","https://openalex.org/W2032477436","https://openalex.org/W2416582102","https://openalex.org/W3136137400"],"abstract_inverted_index":{"Metastatic":[0],"spread":[1],"to":[2,46,84,154],"the":[3,18,75,90,95,108,116,123,135,162,168,177,182],"liver":[4],"is":[5],"a":[6,70],"frequent":[7],"complication":[8],"of":[9,17,40,53,102,115,122,134,143,191],"colorectal":[10],"cancer":[11],"(CRC),":[12],"occurring":[13],"in":[14,60,100],"almost":[15],"half":[16],"cases,":[19],"for":[20,131],"which":[21],"personalized":[22],"treatment":[23],"strategies":[24],"are":[25],"highly":[26],"desirable.":[27],"To":[28,56],"this":[29],"aim,":[30],"it":[31],"has":[32],"been":[33],"proven":[34],"that":[35,73,93],"patient-derived":[36],"mouse":[37,91],"xenografts":[38],"(PDX)":[39],"liver-metastatic":[41],"CRC":[42],"can":[43],"be":[44],"used":[45],"discover":[47],"new":[48],"therapeutic":[49],"targets":[50],"and":[51,118,146],"determinants":[52],"drug":[54],"resistance.":[55],"identify":[57],"gene":[58],"fusions":[59],"RNA-Seq":[61,104],"data":[62,156],"obtained":[63],"from":[64,81,157],"such":[65],"PDX":[66,159],"samples,":[67],"we":[68],"propose":[69],"novel":[71],"pipeline":[72,184],"tackles":[74],"following":[76],"issues:":[77],"(i)":[78],"discriminating":[79],"human":[80],"murine":[82],"RNA,":[83],"filter":[85],"out":[86],"transcripts":[87,111],"contributed":[88],"by":[89,112,119,167],"stroma":[92],"supports":[94],"PDX;":[96],"(ii)":[97],"increasing":[98],"sensitivity":[99],"case":[101],"suboptimal":[103],"coverage;":[105],"(iii)":[106],"prioritizing":[107],"detected":[109],"chimeric":[110],"molecular":[113],"features":[114],"fusion":[117,164],"functional":[120],"relevance":[121],"involved":[124],"genes;":[125],"(iv)":[126],"providing":[127],"appropriate":[128],"sequence":[129],"information":[130],"subsequent":[132],"validation":[133],"identified":[136,166],"fusions.":[137,189],"The":[138],"pipeline,":[139],"built":[140],"on":[141],"top":[142],"Chimerascan(R.Iyer,":[144],"2011)":[145,148],"deFuse(McPherson,":[147],"aligner":[149],"tools,":[150],"was":[151],"successfully":[152],"applied":[153],"RNASeq":[155],"11":[158],"samples.":[160],"Among":[161],"299":[163],"genes":[165],"aforementioned":[169],"softwares,":[170],"five":[171],"were":[172,193],"selected":[173],"since":[174],"passed":[175],"all":[176],"filtering":[178],"stages":[179],"implemented":[180],"into":[181],"proposed":[183],"resulting":[185],"as":[186],"biologically":[187],"relevant":[188],"Three":[190],"them":[192],"experimentally":[194],"confirmed.":[195]},"counts_by_year":[],"updated_date":"2026-03-10T16:38:18.471706","created_date":"2016-06-24T00:00:00"}
