{"id":"https://openalex.org/W2768834792","doi":"https://doi.org/10.1142/9789813235533_0002","title":"Characterization of drug-induced splicing complexity in prostate cancer cell line using long read technology","display_name":"Characterization of drug-induced splicing complexity in prostate cancer cell line using long read technology","publication_year":2017,"publication_date":"2017-11-17","ids":{"openalex":"https://openalex.org/W2768834792","doi":"https://doi.org/10.1142/9789813235533_0002","mag":"2768834792","pmid":"https://pubmed.ncbi.nlm.nih.gov/29218865"},"language":"en","primary_location":{"id":"doi:10.1142/9789813235533_0002","doi":"https://doi.org/10.1142/9789813235533_0002","is_oa":true,"landing_page_url":"https://doi.org/10.1142/9789813235533_0002","pdf_url":null,"source":{"id":"https://openalex.org/S7407088813","display_name":"Pacific Symposium on Biocomputing (PSB)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Biocomputing 2018","raw_type":"proceedings-article"},"volume":null,"type":"conference-paper","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://doi.org/10.1142/9789813235533_0002","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100692845","display_name":"Xintong Chen","orcid":"https://orcid.org/0000-0002-2536-165X","observed_orcids":["https://orcid.org/0000-0002-2536-165X","https://orcid.org/0009-0007-0344-7237"]},"institutions":[{"id":"https://openalex.org/I98704320","display_name":"Icahn School of Medicine at Mount Sinai","ror":"https://ror.org/04a9tmd77","country_code":"US","type":"education","lineage":["https://openalex.org/I1320796813","https://openalex.org/I98704320"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xintong Chen","raw_affiliation_strings":["Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, New York, NY 10029, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, New York, NY 10029, USA","institution_ids":["https://openalex.org/I98704320"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027726446","display_name":"Sander M. Houten","orcid":"https://orcid.org/0000-0002-6167-9147","observed_orcids":["https://orcid.org/0000-0002-6167-9147"]},"institutions":[{"id":"https://openalex.org/I98704320","display_name":"Icahn School of Medicine at Mount Sinai","ror":"https://ror.org/04a9tmd77","country_code":"US","type":"education","lineage":["https://openalex.org/I1320796813","https://openalex.org/I98704320"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sander Houten","raw_affiliation_strings":["Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, New York, NY 10029, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, New York, NY 10029, USA","institution_ids":["https://openalex.org/I98704320"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017044767","display_name":"Kimaada Allette","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I98704320","display_name":"Icahn School of Medicine at Mount Sinai","ror":"https://ror.org/04a9tmd77","country_code":"US","type":"education","lineage":["https://openalex.org/I1320796813","https://openalex.org/I98704320"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kimaada Allette","raw_affiliation_strings":["Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, New York, NY 10029, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, New York, NY 10029, USA","institution_ids":["https://openalex.org/I98704320"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076788078","display_name":"Robert Sebra","orcid":"https://orcid.org/0000-0001-9267-2426","observed_orcids":["https://orcid.org/0000-0001-9267-2426"]},"institutions":[{"id":"https://openalex.org/I98704320","display_name":"Icahn School of Medicine at Mount Sinai","ror":"https://ror.org/04a9tmd77","country_code":"US","type":"education","lineage":["https://openalex.org/I1320796813","https://openalex.org/I98704320"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Robert P. Sebra","raw_affiliation_strings":["Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, New York, NY 10029, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, New York, NY 10029, USA","institution_ids":["https://openalex.org/I98704320"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000065699","display_name":"Gustavo A. Stolovitzky","orcid":"https://orcid.org/0000-0002-9618-2819","observed_orcids":["https://orcid.org/0000-0002-9618-2819"]},"institutions":[{"id":"https://openalex.org/I1341412227","display_name":"IBM (United States)","ror":"https://ror.org/05hh8d621","country_code":"US","type":"company","lineage":["https://openalex.org/I1341412227"]},{"id":"https://openalex.org/I4210114115","display_name":"IBM Research - Thomas J. Watson Research Center","ror":"https://ror.org/0265w5591","country_code":"US","type":"facility","lineage":["https://openalex.org/I1341412227","https://openalex.org/I4210114115"]},{"id":"https://openalex.org/I98704320","display_name":"Icahn School of Medicine at Mount Sinai","ror":"https://ror.org/04a9tmd77","country_code":"US","type":"education","lineage":["https://openalex.org/I1320796813","https://openalex.org/I98704320"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gustavo Stolovitzky","raw_affiliation_strings":["Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, New York, NY 10029, USA","IBM Translational Systems Biology and Nanobiotechnology Research, Yorktown Heights, NY 10598, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, New York, NY 10029, USA","institution_ids":["https://openalex.org/I98704320"]},{"raw_affiliation_string":"IBM Translational Systems Biology and Nanobiotechnology Research, Yorktown Heights, NY 10598, USA","institution_ids":["https://openalex.org/I1341412227","https://openalex.org/I4210114115"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5043236874","display_name":"Bojan Losic","orcid":"https://orcid.org/0000-0002-8282-7874","observed_orcids":["https://orcid.org/0000-0002-8282-7874"]},"institutions":[{"id":"https://openalex.org/I98704320","display_name":"Icahn School of Medicine at Mount Sinai","ror":"https://ror.org/04a9tmd77","country_code":"US","type":"education","lineage":["https://openalex.org/I1320796813","https://openalex.org/I98704320"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bojan Losic","raw_affiliation_strings":["Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, New York, NY 10029, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, New York, NY 10029, USA","institution_ids":["https://openalex.org/I98704320"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":2.0433,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.87327782,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":95},"biblio":{"volume":"23","issue":null,"first_page":"8","last_page":"19"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":0.9878000020980835,"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"}},"topics":[{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":0.9878000020980835,"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/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.006599999964237213,"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/T10543","display_name":"Prostate Cancer Treatment and Research","score":0.000699999975040555,"subfield":{"id":"https://openalex.org/subfields/2740","display_name":"Pulmonary and Respiratory Medicine"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/prostate-cancer","display_name":"prostate cancer","score":0.718999981880188},{"id":"https://openalex.org/keywords/alternative-splicing","display_name":"alternative splicing","score":0.8849999904632568},{"id":"https://openalex.org/keywords/long-read-rna-sequencing","display_name":"long-read RNA sequencing","score":0.8069999814033508},{"id":"https://openalex.org/keywords/transcript-isoforms","display_name":"mRNA isoforms","score":0.6499999761581421},{"id":"https://openalex.org/keywords/gene-fusion","display_name":"gene fusion","score":0.8240000009536743},{"id":"https://openalex.org/keywords/synergistic-drug-combination","display_name":"synergistic drug combination","score":0.8370000123977661},{"id":"https://openalex.org/keywords/novel-transcripts","display_name":"novel transcripts","score":0.4779999852180481},{"id":"https://openalex.org/keywords/cancer-cell-lines","display_name":"cancer cell lines","score":0.5759999752044678}],"concepts":[{"id":"https://openalex.org/C54458228","wikidata":"https://www.wikidata.org/wiki/Q237218","display_name":"RNA splicing","level":4,"score":0.901032567024231},{"id":"https://openalex.org/C194583182","wikidata":"https://www.wikidata.org/wiki/Q21114084","display_name":"Alternative splicing","level":4,"score":0.6527222990989685},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5798472762107849},{"id":"https://openalex.org/C36823959","wikidata":"https://www.wikidata.org/wiki/Q373027","display_name":"Exon","level":3,"score":0.5128453373908997},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4545894265174866},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.4242402911186218},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3257077932357788},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2719573378562927}],"mesh":[{"descriptor_ui":"D000971","descriptor_name":"Antineoplastic Combined Chemotherapy Protocols","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":"D008297","descriptor_name":"Male","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011471","descriptor_name":"Prostatic Neoplasms","qualifier_ui":"Q000188","qualifier_name":"drug therapy","is_major_topic":true},{"descriptor_ui":"D011471","descriptor_name":"Prostatic Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012326","descriptor_name":"RNA Splicing","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D012326","descriptor_name":"RNA Splicing","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012334","descriptor_name":"RNA, Neoplasm","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D013629","descriptor_name":"Tamoxifen","qualifier_ui":"Q000008","qualifier_name":"administration & dosage","is_major_topic":false},{"descriptor_ui":"D015767","descriptor_name":"Mefloquine","qualifier_ui":"Q000008","qualifier_name":"administration & dosage","is_major_topic":false},{"descriptor_ui":"D017398","descriptor_name":"Alternative Splicing","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":true},{"descriptor_ui":"D017398","descriptor_name":"Alternative Splicing","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D045744","descriptor_name":"Cell Line, Tumor","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D050939","descriptor_name":"Gene Fusion","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1142/9789813235533_0002","doi":"https://doi.org/10.1142/9789813235533_0002","is_oa":true,"landing_page_url":"https://doi.org/10.1142/9789813235533_0002","pdf_url":null,"source":{"id":"https://openalex.org/S7407088813","display_name":"Pacific Symposium on Biocomputing (PSB)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Biocomputing 2018","raw_type":"proceedings-article"},{"id":"pmid:29218865","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29218865","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,"listed_in":[],"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":"Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing","raw_type":"Journal Article"}],"best_oa_location":{"id":"doi:10.1142/9789813235533_0002","doi":"https://doi.org/10.1142/9789813235533_0002","is_oa":true,"landing_page_url":"https://doi.org/10.1142/9789813235533_0002","pdf_url":null,"source":{"id":"https://openalex.org/S7407088813","display_name":"Pacific Symposium on Biocomputing (PSB)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Biocomputing 2018","raw_type":"proceedings-article"},"sustainable_development_goals":[{"score":0.6240000128746033,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":28,"referenced_works":["https://openalex.org/W1944880632","https://openalex.org/W2023768482","https://openalex.org/W2036291018","https://openalex.org/W2042160423","https://openalex.org/W2048120844","https://openalex.org/W2051541780","https://openalex.org/W2054841963","https://openalex.org/W2064089886","https://openalex.org/W2064469303","https://openalex.org/W2073548049","https://openalex.org/W2080266689","https://openalex.org/W2090906911","https://openalex.org/W2096465161","https://openalex.org/W2101291993","https://openalex.org/W2102424043","https://openalex.org/W2103441770","https://openalex.org/W2106678197","https://openalex.org/W2109293112","https://openalex.org/W2121604817","https://openalex.org/W2123128942","https://openalex.org/W2137526110","https://openalex.org/W2165463056","https://openalex.org/W2169456326","https://openalex.org/W2169810552","https://openalex.org/W2177272234","https://openalex.org/W2337011385","https://openalex.org/W2521298622","https://openalex.org/W2557496587"],"related_works":["https://openalex.org/W4393090630","https://openalex.org/W2500579956","https://openalex.org/W7204690942","https://openalex.org/W4289638669","https://openalex.org/W2794114531","https://openalex.org/W2493935502","https://openalex.org/W4409627423","https://openalex.org/W7124249335","https://openalex.org/W4225716355","https://openalex.org/W4239998438"],"abstract_inverted_index":{"We":[0,20,51],"characterize":[1],"the":[2,62],"transcriptional":[3],"splicing":[4,46,58],"landscape":[5],"of":[6,24,39,64],"a":[7,14,22,36],"prostate":[8],"cancer":[9],"cell":[10],"line":[11],"treated":[12],"with":[13],"previously":[15,73],"identified":[16],"synergistic":[17],"drug":[18],"combination.":[19],"use":[21],"combination":[23],"third":[25],"generation":[26],"long-read":[27],"RNA":[28],"sequencing":[29],"technology":[30],"and":[31,42,67],"short-read":[32],"RNAseq":[33],"to":[34,44],"create":[35],"high-fidelity":[37],"map":[38],"expressed":[40],"isoforms":[41],"fusions":[43],"quantify":[45],"events":[47],"triggered":[48],"by":[49],"treatment.":[50],"find":[52],"strong":[53],"evidence":[54],"for":[55],"drug-induced,":[56],"coherent":[57],"changes":[59],"which":[60],"disrupt":[61],"function":[63],"oncogenic":[65],"proteins,":[66],"detect":[68],"novel":[69],"transcripts":[70],"arising":[71],"from":[72],"unreported":[74],"fusion":[75],"events.":[76]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2017,"cited_by_count":1}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2017-12-04T00:00:00"}