{"id":"https://openalex.org/W2952713926","doi":"https://doi.org/10.1093/bioinformatics/bty244","title":"COSSMO: predicting competitive alternative splice site selection using deep learning","display_name":"COSSMO: predicting competitive alternative splice site selection using deep learning","publication_year":2018,"publication_date":"2018-04-16","ids":{"openalex":"https://openalex.org/W2952713926","doi":"https://doi.org/10.1093/bioinformatics/bty244","mag":"2952713926","pmid":"https://pubmed.ncbi.nlm.nih.gov/29949959"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty244","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty244","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/13/i429/25097973/bty244.pdf","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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/34/13/i429/25097973/bty244.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5034394920","display_name":"Hannes Bretschneider","orcid":"https://orcid.org/0000-0003-0109-3774"},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]},{"id":"https://openalex.org/I2802127592","display_name":"Ontario Genomics","ror":"https://ror.org/00c68jz96","country_code":"CA","type":"nonprofit","lineage":["https://openalex.org/I2802127592"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Hannes Bretschneider","raw_affiliation_strings":["Deep Genomics Inc, Toronto, Canada","Department of Computer Science, University of Toronto, Toronto, Canada"],"affiliations":[{"raw_affiliation_string":"Deep Genomics Inc, Toronto, Canada","institution_ids":["https://openalex.org/I2802127592"]},{"raw_affiliation_string":"Department of Computer Science, University of Toronto, Toronto, Canada","institution_ids":["https://openalex.org/I185261750"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037238850","display_name":"Shreshth Gandhi","orcid":"https://orcid.org/0009-0004-2625-4575"},"institutions":[{"id":"https://openalex.org/I2802127592","display_name":"Ontario Genomics","ror":"https://ror.org/00c68jz96","country_code":"CA","type":"nonprofit","lineage":["https://openalex.org/I2802127592"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Shreshth Gandhi","raw_affiliation_strings":["Deep Genomics Inc, Toronto, Canada"],"affiliations":[{"raw_affiliation_string":"Deep Genomics Inc, Toronto, Canada","institution_ids":["https://openalex.org/I2802127592"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051128953","display_name":"Amit G. Deshwar","orcid":"https://orcid.org/0000-0002-7031-5863"},"institutions":[{"id":"https://openalex.org/I2802127592","display_name":"Ontario Genomics","ror":"https://ror.org/00c68jz96","country_code":"CA","type":"nonprofit","lineage":["https://openalex.org/I2802127592"]},{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Amit G Deshwar","raw_affiliation_strings":["Deep Genomics Inc, Toronto, Canada","Edward S. Rogers Sr. Department of Electrical and Computer Engineering, University of Toronto, Toronto, Canada"],"affiliations":[{"raw_affiliation_string":"Deep Genomics Inc, Toronto, Canada","institution_ids":["https://openalex.org/I2802127592"]},{"raw_affiliation_string":"Edward S. Rogers Sr. Department of Electrical and Computer Engineering, University of Toronto, Toronto, Canada","institution_ids":["https://openalex.org/I185261750"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084666204","display_name":"Khalid Zuberi","orcid":null},"institutions":[{"id":"https://openalex.org/I2802127592","display_name":"Ontario Genomics","ror":"https://ror.org/00c68jz96","country_code":"CA","type":"nonprofit","lineage":["https://openalex.org/I2802127592"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Khalid Zuberi","raw_affiliation_strings":["Deep Genomics Inc, Toronto, Canada"],"affiliations":[{"raw_affiliation_string":"Deep Genomics Inc, Toronto, Canada","institution_ids":["https://openalex.org/I2802127592"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5003361977","display_name":"Brendan J. Frey","orcid":null},"institutions":[{"id":"https://openalex.org/I2802127592","display_name":"Ontario Genomics","ror":"https://ror.org/00c68jz96","country_code":"CA","type":"nonprofit","lineage":["https://openalex.org/I2802127592"]},{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Brendan J Frey","raw_affiliation_strings":["Deep Genomics Inc, Toronto, Canada","Department of Computer Science, University of Toronto, Toronto, Canada","Edward S. Rogers Sr. Department of Electrical and Computer Engineering, University of Toronto, Toronto, Canada"],"affiliations":[{"raw_affiliation_string":"Deep Genomics Inc, Toronto, Canada","institution_ids":["https://openalex.org/I2802127592"]},{"raw_affiliation_string":"Department of Computer Science, University of Toronto, Toronto, Canada","institution_ids":["https://openalex.org/I185261750"]},{"raw_affiliation_string":"Edward S. Rogers Sr. Department of Electrical and Computer Engineering, University of Toronto, Toronto, Canada","institution_ids":["https://openalex.org/I185261750"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5003361977"],"corresponding_institution_ids":["https://openalex.org/I185261750","https://openalex.org/I2802127592"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":2.7836,"has_fulltext":true,"cited_by_count":63,"citation_normalized_percentile":{"value":0.91654175,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"34","issue":"13","first_page":"i429","last_page":"i437"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":1.0,"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":1.0,"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/T11482","display_name":"RNA modifications and cancer","score":0.9998999834060669,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9998000264167786,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/splice","display_name":"splice","score":0.8126527070999146},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6658588647842407},{"id":"https://openalex.org/keywords/rna-splicing","display_name":"RNA splicing","score":0.6370594501495361},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5269915461540222},{"id":"https://openalex.org/keywords/alternative-splicing","display_name":"Alternative splicing","score":0.4630662798881531},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4629994034767151},{"id":"https://openalex.org/keywords/selection","display_name":"Selection (genetic algorithm)","score":0.4359779953956604},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4275255799293518},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3615608811378479},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2067175805568695},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.19082972407341003},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1883903443813324},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.1639193296432495}],"concepts":[{"id":"https://openalex.org/C2780989783","wikidata":"https://www.wikidata.org/wiki/Q7578557","display_name":"splice","level":3,"score":0.8126527070999146},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6658588647842407},{"id":"https://openalex.org/C54458228","wikidata":"https://www.wikidata.org/wiki/Q237218","display_name":"RNA splicing","level":4,"score":0.6370594501495361},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5269915461540222},{"id":"https://openalex.org/C194583182","wikidata":"https://www.wikidata.org/wiki/Q21114084","display_name":"Alternative splicing","level":4,"score":0.4630662798881531},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4629994034767151},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.4359779953956604},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4275255799293518},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3615608811378479},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2067175805568695},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.19082972407341003},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1883903443813324},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.1639193296432495},{"id":"https://openalex.org/C105580179","wikidata":"https://www.wikidata.org/wiki/Q188928","display_name":"Messenger RNA","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","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":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017398","descriptor_name":"Alternative Splicing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017398","descriptor_name":"Alternative Splicing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017398","descriptor_name":"Alternative Splicing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D022821","descriptor_name":"RNA Splice Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D022821","descriptor_name":"RNA Splice Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D022821","descriptor_name":"RNA Splice Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bty244","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty244","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/13/i429/25097973/bty244.pdf","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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:29949959","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29949959","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:europepmc.org:4991056","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6022534","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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty244","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty244","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/13/i429/25097973/bty244.pdf","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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2952713926.pdf","grobid_xml":"https://content.openalex.org/works/W2952713926.grobid-xml"},"referenced_works_count":28,"referenced_works":["https://openalex.org/W1019830208","https://openalex.org/W1966123525","https://openalex.org/W1968569455","https://openalex.org/W2018838463","https://openalex.org/W2034691490","https://openalex.org/W2064675550","https://openalex.org/W2066876408","https://openalex.org/W2069696438","https://openalex.org/W2088338354","https://openalex.org/W2092616354","https://openalex.org/W2095998476","https://openalex.org/W2096465161","https://openalex.org/W2102278945","https://openalex.org/W2103777723","https://openalex.org/W2105694586","https://openalex.org/W2115820057","https://openalex.org/W2121114391","https://openalex.org/W2139727828","https://openalex.org/W2144015117","https://openalex.org/W2150717117","https://openalex.org/W2197459998","https://openalex.org/W2336509392","https://openalex.org/W2337463877","https://openalex.org/W2559655401","https://openalex.org/W2613432108","https://openalex.org/W2952239877","https://openalex.org/W6681387118","https://openalex.org/W6682257986"],"related_works":["https://openalex.org/W2001319824","https://openalex.org/W2067501355","https://openalex.org/W2008389025","https://openalex.org/W2159668471","https://openalex.org/W1943031701","https://openalex.org/W2136950317","https://openalex.org/W2321791250","https://openalex.org/W4213427798","https://openalex.org/W2023199111","https://openalex.org/W2564462691"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":10},{"year":2024,"cited_by_count":12},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":11},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":11},{"year":2018,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
