{"id":"https://openalex.org/W2954055267","doi":"https://doi.org/10.1093/bioinformatics/btz367","title":"DIFFUSE: predicting isoform functions from sequences and expression profiles via deep learning","display_name":"DIFFUSE: predicting isoform functions from sequences and expression profiles via deep learning","publication_year":2019,"publication_date":"2019-05-09","ids":{"openalex":"https://openalex.org/W2954055267","doi":"https://doi.org/10.1093/bioinformatics/btz367","mag":"2954055267","pmid":"https://pubmed.ncbi.nlm.nih.gov/31510699"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz367","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz367","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/14/i284/28913629/btz367.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":null,"license_id":null,"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":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/35/14/i284/28913629/btz367.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100353484","display_name":"Hao Chen","orcid":"https://orcid.org/0000-0001-7436-5895"},"institutions":[{"id":"https://openalex.org/I103635307","display_name":"University of California, Riverside","ror":"https://ror.org/03nawhv43","country_code":"US","type":"education","lineage":["https://openalex.org/I103635307"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hao Chen","raw_affiliation_strings":["Department of Compute Science and Engineering, University of California, Riverside, CA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Compute Science and Engineering, University of California, Riverside, CA, USA","institution_ids":["https://openalex.org/I103635307"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056732178","display_name":"Dipan Shaw","orcid":"https://orcid.org/0000-0001-9556-0243"},"institutions":[{"id":"https://openalex.org/I103635307","display_name":"University of California, Riverside","ror":"https://ror.org/03nawhv43","country_code":"US","type":"education","lineage":["https://openalex.org/I103635307"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dipan Shaw","raw_affiliation_strings":["Department of Compute Science and Engineering, University of California, Riverside, CA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Compute Science and Engineering, University of California, Riverside, CA, USA","institution_ids":["https://openalex.org/I103635307"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009826239","display_name":"Jianyang Zeng","orcid":null},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jianyang Zeng","raw_affiliation_strings":["Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China"],"affiliations":[{"raw_affiliation_string":"Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076729236","display_name":"Dongbo Bu","orcid":"https://orcid.org/0000-0003-4119-4238"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210090176","display_name":"Institute of Computing Technology","ror":"https://ror.org/0090r4d87","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210090176"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Dongbo Bu","raw_affiliation_strings":["Key Lab of Intelligent Information Process, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China","University of Chinese Academy of Sciences, Beijing, China"],"affiliations":[{"raw_affiliation_string":"Key Lab of Intelligent Information Process, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China","institution_ids":["https://openalex.org/I4210090176","https://openalex.org/I19820366"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences, Beijing, China","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101911266","display_name":"Tao Jiang","orcid":"https://orcid.org/0000-0003-3833-4498"},"institutions":[{"id":"https://openalex.org/I103635307","display_name":"University of California, Riverside","ror":"https://ror.org/03nawhv43","country_code":"US","type":"education","lineage":["https://openalex.org/I103635307"]},{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN","US"],"is_corresponding":true,"raw_author_name":"Tao Jiang","raw_affiliation_strings":["Bioinformatics Division, BNRIST/Department of Computer Science and Technology, Tsinghua University, Beijing, China","Department of Compute Science and Engineering, University of California, Riverside, CA, USA"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Division, BNRIST/Department of Computer Science and Technology, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]},{"raw_affiliation_string":"Department of Compute Science and Engineering, University of California, Riverside, CA, USA","institution_ids":["https://openalex.org/I103635307"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5101911266"],"corresponding_institution_ids":["https://openalex.org/I103635307","https://openalex.org/I99065089"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.2331,"has_fulltext":false,"cited_by_count":45,"citation_normalized_percentile":{"value":0.88675009,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"35","issue":"14","first_page":"i284","last_page":"i294"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":0.9987999796867371,"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":0.9987999796867371,"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/T10222","display_name":"Genomics and Chromatin Dynamics","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"}}],"keywords":[{"id":"https://openalex.org/keywords/gene-isoform","display_name":"Gene isoform","score":0.6955838203430176},{"id":"https://openalex.org/keywords/focus","display_name":"Focus (optics)","score":0.5919326543807983},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.5764816403388977},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5520398020744324},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5424073934555054},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5300756692886353},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.49510255455970764},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.36188942193984985},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3127128481864929},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2087438702583313},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.14344996213912964},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.07753682136535645},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.06822428107261658}],"concepts":[{"id":"https://openalex.org/C53345823","wikidata":"https://www.wikidata.org/wiki/Q5531554","display_name":"Gene isoform","level":3,"score":0.6955838203430176},{"id":"https://openalex.org/C192209626","wikidata":"https://www.wikidata.org/wiki/Q190909","display_name":"Focus (optics)","level":2,"score":0.5919326543807983},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.5764816403388977},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5520398020744324},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5424073934555054},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5300756692886353},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.49510255455970764},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.36188942193984985},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3127128481864929},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2087438702583313},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.14344996213912964},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.07753682136535645},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.06822428107261658},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"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":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","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":false},{"descriptor_ui":"D017398","descriptor_name":"Alternative Splicing","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":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btz367","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz367","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/14/i284/28913629/btz367.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31510699","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31510699","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:ark:/13030/qt33n6m8xx","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:escholarship.org/ark:/13030/qt33n6m8xx","is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/33n6m8xx","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics (Oxford, England), vol 35, iss 14","raw_type":"article"},{"id":"pmh:oai:europepmc.org:5588732","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6612874","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/btz367","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz367","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/14/i284/28913629/btz367.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1117163193","display_name":null,"funder_award_id":"IIS-1646333","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3049739919","display_name":null,"funder_award_id":"2018YFC0910404 and 2018YFC0910405","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G58594601","display_name":null,"funder_award_id":"61772197, 31671369, 31770775, 61872216, 61472205 and 81630103","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2954055267.pdf","grobid_xml":"https://content.openalex.org/works/W2954055267.grobid-xml"},"referenced_works_count":57,"referenced_works":["https://openalex.org/W1527927437","https://openalex.org/W1784654175","https://openalex.org/W1964362163","https://openalex.org/W1966327575","https://openalex.org/W1970108358","https://openalex.org/W1988579430","https://openalex.org/W1996791859","https://openalex.org/W2005126631","https://openalex.org/W2027898937","https://openalex.org/W2037047673","https://openalex.org/W2041399050","https://openalex.org/W2042160423","https://openalex.org/W2095705004","https://openalex.org/W2097270746","https://openalex.org/W2100691482","https://openalex.org/W2101378463","https://openalex.org/W2108984616","https://openalex.org/W2109255472","https://openalex.org/W2116041602","https://openalex.org/W2124649441","https://openalex.org/W2129999749","https://openalex.org/W2133790733","https://openalex.org/W2138459937","https://openalex.org/W2143892152","https://openalex.org/W2152811165","https://openalex.org/W2153499010","https://openalex.org/W2153544371","https://openalex.org/W2155804510","https://openalex.org/W2158714788","https://openalex.org/W2159482845","https://openalex.org/W2161062388","https://openalex.org/W2161538187","https://openalex.org/W2223752691","https://openalex.org/W2280321189","https://openalex.org/W2280346092","https://openalex.org/W2402144811","https://openalex.org/W2472351724","https://openalex.org/W2516432504","https://openalex.org/W2615066396","https://openalex.org/W2743273864","https://openalex.org/W2744744159","https://openalex.org/W2809400819","https://openalex.org/W2904341255","https://openalex.org/W2914059076","https://openalex.org/W2949867299","https://openalex.org/W2950890882","https://openalex.org/W2953384591","https://openalex.org/W2963468488","https://openalex.org/W2998704965","https://openalex.org/W4206192903","https://openalex.org/W4285719527","https://openalex.org/W4294216483","https://openalex.org/W6674330103","https://openalex.org/W6680532216","https://openalex.org/W6694890867","https://openalex.org/W6713134421","https://openalex.org/W6752482755"],"related_works":["https://openalex.org/W1540936366","https://openalex.org/W2079625624","https://openalex.org/W2004254765","https://openalex.org/W2126407448","https://openalex.org/W2125691904","https://openalex.org/W200174347","https://openalex.org/W2048132363","https://openalex.org/W2953122964","https://openalex.org/W1971262350","https://openalex.org/W2507850257"],"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":3},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":14},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":2}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}
