{"id":"https://openalex.org/W2950890882","doi":"https://doi.org/10.1093/bioinformatics/btx247","title":"TITER: predicting translation initiation sites by deep learning","display_name":"TITER: predicting translation initiation sites by deep learning","publication_year":2017,"publication_date":"2017-04-24","ids":{"openalex":"https://openalex.org/W2950890882","doi":"https://doi.org/10.1093/bioinformatics/btx247","mag":"2950890882","pmid":"https://pubmed.ncbi.nlm.nih.gov/28881981"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btx247","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx247","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/14/i234/25157333/btx247.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/33/14/i234/25157333/btx247.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100369648","display_name":"Sai Zhang","orcid":"https://orcid.org/0000-0001-5996-6086"},"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":"Sai Zhang","raw_affiliation_strings":["Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China"],"raw_orcid":null,"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/A5046702976","display_name":"Hailin Hu","orcid":"https://orcid.org/0000-0002-5768-4437"},"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":"Hailin Hu","raw_affiliation_strings":["School of Medicine, Tsinghua University, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Medicine, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"middle","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":false,"raw_author_name":"Tao Jiang","raw_affiliation_strings":["Department of Computer Science and Engineering, University of California, Riverside, CA, USA","Institute of Integrative Genome Biology, University of California, Riverside, CA, USA","MOE Key Lab of Bioinformatics and Bioinformatics Division, TNLIST/Department of Computer Science and Technology, Tsinghua University, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, University of California, Riverside, CA, USA","institution_ids":["https://openalex.org/I103635307"]},{"raw_affiliation_string":"Institute of Integrative Genome Biology, University of California, Riverside, CA, USA","institution_ids":["https://openalex.org/I103635307"]},{"raw_affiliation_string":"MOE Key Lab of Bioinformatics and Bioinformatics Division, TNLIST/Department of Computer Science and Technology, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100434028","display_name":"Lei Zhang","orcid":"https://orcid.org/0000-0003-2343-084X"},"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":true,"raw_author_name":"Lei Zhang","raw_affiliation_strings":["School of Medicine, Tsinghua University, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Medicine, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5009826239","display_name":"Jianyang Zeng","orcid":"https://orcid.org/0000-0003-0950-7716"},"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":true,"raw_author_name":"Jianyang Zeng","raw_affiliation_strings":["Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5009826239","https://openalex.org/A5100434028"],"corresponding_institution_ids":["https://openalex.org/I99065089"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":3.6952,"has_fulltext":true,"cited_by_count":122,"citation_normalized_percentile":{"value":0.94184504,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"33","issue":"14","first_page":"i234","last_page":"i242"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9472000002861023,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9472000002861023,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.023800000548362732,"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":0.006099999882280827,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/open-reading-frame","display_name":"Open reading frame","score":0.5694367289543152},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.549706220626831},{"id":"https://openalex.org/keywords/translation","display_name":"Translation (biology)","score":0.5467104911804199},{"id":"https://openalex.org/keywords/titer","display_name":"Titer","score":0.5445459485054016},{"id":"https://openalex.org/keywords/start-codon","display_name":"Start codon","score":0.5024521350860596},{"id":"https://openalex.org/keywords/eukaryotic-translation","display_name":"Eukaryotic translation","score":0.4897637367248535},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.44645583629608154},{"id":"https://openalex.org/keywords/stop-codon","display_name":"Stop codon","score":0.444334477186203},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4363241493701935},{"id":"https://openalex.org/keywords/ribosome-profiling","display_name":"Ribosome profiling","score":0.43036922812461853},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.4134683609008789},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.38748639822006226},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3516612648963928},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3340255320072174},{"id":"https://openalex.org/keywords/messenger-rna","display_name":"Messenger RNA","score":0.24746403098106384},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.17082789540290833}],"concepts":[{"id":"https://openalex.org/C47289529","wikidata":"https://www.wikidata.org/wiki/Q908550","display_name":"Open reading frame","level":4,"score":0.5694367289543152},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.549706220626831},{"id":"https://openalex.org/C149364088","wikidata":"https://www.wikidata.org/wiki/Q185917","display_name":"Translation (biology)","level":4,"score":0.5467104911804199},{"id":"https://openalex.org/C32611913","wikidata":"https://www.wikidata.org/wiki/Q2166189","display_name":"Titer","level":3,"score":0.5445459485054016},{"id":"https://openalex.org/C176990463","wikidata":"https://www.wikidata.org/wiki/Q1854186","display_name":"Start codon","level":4,"score":0.5024521350860596},{"id":"https://openalex.org/C4718897","wikidata":"https://www.wikidata.org/wiki/Q5408698","display_name":"Eukaryotic translation","level":5,"score":0.4897637367248535},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.44645583629608154},{"id":"https://openalex.org/C20580545","wikidata":"https://www.wikidata.org/wiki/Q28354","display_name":"Stop codon","level":3,"score":0.444334477186203},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4363241493701935},{"id":"https://openalex.org/C182325514","wikidata":"https://www.wikidata.org/wiki/Q7322425","display_name":"Ribosome profiling","level":5,"score":0.43036922812461853},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.4134683609008789},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.38748639822006226},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3516612648963928},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3340255320072174},{"id":"https://openalex.org/C105580179","wikidata":"https://www.wikidata.org/wiki/Q188928","display_name":"Messenger RNA","level":3,"score":0.24746403098106384},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.17082789540290833},{"id":"https://openalex.org/C159654299","wikidata":"https://www.wikidata.org/wiki/Q79460","display_name":"Antibody","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","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":"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":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010442","descriptor_name":"Peptide Chain Initiation, Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010442","descriptor_name":"Peptide Chain Initiation, Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010442","descriptor_name":"Peptide Chain Initiation, Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010442","descriptor_name":"Peptide Chain Initiation, Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016366","descriptor_name":"Open Reading Frames","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016366","descriptor_name":"Open Reading Frames","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016366","descriptor_name":"Open Reading Frames","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016366","descriptor_name":"Open Reading Frames","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":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","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":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018387","descriptor_name":"Codon, Initiator","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018387","descriptor_name":"Codon, Initiator","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018387","descriptor_name":"Codon, Initiator","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018387","descriptor_name":"Codon, Initiator","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btx247","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx247","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/14/i234/25157333/btx247.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:28881981","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28881981","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:escholarship.org:ark:/13030/qt5qt468bt","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/5qt468bt","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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, vol 33, iss 14","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:5870772","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5870772","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btx247","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx247","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/14/i234/25157333/btx247.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":[{"display_name":"Quality Education","score":0.5799999833106995,"id":"https://metadata.un.org/sdg/4"}],"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/G3236980053","display_name":null,"funder_award_id":"DBI-1262107","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G325743107","display_name":null,"funder_award_id":"61033001","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G3444118898","display_name":"EAGER: Transcript-Based Differential Expression Analysis for Population Data Without Predefined Conditions","funder_award_id":"1646333","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4886626501","display_name":null,"funder_award_id":"2011CBA00301","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G680756813","display_name":null,"funder_award_id":"61033001","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7219872841","display_name":null,"funder_award_id":"61361136003","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7798674883","display_name":null,"funder_award_id":"61033001, 61361136003","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8514270459","display_name":null,"funder_award_id":"61361136003","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G8552498057","display_name":"Collaborative Research: ABI Innovation: Genome-Wide Inference of mRNA Isoforms and Abundance Estimation from Biased RNA-Seq Reads","funder_award_id":"1262107","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8623030917","display_name":null,"funder_award_id":"2011CBA00300","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G8755943873","display_name":null,"funder_award_id":"61472205","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},{"id":"https://openalex.org/F4320336066","display_name":"Beijing Advanced Innovation Center for Structural Biology, Tsinghua University","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2950890882.pdf","grobid_xml":"https://content.openalex.org/works/W2950890882.grobid-xml"},"referenced_works_count":56,"referenced_works":["https://openalex.org/W1019830208","https://openalex.org/W1498436455","https://openalex.org/W1668594850","https://openalex.org/W1806891645","https://openalex.org/W1944327053","https://openalex.org/W1951403192","https://openalex.org/W1966618675","https://openalex.org/W1989621875","https://openalex.org/W1997465134","https://openalex.org/W2007959190","https://openalex.org/W2008410413","https://openalex.org/W2013310179","https://openalex.org/W2024751967","https://openalex.org/W2031374133","https://openalex.org/W2037313242","https://openalex.org/W2068138304","https://openalex.org/W2076455712","https://openalex.org/W2079517684","https://openalex.org/W2086157203","https://openalex.org/W2095705004","https://openalex.org/W2100495367","https://openalex.org/W2101234009","https://openalex.org/W2104544277","https://openalex.org/W2106806242","https://openalex.org/W2114281975","https://openalex.org/W2118151336","https://openalex.org/W2122090912","https://openalex.org/W2127986230","https://openalex.org/W2136922672","https://openalex.org/W2137259955","https://openalex.org/W2141327598","https://openalex.org/W2145991872","https://openalex.org/W2151619201","https://openalex.org/W2152974197","https://openalex.org/W2154071538","https://openalex.org/W2158899491","https://openalex.org/W2160815625","https://openalex.org/W2170472690","https://openalex.org/W2198606573","https://openalex.org/W2262417550","https://openalex.org/W2336509392","https://openalex.org/W2398612826","https://openalex.org/W2427010553","https://openalex.org/W2464717012","https://openalex.org/W2537562414","https://openalex.org/W2554247923","https://openalex.org/W2596585349","https://openalex.org/W2604272474","https://openalex.org/W2739999456","https://openalex.org/W2951650375","https://openalex.org/W2952230511","https://openalex.org/W6640743173","https://openalex.org/W6674330103","https://openalex.org/W6675354045","https://openalex.org/W6677671969","https://openalex.org/W6683738474"],"related_works":["https://openalex.org/W2100776225","https://openalex.org/W2085053769","https://openalex.org/W2386425209","https://openalex.org/W2993421742","https://openalex.org/W1854619266","https://openalex.org/W2951934001","https://openalex.org/W2768144926","https://openalex.org/W2005952992","https://openalex.org/W2134864490","https://openalex.org/W2063906088"],"abstract_inverted_index":{"MOTIVATION:":[0],"Translation":[1],"initiation":[2,19,81,120,201,225],"is":[3,231],"a":[4,95,106,129,144,181],"key":[5],"step":[6],"in":[7,161,202],"the":[8,16,22,47,52,76,83,115,122,136,157,189,197,207,211,220],"regulation":[9],"of":[10,54,79,85,118,126,139,177,199,210],"gene":[11,217],"expression.":[12],"In":[13,164],"addition":[14],"to":[15,42,169,196],"annotated":[17],"translation":[18,23,80,119,200,224],"sites":[20],"(TISs),":[21],"process":[24],"may":[25],"also":[26],"start":[27,186],"at":[28,63,254],"multiple":[29],"alternative":[30],"TISs":[31,44,104,127],"(including":[32],"both":[33],"AUG":[34,185],"and":[35,45,68,82,133,219,237],"non-AUG":[36],"codons),":[37],"which":[38],"makes":[39],"it":[40],"challenging":[41],"predict":[43],"study":[46],"underlying":[48],"regulatory":[49],"mechanisms.":[50],"Meanwhile,":[51],"advent":[53],"several":[55],"high-throughput":[56],"sequencing":[57],"techniques":[58],"for":[59,73,88,101,174,184],"profiling":[60],"initiating":[61],"ribosomes":[62],"single-nucleotide":[64],"resolution,":[65],"e.g.":[66],"GTI-seq":[67],"QTI-seq,":[69],"provides":[70],"abundant":[71],"data":[72,251],"systematically":[74],"studying":[75],"general":[77],"principles":[78],"development":[84],"computational":[86],"method":[87],"TIS":[89,140,178],"identification.":[90],"METHODS:":[91],"We":[92],"have":[93],"developed":[94],"deep":[96],"learning-based":[97],"framework,":[98],"named":[99],"TITER,":[100],"accurately":[102],"predicting":[103],"on":[105,110,216],"genome-wide":[107],"scale":[108],"based":[109],"QTI-seq":[111],"data.":[112],"TITER":[113,153,166,190,230],"extracts":[114],"sequence":[116,124,172],"features":[117],"from":[121,241],"surrounding":[123],"contexts":[125],"using":[128],"hybrid":[130],"neural":[131],"network":[132],"further":[134],"integrates":[135],"prior":[137],"preference":[138],"codon":[141],"composition":[142],"into":[143],"unified":[145],"prediction":[146,159,191],"framework.":[147],"RESULTS:":[148],"Extensive":[149],"tests":[150],"demonstrated":[151],"that":[152],"can":[154,193,238],"greatly":[155],"outperform":[156],"state-of-the-art":[158],"methods":[160],"identifying":[162],"TISs.":[163],"addition,":[165],"was":[167],"able":[168],"identify":[170],"important":[171],"signatures":[173],"individual":[175],"types":[176],"codons,":[179],"including":[180,206],"Kozak-sequence-like":[182],"motif":[183],"codon.":[187],"Furthermore,":[188],"score":[192],"be":[194,239],"related":[195],"strength":[198],"various":[203],"biological":[204],"scenarios,":[205],"repressive":[208],"effect":[209],"upstream":[212],"open":[213],"reading":[214],"frames":[215],"expression":[218],"mutational":[221],"effects":[222],"influencing":[223],"efficiency.":[226],"AVAILABILITY":[227],"AND":[228],"IMPLEMENTATION:":[229],"available":[232,253],"as":[233],"an":[234],"open-source":[235],"software":[236],"downloaded":[240],"https://github.com/zhangsaithu/titer":[242],".":[243],"CONTACT:":[244],"lzhang20@mail.tsinghua.edu.cn":[245],"or":[246],"zengjy321@tsinghua.edu.cn.":[247],"SUPPLEMENTARY":[248],"INFORMATION:":[249],"Supplementary":[250],"are":[252],"Bioinformatics":[255],"online.":[256]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":18},{"year":2023,"cited_by_count":25},{"year":2022,"cited_by_count":18},{"year":2021,"cited_by_count":16},{"year":2020,"cited_by_count":11},{"year":2019,"cited_by_count":9},{"year":2018,"cited_by_count":9},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":1}],"updated_date":"2026-04-29T09:16:38.111599","created_date":"2025-10-10T00:00:00"}