{"id":"https://openalex.org/W3137883089","doi":"https://doi.org/10.1371/journal.pcbi.1008842","title":"Full-length ribosome density prediction by a multi-input and multi-output model","display_name":"Full-length ribosome density prediction by a multi-input and multi-output model","publication_year":2021,"publication_date":"2021-03-26","ids":{"openalex":"https://openalex.org/W3137883089","doi":"https://doi.org/10.1371/journal.pcbi.1008842","mag":"3137883089","pmid":"https://pubmed.ncbi.nlm.nih.gov/33770074"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1008842","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1008842","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1008842&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1008842&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5045213879","display_name":"Tingzhong Tian","orcid":"https://orcid.org/0000-0003-4899-0632"},"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":"Tingzhong Tian","raw_affiliation_strings":["Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China"],"raw_orcid":"https://orcid.org/0000-0003-4899-0632","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/A5101531700","display_name":"Shuya Li","orcid":"https://orcid.org/0009-0003-2878-0926"},"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":"Shuya Li","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/A5006350534","display_name":"Lang Peng","orcid":"https://orcid.org/0000-0002-8289-0160"},"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":"Peng Lang","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/A5067578751","display_name":"Dan Zhao","orcid":"https://orcid.org/0000-0003-0195-6031"},"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":"Dan Zhao","raw_affiliation_strings":["Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China"],"raw_orcid":"https://orcid.org/0000-0003-0195-6031","affiliations":[{"raw_affiliation_string":"Institute for Interdisciplinary Information Sciences, 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","MOE Key Laboratory of Bioinformatics, 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"]},{"raw_affiliation_string":"MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5009826239","https://openalex.org/A5067578751"],"corresponding_institution_ids":["https://openalex.org/I99065089"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.6514,"has_fulltext":true,"cited_by_count":12,"citation_normalized_percentile":{"value":0.66190451,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"17","issue":"3","first_page":"e1008842","last_page":"e1008842"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","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/T10521","display_name":"RNA and protein synthesis mechanisms","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":0.9991999864578247,"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/T10604","display_name":"RNA Research and Splicing","score":0.9965999722480774,"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/ribosome-profiling","display_name":"Ribosome profiling","score":0.8245522975921631},{"id":"https://openalex.org/keywords/ribosome","display_name":"Ribosome","score":0.587681770324707},{"id":"https://openalex.org/keywords/translation","display_name":"Translation (biology)","score":0.5356893539428711},{"id":"https://openalex.org/keywords/coding-region","display_name":"Coding region","score":0.5118545889854431},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4842536151409149},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.46488142013549805},{"id":"https://openalex.org/keywords/messenger-rna","display_name":"Messenger RNA","score":0.32987266778945923},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.32724320888519287},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.32104140520095825},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2868853807449341},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1494523286819458},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.12812519073486328}],"concepts":[{"id":"https://openalex.org/C182325514","wikidata":"https://www.wikidata.org/wiki/Q7322425","display_name":"Ribosome profiling","level":5,"score":0.8245522975921631},{"id":"https://openalex.org/C88478588","wikidata":"https://www.wikidata.org/wiki/Q42244","display_name":"Ribosome","level":4,"score":0.587681770324707},{"id":"https://openalex.org/C149364088","wikidata":"https://www.wikidata.org/wiki/Q185917","display_name":"Translation (biology)","level":4,"score":0.5356893539428711},{"id":"https://openalex.org/C91779695","wikidata":"https://www.wikidata.org/wiki/Q3780824","display_name":"Coding region","level":3,"score":0.5118545889854431},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4842536151409149},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.46488142013549805},{"id":"https://openalex.org/C105580179","wikidata":"https://www.wikidata.org/wiki/Q188928","display_name":"Messenger RNA","level":3,"score":0.32987266778945923},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.32724320888519287},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.32104140520095825},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2868853807449341},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1494523286819458},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.12812519073486328}],"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":"D003062","descriptor_name":"Codon","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D003062","descriptor_name":"Codon","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D003062","descriptor_name":"Codon","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D003062","descriptor_name":"Codon","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D003062","descriptor_name":"Codon","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D003062","descriptor_name":"Codon","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010441","descriptor_name":"Peptide Chain Elongation, Translational","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010441","descriptor_name":"Peptide Chain Elongation, Translational","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010441","descriptor_name":"Peptide Chain Elongation, Translational","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012270","descriptor_name":"Ribosomes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012270","descriptor_name":"Ribosomes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012270","descriptor_name":"Ribosomes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012270","descriptor_name":"Ribosomes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D012270","descriptor_name":"Ribosomes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D012270","descriptor_name":"Ribosomes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","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}],"locations_count":4,"locations":[{"id":"doi:10.1371/journal.pcbi.1008842","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1008842","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1008842&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:33770074","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33770074","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:doaj.org/article:99c0101d8448448d9b9aa3d81c36629a","is_oa":true,"landing_page_url":"https://doaj.org/article/99c0101d8448448d9b9aa3d81c36629a","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 17, Iss 3, p e1008842 (2021)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8026034","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8026034","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1008842","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1008842","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1008842&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3927232695","display_name":"\u89e3\u6790\u57fa\u56e0\u7ec4\u4e09\u7ef4\u6298\u53e0\u7684\u8ba1\u7b97\u6a21\u578b\u7814\u7a76","funder_award_id":"61872216","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6429079033","display_name":"\u57fa\u4e8e\u751f\u7269\u7f51\u7edc\u7684\u75c5\u8bc1\u7ed3\u5408\u7814\u7a76\u65b9\u6cd5","funder_award_id":"81630103","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7314568505","display_name":null,"funder_award_id":"31900862","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3137883089.pdf","grobid_xml":"https://content.openalex.org/works/W3137883089.grobid-xml"},"referenced_works_count":63,"referenced_works":["https://openalex.org/W1491459594","https://openalex.org/W1879501137","https://openalex.org/W1924770834","https://openalex.org/W1956613997","https://openalex.org/W1974394989","https://openalex.org/W1975304761","https://openalex.org/W1981473906","https://openalex.org/W1999143685","https://openalex.org/W2018590530","https://openalex.org/W2025569664","https://openalex.org/W2047405192","https://openalex.org/W2058852389","https://openalex.org/W2060421156","https://openalex.org/W2063779182","https://openalex.org/W2065371606","https://openalex.org/W2068103032","https://openalex.org/W2071656832","https://openalex.org/W2075839343","https://openalex.org/W2079517684","https://openalex.org/W2086471971","https://openalex.org/W2086561953","https://openalex.org/W2092035637","https://openalex.org/W2098906326","https://openalex.org/W2100908594","https://openalex.org/W2110803333","https://openalex.org/W2112220686","https://openalex.org/W2116486533","https://openalex.org/W2147837708","https://openalex.org/W2161616648","https://openalex.org/W2167858459","https://openalex.org/W2168138973","https://openalex.org/W2169393322","https://openalex.org/W2170089172","https://openalex.org/W2170513170","https://openalex.org/W2170551349","https://openalex.org/W2233287223","https://openalex.org/W2306137721","https://openalex.org/W2434834409","https://openalex.org/W2466333954","https://openalex.org/W2482511961","https://openalex.org/W2520264800","https://openalex.org/W2529618169","https://openalex.org/W2562038667","https://openalex.org/W2607314890","https://openalex.org/W2619850245","https://openalex.org/W2747361679","https://openalex.org/W2757221062","https://openalex.org/W2761423809","https://openalex.org/W2762868004","https://openalex.org/W2768325741","https://openalex.org/W2769217290","https://openalex.org/W2784103660","https://openalex.org/W2914948079","https://openalex.org/W2962101943","https://openalex.org/W2964849163","https://openalex.org/W2970971581","https://openalex.org/W2999194912","https://openalex.org/W3015217127","https://openalex.org/W3105907097","https://openalex.org/W3149173706","https://openalex.org/W4212774754","https://openalex.org/W4241497765","https://openalex.org/W7073627059"],"related_works":["https://openalex.org/W2951085267","https://openalex.org/W2010594594","https://openalex.org/W2625763766","https://openalex.org/W3174925618","https://openalex.org/W2764188251","https://openalex.org/W1666668357","https://openalex.org/W2020663470","https://openalex.org/W2884058580","https://openalex.org/W2053920173","https://openalex.org/W93974876"],"abstract_inverted_index":{"Translation":[0],"elongation":[1,40,56,73,86,205,262,271,301],"is":[2],"regulated":[3],"by":[4],"a":[5,109,115,246,292],"series":[6],"of":[7,39,48,71,80,101,128,183,190,237,266,281,299,305],"complicated":[8],"mechanisms":[9,280],"in":[10,18,88,138,302],"both":[11],"prokaryotes":[12],"and":[13,75,117,143,146,164],"eukaryotes.":[14],"Although":[15],"recent":[16],"advance":[17],"ribosome":[19,29,58,78,125,168,192],"profiling":[20,59],"techniques":[21],"has":[22,94],"enabled":[23],"one":[24],"to":[25,98,187],"capture":[26],"the":[27,36,49,69,72,84,99,124,135,151,160,167,172,181,188,203,225,231,235,242,250,260,278,297,303],"genome-wide":[28],"footprints":[30],"along":[31,171],"transcripts":[32],"at":[33,245],"codon":[34,215],"resolution,":[35],"regulatory":[37,279],"codes":[38],"dynamics":[41],"are":[42],"still":[43],"not":[44,95,218],"fully":[45],"understood.":[46],"Most":[47],"existing":[50],"computational":[51],"approaches":[52,163],"for":[53,122,230,295],"modeling":[54,123],"translation":[55,85,139,204,261,270,300],"from":[57,150,249],"data":[60],"mainly":[61],"focus":[62],"on":[63,210,259,269,277],"local":[64],"contextual":[65],"patterns,":[66],"while":[67],"ignoring":[68],"continuity":[70],"process":[74,87],"relations":[76],"between":[77],"densities":[79],"remote":[81,144],"codons.":[82],"Modeling":[83],"full-length":[89,129,153,306],"coding":[90,154],"sequence":[91],"(CDS)":[92],"level":[93],"been":[96],"studied":[97],"best":[100,236],"our":[102,211,238],"knowledge.":[103],"In":[104,177],"this":[105],"paper,":[106],"we":[107],"developed":[108],"deep":[110],"learning":[111],"based":[112,209],"approach":[113],"with":[114,224],"multi-input":[116],"multi-output":[118],"framework,":[119],"named":[120,214],"RiboMIMO,":[121],"density":[126,169],"distributions":[127,170],"mRNA":[130,174],"CDS":[131,175],"regions.":[132,176],"Through":[133],"considering":[134],"underlying":[136],"correlations":[137],"efficiency":[140],"among":[141],"neighboring":[142],"codons":[145,186,243],"extracting":[147],"hidden":[148],"features":[149],"input":[152,185],"sequence,":[155],"RiboMIMO":[156,179,289],"can":[157,196,290],"greatly":[158],"outperform":[159],"state-of-the-art":[161],"baseline":[162],"accurately":[165],"predict":[166],"whole":[173],"addition,":[178],"explores":[180],"contributions":[182],"individual":[184],"predictions":[189],"output":[191],"densities,":[193],"which":[194],"thus":[195],"help":[197],"reveal":[198],"important":[199],"biological":[200],"factors":[201],"influencing":[202],"process.":[206],"The":[207],"analyses,":[208],"interpretable":[212],"metric":[213],"impact":[216,268],"score,":[217],"only":[219],"identified":[220],"several":[221],"patterns":[222],"consistent":[223],"previously-published":[226],"literatures,":[227],"but":[228],"also":[229,255],"first":[232],"time":[233],"(to":[234],"knowledge)":[239],"revealed":[240],"that":[241,288],"located":[244],"long":[247],"distance":[248],"ribosomal":[251],"A":[252],"site":[253],"may":[254,273],"have":[256],"an":[257],"association":[258],"rate.":[263],"This":[264],"finding":[265],"long-range":[267],"velocity":[272],"shed":[274],"new":[275],"light":[276],"protein":[282],"synthesis.":[283],"Overall,":[284],"these":[285],"results":[286],"indicated":[287],"provide":[291],"useful":[293],"tool":[294],"studying":[296],"regulation":[298],"range":[304],"CDS.":[307]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":5},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1}],"updated_date":"2026-06-06T09:05:17.133730","created_date":"2025-10-10T00:00:00"}