{"id":"https://openalex.org/W4205773061","doi":"https://doi.org/10.1093/bioinformatics/btac020","title":"ProteinBERT: a universal deep-learning model of protein sequence and function","display_name":"ProteinBERT: a universal deep-learning model of protein sequence and function","publication_year":2022,"publication_date":"2022-01-08","ids":{"openalex":"https://openalex.org/W4205773061","doi":"https://doi.org/10.1093/bioinformatics/btac020","pmid":"https://pubmed.ncbi.nlm.nih.gov/35020807"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac020","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac020","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/8/2102/49009610/btac020.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","license_id":"https://openalex.org/licenses/cc-by","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/38/8/2102/49009610/btac020.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5058480616","display_name":"Nadav Brandes","orcid":"https://orcid.org/0000-0002-0510-2546"},"institutions":[{"id":"https://openalex.org/I197251160","display_name":"Hebrew University of Jerusalem","ror":"https://ror.org/03qxff017","country_code":"IL","type":"education","lineage":["https://openalex.org/I197251160"]}],"countries":["IL"],"is_corresponding":true,"raw_author_name":"Nadav Brandes","raw_affiliation_strings":["School of Computer Science and Engineering, The Hebrew University of Jerusalem , Jerusalem 9190401, Israel"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, The Hebrew University of Jerusalem , Jerusalem 9190401, Israel","institution_ids":["https://openalex.org/I197251160"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045008246","display_name":"Dan Ofer","orcid":"https://orcid.org/0000-0001-5136-8014"},"institutions":[{"id":"https://openalex.org/I197251160","display_name":"Hebrew University of Jerusalem","ror":"https://ror.org/03qxff017","country_code":"IL","type":"education","lineage":["https://openalex.org/I197251160"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Dan Ofer","raw_affiliation_strings":["Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel"],"affiliations":[{"raw_affiliation_string":"Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel","institution_ids":["https://openalex.org/I197251160"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015862526","display_name":"Yam Peleg","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yam Peleg","raw_affiliation_strings":["Deep Trading Ltd. , Haifa 3508401, Israel"],"affiliations":[{"raw_affiliation_string":"Deep Trading Ltd. , Haifa 3508401, Israel","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080111333","display_name":"Nadav Rappoport","orcid":"https://orcid.org/0000-0002-7218-2558"},"institutions":[{"id":"https://openalex.org/I124227911","display_name":"Ben-Gurion University of the Negev","ror":"https://ror.org/05tkyf982","country_code":"IL","type":"education","lineage":["https://openalex.org/I124227911"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Nadav Rappoport","raw_affiliation_strings":["Department of Software and Information Systems Engineering, Faculty of Engineering Sciences, Ben-Gurion University of the Negev , Beer Sheva 8410501, Israel"],"affiliations":[{"raw_affiliation_string":"Department of Software and Information Systems Engineering, Faculty of Engineering Sciences, Ben-Gurion University of the Negev , Beer Sheva 8410501, Israel","institution_ids":["https://openalex.org/I124227911"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5085924022","display_name":"Michal Linial","orcid":"https://orcid.org/0000-0002-9357-4526"},"institutions":[{"id":"https://openalex.org/I197251160","display_name":"Hebrew University of Jerusalem","ror":"https://ror.org/03qxff017","country_code":"IL","type":"education","lineage":["https://openalex.org/I197251160"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Michal Linial","raw_affiliation_strings":["Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel"],"affiliations":[{"raw_affiliation_string":"Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel","institution_ids":["https://openalex.org/I197251160"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5058480616"],"corresponding_institution_ids":["https://openalex.org/I197251160"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":73.3459,"has_fulltext":true,"cited_by_count":914,"citation_normalized_percentile":{"value":0.99976063,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"38","issue":"8","first_page":"2102","last_page":"2110"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9991000294685364,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9991000294685364,"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":0.998199999332428,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9977999925613403,"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/computer-science","display_name":"Computer science","score":0.8065807819366455},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.632149338722229},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.62718266248703},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.552136242389679},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.535293698310852},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.5283799171447754},{"id":"https://openalex.org/keywords/language-model","display_name":"Language model","score":0.505886971950531},{"id":"https://openalex.org/keywords/scheme","display_name":"Scheme (mathematics)","score":0.4881149232387543},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.46351706981658936},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.4075477719306946},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3917381167411804}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8065807819366455},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.632149338722229},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.62718266248703},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.552136242389679},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.535293698310852},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.5283799171447754},{"id":"https://openalex.org/C137293760","wikidata":"https://www.wikidata.org/wiki/Q3621696","display_name":"Language model","level":2,"score":0.505886971950531},{"id":"https://openalex.org/C77618280","wikidata":"https://www.wikidata.org/wiki/Q1155772","display_name":"Scheme (mathematics)","level":2,"score":0.4881149232387543},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.46351706981658936},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.4075477719306946},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3917381167411804},{"id":"https://openalex.org/C187736073","wikidata":"https://www.wikidata.org/wiki/Q2920921","display_name":"Management","level":1,"score":0.0},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","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":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btac020","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac020","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/8/2102/49009610/btac020.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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:35020807","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35020807","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:pubmedcentral.nih.gov:9386727","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9386727","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btac020","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac020","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/8/2102/49009610/btac020.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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Quality Education","id":"https://metadata.un.org/sdg/4","score":0.7799999713897705}],"awards":[{"id":"https://openalex.org/G1632440799","display_name":null,"funder_award_id":"2753/20","funder_id":"https://openalex.org/F4320322252","funder_display_name":"Israel Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320322252","display_name":"Israel Science Foundation","ror":"https://ror.org/04sazxf24"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4205773061.pdf","grobid_xml":"https://content.openalex.org/works/W4205773061.grobid-xml"},"referenced_works_count":32,"referenced_works":["https://openalex.org/W1971784866","https://openalex.org/W2043274355","https://openalex.org/W2055043387","https://openalex.org/W2076048958","https://openalex.org/W2097632784","https://openalex.org/W2103017472","https://openalex.org/W2113765418","https://openalex.org/W2135530477","https://openalex.org/W2147526198","https://openalex.org/W2158714788","https://openalex.org/W2165698076","https://openalex.org/W2252523470","https://openalex.org/W2379594833","https://openalex.org/W2472351724","https://openalex.org/W2527759989","https://openalex.org/W2735621019","https://openalex.org/W2912990441","https://openalex.org/W2951433247","https://openalex.org/W2971227267","https://openalex.org/W2980789587","https://openalex.org/W2984761660","https://openalex.org/W2989156240","https://openalex.org/W2995514860","https://openalex.org/W2997234557","https://openalex.org/W2999481648","https://openalex.org/W3144701084","https://openalex.org/W3146944767","https://openalex.org/W3177500196","https://openalex.org/W3198971594","https://openalex.org/W4212774754","https://openalex.org/W4285651992","https://openalex.org/W6763868836"],"related_works":["https://openalex.org/W2361861616","https://openalex.org/W2263699433","https://openalex.org/W2377979023","https://openalex.org/W2218034408","https://openalex.org/W2392921965","https://openalex.org/W2358755282","https://openalex.org/W1570025324","https://openalex.org/W2116902754","https://openalex.org/W2740145017","https://openalex.org/W2166185180"],"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":77},{"year":2025,"cited_by_count":376},{"year":2024,"cited_by_count":269},{"year":2023,"cited_by_count":157},{"year":2022,"cited_by_count":33},{"year":2021,"cited_by_count":2}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}