{"id":"https://openalex.org/W4416504075","doi":"https://doi.org/10.1093/bioinformatics/btaf631","title":"PLM-eXplain: divide and conquer the protein embedding space","display_name":"PLM-eXplain: divide and conquer the protein embedding space","publication_year":2025,"publication_date":"2025-11-21","ids":{"openalex":"https://openalex.org/W4416504075","doi":"https://doi.org/10.1093/bioinformatics/btaf631","pmid":"https://pubmed.ncbi.nlm.nih.gov/41269097"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf631","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf631","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf631/65450439/btaf631.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf631/65450439/btaf631.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5073681336","display_name":"Jan van Eck","orcid":"https://orcid.org/0009-0002-3877-2965"},"institutions":[{"id":"https://openalex.org/I173063890","display_name":"University of Applied Sciences Utrecht","ror":"https://ror.org/028z9kw20","country_code":"NL","type":"education","lineage":["https://openalex.org/I173063890"]},{"id":"https://openalex.org/I193662353","display_name":"Utrecht University","ror":"https://ror.org/04pp8hn57","country_code":"NL","type":"education","lineage":["https://openalex.org/I193662353"]}],"countries":["NL"],"is_corresponding":true,"raw_author_name":"Jan van Eck","raw_affiliation_strings":["AI Technology for Life, Department of Computing and Information Sciences, Department of Biology, Utrecht University , Utrecht, 3584CC,","AI Technology for Life, Department of Computing and Information Sciences, Department of Biology, Utrecht University, Utrecht, Netherlands"],"affiliations":[{"raw_affiliation_string":"AI Technology for Life, Department of Computing and Information Sciences, Department of Biology, Utrecht University , Utrecht, 3584CC,","institution_ids":["https://openalex.org/I193662353","https://openalex.org/I173063890"]},{"raw_affiliation_string":"AI Technology for Life, Department of Computing and Information Sciences, Department of Biology, Utrecht University, Utrecht, Netherlands","institution_ids":["https://openalex.org/I173063890","https://openalex.org/I193662353"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084663159","display_name":"Dea Gogishvili","orcid":"https://orcid.org/0000-0001-8809-0861"},"institutions":[{"id":"https://openalex.org/I173063890","display_name":"University of Applied Sciences Utrecht","ror":"https://ror.org/028z9kw20","country_code":"NL","type":"education","lineage":["https://openalex.org/I173063890"]},{"id":"https://openalex.org/I193662353","display_name":"Utrecht University","ror":"https://ror.org/04pp8hn57","country_code":"NL","type":"education","lineage":["https://openalex.org/I193662353"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Dea Gogishvili","raw_affiliation_strings":["AI Technology for Life, Department of Computing and Information Sciences, Department of Biology, Utrecht University , Utrecht, 3584CC,","AI Technology for Life, Department of Computing and Information Sciences, Department of Biology, Utrecht University, Utrecht, Netherlands"],"affiliations":[{"raw_affiliation_string":"AI Technology for Life, Department of Computing and Information Sciences, Department of Biology, Utrecht University , Utrecht, 3584CC,","institution_ids":["https://openalex.org/I193662353","https://openalex.org/I173063890"]},{"raw_affiliation_string":"AI Technology for Life, Department of Computing and Information Sciences, Department of Biology, Utrecht University, Utrecht, Netherlands","institution_ids":["https://openalex.org/I173063890","https://openalex.org/I193662353"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014798951","display_name":"Wilson Silva","orcid":"https://orcid.org/0000-0002-4080-9328"},"institutions":[{"id":"https://openalex.org/I173063890","display_name":"University of Applied Sciences Utrecht","ror":"https://ror.org/028z9kw20","country_code":"NL","type":"education","lineage":["https://openalex.org/I173063890"]},{"id":"https://openalex.org/I193662353","display_name":"Utrecht University","ror":"https://ror.org/04pp8hn57","country_code":"NL","type":"education","lineage":["https://openalex.org/I193662353"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Wilson Silva","raw_affiliation_strings":["AI Technology for Life, Department of Computing and Information Sciences, Department of Biology, Utrecht University , Utrecht, 3584CC,","AI Technology for Life, Department of Computing and Information Sciences, Department of Biology, Utrecht University, Utrecht, Netherlands"],"affiliations":[{"raw_affiliation_string":"AI Technology for Life, Department of Computing and Information Sciences, Department of Biology, Utrecht University , Utrecht, 3584CC,","institution_ids":["https://openalex.org/I193662353","https://openalex.org/I173063890"]},{"raw_affiliation_string":"AI Technology for Life, Department of Computing and Information Sciences, Department of Biology, Utrecht University, Utrecht, Netherlands","institution_ids":["https://openalex.org/I173063890","https://openalex.org/I193662353"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5014978488","display_name":"Sanne Abeln","orcid":"https://orcid.org/0000-0002-2779-7174"},"institutions":[{"id":"https://openalex.org/I173063890","display_name":"University of Applied Sciences Utrecht","ror":"https://ror.org/028z9kw20","country_code":"NL","type":"education","lineage":["https://openalex.org/I173063890"]},{"id":"https://openalex.org/I193662353","display_name":"Utrecht University","ror":"https://ror.org/04pp8hn57","country_code":"NL","type":"education","lineage":["https://openalex.org/I193662353"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Sanne Abeln","raw_affiliation_strings":["AI Technology for Life, Department of Computing and Information Sciences, Department of Biology, Utrecht University , Utrecht, 3584CC,","AI Technology for Life, Department of Computing and Information Sciences, Department of Biology, Utrecht University, Utrecht, Netherlands"],"affiliations":[{"raw_affiliation_string":"AI Technology for Life, Department of Computing and Information Sciences, Department of Biology, Utrecht University , Utrecht, 3584CC,","institution_ids":["https://openalex.org/I193662353","https://openalex.org/I173063890"]},{"raw_affiliation_string":"AI Technology for Life, Department of Computing and Information Sciences, Department of Biology, Utrecht University, Utrecht, Netherlands","institution_ids":["https://openalex.org/I173063890","https://openalex.org/I193662353"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5073681336"],"corresponding_institution_ids":["https://openalex.org/I173063890","https://openalex.org/I193662353"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.7371,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.77150494,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":98},"biblio":{"volume":"42","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.5016999840736389,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.5016999840736389,"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.04230000078678131,"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":0.027699999511241913,"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/divide-and-conquer-algorithms","display_name":"Divide and conquer algorithms","score":0.870199978351593},{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.6345999836921692},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.6241999864578247},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.6035000085830688},{"id":"https://openalex.org/keywords/space","display_name":"Space (punctuation)","score":0.5073000192642212},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4174000024795532}],"concepts":[{"id":"https://openalex.org/C71559656","wikidata":"https://www.wikidata.org/wiki/Q671298","display_name":"Divide and conquer algorithms","level":2,"score":0.870199978351593},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7434999942779541},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.6345999836921692},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.6241999864578247},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.6035000085830688},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.5591999888420105},{"id":"https://openalex.org/C2778572836","wikidata":"https://www.wikidata.org/wiki/Q380933","display_name":"Space (punctuation)","level":2,"score":0.5073000192642212},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4296000003814697},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4174000024795532},{"id":"https://openalex.org/C2988963302","wikidata":"https://www.wikidata.org/wiki/Q629206","display_name":"Program code","level":2,"score":0.2565000057220459},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.25619998574256897},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.25110000371932983},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.2506999969482422}],"mesh":[{"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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btaf631","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf631","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf631/65450439/btaf631.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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:41269097","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41269097","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:dspace.library.uu.nl:1874/463373","is_oa":true,"landing_page_url":"https://dspace.library.uu.nl/handle/1874/463373","pdf_url":null,"source":{"id":"https://openalex.org/S4306401649","display_name":"Utrecht University Repository (Utrecht University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I193662353","host_organization_name":"Utrecht University","host_organization_lineage":["https://openalex.org/I193662353"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"/dk/atira/pure/researchoutput/researchoutputtypes/workingpaper/preprint"},{"id":"pmh:oai:dspace.library.uu.nl:1874/480132","is_oa":true,"landing_page_url":"https://dspace.library.uu.nl/handle/1874/480132","pdf_url":null,"source":{"id":"https://openalex.org/S4306401649","display_name":"Utrecht University Repository (Utrecht University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I193662353","host_organization_name":"Utrecht University","host_organization_lineage":["https://openalex.org/I193662353"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12790820","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12790820/","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/btaf631","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf631","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf631/65450439/btaf631.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":[],"awards":[{"id":"https://openalex.org/G5616476150","display_name":null,"funder_award_id":"01ED2407A","funder_id":"https://openalex.org/F4320314158","funder_display_name":"EU Joint Programme \u2013 Neurodegenerative Disease Research"}],"funders":[{"id":"https://openalex.org/F4320314158","display_name":"EU Joint Programme \u2013 Neurodegenerative Disease Research","ror":null},{"id":"https://openalex.org/F4320321007","display_name":"ZonMw","ror":"https://ror.org/01yaj9a77"},{"id":"https://openalex.org/F4320326729","display_name":"Alzheimer Nederland","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4416504075.pdf","grobid_xml":"https://content.openalex.org/works/W4416504075.grobid-xml"},"referenced_works_count":35,"referenced_works":["https://openalex.org/W1975304761","https://openalex.org/W2068265376","https://openalex.org/W2114850508","https://openalex.org/W2159041173","https://openalex.org/W2170852633","https://openalex.org/W2614053601","https://openalex.org/W2786514708","https://openalex.org/W2897521776","https://openalex.org/W2913240367","https://openalex.org/W2933712037","https://openalex.org/W2943717199","https://openalex.org/W2972174635","https://openalex.org/W3022640420","https://openalex.org/W3038168026","https://openalex.org/W3166142427","https://openalex.org/W3177500196","https://openalex.org/W3177828909","https://openalex.org/W4212946592","https://openalex.org/W4223644783","https://openalex.org/W4225264859","https://openalex.org/W4281993476","https://openalex.org/W4311070988","https://openalex.org/W4317369987","https://openalex.org/W4327550249","https://openalex.org/W4362471278","https://openalex.org/W4366823175","https://openalex.org/W4385667255","https://openalex.org/W4388464011","https://openalex.org/W4391152432","https://openalex.org/W4392240076","https://openalex.org/W4395118066","https://openalex.org/W4403394716","https://openalex.org/W4406440058","https://openalex.org/W4409982859","https://openalex.org/W4414589084"],"related_works":[],"abstract_inverted_index":{"Source":[0],"code":[1],"and":[2],"models":[3],"are":[4],"available":[5],"at":[6],"https://github.com/AIT4LIFE-UU/PLM-eXplain/.":[7]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-04-17T18:11:37.981687","created_date":"2025-11-23T00:00:00"}
