{"id":"https://openalex.org/W4412888838","doi":"https://doi.org/10.18653/v1/2025.findings-acl.184","title":"Large Language Models in Bioinformatics: A Survey","display_name":"Large Language Models in Bioinformatics: A Survey","publication_year":2025,"publication_date":"2025-01-01","ids":{"openalex":"https://openalex.org/W4412888838","doi":"https://doi.org/10.18653/v1/2025.findings-acl.184"},"language":"en","primary_location":{"id":"doi:10.18653/v1/2025.findings-acl.184","is_oa":true,"landing_page_url":"https://doi.org/10.18653/v1/2025.findings-acl.184","pdf_url":"https://aclanthology.org/2025.findings-acl.184.pdf","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Findings of the Association for Computational Linguistics: ACL 2025","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://aclanthology.org/2025.findings-acl.184.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100344990","display_name":"Zhenyu Wang","orcid":"https://orcid.org/0000-0003-3433-5362"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Zhenyu Wang","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056285519","display_name":"Zikang Wang","orcid":"https://orcid.org/0000-0003-1406-1237"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Zikang Wang","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":null,"display_name":"Jiyue Jiang","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jiyue Jiang","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053263555","display_name":"Pengan Chen","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Pengan Chen","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101684411","display_name":"Xiangyu Shi","orcid":"https://orcid.org/0000-0002-1496-6194"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Xiangyu Shi","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5043237792","display_name":"Yu Li","orcid":"https://orcid.org/0000-0001-5788-8424"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yu Li","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":9,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"3602","last_page":"3615"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9138000011444092,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9138000011444092,"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":0.6614194512367249},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3701598048210144}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6614194512367249},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3701598048210144}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.18653/v1/2025.findings-acl.184","is_oa":true,"landing_page_url":"https://doi.org/10.18653/v1/2025.findings-acl.184","pdf_url":"https://aclanthology.org/2025.findings-acl.184.pdf","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Findings of the Association for Computational Linguistics: ACL 2025","raw_type":"proceedings-article"},{"id":"pmh:doi:10.48550/arxiv.2503.04490","is_oa":true,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4406922384","display_name":"Open MIND","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":"publisher-specific-oa","license_id":"https://openalex.org/licenses/publisher-specific-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Article"}],"best_oa_location":{"id":"doi:10.18653/v1/2025.findings-acl.184","is_oa":true,"landing_page_url":"https://doi.org/10.18653/v1/2025.findings-acl.184","pdf_url":"https://aclanthology.org/2025.findings-acl.184.pdf","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Findings of the Association for Computational Linguistics: ACL 2025","raw_type":"proceedings-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1495595508","display_name":null,"funder_award_id":"5501329","funder_id":"https://openalex.org/F4320322942","funder_display_name":"Chinese University of Hong Kong"},{"id":"https://openalex.org/G2978361218","display_name":null,"funder_award_id":"8601663","funder_id":"https://openalex.org/F4320322942","funder_display_name":"Chinese University of Hong Kong"},{"id":"https://openalex.org/G4809109598","display_name":null,"funder_award_id":"4937026","funder_id":"https://openalex.org/F4320322942","funder_display_name":"Chinese University of Hong Kong"},{"id":"https://openalex.org/G5248485515","display_name":null,"funder_award_id":"5501517","funder_id":"https://openalex.org/F4320322942","funder_display_name":"Chinese University of Hong Kong"},{"id":"https://openalex.org/G5808829462","display_name":"Deep Learning-Assisted RNA and Protein Structure Prediction, and High Protein Binding-Affinity RNA Design","funder_award_id":"GHP/065/21SZ","funder_id":"https://openalex.org/F4320321920","funder_display_name":"Innovation and Technology Commission"},{"id":"https://openalex.org/G6562111534","display_name":null,"funder_award_id":"8601603","funder_id":"https://openalex.org/F4320322942","funder_display_name":"Chinese University of Hong Kong"},{"id":"https://openalex.org/G6709416133","display_name":null,"funder_award_id":"4937025","funder_id":"https://openalex.org/F4320322942","funder_display_name":"Chinese University of Hong Kong"}],"funders":[{"id":"https://openalex.org/F4320321920","display_name":"Innovation and Technology Commission","ror":"https://ror.org/04vf9tr09"},{"id":"https://openalex.org/F4320322942","display_name":"Chinese University of Hong Kong","ror":"https://ror.org/00t33hh48"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4412888838.pdf","grobid_xml":"https://content.openalex.org/works/W4412888838.grobid-xml"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"Large":[0],"Language":[1],"Models":[2],"(LLMs)":[3],"are":[4],"revolutionizing":[5],"bioinformatics,":[6],"enabling":[7],"advanced":[8],"analysis":[9],"of":[10,22,77],"DNA,":[11],"RNA,":[12],"proteins,":[13],"and":[14,36,50,53,64,84],"single-cell":[15,37],"data.This":[16],"survey":[17],"provides":[18],"a":[19,68],"systematic":[20],"review":[21],"recent":[23],"advancements,":[24],"focusing":[25],"on":[26],"genomic":[27],"sequence":[28],"modeling,":[29],"RNA":[30],"structure":[31],"prediction,":[32],"protein":[33],"function":[34],"inference,":[35],"transcriptomics.Meanwhile,":[38],"we":[39],"also":[40],"discuss":[41],"several":[42],"key":[43],"challenges,":[44],"including":[45],"data":[46],"scarcity,":[47],"computational":[48],"complexity,":[49],"cross-omics":[51],"integration,":[52],"explore":[54],"future":[55],"directions":[56],"such":[57],"as":[58],"multimodal":[59],"learning,":[60],"hybrid":[61],"AI":[62],"models,":[63],"clinical":[65],"applications.By":[66],"offering":[67],"comprehensive":[69],"perspective,":[70],"this":[71],"paper":[72],"underscores":[73],"the":[74],"transformative":[75],"potential":[76],"LLMs":[78],"in":[79,82],"driving":[80],"innovations":[81],"bioinformatics":[83],"precision":[85],"medicine.":[86]},"counts_by_year":[{"year":2026,"cited_by_count":6},{"year":2025,"cited_by_count":3}],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}
