Fast, sensitive detection of protein homologs using deep dense retrieval Article Swipe
Liang Hong
,
Zhigang Hu
,
Siqi Sun
,
Xiangru Tang
,
Jiuming Wang
,
Qingxiong Tan
,
Liangzhen Zheng
,
Sheng Wang
,
Sheng Xu
,
Irwin King
,
Mark Gerstein
,
Yu Li
·
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1038/s41587-024-02353-6
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1038/s41587-024-02353-6
The identification of protein homologs in large databases using conventional methods, such as protein sequence comparison, often misses remote homologs. Here, we offer an ultrafast, highly sensitive method, dense homolog retriever (DHR), for detecting homologs on the basis of a protein language model and dense retrieval techniques. Its dual-encoder architecture generates different embeddings for the same protein sequence and easily locates homologs by comparing these representations. Its alignment-free nature improves speed and the protein language model incorporates rich evolutionary and structural information within DHR embeddings. DHR achieves a >10% increase in sensitivity compared to previous methods and a >56% increase in sensitivity at the superfamily level for samples that are challenging to identify using alignment-based approaches. It is up to 22 times faster than traditional methods such as PSI-BLAST and DIAMOND and up to 28,700 times faster than HMMER. The new remote homologs exclusively found by DHR are useful for revealing connections between well-characterized proteins and improving our knowledge of protein evolution, structure and function.
Related Topics
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1038/s41587-024-02353-6
- OA Status
- hybrid
- Cited By
- 25
- References
- 59
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4401463754
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
-
https://openalex.org/W4401463754Canonical identifier for this work in OpenAlex
- DOI
-
https://doi.org/10.1038/s41587-024-02353-6Digital Object Identifier
- Title
-
Fast, sensitive detection of protein homologs using deep dense retrievalWork title
- Type
-
articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2024Year of publication
- Publication date
-
2024-08-09Full publication date if available
- Authors
-
Liang Hong, Zhigang Hu, Siqi Sun, Xiangru Tang, Jiuming Wang, Qingxiong Tan, Liangzhen Zheng, Sheng Wang, Sheng Xu, Irwin King, Mark Gerstein, Yu LiList of authors in order
- Landing page
-
https://doi.org/10.1038/s41587-024-02353-6Publisher landing page
- Open access
-
YesWhether a free full text is available
- OA status
-
hybridOpen access status per OpenAlex
- OA URL
-
https://doi.org/10.1038/s41587-024-02353-6Direct OA link when available
- Concepts
-
Homologous chromosome, Computational biology, Computer science, Biology, Genetics, GeneTop concepts (fields/topics) attached by OpenAlex
- Cited by
-
25Total citation count in OpenAlex
- Citations by year (recent)
-
2025: 24, 2024: 1Per-year citation counts (last 5 years)
- References (count)
-
59Number of works referenced by this work
- Related works (count)
-
10Other works algorithmically related by OpenAlex
Full payload
| id | https://openalex.org/W4401463754 |
|---|---|
| doi | https://doi.org/10.1038/s41587-024-02353-6 |
| ids.doi | https://doi.org/10.1038/s41587-024-02353-6 |
| ids.pmid | https://pubmed.ncbi.nlm.nih.gov/39123049 |
| ids.openalex | https://openalex.org/W4401463754 |
| fwci | 12.00618063 |
| mesh[0].qualifier_ui | Q000737 |
| mesh[0].descriptor_ui | D011506 |
| mesh[0].is_major_topic | True |
| mesh[0].qualifier_name | chemistry |
| mesh[0].descriptor_name | Proteins |
| mesh[1].qualifier_ui | Q000235 |
| mesh[1].descriptor_ui | D011506 |
| mesh[1].is_major_topic | True |
| mesh[1].qualifier_name | genetics |
| mesh[1].descriptor_name | Proteins |
| mesh[2].qualifier_ui | |
| mesh[2].descriptor_ui | D030562 |
| mesh[2].is_major_topic | False |
| mesh[2].qualifier_name | |
| mesh[2].descriptor_name | Databases, Protein |
| mesh[3].qualifier_ui | |
| mesh[3].descriptor_ui | D000465 |
| mesh[3].is_major_topic | False |
| mesh[3].qualifier_name | |
| mesh[3].descriptor_name | Algorithms |
| mesh[4].qualifier_ui | Q000379 |
| mesh[4].descriptor_ui | D016415 |
| mesh[4].is_major_topic | False |
| mesh[4].qualifier_name | methods |
| mesh[4].descriptor_name | Sequence Alignment |
| mesh[5].qualifier_ui | Q000379 |
| mesh[5].descriptor_ui | D020539 |
| mesh[5].is_major_topic | True |
| mesh[5].qualifier_name | methods |
| mesh[5].descriptor_name | Sequence Analysis, Protein |
| mesh[6].qualifier_ui | |
| mesh[6].descriptor_ui | D017386 |
| mesh[6].is_major_topic | True |
| mesh[6].qualifier_name | |
| mesh[6].descriptor_name | Sequence Homology, Amino Acid |
| mesh[7].qualifier_ui | Q000379 |
| mesh[7].descriptor_ui | D019295 |
| mesh[7].is_major_topic | True |
| mesh[7].qualifier_name | methods |
| mesh[7].descriptor_name | Computational Biology |
| mesh[8].qualifier_ui | Q000737 |
| mesh[8].descriptor_ui | D011506 |
| mesh[8].is_major_topic | True |
| mesh[8].qualifier_name | chemistry |
| mesh[8].descriptor_name | Proteins |
| mesh[9].qualifier_ui | Q000235 |
| mesh[9].descriptor_ui | D011506 |
| mesh[9].is_major_topic | True |
| mesh[9].qualifier_name | genetics |
| mesh[9].descriptor_name | Proteins |
| mesh[10].qualifier_ui | |
| mesh[10].descriptor_ui | D030562 |
| mesh[10].is_major_topic | False |
| mesh[10].qualifier_name | |
| mesh[10].descriptor_name | Databases, Protein |
| mesh[11].qualifier_ui | |
| mesh[11].descriptor_ui | D000465 |
| mesh[11].is_major_topic | False |
| mesh[11].qualifier_name | |
| mesh[11].descriptor_name | Algorithms |
| mesh[12].qualifier_ui | Q000379 |
| mesh[12].descriptor_ui | D016415 |
| mesh[12].is_major_topic | False |
| mesh[12].qualifier_name | methods |
| mesh[12].descriptor_name | Sequence Alignment |
| mesh[13].qualifier_ui | Q000379 |
| mesh[13].descriptor_ui | D020539 |
| mesh[13].is_major_topic | True |
| mesh[13].qualifier_name | methods |
| mesh[13].descriptor_name | Sequence Analysis, Protein |
| mesh[14].qualifier_ui | |
| mesh[14].descriptor_ui | D017386 |
| mesh[14].is_major_topic | True |
| mesh[14].qualifier_name | |
| mesh[14].descriptor_name | Sequence Homology, Amino Acid |
| mesh[15].qualifier_ui | Q000379 |
| mesh[15].descriptor_ui | D019295 |
| mesh[15].is_major_topic | True |
| mesh[15].qualifier_name | methods |
| mesh[15].descriptor_name | Computational Biology |
| mesh[16].qualifier_ui | Q000737 |
| mesh[16].descriptor_ui | D011506 |
| mesh[16].is_major_topic | True |
| mesh[16].qualifier_name | chemistry |
| mesh[16].descriptor_name | Proteins |
| mesh[17].qualifier_ui | Q000235 |
| mesh[17].descriptor_ui | D011506 |
| mesh[17].is_major_topic | True |
| mesh[17].qualifier_name | genetics |
| mesh[17].descriptor_name | Proteins |
| mesh[18].qualifier_ui | |
| mesh[18].descriptor_ui | D030562 |
| mesh[18].is_major_topic | False |
| mesh[18].qualifier_name | |
| mesh[18].descriptor_name | Databases, Protein |
| mesh[19].qualifier_ui | |
| mesh[19].descriptor_ui | D000465 |
| mesh[19].is_major_topic | False |
| mesh[19].qualifier_name | |
| mesh[19].descriptor_name | Algorithms |
| mesh[20].qualifier_ui | Q000379 |
| mesh[20].descriptor_ui | D016415 |
| mesh[20].is_major_topic | False |
| mesh[20].qualifier_name | methods |
| mesh[20].descriptor_name | Sequence Alignment |
| mesh[21].qualifier_ui | Q000379 |
| mesh[21].descriptor_ui | D020539 |
| mesh[21].is_major_topic | True |
| mesh[21].qualifier_name | methods |
| mesh[21].descriptor_name | Sequence Analysis, Protein |
| mesh[22].qualifier_ui | |
| mesh[22].descriptor_ui | D017386 |
| mesh[22].is_major_topic | True |
| mesh[22].qualifier_name | |
| mesh[22].descriptor_name | Sequence Homology, Amino Acid |
| mesh[23].qualifier_ui | Q000379 |
| mesh[23].descriptor_ui | D019295 |
| mesh[23].is_major_topic | True |
| mesh[23].qualifier_name | methods |
| mesh[23].descriptor_name | Computational Biology |
| type | article |
| title | Fast, sensitive detection of protein homologs using deep dense retrieval |
| awards[0].id | https://openalex.org/G2253502123 |
| awards[0].funder_id | https://openalex.org/F4320326427 |
| awards[0].display_name | |
| awards[0].funder_award_id | GHP/065/21SZ |
| awards[0].funder_display_name | Innovation and Technology Fund |
| awards[1].id | https://openalex.org/G6881691867 |
| awards[1].funder_id | https://openalex.org/F4320321592 |
| awards[1].display_name | |
| awards[1].funder_award_id | CUHK 24204023 |
| awards[1].funder_display_name | Research Grants Council, University Grants Committee |
| awards[2].id | https://openalex.org/G7525817988 |
| awards[2].funder_id | https://openalex.org/F4320321592 |
| awards[2].display_name | |
| awards[2].funder_award_id | PF22-73180 |
| awards[2].funder_display_name | Research Grants Council, University Grants Committee |
| biblio.issue | 6 |
| biblio.volume | 43 |
| biblio.last_page | 995 |
| biblio.first_page | 983 |
| topics[0].id | https://openalex.org/T12254 |
| topics[0].field.id | https://openalex.org/fields/13 |
| topics[0].field.display_name | Biochemistry, Genetics and Molecular Biology |
| topics[0].score | 0.9997000098228455 |
| topics[0].domain.id | https://openalex.org/domains/1 |
| topics[0].domain.display_name | Life Sciences |
| topics[0].subfield.id | https://openalex.org/subfields/1312 |
| topics[0].subfield.display_name | Molecular Biology |
| topics[0].display_name | Machine Learning in Bioinformatics |
| topics[1].id | https://openalex.org/T10044 |
| topics[1].field.id | https://openalex.org/fields/13 |
| topics[1].field.display_name | Biochemistry, Genetics and Molecular Biology |
| topics[1].score | 0.9977999925613403 |
| topics[1].domain.id | https://openalex.org/domains/1 |
| topics[1].domain.display_name | Life Sciences |
| topics[1].subfield.id | https://openalex.org/subfields/1312 |
| topics[1].subfield.display_name | Molecular Biology |
| topics[1].display_name | Protein Structure and Dynamics |
| topics[2].id | https://openalex.org/T10015 |
| topics[2].field.id | https://openalex.org/fields/13 |
| topics[2].field.display_name | Biochemistry, Genetics and Molecular Biology |
| topics[2].score | 0.9925000071525574 |
| topics[2].domain.id | https://openalex.org/domains/1 |
| topics[2].domain.display_name | Life Sciences |
| topics[2].subfield.id | https://openalex.org/subfields/1312 |
| topics[2].subfield.display_name | Molecular Biology |
| topics[2].display_name | Genomics and Phylogenetic Studies |
| funders[0].id | https://openalex.org/F4320321592 |
| funders[0].ror | https://ror.org/00djwmt25 |
| funders[0].display_name | Research Grants Council, University Grants Committee |
| funders[1].id | https://openalex.org/F4320326427 |
| funders[1].ror | |
| funders[1].display_name | Innovation and Technology Fund |
| is_xpac | False |
| apc_list.value | 9750 |
| apc_list.currency | EUR |
| apc_list.value_usd | 11690 |
| apc_paid.value | 9750 |
| apc_paid.currency | EUR |
| apc_paid.value_usd | 11690 |
| concepts[0].id | https://openalex.org/C64894306 |
| concepts[0].level | 3 |
| concepts[0].score | 0.4478304982185364 |
| concepts[0].wikidata | https://www.wikidata.org/wiki/Q849622 |
| concepts[0].display_name | Homologous chromosome |
| concepts[1].id | https://openalex.org/C70721500 |
| concepts[1].level | 1 |
| concepts[1].score | 0.4334469437599182 |
| concepts[1].wikidata | https://www.wikidata.org/wiki/Q177005 |
| concepts[1].display_name | Computational biology |
| concepts[2].id | https://openalex.org/C41008148 |
| concepts[2].level | 0 |
| concepts[2].score | 0.3600435256958008 |
| concepts[2].wikidata | https://www.wikidata.org/wiki/Q21198 |
| concepts[2].display_name | Computer science |
| concepts[3].id | https://openalex.org/C86803240 |
| concepts[3].level | 0 |
| concepts[3].score | 0.2970898449420929 |
| concepts[3].wikidata | https://www.wikidata.org/wiki/Q420 |
| concepts[3].display_name | Biology |
| concepts[4].id | https://openalex.org/C54355233 |
| concepts[4].level | 1 |
| concepts[4].score | 0.27348437905311584 |
| concepts[4].wikidata | https://www.wikidata.org/wiki/Q7162 |
| concepts[4].display_name | Genetics |
| concepts[5].id | https://openalex.org/C104317684 |
| concepts[5].level | 2 |
| concepts[5].score | 0.24562197923660278 |
| concepts[5].wikidata | https://www.wikidata.org/wiki/Q7187 |
| concepts[5].display_name | Gene |
| keywords[0].id | https://openalex.org/keywords/homologous-chromosome |
| keywords[0].score | 0.4478304982185364 |
| keywords[0].display_name | Homologous chromosome |
| keywords[1].id | https://openalex.org/keywords/computational-biology |
| keywords[1].score | 0.4334469437599182 |
| keywords[1].display_name | Computational biology |
| keywords[2].id | https://openalex.org/keywords/computer-science |
| keywords[2].score | 0.3600435256958008 |
| keywords[2].display_name | Computer science |
| keywords[3].id | https://openalex.org/keywords/biology |
| keywords[3].score | 0.2970898449420929 |
| keywords[3].display_name | Biology |
| keywords[4].id | https://openalex.org/keywords/genetics |
| keywords[4].score | 0.27348437905311584 |
| keywords[4].display_name | Genetics |
| keywords[5].id | https://openalex.org/keywords/gene |
| keywords[5].score | 0.24562197923660278 |
| keywords[5].display_name | Gene |
| language | en |
| locations[0].id | doi:10.1038/s41587-024-02353-6 |
| locations[0].is_oa | True |
| locations[0].source.id | https://openalex.org/S106963461 |
| locations[0].source.issn | 1087-0156, 1546-1696 |
| locations[0].source.type | journal |
| locations[0].source.is_oa | False |
| locations[0].source.issn_l | 1087-0156 |
| locations[0].source.is_core | True |
| locations[0].source.is_in_doaj | False |
| locations[0].source.display_name | Nature Biotechnology |
| locations[0].source.host_organization | https://openalex.org/P4310319908 |
| locations[0].source.host_organization_name | Nature Portfolio |
| locations[0].source.host_organization_lineage | https://openalex.org/P4310319908, https://openalex.org/P4310319965 |
| locations[0].source.host_organization_lineage_names | Nature Portfolio, Springer Nature |
| locations[0].license | cc-by-nc-nd |
| locations[0].pdf_url | |
| locations[0].version | publishedVersion |
| locations[0].raw_type | journal-article |
| locations[0].license_id | https://openalex.org/licenses/cc-by-nc-nd |
| locations[0].is_accepted | True |
| locations[0].is_published | True |
| locations[0].raw_source_name | Nature Biotechnology |
| locations[0].landing_page_url | https://doi.org/10.1038/s41587-024-02353-6 |
| locations[1].id | pmid:39123049 |
| locations[1].is_oa | False |
| locations[1].source.id | https://openalex.org/S4306525036 |
| locations[1].source.issn | |
| locations[1].source.type | repository |
| locations[1].source.is_oa | False |
| locations[1].source.issn_l | |
| locations[1].source.is_core | False |
| locations[1].source.is_in_doaj | False |
| locations[1].source.display_name | PubMed |
| locations[1].source.host_organization | https://openalex.org/I1299303238 |
| locations[1].source.host_organization_name | National Institutes of Health |
| locations[1].source.host_organization_lineage | https://openalex.org/I1299303238 |
| locations[1].license | |
| locations[1].pdf_url | |
| locations[1].version | publishedVersion |
| locations[1].raw_type | |
| locations[1].license_id | |
| locations[1].is_accepted | True |
| locations[1].is_published | True |
| locations[1].raw_source_name | Nature biotechnology |
| locations[1].landing_page_url | https://pubmed.ncbi.nlm.nih.gov/39123049 |
| locations[2].id | pmh:oai:pubmedcentral.nih.gov:12167706 |
| locations[2].is_oa | True |
| locations[2].source.id | https://openalex.org/S2764455111 |
| locations[2].source.issn | |
| locations[2].source.type | repository |
| locations[2].source.is_oa | False |
| locations[2].source.issn_l | |
| locations[2].source.is_core | False |
| locations[2].source.is_in_doaj | False |
| locations[2].source.display_name | PubMed Central |
| locations[2].source.host_organization | https://openalex.org/I1299303238 |
| locations[2].source.host_organization_name | National Institutes of Health |
| locations[2].source.host_organization_lineage | https://openalex.org/I1299303238 |
| locations[2].license | other-oa |
| locations[2].pdf_url | |
| locations[2].version | submittedVersion |
| locations[2].raw_type | Text |
| locations[2].license_id | https://openalex.org/licenses/other-oa |
| locations[2].is_accepted | False |
| locations[2].is_published | False |
| locations[2].raw_source_name | Nat Biotechnol |
| locations[2].landing_page_url | https://www.ncbi.nlm.nih.gov/pmc/articles/12167706 |
| indexed_in | crossref, pubmed |
| authorships[0].author.id | https://openalex.org/A5000680377 |
| authorships[0].author.orcid | https://orcid.org/0000-0003-0107-336X |
| authorships[0].author.display_name | Liang Hong |
| authorships[0].countries | HK |
| authorships[0].affiliations[0].institution_ids | https://openalex.org/I177725633 |
| authorships[0].affiliations[0].raw_affiliation_string | Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong SAR, China |
| authorships[0].institutions[0].id | https://openalex.org/I177725633 |
| authorships[0].institutions[0].ror | https://ror.org/00t33hh48 |
| authorships[0].institutions[0].type | education |
| authorships[0].institutions[0].lineage | https://openalex.org/I177725633 |
| authorships[0].institutions[0].country_code | HK |
| authorships[0].institutions[0].display_name | Chinese University of Hong Kong |
| authorships[0].author_position | first |
| authorships[0].raw_author_name | Liang Hong |
| authorships[0].is_corresponding | False |
| authorships[0].raw_affiliation_strings | Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong SAR, China |
| authorships[1].author.id | https://openalex.org/A5100640454 |
| authorships[1].author.orcid | https://orcid.org/0000-0002-4482-1535 |
| authorships[1].author.display_name | Zhigang Hu |
| authorships[1].countries | HK |
| authorships[1].affiliations[0].institution_ids | https://openalex.org/I177725633 |
| authorships[1].affiliations[0].raw_affiliation_string | Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong SAR, China |
| authorships[1].institutions[0].id | https://openalex.org/I177725633 |
| authorships[1].institutions[0].ror | https://ror.org/00t33hh48 |
| authorships[1].institutions[0].type | education |
| authorships[1].institutions[0].lineage | https://openalex.org/I177725633 |
| authorships[1].institutions[0].country_code | HK |
| authorships[1].institutions[0].display_name | Chinese University of Hong Kong |
| authorships[1].author_position | middle |
| authorships[1].raw_author_name | Zhihang Hu |
| authorships[1].is_corresponding | False |
| authorships[1].raw_affiliation_strings | Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong SAR, China |
| authorships[2].author.id | https://openalex.org/A5023777406 |
| authorships[2].author.orcid | https://orcid.org/0000-0001-7240-8724 |
| authorships[2].author.display_name | Siqi Sun |
| authorships[2].countries | CN |
| authorships[2].affiliations[0].institution_ids | https://openalex.org/I24943067 |
| authorships[2].affiliations[0].raw_affiliation_string | Research Institute of Intelligent Complex Systems, Fudan University, Shanghai, China |
| authorships[2].institutions[0].id | https://openalex.org/I24943067 |
| authorships[2].institutions[0].ror | https://ror.org/013q1eq08 |
| authorships[2].institutions[0].type | education |
| authorships[2].institutions[0].lineage | https://openalex.org/I24943067 |
| authorships[2].institutions[0].country_code | CN |
| authorships[2].institutions[0].display_name | Fudan University |
| authorships[2].author_position | middle |
| authorships[2].raw_author_name | Siqi Sun |
| authorships[2].is_corresponding | False |
| authorships[2].raw_affiliation_strings | Research Institute of Intelligent Complex Systems, Fudan University, Shanghai, China |
| authorships[3].author.id | https://openalex.org/A5108999586 |
| authorships[3].author.orcid | https://orcid.org/0009-0006-2700-4513 |
| authorships[3].author.display_name | Xiangru Tang |
| authorships[3].countries | US |
| authorships[3].affiliations[0].institution_ids | https://openalex.org/I32971472 |
| authorships[3].affiliations[0].raw_affiliation_string | Department of Computer Science, Yale University, New Haven, CT, USA |
| authorships[3].institutions[0].id | https://openalex.org/I32971472 |
| authorships[3].institutions[0].ror | https://ror.org/03v76x132 |
| authorships[3].institutions[0].type | education |
| authorships[3].institutions[0].lineage | https://openalex.org/I32971472 |
| authorships[3].institutions[0].country_code | US |
| authorships[3].institutions[0].display_name | Yale University |
| authorships[3].author_position | middle |
| authorships[3].raw_author_name | Xiangru Tang |
| authorships[3].is_corresponding | False |
| authorships[3].raw_affiliation_strings | Department of Computer Science, Yale University, New Haven, CT, USA |
| authorships[4].author.id | https://openalex.org/A5078001917 |
| authorships[4].author.orcid | https://orcid.org/0009-0003-9591-156X |
| authorships[4].author.display_name | Jiuming Wang |
| authorships[4].countries | HK |
| authorships[4].affiliations[0].institution_ids | https://openalex.org/I177725633 |
| authorships[4].affiliations[0].raw_affiliation_string | Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong SAR, China |
| authorships[4].institutions[0].id | https://openalex.org/I177725633 |
| authorships[4].institutions[0].ror | https://ror.org/00t33hh48 |
| authorships[4].institutions[0].type | education |
| authorships[4].institutions[0].lineage | https://openalex.org/I177725633 |
| authorships[4].institutions[0].country_code | HK |
| authorships[4].institutions[0].display_name | Chinese University of Hong Kong |
| authorships[4].author_position | middle |
| authorships[4].raw_author_name | Jiuming Wang |
| authorships[4].is_corresponding | False |
| authorships[4].raw_affiliation_strings | Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong SAR, China |
| authorships[5].author.id | https://openalex.org/A5101846980 |
| authorships[5].author.orcid | |
| authorships[5].author.display_name | Qingxiong Tan |
| authorships[5].countries | HK |
| authorships[5].affiliations[0].institution_ids | https://openalex.org/I177725633 |
| authorships[5].affiliations[0].raw_affiliation_string | Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong SAR, China |
| authorships[5].institutions[0].id | https://openalex.org/I177725633 |
| authorships[5].institutions[0].ror | https://ror.org/00t33hh48 |
| authorships[5].institutions[0].type | education |
| authorships[5].institutions[0].lineage | https://openalex.org/I177725633 |
| authorships[5].institutions[0].country_code | HK |
| authorships[5].institutions[0].display_name | Chinese University of Hong Kong |
| authorships[5].author_position | middle |
| authorships[5].raw_author_name | Qingxiong Tan |
| authorships[5].is_corresponding | False |
| authorships[5].raw_affiliation_strings | Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong SAR, China |
| authorships[6].author.id | https://openalex.org/A5029472602 |
| authorships[6].author.orcid | https://orcid.org/0000-0003-1179-2106 |
| authorships[6].author.display_name | Liangzhen Zheng |
| authorships[6].countries | CN |
| authorships[6].affiliations[0].institution_ids | https://openalex.org/I19820366, https://openalex.org/I4210145761 |
| authorships[6].affiliations[0].raw_affiliation_string | Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China |
| authorships[6].institutions[0].id | https://openalex.org/I19820366 |
| authorships[6].institutions[0].ror | https://ror.org/034t30j35 |
| authorships[6].institutions[0].type | government |
| authorships[6].institutions[0].lineage | https://openalex.org/I19820366 |
| authorships[6].institutions[0].country_code | CN |
| authorships[6].institutions[0].display_name | Chinese Academy of Sciences |
| authorships[6].institutions[1].id | https://openalex.org/I4210145761 |
| authorships[6].institutions[1].ror | https://ror.org/04gh4er46 |
| authorships[6].institutions[1].type | facility |
| authorships[6].institutions[1].lineage | https://openalex.org/I19820366, https://openalex.org/I4210145761 |
| authorships[6].institutions[1].country_code | CN |
| authorships[6].institutions[1].display_name | Shenzhen Institutes of Advanced Technology |
| authorships[6].author_position | middle |
| authorships[6].raw_author_name | Liangzhen Zheng |
| authorships[6].is_corresponding | False |
| authorships[6].raw_affiliation_strings | Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China |
| authorships[7].author.id | https://openalex.org/A5100371324 |
| authorships[7].author.orcid | https://orcid.org/0000-0003-4210-1670 |
| authorships[7].author.display_name | Sheng Wang |
| authorships[7].countries | CN |
| authorships[7].affiliations[0].institution_ids | https://openalex.org/I19820366, https://openalex.org/I4210145761 |
| authorships[7].affiliations[0].raw_affiliation_string | Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China |
| authorships[7].institutions[0].id | https://openalex.org/I19820366 |
| authorships[7].institutions[0].ror | https://ror.org/034t30j35 |
| authorships[7].institutions[0].type | government |
| authorships[7].institutions[0].lineage | https://openalex.org/I19820366 |
| authorships[7].institutions[0].country_code | CN |
| authorships[7].institutions[0].display_name | Chinese Academy of Sciences |
| authorships[7].institutions[1].id | https://openalex.org/I4210145761 |
| authorships[7].institutions[1].ror | https://ror.org/04gh4er46 |
| authorships[7].institutions[1].type | facility |
| authorships[7].institutions[1].lineage | https://openalex.org/I19820366, https://openalex.org/I4210145761 |
| authorships[7].institutions[1].country_code | CN |
| authorships[7].institutions[1].display_name | Shenzhen Institutes of Advanced Technology |
| authorships[7].author_position | middle |
| authorships[7].raw_author_name | Sheng Wang |
| authorships[7].is_corresponding | False |
| authorships[7].raw_affiliation_strings | Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China |
| authorships[8].author.id | https://openalex.org/A5100604665 |
| authorships[8].author.orcid | https://orcid.org/0000-0002-6507-9122 |
| authorships[8].author.display_name | Sheng Xu |
| authorships[8].countries | CN |
| authorships[8].affiliations[0].institution_ids | https://openalex.org/I24943067 |
| authorships[8].affiliations[0].raw_affiliation_string | Research Institute of Intelligent Complex Systems, Fudan University, Shanghai, China |
| authorships[8].institutions[0].id | https://openalex.org/I24943067 |
| authorships[8].institutions[0].ror | https://ror.org/013q1eq08 |
| authorships[8].institutions[0].type | education |
| authorships[8].institutions[0].lineage | https://openalex.org/I24943067 |
| authorships[8].institutions[0].country_code | CN |
| authorships[8].institutions[0].display_name | Fudan University |
| authorships[8].author_position | middle |
| authorships[8].raw_author_name | Sheng Xu |
| authorships[8].is_corresponding | False |
| authorships[8].raw_affiliation_strings | Research Institute of Intelligent Complex Systems, Fudan University, Shanghai, China |
| authorships[9].author.id | https://openalex.org/A5042251906 |
| authorships[9].author.orcid | https://orcid.org/0000-0001-8106-6447 |
| authorships[9].author.display_name | Irwin King |
| authorships[9].countries | HK |
| authorships[9].affiliations[0].institution_ids | https://openalex.org/I177725633 |
| authorships[9].affiliations[0].raw_affiliation_string | Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong SAR, China |
| authorships[9].institutions[0].id | https://openalex.org/I177725633 |
| authorships[9].institutions[0].ror | https://ror.org/00t33hh48 |
| authorships[9].institutions[0].type | education |
| authorships[9].institutions[0].lineage | https://openalex.org/I177725633 |
| authorships[9].institutions[0].country_code | HK |
| authorships[9].institutions[0].display_name | Chinese University of Hong Kong |
| authorships[9].author_position | middle |
| authorships[9].raw_author_name | Irwin King |
| authorships[9].is_corresponding | False |
| authorships[9].raw_affiliation_strings | Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong SAR, China |
| authorships[10].author.id | https://openalex.org/A5042321575 |
| authorships[10].author.orcid | https://orcid.org/0000-0002-9746-3719 |
| authorships[10].author.display_name | Mark Gerstein |
| authorships[10].countries | US |
| authorships[10].affiliations[0].institution_ids | https://openalex.org/I32971472 |
| authorships[10].affiliations[0].raw_affiliation_string | Department of Computer Science, Yale University, New Haven, CT, USA |
| authorships[10].institutions[0].id | https://openalex.org/I32971472 |
| authorships[10].institutions[0].ror | https://ror.org/03v76x132 |
| authorships[10].institutions[0].type | education |
| authorships[10].institutions[0].lineage | https://openalex.org/I32971472 |
| authorships[10].institutions[0].country_code | US |
| authorships[10].institutions[0].display_name | Yale University |
| authorships[10].author_position | middle |
| authorships[10].raw_author_name | Mark Gerstein |
| authorships[10].is_corresponding | False |
| authorships[10].raw_affiliation_strings | Department of Computer Science, Yale University, New Haven, CT, USA |
| authorships[11].author.id | https://openalex.org/A5100345753 |
| authorships[11].author.orcid | https://orcid.org/0000-0002-3664-6722 |
| authorships[11].author.display_name | Yu Li |
| authorships[11].affiliations[0].institution_ids | https://openalex.org/I4391012619 |
| authorships[11].affiliations[0].raw_affiliation_string | Shanghai AI Laboratory, Shanghai, China |
| authorships[11].institutions[0].id | https://openalex.org/I4391012619 |
| authorships[11].institutions[0].ror | https://ror.org/03wkvpx79 |
| authorships[11].institutions[0].type | facility |
| authorships[11].institutions[0].lineage | https://openalex.org/I4391012619 |
| authorships[11].institutions[0].country_code | |
| authorships[11].institutions[0].display_name | Shanghai Artificial Intelligence Laboratory |
| authorships[11].author_position | last |
| authorships[11].raw_author_name | Yu Li |
| authorships[11].is_corresponding | False |
| authorships[11].raw_affiliation_strings | Shanghai AI Laboratory, Shanghai, China |
| has_content.pdf | False |
| has_content.grobid_xml | False |
| is_paratext | False |
| open_access.is_oa | True |
| open_access.oa_url | https://doi.org/10.1038/s41587-024-02353-6 |
| open_access.oa_status | hybrid |
| open_access.any_repository_has_fulltext | False |
| created_date | 2025-10-10T00:00:00 |
| display_name | Fast, sensitive detection of protein homologs using deep dense retrieval |
| has_fulltext | False |
| is_retracted | False |
| updated_date | 2025-11-06T03:46:38.306776 |
| primary_topic.id | https://openalex.org/T12254 |
| primary_topic.field.id | https://openalex.org/fields/13 |
| primary_topic.field.display_name | Biochemistry, Genetics and Molecular Biology |
| primary_topic.score | 0.9997000098228455 |
| primary_topic.domain.id | https://openalex.org/domains/1 |
| primary_topic.domain.display_name | Life Sciences |
| primary_topic.subfield.id | https://openalex.org/subfields/1312 |
| primary_topic.subfield.display_name | Molecular Biology |
| primary_topic.display_name | Machine Learning in Bioinformatics |
| related_works | https://openalex.org/W4391375266, https://openalex.org/W2748952813, https://openalex.org/W2390279801, https://openalex.org/W2358668433, https://openalex.org/W4396701345, https://openalex.org/W2376932109, https://openalex.org/W2001405890, https://openalex.org/W4396696052, https://openalex.org/W2382290278, https://openalex.org/W4395014643 |
| cited_by_count | 25 |
| counts_by_year[0].year | 2025 |
| counts_by_year[0].cited_by_count | 24 |
| counts_by_year[1].year | 2024 |
| counts_by_year[1].cited_by_count | 1 |
| locations_count | 3 |
| best_oa_location.id | doi:10.1038/s41587-024-02353-6 |
| best_oa_location.is_oa | True |
| best_oa_location.source.id | https://openalex.org/S106963461 |
| best_oa_location.source.issn | 1087-0156, 1546-1696 |
| best_oa_location.source.type | journal |
| best_oa_location.source.is_oa | False |
| best_oa_location.source.issn_l | 1087-0156 |
| best_oa_location.source.is_core | True |
| best_oa_location.source.is_in_doaj | False |
| best_oa_location.source.display_name | Nature Biotechnology |
| best_oa_location.source.host_organization | https://openalex.org/P4310319908 |
| best_oa_location.source.host_organization_name | Nature Portfolio |
| best_oa_location.source.host_organization_lineage | https://openalex.org/P4310319908, https://openalex.org/P4310319965 |
| best_oa_location.source.host_organization_lineage_names | Nature Portfolio, Springer Nature |
| best_oa_location.license | cc-by-nc-nd |
| best_oa_location.pdf_url | |
| best_oa_location.version | publishedVersion |
| best_oa_location.raw_type | journal-article |
| best_oa_location.license_id | https://openalex.org/licenses/cc-by-nc-nd |
| best_oa_location.is_accepted | True |
| best_oa_location.is_published | True |
| best_oa_location.raw_source_name | Nature Biotechnology |
| best_oa_location.landing_page_url | https://doi.org/10.1038/s41587-024-02353-6 |
| primary_location.id | doi:10.1038/s41587-024-02353-6 |
| primary_location.is_oa | True |
| primary_location.source.id | https://openalex.org/S106963461 |
| primary_location.source.issn | 1087-0156, 1546-1696 |
| primary_location.source.type | journal |
| primary_location.source.is_oa | False |
| primary_location.source.issn_l | 1087-0156 |
| primary_location.source.is_core | True |
| primary_location.source.is_in_doaj | False |
| primary_location.source.display_name | Nature Biotechnology |
| primary_location.source.host_organization | https://openalex.org/P4310319908 |
| primary_location.source.host_organization_name | Nature Portfolio |
| primary_location.source.host_organization_lineage | https://openalex.org/P4310319908, https://openalex.org/P4310319965 |
| primary_location.source.host_organization_lineage_names | Nature Portfolio, Springer Nature |
| primary_location.license | cc-by-nc-nd |
| primary_location.pdf_url | |
| primary_location.version | publishedVersion |
| primary_location.raw_type | journal-article |
| primary_location.license_id | https://openalex.org/licenses/cc-by-nc-nd |
| primary_location.is_accepted | True |
| primary_location.is_published | True |
| primary_location.raw_source_name | Nature Biotechnology |
| primary_location.landing_page_url | https://doi.org/10.1038/s41587-024-02353-6 |
| publication_date | 2024-08-09 |
| publication_year | 2024 |
| referenced_works | https://openalex.org/W3177828909, https://openalex.org/W2922258649, https://openalex.org/W2085448729, https://openalex.org/W3049002444, https://openalex.org/W2068577315, https://openalex.org/W4252395482, https://openalex.org/W2043951056, https://openalex.org/W2158714788, https://openalex.org/W2170471837, https://openalex.org/W1987134040, https://openalex.org/W2950954328, https://openalex.org/W2138122982, https://openalex.org/W2133075481, https://openalex.org/W2766284073, https://openalex.org/W2077235131, https://openalex.org/W2258865027, https://openalex.org/W2103486885, https://openalex.org/W2156563976, https://openalex.org/W2112011435, https://openalex.org/W3111174583, https://openalex.org/W3146944767, https://openalex.org/W4327550249, https://openalex.org/W2980789587, https://openalex.org/W4213112325, https://openalex.org/W4282984452, https://openalex.org/W4386496033, https://openalex.org/W2142678478, https://openalex.org/W6791955017, https://openalex.org/W4286669150, https://openalex.org/W3136918052, https://openalex.org/W2949342052, https://openalex.org/W2953008890, https://openalex.org/W4300861364, https://openalex.org/W2559007573, https://openalex.org/W2902353954, https://openalex.org/W2021312899, https://openalex.org/W2045204781, https://openalex.org/W2069458148, https://openalex.org/W4375858802, https://openalex.org/W2051210555, https://openalex.org/W2161151688, https://openalex.org/W2115540209, https://openalex.org/W2097632784, https://openalex.org/W3199799076, https://openalex.org/W2008545402, https://openalex.org/W2140673705, https://openalex.org/W3156051371, https://openalex.org/W3127238141, https://openalex.org/W3207661553, https://openalex.org/W2969895640, https://openalex.org/W3099700870, https://openalex.org/W3038572442, https://openalex.org/W3027879771, https://openalex.org/W4206890427, https://openalex.org/W2995514860, https://openalex.org/W3106743555, https://openalex.org/W2998702515, https://openalex.org/W2102461176, https://openalex.org/W3098851962 |
| referenced_works_count | 59 |
| abstract_inverted_index.a | 39, 87, 97 |
| abstract_inverted_index.22 | 120 |
| abstract_inverted_index.It | 116 |
| abstract_inverted_index.an | 23 |
| abstract_inverted_index.as | 12, 127 |
| abstract_inverted_index.at | 102 |
| abstract_inverted_index.by | 62, 145 |
| abstract_inverted_index.in | 5, 90, 100 |
| abstract_inverted_index.is | 117 |
| abstract_inverted_index.of | 2, 38, 159 |
| abstract_inverted_index.on | 35 |
| abstract_inverted_index.to | 93, 111, 119, 133 |
| abstract_inverted_index.up | 118, 132 |
| abstract_inverted_index.we | 21 |
| abstract_inverted_index.DHR | 83, 85, 146 |
| abstract_inverted_index.Its | 47, 66 |
| abstract_inverted_index.The | 0, 139 |
| abstract_inverted_index.and | 43, 58, 71, 79, 96, 129, 131, 155, 163 |
| abstract_inverted_index.are | 109, 147 |
| abstract_inverted_index.for | 32, 53, 106, 149 |
| abstract_inverted_index.new | 140 |
| abstract_inverted_index.our | 157 |
| abstract_inverted_index.the | 36, 54, 72, 103 |
| abstract_inverted_index.>10% | 88 |
| abstract_inverted_index.>56% | 98 |
| abstract_inverted_index.rich | 77 |
| abstract_inverted_index.same | 55 |
| abstract_inverted_index.such | 11, 126 |
| abstract_inverted_index.than | 123, 137 |
| abstract_inverted_index.that | 108 |
| abstract_inverted_index.Here, | 20 |
| abstract_inverted_index.basis | 37 |
| abstract_inverted_index.dense | 28, 44 |
| abstract_inverted_index.found | 144 |
| abstract_inverted_index.large | 6 |
| abstract_inverted_index.level | 105 |
| abstract_inverted_index.model | 42, 75 |
| abstract_inverted_index.offer | 22 |
| abstract_inverted_index.often | 16 |
| abstract_inverted_index.speed | 70 |
| abstract_inverted_index.these | 64 |
| abstract_inverted_index.times | 121, 135 |
| abstract_inverted_index.using | 8, 113 |
| abstract_inverted_index.(DHR), | 31 |
| abstract_inverted_index.28,700 | 134 |
| abstract_inverted_index.HMMER. | 138 |
| abstract_inverted_index.easily | 59 |
| abstract_inverted_index.faster | 122, 136 |
| abstract_inverted_index.highly | 25 |
| abstract_inverted_index.misses | 17 |
| abstract_inverted_index.nature | 68 |
| abstract_inverted_index.remote | 18, 141 |
| abstract_inverted_index.useful | 148 |
| abstract_inverted_index.within | 82 |
| abstract_inverted_index.DIAMOND | 130 |
| abstract_inverted_index.between | 152 |
| abstract_inverted_index.homolog | 29 |
| abstract_inverted_index.locates | 60 |
| abstract_inverted_index.method, | 27 |
| abstract_inverted_index.methods | 95, 125 |
| abstract_inverted_index.protein | 3, 13, 40, 56, 73, 160 |
| abstract_inverted_index.samples | 107 |
| abstract_inverted_index.achieves | 86 |
| abstract_inverted_index.compared | 92 |
| abstract_inverted_index.homologs | 4, 34, 61, 142 |
| abstract_inverted_index.identify | 112 |
| abstract_inverted_index.improves | 69 |
| abstract_inverted_index.increase | 89, 99 |
| abstract_inverted_index.language | 41, 74 |
| abstract_inverted_index.methods, | 10 |
| abstract_inverted_index.previous | 94 |
| abstract_inverted_index.proteins | 154 |
| abstract_inverted_index.sequence | 14, 57 |
| abstract_inverted_index.PSI-BLAST | 128 |
| abstract_inverted_index.comparing | 63 |
| abstract_inverted_index.databases | 7 |
| abstract_inverted_index.detecting | 33 |
| abstract_inverted_index.different | 51 |
| abstract_inverted_index.function. | 164 |
| abstract_inverted_index.generates | 50 |
| abstract_inverted_index.homologs. | 19 |
| abstract_inverted_index.improving | 156 |
| abstract_inverted_index.knowledge | 158 |
| abstract_inverted_index.retrieval | 45 |
| abstract_inverted_index.retriever | 30 |
| abstract_inverted_index.revealing | 150 |
| abstract_inverted_index.sensitive | 26 |
| abstract_inverted_index.structure | 162 |
| abstract_inverted_index.embeddings | 52 |
| abstract_inverted_index.evolution, | 161 |
| abstract_inverted_index.structural | 80 |
| abstract_inverted_index.ultrafast, | 24 |
| abstract_inverted_index.approaches. | 115 |
| abstract_inverted_index.challenging | 110 |
| abstract_inverted_index.comparison, | 15 |
| abstract_inverted_index.connections | 151 |
| abstract_inverted_index.embeddings. | 84 |
| abstract_inverted_index.exclusively | 143 |
| abstract_inverted_index.information | 81 |
| abstract_inverted_index.sensitivity | 91, 101 |
| abstract_inverted_index.superfamily | 104 |
| abstract_inverted_index.techniques. | 46 |
| abstract_inverted_index.traditional | 124 |
| abstract_inverted_index.architecture | 49 |
| abstract_inverted_index.conventional | 9 |
| abstract_inverted_index.dual-encoder | 48 |
| abstract_inverted_index.evolutionary | 78 |
| abstract_inverted_index.incorporates | 76 |
| abstract_inverted_index.alignment-free | 67 |
| abstract_inverted_index.identification | 1 |
| abstract_inverted_index.alignment-based | 114 |
| abstract_inverted_index.representations. | 65 |
| abstract_inverted_index.well-characterized | 153 |
| cited_by_percentile_year.max | 100 |
| cited_by_percentile_year.min | 90 |
| countries_distinct_count | 3 |
| institutions_distinct_count | 12 |
| citation_normalized_percentile.value | 0.98264288 |
| citation_normalized_percentile.is_in_top_1_percent | True |
| citation_normalized_percentile.is_in_top_10_percent | True |