{"id":"https://openalex.org/W3176388985","doi":"https://doi.org/10.1093/bioinformatics/btab439","title":"Embeddings of genomic region sets capture rich biological associations in lower dimensions","display_name":"Embeddings of genomic region sets capture rich biological associations in lower dimensions","publication_year":2021,"publication_date":"2021-06-15","ids":{"openalex":"https://openalex.org/W3176388985","doi":"https://doi.org/10.1093/bioinformatics/btab439","mag":"3176388985","pmid":"https://pubmed.ncbi.nlm.nih.gov/34156475"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab439","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab439","pdf_url":null,"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":null,"license_id":null,"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":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8652032","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5070459760","display_name":"Erfaneh Gharavi","orcid":"https://orcid.org/0000-0003-4444-2751"},"institutions":[{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Erfaneh Gharavi","raw_affiliation_strings":["Center for Public Health Genomics, University of Virginia , Charlottesville, VA 22903, USA","School of Data Science, University of Virginia , Charlottesville, VA 22903, USA"],"affiliations":[{"raw_affiliation_string":"Center for Public Health Genomics, University of Virginia , Charlottesville, VA 22903, USA","institution_ids":["https://openalex.org/I51556381"]},{"raw_affiliation_string":"School of Data Science, University of Virginia , Charlottesville, VA 22903, USA","institution_ids":["https://openalex.org/I51556381"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076690302","display_name":"Aaron Gu","orcid":"https://orcid.org/0000-0002-4918-4010"},"institutions":[{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Aaron Gu","raw_affiliation_strings":["Center for Public Health Genomics, University of Virginia , Charlottesville, VA 22903, USA","Department of Computer Science, University of Virginia , Charlottesville, VA 22903, USA"],"affiliations":[{"raw_affiliation_string":"Center for Public Health Genomics, University of Virginia , Charlottesville, VA 22903, USA","institution_ids":["https://openalex.org/I51556381"]},{"raw_affiliation_string":"Department of Computer Science, University of Virginia , Charlottesville, VA 22903, USA","institution_ids":["https://openalex.org/I51556381"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028570408","display_name":"Guangtao Zheng","orcid":"https://orcid.org/0000-0002-1287-4931"},"institutions":[{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Guangtao Zheng","raw_affiliation_strings":["Department of Computer Science, University of Virginia , Charlottesville, VA 22903, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Virginia , Charlottesville, VA 22903, USA","institution_ids":["https://openalex.org/I51556381"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079643437","display_name":"Jason P. Smith","orcid":"https://orcid.org/0000-0002-2688-0988"},"institutions":[{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jason P Smith","raw_affiliation_strings":["Center for Public Health Genomics, University of Virginia , Charlottesville, VA 22903, USA","Department of Biochemistry and Molecular Genetics, University of Virginia , Charlottesville, VA 22903, USA"],"affiliations":[{"raw_affiliation_string":"Center for Public Health Genomics, University of Virginia , Charlottesville, VA 22903, USA","institution_ids":["https://openalex.org/I51556381"]},{"raw_affiliation_string":"Department of Biochemistry and Molecular Genetics, University of Virginia , Charlottesville, VA 22903, USA","institution_ids":["https://openalex.org/I51556381"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102838529","display_name":"Hyun Jae Cho","orcid":"https://orcid.org/0000-0002-9537-1781"},"institutions":[{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hyun Jae Cho","raw_affiliation_strings":["Center for Public Health Genomics, University of Virginia , Charlottesville, VA 22903, USA","Department of Computer Science, University of Virginia , Charlottesville, VA 22903, USA"],"affiliations":[{"raw_affiliation_string":"Center for Public Health Genomics, University of Virginia , Charlottesville, VA 22903, USA","institution_ids":["https://openalex.org/I51556381"]},{"raw_affiliation_string":"Department of Computer Science, University of Virginia , Charlottesville, VA 22903, USA","institution_ids":["https://openalex.org/I51556381"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013588572","display_name":"Aidong Zhang","orcid":"https://orcid.org/0000-0001-9723-3246"},"institutions":[{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Aidong Zhang","raw_affiliation_strings":["Department of Computer Science, University of Virginia , Charlottesville, VA 22903, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Virginia , Charlottesville, VA 22903, USA","institution_ids":["https://openalex.org/I51556381"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086462231","display_name":"Donald E. Brown","orcid":"https://orcid.org/0000-0002-9140-2632"},"institutions":[{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Donald E Brown","raw_affiliation_strings":["School of Data Science, University of Virginia , Charlottesville, VA 22903, USA"],"affiliations":[{"raw_affiliation_string":"School of Data Science, University of Virginia , Charlottesville, VA 22903, USA","institution_ids":["https://openalex.org/I51556381"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5055872618","display_name":"Nathan C. Sheffield","orcid":"https://orcid.org/0000-0001-5643-4068"},"institutions":[{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Nathan C Sheffield","raw_affiliation_strings":["Center for Public Health Genomics, University of Virginia , Charlottesville, VA 22903, USA","Department of Biochemistry and Molecular Genetics, University of Virginia , Charlottesville, VA 22903, USA","Department of Biomedical Engineering, University of Virginia , Charlottesville, VA 22903, USA","Department of Public Health Sciences, University of Virginia , Charlottesville, VA 22903, USA","School of Data Science, University of Virginia , Charlottesville, VA 22903, USA"],"affiliations":[{"raw_affiliation_string":"Center for Public Health Genomics, University of Virginia , Charlottesville, VA 22903, USA","institution_ids":["https://openalex.org/I51556381"]},{"raw_affiliation_string":"Department of Biochemistry and Molecular Genetics, University of Virginia , Charlottesville, VA 22903, USA","institution_ids":["https://openalex.org/I51556381"]},{"raw_affiliation_string":"Department of Biomedical Engineering, University of Virginia , Charlottesville, VA 22903, USA","institution_ids":["https://openalex.org/I51556381"]},{"raw_affiliation_string":"Department of Public Health Sciences, University of Virginia , Charlottesville, VA 22903, USA","institution_ids":["https://openalex.org/I51556381"]},{"raw_affiliation_string":"School of Data Science, University of Virginia , Charlottesville, VA 22903, USA","institution_ids":["https://openalex.org/I51556381"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5055872618"],"corresponding_institution_ids":["https://openalex.org/I51556381"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.2775,"has_fulltext":false,"cited_by_count":33,"citation_normalized_percentile":{"value":0.89205784,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"37","issue":"23","first_page":"4299","last_page":"4306"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","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/T10885","display_name":"Gene expression and cancer classification","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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9987000226974487,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9980000257492065,"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/computational-biology","display_name":"Computational biology","score":0.537641704082489},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4567696750164032},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.42212191224098206},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.40293025970458984}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.537641704082489},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4567696750164032},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.42212191224098206},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.40293025970458984}],"mesh":[{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btab439","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab439","pdf_url":null,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34156475","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34156475","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:8652032","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8652032","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:8652032","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8652032","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1291062413","display_name":null,"funder_award_id":"IIS-1955151","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G2292165592","display_name":null,"funder_award_id":"OAC-1934600","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3383124427","display_name":null,"funder_award_id":"GM128636","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7312491463","display_name":null,"funder_award_id":"UL1TR003015","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":32,"referenced_works":["https://openalex.org/W1978394996","https://openalex.org/W2032345031","https://openalex.org/W2092988184","https://openalex.org/W2115394533","https://openalex.org/W2117757143","https://openalex.org/W2128728535","https://openalex.org/W2163922914","https://openalex.org/W2184563578","https://openalex.org/W2259938310","https://openalex.org/W2514448720","https://openalex.org/W2724377567","https://openalex.org/W2727352277","https://openalex.org/W2739636023","https://openalex.org/W2789774764","https://openalex.org/W2791796577","https://openalex.org/W2884001105","https://openalex.org/W2889326414","https://openalex.org/W2890044969","https://openalex.org/W2900310474","https://openalex.org/W2902652978","https://openalex.org/W2923300855","https://openalex.org/W2942801317","https://openalex.org/W2943766116","https://openalex.org/W2949346354","https://openalex.org/W2950630354","https://openalex.org/W2952631022","https://openalex.org/W2979464975","https://openalex.org/W2989061519","https://openalex.org/W3013674494","https://openalex.org/W3013690547","https://openalex.org/W3034511617","https://openalex.org/W3042374971"],"related_works":["https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W4391375266","https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W2061542922"],"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":1},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":20},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":1}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
