{"id":"https://openalex.org/W4417200322","doi":"https://doi.org/10.1145/3765612.3767789","title":"A novel approach to highly variable genes selection for scRNA-Seq analysis","display_name":"A novel approach to highly variable genes selection for scRNA-Seq analysis","publication_year":2025,"publication_date":"2025-10-12","ids":{"openalex":"https://openalex.org/W4417200322","doi":"https://doi.org/10.1145/3765612.3767789"},"language":"en","primary_location":{"id":"doi:10.1145/3765612.3767789","doi":"https://doi.org/10.1145/3765612.3767789","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3765612.3767789","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3765612.3767789","source":{"id":"https://openalex.org/S7407087958","display_name":"ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 16th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics","raw_type":"proceedings-article"},"volume":null,"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://dl.acm.org/doi/pdf/10.1145/3765612.3767789","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5120743255","display_name":"Enos Dk Kakwambi","orcid":"https://orcid.org/0009-0008-1404-5118","observed_orcids":["https://orcid.org/0009-0008-1404-5118"]},"institutions":[{"id":"https://openalex.org/I8692664","display_name":"University of Oklahoma","ror":"https://ror.org/02aqsxs83","country_code":"US","type":"education","lineage":["https://openalex.org/I8692664"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Enos Dk Kakwambi","raw_affiliation_strings":["University of Oklahoma, Norman, OK, USA"],"raw_orcid":"https://orcid.org/0009-0008-1404-5118","affiliations":[{"raw_affiliation_string":"University of Oklahoma, Norman, OK, USA","institution_ids":["https://openalex.org/I8692664"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Tuan Nguyen","orcid":"https://orcid.org/0009-0006-5196-635X","observed_orcids":["https://orcid.org/0009-0006-5196-635X"]},"institutions":[{"id":"https://openalex.org/I8692664","display_name":"University of Oklahoma","ror":"https://ror.org/02aqsxs83","country_code":"US","type":"education","lineage":["https://openalex.org/I8692664"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tuan Nguyen","raw_affiliation_strings":["University of Oklahoma, Norman, OK, USA"],"raw_orcid":"https://orcid.org/0009-0006-5196-635X","affiliations":[{"raw_affiliation_string":"University of Oklahoma, Norman, OK, USA","institution_ids":["https://openalex.org/I8692664"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5120743251","display_name":"Suryaveer Kapoor","orcid":"https://orcid.org/0009-0004-7995-6896","observed_orcids":["https://orcid.org/0009-0004-7995-6896"]},"institutions":[{"id":"https://openalex.org/I8692664","display_name":"University of Oklahoma","ror":"https://ror.org/02aqsxs83","country_code":"US","type":"education","lineage":["https://openalex.org/I8692664"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Suryaveer Kapoor","raw_affiliation_strings":["University of Oklahoma, Norman, OK, USA"],"raw_orcid":"https://orcid.org/0009-0004-7995-6896","affiliations":[{"raw_affiliation_string":"University of Oklahoma, Norman, OK, USA","institution_ids":["https://openalex.org/I8692664"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5018308989","display_name":"Marmar R. Moussa","orcid":"https://orcid.org/0000-0003-0574-6656","observed_orcids":["https://orcid.org/0000-0003-0574-6656"]},"institutions":[{"id":"https://openalex.org/I8692664","display_name":"University of Oklahoma","ror":"https://ror.org/02aqsxs83","country_code":"US","type":"education","lineage":["https://openalex.org/I8692664"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Marmar R. Moussa","raw_affiliation_strings":["University of Oklahoma, Norman, OK, USA"],"raw_orcid":"https://orcid.org/0000-0003-0574-6656","affiliations":[{"raw_affiliation_string":"University of Oklahoma, Norman, OK, USA","institution_ids":["https://openalex.org/I8692664"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I8692664"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.32991986,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"1"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9994999766349792,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9994999766349792,"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/T10885","display_name":"Gene expression and cancer classification","score":0.0003000000142492354,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.0,"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/highly-variable-genes","display_name":"highly variable genes","score":0.8970000147819519},{"id":"https://openalex.org/keywords/gene-selection","display_name":"gene selection","score":0.9419999718666077},{"id":"https://openalex.org/keywords/single-cell-rna-sequencing","display_name":"single-cell RNA sequencing","score":0.8669999837875366},{"id":"https://openalex.org/keywords/mean-variance-relationship","display_name":"mean-variance relationship","score":0.7739999890327454},{"id":"https://openalex.org/keywords/dispersion","display_name":"dispersion","score":0.4090000092983246},{"id":"https://openalex.org/keywords/dimensionality-reduction","display_name":"dimensionality reduction","score":0.8539999723434448},{"id":"https://openalex.org/keywords/cell-clustering","display_name":"cell clustering","score":0.492000013589859}],"concepts":[{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.6010000109672546},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.5942000150680542},{"id":"https://openalex.org/C148483581","wikidata":"https://www.wikidata.org/wiki/Q446488","display_name":"Feature selection","level":2,"score":0.5684999823570251},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.5329999923706055},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5281000137329102},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.5127999782562256},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4422999918460846},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.42410001158714294},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4074000120162964},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.40689998865127563},{"id":"https://openalex.org/C182365436","wikidata":"https://www.wikidata.org/wiki/Q50701","display_name":"Variable (mathematics)","level":2,"score":0.40209999680519104},{"id":"https://openalex.org/C2984324147","wikidata":"https://www.wikidata.org/wiki/Q3080021","display_name":"Gene selection","level":5,"score":0.39010000228881836},{"id":"https://openalex.org/C196083921","wikidata":"https://www.wikidata.org/wiki/Q7915758","display_name":"Variance (accounting)","level":2,"score":0.38839998841285706},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.3700999915599823},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.3425999879837036},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.2976999878883362},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.26829999685287476},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2623000144958496}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3765612.3767789","doi":"https://doi.org/10.1145/3765612.3767789","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3765612.3767789","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3765612.3767789","source":{"id":"https://openalex.org/S7407087958","display_name":"ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 16th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics","raw_type":"proceedings-article"}],"best_oa_location":{"id":"doi:10.1145/3765612.3767789","doi":"https://doi.org/10.1145/3765612.3767789","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3765612.3767789","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3765612.3767789","source":{"id":"https://openalex.org/S7407087958","display_name":"ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 16th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics","raw_type":"proceedings-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G212617057","display_name":"CAREER: Computational and statistical methods for studying single cell genomics data in the context of tissue organization","funder_award_id":"2443386","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4626365307","display_name":"Collaborative Research: III: Medium: Algorithms for scalable inference and phylodynamic analysis of tumor haplotypes using low-coverage single cell sequencing data","funder_award_id":"2341725","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6671297155","display_name":null,"funder_award_id":"CAREER","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G894646939","display_name":null,"funder_award_id":"BIC2.0","funder_id":"https://openalex.org/F4320310179","funder_display_name":"University of Oklahoma"},{"id":"https://openalex.org/G9000886141","display_name":"Computational approaches to the mechanistic elucidation of the serrated pathway of human colon carcinogenesis","funder_award_id":"K25CA270079","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320310179","display_name":"University of Oklahoma","ror":"https://ror.org/02aqsxs83"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4417200322.pdf","grobid_xml":"https://content.openalex.org/works/W4417200322.grobid-xml"},"referenced_works_count":5,"referenced_works":["https://openalex.org/W1977361006","https://openalex.org/W2007439698","https://openalex.org/W2949177718","https://openalex.org/W3071636267","https://openalex.org/W3202498768"],"related_works":["https://openalex.org/W7202362534","https://openalex.org/W4417241661","https://openalex.org/W2791285756","https://openalex.org/W7114986591","https://openalex.org/W7114988266","https://openalex.org/W7115013744","https://openalex.org/W4210932541","https://openalex.org/W4308337362","https://openalex.org/W2914371208","https://openalex.org/W3158549903"],"abstract_inverted_index":{"Single":[0],"cell":[1,32,35],"RNA-sequencing":[2],"(scRNA-Seq)":[3],"data":[4],"are":[5,113],"typically":[6],"represented":[7],"as":[8,19],"cell-by-gene":[9],"count":[10],"matrices,":[11],"which":[12,52],"capture":[13],"the":[14,22,62,86],"expression":[15,82],"of":[16,29,73,88,106,108],"each":[17,89],"gene":[18,44,64,91,100],"detected":[20],"in":[21],"sampled":[23],"cells;":[24],"often":[25],"a":[26,43],"heterogeneous":[27],"population":[28],"multiple":[30],"different":[31],"types":[33],"or":[34],"states.":[36],"Almost":[37],"all":[38],"scRNA-Seq":[39],"analysis":[40],"workflows":[41],"have":[42],"selection":[45,72,101],"step":[46],"prior":[47],"to":[48,84,110,115],"applying":[49],"clustering":[50],"algorithms":[51],"helps":[53],"remove":[54],"genes":[55,76,109],"with":[56],"low":[57],"variability":[58,87],"and":[59,80,112],"hence":[60],"reduce":[61],"high-dimensional":[63],"space.":[65],"A":[66],"defacto":[67],"method":[68],"for":[69,99],"achieving":[70],"this":[71],"highly":[74],"variable":[75],"(HVG)":[77],"uses":[78],"dispersion":[79],"mean":[81],"scores":[83],"evaluate":[85],"individual":[90],"[3].":[92],"However,":[93],"methods":[94],"based":[95],"on":[96],"mean-variance":[97],"relationship":[98],"suffer":[102],"from":[103],"arbitrary":[104],"determination":[105],"number":[107],"use":[111],"susceptible":[114],"variance":[116],"instability.":[117]},"counts_by_year":[],"updated_date":"2026-10-28T10:33:24.094632","created_date":"2025-12-10T00:00:00"}