{"id":"https://openalex.org/W4411136978","doi":"https://doi.org/10.1186/s12859-025-06160-x","title":"SEQSIM: A novel bioinformatics tool for comparisons of promoter regions\u2014a case study of calcium binding protein spermatid associated 1 (CABS1)","display_name":"SEQSIM: A novel bioinformatics tool for comparisons of promoter regions\u2014a case study of calcium binding protein spermatid associated 1 (CABS1)","publication_year":2025,"publication_date":"2025-06-09","ids":{"openalex":"https://openalex.org/W4411136978","doi":"https://doi.org/10.1186/s12859-025-06160-x","pmid":"https://pubmed.ncbi.nlm.nih.gov/40490738"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-025-06160-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06160-x","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06160-x","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06160-x","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5086421317","display_name":"Joy Ramielle L. Santos","orcid":"https://orcid.org/0009-0009-3155-187X"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Joy Ramielle L. Santos","raw_affiliation_strings":["Department of Medicine, University of Alberta, Edmonton, T6G 2R3, Canada. joyramie@ualberta.ca"],"affiliations":[{"raw_affiliation_string":"Department of Medicine, University of Alberta, Edmonton, T6G 2R3, Canada. joyramie@ualberta.ca","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059121720","display_name":"Weijie Sun","orcid":"https://orcid.org/0000-0003-3099-0298"},"institutions":[{"id":"https://openalex.org/I154425047","display_name":"University of Alberta","ror":"https://ror.org/0160cpw27","country_code":"CA","type":"education","lineage":["https://openalex.org/I154425047"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Weijie Sun","raw_affiliation_strings":["Department of Computer Sciences, University of Alberta, Edmonton, T6G 2E1, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Computer Sciences, University of Alberta, Edmonton, T6G 2E1, Canada","institution_ids":["https://openalex.org/I154425047"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006782649","display_name":"A. Dean Befus","orcid":"https://orcid.org/0000-0002-1611-2897"},"institutions":[{"id":"https://openalex.org/I154425047","display_name":"University of Alberta","ror":"https://ror.org/0160cpw27","country_code":"CA","type":"education","lineage":["https://openalex.org/I154425047"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"A. Dean Befus","raw_affiliation_strings":["Department of Medicine, University of Alberta, Edmonton, T6G 2R3, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Medicine, University of Alberta, Edmonton, T6G 2R3, Canada","institution_ids":["https://openalex.org/I154425047"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5026845136","display_name":"Marcelo Marcet\u2010Palacios","orcid":"https://orcid.org/0000-0002-4048-4658"},"institutions":[{"id":"https://openalex.org/I154425047","display_name":"University of Alberta","ror":"https://ror.org/0160cpw27","country_code":"CA","type":"education","lineage":["https://openalex.org/I154425047"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Marcelo Marcet-Palacios","raw_affiliation_strings":["Department of Medicine, University of Alberta, Edmonton, T6G 2R3, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Medicine, University of Alberta, Edmonton, T6G 2R3, Canada","institution_ids":["https://openalex.org/I154425047"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5086421317"],"corresponding_institution_ids":[],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.7625,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.71837007,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":98},"biblio":{"volume":"26","issue":"1","first_page":"156","last_page":"156"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9983000159263611,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9983000159263611,"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/T12929","display_name":"Animal Genetics and Reproduction","score":0.9979000091552734,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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":0.9932000041007996,"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/spermatid","display_name":"Spermatid","score":0.6491056680679321},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.5965656042098999},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5643702149391174},{"id":"https://openalex.org/keywords/calcium-binding-protein","display_name":"Calcium-binding protein","score":0.5487223863601685},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.5245944857597351},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.49294161796569824},{"id":"https://openalex.org/keywords/calcium","display_name":"Calcium","score":0.4503518342971802},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.32169365882873535},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.12558576464653015},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1187376081943512},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.11523929238319397},{"id":"https://openalex.org/keywords/internal-medicine","display_name":"Internal medicine","score":0.05614537000656128}],"concepts":[{"id":"https://openalex.org/C2777394357","wikidata":"https://www.wikidata.org/wiki/Q1494188","display_name":"Spermatid","level":3,"score":0.6491056680679321},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.5965656042098999},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5643702149391174},{"id":"https://openalex.org/C122229402","wikidata":"https://www.wikidata.org/wiki/Q5018802","display_name":"Calcium-binding protein","level":3,"score":0.5487223863601685},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.5245944857597351},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.49294161796569824},{"id":"https://openalex.org/C519063684","wikidata":"https://www.wikidata.org/wiki/Q706","display_name":"Calcium","level":2,"score":0.4503518342971802},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.32169365882873535},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.12558576464653015},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1187376081943512},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.11523929238319397},{"id":"https://openalex.org/C126322002","wikidata":"https://www.wikidata.org/wiki/Q11180","display_name":"Internal medicine","level":1,"score":0.05614537000656128},{"id":"https://openalex.org/C2781087480","wikidata":"https://www.wikidata.org/wiki/Q17145","display_name":"Sperm","level":2,"score":0.0}],"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":"D002135","descriptor_name":"Calcium-Binding Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D002135","descriptor_name":"Calcium-Binding Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D002135","descriptor_name":"Calcium-Binding Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008297","descriptor_name":"Male","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008297","descriptor_name":"Male","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008297","descriptor_name":"Male","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","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":"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":4,"locations":[{"id":"doi:10.1186/s12859-025-06160-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06160-x","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06160-x","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40490738","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40490738","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:5d269a955c094b7b885152a87010e22f","is_oa":true,"landing_page_url":"https://doaj.org/article/5d269a955c094b7b885152a87010e22f","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 26, Iss 1, Pp 1-20 (2025)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:10963356","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12150522","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-025-06160-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06160-x","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06160-x","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.7400000095367432,"display_name":"Zero hunger","id":"https://metadata.un.org/sdg/2"}],"awards":[{"id":"https://openalex.org/G1597412403","display_name":null,"funder_award_id":"RGPIN-","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G2165548363","display_name":null,"funder_award_id":"Canada","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G3028888727","display_name":null,"funder_award_id":"RGPIN-2020-0","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G3525686075","display_name":null,"funder_award_id":"RGPIN-2020","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G6221715925","display_name":null,"funder_award_id":"RGPIN","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G675966558","display_name":null,"funder_award_id":"RGPIN-2020-04553","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G8105784103","display_name":null,"funder_award_id":"RGPIN-202","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"}],"funders":[{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4411136978.pdf","grobid_xml":"https://content.openalex.org/works/W4411136978.grobid-xml"},"referenced_works_count":58,"referenced_works":["https://openalex.org/W994757099","https://openalex.org/W1922068952","https://openalex.org/W1979076392","https://openalex.org/W1985577061","https://openalex.org/W2011473978","https://openalex.org/W2028695285","https://openalex.org/W2065849734","https://openalex.org/W2070164706","https://openalex.org/W2072357155","https://openalex.org/W2074231493","https://openalex.org/W2084332810","https://openalex.org/W2088111540","https://openalex.org/W2088338161","https://openalex.org/W2089064575","https://openalex.org/W2103438787","https://openalex.org/W2107032654","https://openalex.org/W2107578440","https://openalex.org/W2107950128","https://openalex.org/W2114016259","https://openalex.org/W2120772351","https://openalex.org/W2134977238","https://openalex.org/W2137465688","https://openalex.org/W2137910529","https://openalex.org/W2147838733","https://openalex.org/W2152926641","https://openalex.org/W2154074258","https://openalex.org/W2158217645","https://openalex.org/W2159164310","https://openalex.org/W2159619387","https://openalex.org/W2164814636","https://openalex.org/W2167241965","https://openalex.org/W2169742902","https://openalex.org/W2293605963","https://openalex.org/W2356355115","https://openalex.org/W2474747771","https://openalex.org/W2587668080","https://openalex.org/W2761430568","https://openalex.org/W2901901698","https://openalex.org/W2903832988","https://openalex.org/W2951856336","https://openalex.org/W2962807110","https://openalex.org/W3004002906","https://openalex.org/W3045327650","https://openalex.org/W3119324088","https://openalex.org/W3129730550","https://openalex.org/W4220831425","https://openalex.org/W4283374035","https://openalex.org/W4318477830","https://openalex.org/W4319298586","https://openalex.org/W4379653175","https://openalex.org/W4383505098","https://openalex.org/W4386379020","https://openalex.org/W4386591788","https://openalex.org/W4386771831","https://openalex.org/W4388328068","https://openalex.org/W4390670656","https://openalex.org/W4396977546","https://openalex.org/W4399437516"],"related_works":["https://openalex.org/W2068657252","https://openalex.org/W2063950472","https://openalex.org/W3120864646","https://openalex.org/W2024050351","https://openalex.org/W2160520610","https://openalex.org/W1977806942","https://openalex.org/W2057555038","https://openalex.org/W2097841878","https://openalex.org/W2011481364","https://openalex.org/W2000967002"],"abstract_inverted_index":{"These":[0],"results":[1],"provide":[2],"insight":[3],"into":[4],"potential":[5],"gene":[6,35],"regulation":[7],"mechanisms,":[8],"enhancing":[9],"our":[10],"understanding":[11],"of":[12],"transcriptional":[13],"control":[14],"and":[15,30],"suggesting":[16],"new":[17],"pathways":[18],"for":[19],"functional":[20],"exploration.":[21],"Future":[22],"studies":[23],"incorporating":[24],"SEQSIM":[25],"could":[26],"elucidate":[27],"co-regulatory":[28],"networks":[29],"chromatin":[31],"interactions":[32],"that":[33],"impact":[34],"expression.":[36]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
