{"id":"https://openalex.org/W4297965067","doi":"https://doi.org/10.1093/bioinformatics/btac644","title":"SCAFE: a software suite for analysis of transcribed cis-regulatory elements in single cells","display_name":"SCAFE: a software suite for analysis of transcribed cis-regulatory elements in single cells","publication_year":2022,"publication_date":"2022-09-28","ids":{"openalex":"https://openalex.org/W4297965067","doi":"https://doi.org/10.1093/bioinformatics/btac644","pmid":"https://pubmed.ncbi.nlm.nih.gov/36173306"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac644","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac644","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/22/5126/47153763/btac644.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/38/22/5126/47153763/btac644.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5037016745","display_name":"Jonathan Moody","orcid":"https://orcid.org/0000-0001-9261-711X"},"institutions":[{"id":"https://openalex.org/I4210150921","display_name":"RIKEN Center for Integrative Medical Sciences","ror":"https://ror.org/04mb6s476","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652","https://openalex.org/I4210150921"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Jonathan Moody","raw_affiliation_strings":["RIKEN Center for Integrative Medical Sciences , Yokohama City, Kanagawa 230-0045, Japan"],"affiliations":[{"raw_affiliation_string":"RIKEN Center for Integrative Medical Sciences , Yokohama City, Kanagawa 230-0045, Japan","institution_ids":["https://openalex.org/I4210150921"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110685157","display_name":"Tsukasa Kouno","orcid":null},"institutions":[{"id":"https://openalex.org/I4210150921","display_name":"RIKEN Center for Integrative Medical Sciences","ror":"https://ror.org/04mb6s476","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652","https://openalex.org/I4210150921"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Tsukasa Kouno","raw_affiliation_strings":["RIKEN Center for Integrative Medical Sciences , Yokohama City, Kanagawa 230-0045, Japan"],"affiliations":[{"raw_affiliation_string":"RIKEN Center for Integrative Medical Sciences , Yokohama City, Kanagawa 230-0045, Japan","institution_ids":["https://openalex.org/I4210150921"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054082582","display_name":"Jen-Chien Chang","orcid":"https://orcid.org/0000-0002-6986-8479"},"institutions":[{"id":"https://openalex.org/I4210150921","display_name":"RIKEN Center for Integrative Medical Sciences","ror":"https://ror.org/04mb6s476","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652","https://openalex.org/I4210150921"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Jen-Chien Chang","raw_affiliation_strings":["RIKEN Center for Integrative Medical Sciences , Yokohama City, Kanagawa 230-0045, Japan"],"affiliations":[{"raw_affiliation_string":"RIKEN Center for Integrative Medical Sciences , Yokohama City, Kanagawa 230-0045, Japan","institution_ids":["https://openalex.org/I4210150921"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051765798","display_name":"Yoshinari Ando","orcid":"https://orcid.org/0000-0002-8128-6201"},"institutions":[{"id":"https://openalex.org/I4210150921","display_name":"RIKEN Center for Integrative Medical Sciences","ror":"https://ror.org/04mb6s476","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652","https://openalex.org/I4210150921"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yoshinari Ando","raw_affiliation_strings":["RIKEN Center for Integrative Medical Sciences , Yokohama City, Kanagawa 230-0045, Japan"],"affiliations":[{"raw_affiliation_string":"RIKEN Center for Integrative Medical Sciences , Yokohama City, Kanagawa 230-0045, Japan","institution_ids":["https://openalex.org/I4210150921"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072131150","display_name":"Piero Carninci","orcid":"https://orcid.org/0000-0001-7202-7243"},"institutions":[{"id":"https://openalex.org/I4210115812","display_name":"Human Technopole","ror":"https://ror.org/029gmnc79","country_code":"IT","type":"facility","lineage":["https://openalex.org/I4210115812"]},{"id":"https://openalex.org/I4210150921","display_name":"RIKEN Center for Integrative Medical Sciences","ror":"https://ror.org/04mb6s476","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652","https://openalex.org/I4210150921"]}],"countries":["IT","JP"],"is_corresponding":false,"raw_author_name":"Piero Carninci","raw_affiliation_strings":["Human Technopole , Milan 20157, Italy","RIKEN Center for Integrative Medical Sciences , Yokohama City, Kanagawa 230-0045, Japan"],"affiliations":[{"raw_affiliation_string":"Human Technopole , Milan 20157, Italy","institution_ids":["https://openalex.org/I4210115812"]},{"raw_affiliation_string":"RIKEN Center for Integrative Medical Sciences , Yokohama City, Kanagawa 230-0045, Japan","institution_ids":["https://openalex.org/I4210150921"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007530779","display_name":"Jay W. Shin","orcid":"https://orcid.org/0000-0003-4037-3533"},"institutions":[{"id":"https://openalex.org/I115228651","display_name":"Agency for Science, Technology and Research","ror":"https://ror.org/036wvzt09","country_code":"SG","type":"government","lineage":["https://openalex.org/I115228651"]},{"id":"https://openalex.org/I4210150921","display_name":"RIKEN Center for Integrative Medical Sciences","ror":"https://ror.org/04mb6s476","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652","https://openalex.org/I4210150921"]},{"id":"https://openalex.org/I66068411","display_name":"Genome Institute of Singapore","ror":"https://ror.org/05k8wg936","country_code":"SG","type":"facility","lineage":["https://openalex.org/I115228651","https://openalex.org/I2801752549","https://openalex.org/I66068411"]}],"countries":["JP","SG"],"is_corresponding":true,"raw_author_name":"Jay W Shin","raw_affiliation_strings":["Genome Institute of Singapore, A*STAR Singapore , 60 Biopolis Street, Genome, #02-01, Singapore","RIKEN Center for Integrative Medical Sciences , Yokohama City, Kanagawa 230-0045, Japan"],"affiliations":[{"raw_affiliation_string":"Genome Institute of Singapore, A*STAR Singapore , 60 Biopolis Street, Genome, #02-01, Singapore","institution_ids":["https://openalex.org/I66068411","https://openalex.org/I115228651"]},{"raw_affiliation_string":"RIKEN Center for Integrative Medical Sciences , Yokohama City, Kanagawa 230-0045, Japan","institution_ids":["https://openalex.org/I4210150921"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5019767879","display_name":"Chung-Chau Hon","orcid":"https://orcid.org/0000-0002-3741-7577"},"institutions":[{"id":"https://openalex.org/I4210150921","display_name":"RIKEN Center for Integrative Medical Sciences","ror":"https://ror.org/04mb6s476","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652","https://openalex.org/I4210150921"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Chung-Chau Hon","raw_affiliation_strings":["RIKEN Center for Integrative Medical Sciences , Yokohama City, Kanagawa 230-0045, Japan"],"affiliations":[{"raw_affiliation_string":"RIKEN Center for Integrative Medical Sciences , Yokohama City, Kanagawa 230-0045, Japan","institution_ids":["https://openalex.org/I4210150921"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5007530779","https://openalex.org/A5019767879"],"corresponding_institution_ids":["https://openalex.org/I115228651","https://openalex.org/I4210150921","https://openalex.org/I66068411"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.2997,"has_fulltext":false,"cited_by_count":19,"citation_normalized_percentile":{"value":0.79585313,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"38","issue":"22","first_page":"5126","last_page":"5128"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9998999834060669,"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":0.9998999834060669,"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/T10878","display_name":"CRISPR and Genetic Engineering","score":0.9896000027656555,"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/T10604","display_name":"RNA Research and Splicing","score":0.9854000210762024,"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/mit-license","display_name":"MIT License","score":0.7073490619659424},{"id":"https://openalex.org/keywords/suite","display_name":"Suite","score":0.6628501415252686},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6577469110488892},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.6488271355628967},{"id":"https://openalex.org/keywords/perl","display_name":"Perl","score":0.630092978477478},{"id":"https://openalex.org/keywords/software-suite","display_name":"Software suite","score":0.5722422003746033},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5662602782249451},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.4628303349018097},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.44333845376968384},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4372456669807434},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3804381489753723},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.3511672019958496},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.3324185609817505},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.32291221618652344},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.28504419326782227},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.25482431054115295}],"concepts":[{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.7073490619659424},{"id":"https://openalex.org/C79581498","wikidata":"https://www.wikidata.org/wiki/Q1367530","display_name":"Suite","level":2,"score":0.6628501415252686},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6577469110488892},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.6488271355628967},{"id":"https://openalex.org/C2777002779","wikidata":"https://www.wikidata.org/wiki/Q42478","display_name":"Perl","level":2,"score":0.630092978477478},{"id":"https://openalex.org/C2778736646","wikidata":"https://www.wikidata.org/wiki/Q1143070","display_name":"Software suite","level":3,"score":0.5722422003746033},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5662602782249451},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.4628303349018097},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.44333845376968384},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4372456669807434},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3804381489753723},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.3511672019958496},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.3324185609817505},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.32291221618652344},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.28504419326782227},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.25482431054115295},{"id":"https://openalex.org/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","level":1,"score":0.0},{"id":"https://openalex.org/C95457728","wikidata":"https://www.wikidata.org/wiki/Q309","display_name":"History","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","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":"D024363","descriptor_name":"Transcription Initiation Site","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D024363","descriptor_name":"Transcription Initiation Site","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D024363","descriptor_name":"Transcription Initiation Site","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btac644","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac644","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/22/5126/47153763/btac644.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36173306","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36173306","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:9665856","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9665856","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btac644","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac644","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/22/5126/47153763/btac644.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.46000000834465027,"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320315474","display_name":"Chan Zuckerberg Initiative","ror":"https://ror.org/02qenvm24"},{"id":"https://openalex.org/F4320320912","display_name":"Ministry of Education, Culture, Sports, Science and Technology","ror":"https://ror.org/048rj2z13"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4297965067.pdf","grobid_xml":"https://content.openalex.org/works/W4297965067.grobid-xml"},"referenced_works_count":14,"referenced_works":["https://openalex.org/W1602702667","https://openalex.org/W1834189509","https://openalex.org/W1986223165","https://openalex.org/W2015845481","https://openalex.org/W2053408851","https://openalex.org/W2059478037","https://openalex.org/W2064390432","https://openalex.org/W2114703458","https://openalex.org/W2131356974","https://openalex.org/W2146975379","https://openalex.org/W2807138843","https://openalex.org/W2950843205","https://openalex.org/W2952014119","https://openalex.org/W2997704617"],"related_works":["https://openalex.org/W1516095885","https://openalex.org/W4231704780","https://openalex.org/W2158573927","https://openalex.org/W2108921801","https://openalex.org/W2398058485","https://openalex.org/W4206079007","https://openalex.org/W254965819","https://openalex.org/W4309247532","https://openalex.org/W3156231268","https://openalex.org/W1981336497"],"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":4},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":6}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
