{"id":"https://openalex.org/W4223543947","doi":"https://doi.org/10.1093/bioinformatics/btac209","title":"TRANSDIRE: data-driven direct reprogramming by a pioneer factor-guided trans-omics approach","display_name":"TRANSDIRE: data-driven direct reprogramming by a pioneer factor-guided trans-omics approach","publication_year":2022,"publication_date":"2022-04-12","ids":{"openalex":"https://openalex.org/W4223543947","doi":"https://doi.org/10.1093/bioinformatics/btac209","pmid":"https://pubmed.ncbi.nlm.nih.gov/35561200"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac209","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac209","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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5020556406","display_name":"Ryohei Eguchi","orcid":"https://orcid.org/0000-0002-7387-7562"},"institutions":[{"id":"https://openalex.org/I207014233","display_name":"Kyushu Institute of Technology","ror":"https://ror.org/02278tr80","country_code":"JP","type":"education","lineage":["https://openalex.org/I207014233"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Ryohei Eguchi","raw_affiliation_strings":["Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology , Fukuoka 820-8502, Japan"],"affiliations":[{"raw_affiliation_string":"Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology , Fukuoka 820-8502, Japan","institution_ids":["https://openalex.org/I207014233"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063865670","display_name":"Momoko Hamano","orcid":"https://orcid.org/0000-0002-8752-7053"},"institutions":[{"id":"https://openalex.org/I207014233","display_name":"Kyushu Institute of Technology","ror":"https://ror.org/02278tr80","country_code":"JP","type":"education","lineage":["https://openalex.org/I207014233"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Momoko Hamano","raw_affiliation_strings":["Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology , Fukuoka 820-8502, Japan"],"affiliations":[{"raw_affiliation_string":"Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology , Fukuoka 820-8502, Japan","institution_ids":["https://openalex.org/I207014233"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088317641","display_name":"M Iwata","orcid":"https://orcid.org/0000-0001-6500-4692"},"institutions":[{"id":"https://openalex.org/I207014233","display_name":"Kyushu Institute of Technology","ror":"https://ror.org/02278tr80","country_code":"JP","type":"education","lineage":["https://openalex.org/I207014233"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Michio Iwata","raw_affiliation_strings":["Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology , Fukuoka 820-8502, Japan"],"affiliations":[{"raw_affiliation_string":"Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology , Fukuoka 820-8502, Japan","institution_ids":["https://openalex.org/I207014233"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060744842","display_name":"T\u00f5ru Nakamura","orcid":"https://orcid.org/0000-0002-9199-4551"},"institutions":[{"id":"https://openalex.org/I207014233","display_name":"Kyushu Institute of Technology","ror":"https://ror.org/02278tr80","country_code":"JP","type":"education","lineage":["https://openalex.org/I207014233"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Toru Nakamura","raw_affiliation_strings":["Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology , Fukuoka 820-8502, Japan"],"affiliations":[{"raw_affiliation_string":"Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology , Fukuoka 820-8502, Japan","institution_ids":["https://openalex.org/I207014233"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044080699","display_name":"Shinya Oki","orcid":"https://orcid.org/0000-0002-4767-3259"},"institutions":[{"id":"https://openalex.org/I22299242","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85","country_code":"JP","type":"education","lineage":["https://openalex.org/I22299242"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Shinya Oki","raw_affiliation_strings":["Department of Drug Discovery Medicine, Graduate School of Medicine, Kyoto University , Kyoto 606-8507, Japan"],"affiliations":[{"raw_affiliation_string":"Department of Drug Discovery Medicine, Graduate School of Medicine, Kyoto University , Kyoto 606-8507, Japan","institution_ids":["https://openalex.org/I22299242"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5035394108","display_name":"Yoshihiro Yamanishi","orcid":"https://orcid.org/0000-0003-2279-8773"},"institutions":[{"id":"https://openalex.org/I207014233","display_name":"Kyushu Institute of Technology","ror":"https://ror.org/02278tr80","country_code":"JP","type":"education","lineage":["https://openalex.org/I207014233"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Yoshihiro Yamanishi","raw_affiliation_strings":["Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology , Fukuoka 820-8502, Japan"],"affiliations":[{"raw_affiliation_string":"Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology , Fukuoka 820-8502, Japan","institution_ids":["https://openalex.org/I207014233"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5035394108"],"corresponding_institution_ids":["https://openalex.org/I207014233"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.6862,"has_fulltext":false,"cited_by_count":9,"citation_normalized_percentile":{"value":0.65715487,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"38","issue":"10","first_page":"2839","last_page":"2846"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10505","display_name":"Pluripotent Stem Cells Research","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/T10505","display_name":"Pluripotent Stem Cells Research","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/T10878","display_name":"CRISPR and Genetic Engineering","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"}},{"id":"https://openalex.org/T12929","display_name":"Animal Genetics and Reproduction","score":0.9836999773979187,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/reprogramming","display_name":"Reprogramming","score":0.8999444246292114},{"id":"https://openalex.org/keywords/induced-pluripotent-stem-cell","display_name":"Induced pluripotent stem cell","score":0.7201455235481262},{"id":"https://openalex.org/keywords/chromatin","display_name":"Chromatin","score":0.6839303374290466},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6611518263816833},{"id":"https://openalex.org/keywords/interactome","display_name":"Interactome","score":0.6217138171195984},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6128947138786316},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.5780553817749023},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.538287878036499},{"id":"https://openalex.org/keywords/epigenome","display_name":"Epigenome","score":0.4945161044597626},{"id":"https://openalex.org/keywords/chromatin-immunoprecipitation","display_name":"Chromatin immunoprecipitation","score":0.47097277641296387},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3138515055179596},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.23814281821250916},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.23756709694862366},{"id":"https://openalex.org/keywords/embryonic-stem-cell","display_name":"Embryonic stem cell","score":0.21928545832633972},{"id":"https://openalex.org/keywords/dna-methylation","display_name":"DNA methylation","score":0.07773396372795105}],"concepts":[{"id":"https://openalex.org/C77255625","wikidata":"https://www.wikidata.org/wiki/Q402093","display_name":"Reprogramming","level":3,"score":0.8999444246292114},{"id":"https://openalex.org/C107459253","wikidata":"https://www.wikidata.org/wiki/Q674925","display_name":"Induced pluripotent stem cell","level":4,"score":0.7201455235481262},{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.6839303374290466},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6611518263816833},{"id":"https://openalex.org/C9760119","wikidata":"https://www.wikidata.org/wiki/Q841382","display_name":"Interactome","level":3,"score":0.6217138171195984},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6128947138786316},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.5780553817749023},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.538287878036499},{"id":"https://openalex.org/C117717151","wikidata":"https://www.wikidata.org/wiki/Q3589155","display_name":"Epigenome","level":5,"score":0.4945161044597626},{"id":"https://openalex.org/C134320426","wikidata":"https://www.wikidata.org/wiki/Q901026","display_name":"Chromatin immunoprecipitation","level":5,"score":0.47097277641296387},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3138515055179596},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.23814281821250916},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.23756709694862366},{"id":"https://openalex.org/C145103041","wikidata":"https://www.wikidata.org/wiki/Q1151519","display_name":"Embryonic stem cell","level":3,"score":0.21928545832633972},{"id":"https://openalex.org/C190727270","wikidata":"https://www.wikidata.org/wiki/Q874745","display_name":"DNA methylation","level":4,"score":0.07773396372795105},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.0}],"mesh":[{"descriptor_ui":"D002454","descriptor_name":"Cell Differentiation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002454","descriptor_name":"Cell Differentiation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002454","descriptor_name":"Cell Differentiation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D057026","descriptor_name":"Induced Pluripotent Stem Cells","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D057026","descriptor_name":"Induced Pluripotent Stem Cells","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D057026","descriptor_name":"Induced Pluripotent Stem Cells","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D065150","descriptor_name":"Cellular Reprogramming","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D065150","descriptor_name":"Cellular Reprogramming","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D065150","descriptor_name":"Cellular Reprogramming","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btac209","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac209","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:35561200","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35561200","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}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17","score":0.5099999904632568}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":35,"referenced_works":["https://openalex.org/W1484009785","https://openalex.org/W1810920534","https://openalex.org/W1979513200","https://openalex.org/W2008365696","https://openalex.org/W2018363492","https://openalex.org/W2023238436","https://openalex.org/W2031195065","https://openalex.org/W2040292168","https://openalex.org/W2076486071","https://openalex.org/W2078697242","https://openalex.org/W2084160423","https://openalex.org/W2091579021","https://openalex.org/W2095546080","https://openalex.org/W2108407164","https://openalex.org/W2113142309","https://openalex.org/W2114206069","https://openalex.org/W2116634113","https://openalex.org/W2125987139","https://openalex.org/W2136541538","https://openalex.org/W2138977668","https://openalex.org/W2154362705","https://openalex.org/W2166676212","https://openalex.org/W2173732482","https://openalex.org/W2287379375","https://openalex.org/W2331147307","https://openalex.org/W2462007197","https://openalex.org/W2596666705","https://openalex.org/W2728193959","https://openalex.org/W2758459988","https://openalex.org/W2806109373","https://openalex.org/W2900310474","https://openalex.org/W2900569176","https://openalex.org/W2908648017","https://openalex.org/W2921426074","https://openalex.org/W3015494912"],"related_works":["https://openalex.org/W3029540856","https://openalex.org/W2418603484","https://openalex.org/W4254937032","https://openalex.org/W2744405843","https://openalex.org/W2415743749","https://openalex.org/W3032669875","https://openalex.org/W2992250893","https://openalex.org/W1888433033","https://openalex.org/W2990520546","https://openalex.org/W2392750004"],"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":2},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
