{"id":"https://openalex.org/W4409311858","doi":"https://doi.org/10.1371/journal.pcbi.1012997","title":"Transcriptomic landscape around wound bed defines regenerative versus non-regenerative outcomes in mouse digit amputation","display_name":"Transcriptomic landscape around wound bed defines regenerative versus non-regenerative outcomes in mouse digit amputation","publication_year":2025,"publication_date":"2025-04-09","ids":{"openalex":"https://openalex.org/W4409311858","doi":"https://doi.org/10.1371/journal.pcbi.1012997","pmid":"https://pubmed.ncbi.nlm.nih.gov/40203060"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1012997","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1012997","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1371/journal.pcbi.1012997","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5031643280","display_name":"Archana Prabahar","orcid":"https://orcid.org/0000-0001-6426-4548"},"institutions":[{"id":"https://openalex.org/I102607778","display_name":"Cleveland State University","ror":"https://ror.org/002tx1f22","country_code":"US","type":"education","lineage":["https://openalex.org/I102607778"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Archana Prabahar","raw_affiliation_strings":["Center for Gene Regulation in Health and Disease, Cleveland State University, Cleveland, Ohio, United States of America","Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, Ohio, United States of America"],"raw_orcid":"https://orcid.org/0000-0001-6426-4548","affiliations":[{"raw_affiliation_string":"Center for Gene Regulation in Health and Disease, Cleveland State University, Cleveland, Ohio, United States of America","institution_ids":["https://openalex.org/I102607778"]},{"raw_affiliation_string":"Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, Ohio, United States of America","institution_ids":["https://openalex.org/I102607778"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016707131","display_name":"Connie S. Chamberlain","orcid":"https://orcid.org/0000-0002-4980-4347"},"institutions":[{"id":"https://openalex.org/I135310074","display_name":"University of Wisconsin\u2013Madison","ror":"https://ror.org/01y2jtd41","country_code":"US","type":"education","lineage":["https://openalex.org/I135310074"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Connie S. Chamberlain","raw_affiliation_strings":["Department of Orthopedics and Rehabilitation, University of Wisconsin, Madison, Wisconsin, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Orthopedics and Rehabilitation, University of Wisconsin, Madison, Wisconsin, United States of America","institution_ids":["https://openalex.org/I135310074"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085115078","display_name":"Ray Vanderby","orcid":null},"institutions":[{"id":"https://openalex.org/I135310074","display_name":"University of Wisconsin\u2013Madison","ror":"https://ror.org/01y2jtd41","country_code":"US","type":"education","lineage":["https://openalex.org/I135310074"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ray Vanderby","raw_affiliation_strings":["Department of Orthopedics and Rehabilitation, University of Wisconsin, Madison, Wisconsin, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Orthopedics and Rehabilitation, University of Wisconsin, Madison, Wisconsin, United States of America","institution_ids":["https://openalex.org/I135310074"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081705219","display_name":"William L. Murphy","orcid":"https://orcid.org/0000-0001-5577-7739"},"institutions":[{"id":"https://openalex.org/I135310074","display_name":"University of Wisconsin\u2013Madison","ror":"https://ror.org/01y2jtd41","country_code":"US","type":"education","lineage":["https://openalex.org/I135310074"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"William L. Murphy","raw_affiliation_strings":["Department of Biomedical Engineering, University of Wisconsin, Madison, Wisconsin, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, University of Wisconsin, Madison, Wisconsin, United States of America","institution_ids":["https://openalex.org/I135310074"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027100037","display_name":"William D\u2019Angelo","orcid":"https://orcid.org/0009-0001-6778-6816"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]},{"id":"https://openalex.org/I4210155891","display_name":"McGowan Institute for Regenerative Medicine","ror":"https://ror.org/04js6xx21","country_code":"US","type":"facility","lineage":["https://openalex.org/I170201317","https://openalex.org/I4210098814","https://openalex.org/I4210134769","https://openalex.org/I4210155891"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"William Dangelo","raw_affiliation_strings":["Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America","McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America","institution_ids":["https://openalex.org/I170201317"]},{"raw_affiliation_string":"McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America","institution_ids":["https://openalex.org/I4210155891","https://openalex.org/I170201317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5115060166","display_name":"Kulkarni Mangesh","orcid":null},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]},{"id":"https://openalex.org/I4210155891","display_name":"McGowan Institute for Regenerative Medicine","ror":"https://ror.org/04js6xx21","country_code":"US","type":"facility","lineage":["https://openalex.org/I170201317","https://openalex.org/I4210098814","https://openalex.org/I4210134769","https://openalex.org/I4210155891"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kulkarni Mangesh","raw_affiliation_strings":["McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America","institution_ids":["https://openalex.org/I4210155891","https://openalex.org/I170201317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008873241","display_name":"Bryan N. Brown","orcid":"https://orcid.org/0000-0002-0845-7828"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]},{"id":"https://openalex.org/I4210155891","display_name":"McGowan Institute for Regenerative Medicine","ror":"https://ror.org/04js6xx21","country_code":"US","type":"facility","lineage":["https://openalex.org/I170201317","https://openalex.org/I4210098814","https://openalex.org/I4210134769","https://openalex.org/I4210155891"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bryan Brown","raw_affiliation_strings":["McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America","institution_ids":["https://openalex.org/I4210155891","https://openalex.org/I170201317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041015307","display_name":"Barsanjit Mazumder","orcid":"https://orcid.org/0000-0003-3069-7833"},"institutions":[{"id":"https://openalex.org/I102607778","display_name":"Cleveland State University","ror":"https://ror.org/002tx1f22","country_code":"US","type":"education","lineage":["https://openalex.org/I102607778"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Barsanjit Mazumder","raw_affiliation_strings":["Center for Gene Regulation in Health and Disease, Cleveland State University, Cleveland, Ohio, United States of America","Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, Ohio, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Gene Regulation in Health and Disease, Cleveland State University, Cleveland, Ohio, United States of America","institution_ids":["https://openalex.org/I102607778"]},{"raw_affiliation_string":"Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, Ohio, United States of America","institution_ids":["https://openalex.org/I102607778"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073097748","display_name":"Stephen F. Badylak","orcid":"https://orcid.org/0000-0003-3555-0689"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]},{"id":"https://openalex.org/I4210155891","display_name":"McGowan Institute for Regenerative Medicine","ror":"https://ror.org/04js6xx21","country_code":"US","type":"facility","lineage":["https://openalex.org/I170201317","https://openalex.org/I4210098814","https://openalex.org/I4210134769","https://openalex.org/I4210155891"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Stephen Badylak","raw_affiliation_strings":["Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America","McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America","institution_ids":["https://openalex.org/I170201317"]},{"raw_affiliation_string":"McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America","institution_ids":["https://openalex.org/I4210155891","https://openalex.org/I170201317"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5077250814","display_name":"Peng Jiang","orcid":"https://orcid.org/0000-0002-6057-7624"},"institutions":[{"id":"https://openalex.org/I102607778","display_name":"Cleveland State University","ror":"https://ror.org/002tx1f22","country_code":"US","type":"education","lineage":["https://openalex.org/I102607778"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Peng Jiang","raw_affiliation_strings":["Center for Gene Regulation in Health and Disease, Cleveland State University, Cleveland, Ohio, United States of America","Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, Ohio, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-6057-7624","affiliations":[{"raw_affiliation_string":"Center for Gene Regulation in Health and Disease, Cleveland State University, Cleveland, Ohio, United States of America","institution_ids":["https://openalex.org/I102607778"]},{"raw_affiliation_string":"Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, Ohio, United States of America","institution_ids":["https://openalex.org/I102607778"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":10,"corresponding_author_ids":["https://openalex.org/A5031643280"],"corresponding_institution_ids":["https://openalex.org/I102607778"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":1.5642,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.82643268,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"21","issue":"4","first_page":"e1012997","last_page":"e1012997"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10771","display_name":"Wound Healing and Treatments","score":0.9908999800682068,"subfield":{"id":"https://openalex.org/subfields/2742","display_name":"Rehabilitation"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T10771","display_name":"Wound Healing and Treatments","score":0.9908999800682068,"subfield":{"id":"https://openalex.org/subfields/2742","display_name":"Rehabilitation"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T11570","display_name":"Periodontal Regeneration and Treatments","score":0.987500011920929,"subfield":{"id":"https://openalex.org/subfields/2748","display_name":"Urology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10105","display_name":"Osteoarthritis Treatment and Mechanisms","score":0.9617000222206116,"subfield":{"id":"https://openalex.org/subfields/2745","display_name":"Rheumatology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/regenerative-medicine","display_name":"Regenerative medicine","score":0.7221241593360901},{"id":"https://openalex.org/keywords/regeneration","display_name":"Regeneration (biology)","score":0.6781467199325562},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6378991603851318},{"id":"https://openalex.org/keywords/regenerative-process","display_name":"Regenerative process","score":0.6217808723449707},{"id":"https://openalex.org/keywords/hox-gene","display_name":"Hox gene","score":0.566274106502533},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.5003907680511475},{"id":"https://openalex.org/keywords/bone-morphogenetic-protein-2","display_name":"Bone morphogenetic protein 2","score":0.4766422212123871},{"id":"https://openalex.org/keywords/wound-healing","display_name":"Wound healing","score":0.45790669322013855},{"id":"https://openalex.org/keywords/cell-biology","display_name":"Cell biology","score":0.4470396935939789},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.4095936715602875},{"id":"https://openalex.org/keywords/stem-cell","display_name":"Stem cell","score":0.35821887850761414},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3469616770744324},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.2961168885231018},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.23295366764068604},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.18175697326660156}],"concepts":[{"id":"https://openalex.org/C10854531","wikidata":"https://www.wikidata.org/wiki/Q1061415","display_name":"Regenerative medicine","level":3,"score":0.7221241593360901},{"id":"https://openalex.org/C171056886","wikidata":"https://www.wikidata.org/wiki/Q193119","display_name":"Regeneration (biology)","level":2,"score":0.6781467199325562},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6378991603851318},{"id":"https://openalex.org/C2780205056","wikidata":"https://www.wikidata.org/wiki/Q7308048","display_name":"Regenerative process","level":3,"score":0.6217808723449707},{"id":"https://openalex.org/C111039654","wikidata":"https://www.wikidata.org/wiki/Q253149","display_name":"Hox gene","level":4,"score":0.566274106502533},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.5003907680511475},{"id":"https://openalex.org/C30352789","wikidata":"https://www.wikidata.org/wiki/Q14903153","display_name":"Bone morphogenetic protein 2","level":3,"score":0.4766422212123871},{"id":"https://openalex.org/C2780269544","wikidata":"https://www.wikidata.org/wiki/Q1509074","display_name":"Wound healing","level":2,"score":0.45790669322013855},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.4470396935939789},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.4095936715602875},{"id":"https://openalex.org/C28328180","wikidata":"https://www.wikidata.org/wiki/Q48196","display_name":"Stem cell","level":2,"score":0.35821887850761414},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3469616770744324},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.2961168885231018},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.23295366764068604},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.18175697326660156},{"id":"https://openalex.org/C202751555","wikidata":"https://www.wikidata.org/wiki/Q221681","display_name":"In vitro","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000671","descriptor_name":"Amputation, Surgical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000671","descriptor_name":"Amputation, Surgical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000671","descriptor_name":"Amputation, Surgical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008264","descriptor_name":"Macrophages","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008264","descriptor_name":"Macrophages","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008264","descriptor_name":"Macrophages","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D008810","descriptor_name":"Mice, Inbred C57BL","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008810","descriptor_name":"Mice, Inbred C57BL","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008810","descriptor_name":"Mice, Inbred C57BL","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012038","descriptor_name":"Regeneration","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012038","descriptor_name":"Regeneration","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012038","descriptor_name":"Regeneration","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D014945","descriptor_name":"Wound Healing","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D014945","descriptor_name":"Wound Healing","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D014945","descriptor_name":"Wound Healing","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1371/journal.pcbi.1012997","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1012997","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:40203060","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40203060","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:doaj.org/article:277653be6dcd4819b74fe6b49abca40a","is_oa":true,"landing_page_url":"https://doaj.org/article/277653be6dcd4819b74fe6b49abca40a","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 21, Iss 4, p e1012997 (2025)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12011309","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12011309","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1012997","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1012997","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.41999998688697815}],"awards":[{"id":"https://openalex.org/G365834559","display_name":null,"funder_award_id":"AWD00001593","funder_id":"https://openalex.org/F4320337531","funder_display_name":"Defense Sciences Office, DARPA"}],"funders":[{"id":"https://openalex.org/F4320337531","display_name":"Defense Sciences Office, DARPA","ror":"https://ror.org/0447fe631"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":52,"referenced_works":["https://openalex.org/W273955616","https://openalex.org/W1456320107","https://openalex.org/W1554671829","https://openalex.org/W1702592964","https://openalex.org/W1753995919","https://openalex.org/W1973666758","https://openalex.org/W1985987855","https://openalex.org/W1999574084","https://openalex.org/W2006557479","https://openalex.org/W2025909669","https://openalex.org/W2064825670","https://openalex.org/W2067452822","https://openalex.org/W2071514232","https://openalex.org/W2073365757","https://openalex.org/W2079364490","https://openalex.org/W2107349791","https://openalex.org/W2124097252","https://openalex.org/W2124985265","https://openalex.org/W2140999940","https://openalex.org/W2166719147","https://openalex.org/W2353982544","https://openalex.org/W2473394283","https://openalex.org/W2585423788","https://openalex.org/W2612559606","https://openalex.org/W2767826728","https://openalex.org/W2781934183","https://openalex.org/W2789489527","https://openalex.org/W2792643794","https://openalex.org/W2899588238","https://openalex.org/W2945883683","https://openalex.org/W2952877459","https://openalex.org/W2998402306","https://openalex.org/W2998632984","https://openalex.org/W3007171906","https://openalex.org/W3033577414","https://openalex.org/W3085579791","https://openalex.org/W3089473423","https://openalex.org/W3101608900","https://openalex.org/W3125837796","https://openalex.org/W3129869677","https://openalex.org/W4229452144","https://openalex.org/W4294287712","https://openalex.org/W4298002814","https://openalex.org/W4306958347","https://openalex.org/W4316019276","https://openalex.org/W4319733385","https://openalex.org/W4384338096","https://openalex.org/W4385475981","https://openalex.org/W4401900147","https://openalex.org/W6610017368","https://openalex.org/W6693953293","https://openalex.org/W6749029207"],"related_works":["https://openalex.org/W76656838","https://openalex.org/W2793655825","https://openalex.org/W2163834077","https://openalex.org/W2399761608","https://openalex.org/W4385618182","https://openalex.org/W4288684134","https://openalex.org/W4292485472","https://openalex.org/W3031456766","https://openalex.org/W3033752604","https://openalex.org/W2550987455"],"abstract_inverted_index":{"In":[0,43],"the":[1,17,30,50,53,58,107,163,200,224,231],"mouse":[2],"distal":[3],"terminal":[4],"phalanx":[5],"(P3),":[6],"it":[7],"remains":[8],"mystery":[9],"why":[10],"amputation":[11,23,71],"at":[12],"less":[13],"than":[14],"33%":[15],"of":[16,153,171,199,213],"digit":[18],"results":[19],"in":[20,73,106,151,180,230],"regeneration,":[21,182],"while":[22],"exceeding":[24],"67%":[25],"leads":[26],"to":[27,48,56,89,111,133,234],"non-regeneration.":[28],"Unraveling":[29],"molecular":[31],"mechanisms":[32],"underlying":[33],"this":[34,44],"disparity":[35],"could":[36],"provide":[37],"crucial":[38],"insights":[39],"for":[40,177],"regenerative":[41,63,112,121,145,201,225],"medicine.":[42],"study,":[45],"we":[46,205],"aim":[47],"investigate":[49],"tissues":[51],"within":[52],"wound":[54,108],"bed":[55,109],"understand":[57],"tissue":[59],"microenvironment":[60],"associated":[61],"with":[62,76,84],"versus":[64],"non-regenerative":[65,97,123,147],"outcomes.":[66,124],"We":[67],"employed":[68],"a":[69,80,100,168,207],"P3-specific":[70],"model":[72,211],"mice,":[74],"integrated":[75],"time-series":[77],"RNA-seq":[78,220],"and":[79,86,122,146,160,190,217],"macrophage":[81,116],"assay":[82],"challenged":[83],"pro-":[85],"anti-inflammatory":[87],"cytokines,":[88],"explore":[90],"these":[91],"mechanisms.":[92],"Our":[93],"findings":[94],"revealed":[95],"that":[96,223],"digits":[98,126,148],"exhibit":[99],"greater":[101],"intense":[102],"early":[103,115],"transcriptional":[104],"response":[105,233],"compared":[110],"ones.":[113],"Furthermore,":[114],"phenotypes":[117],"differ":[118],"distinctly":[119],"between":[120,144],"Regenerative":[125],"also":[127],"display":[128],"unique":[129],"co-expression":[130],"modules":[131],"related":[132],"Bone":[134],"Morphogenetic":[135],"Protein":[136],"2":[137],"(Bmp2).":[138],"The":[139],"differentially":[140],"expressed":[141],"genes":[142],"(DEGs)":[143],"are":[149],"enriched":[150],"targets":[152],"several":[154],"transcription":[155,174],"factors,":[156,175],"such":[157],"as":[158,196],"HOXA11":[159],"HOXD11":[161],"from":[162,219],"HOX":[164],"gene":[165,202],"family,":[166],"showing":[167],"time-dependent":[169],"pattern":[170],"enrichment.":[172],"These":[173],"known":[176],"their":[178],"roles":[179],"bone":[181],"skeletal":[183],"patterning,":[184],"osteoblast":[185],"activity,":[186],"fracture":[187],"healing,":[188],"angiogenesis,":[189],"key":[191],"signaling":[192],"pathways,":[193],"may":[194,227],"act":[195],"master":[197],"regulators":[198],"signatures.":[203],"Additionally,":[204],"developed":[206],"deep":[208],"learning":[209],"AI":[210],"capable":[212],"predicting":[214],"post-amputation":[215],"time":[216],"level":[218],"data,":[221],"indicating":[222],"probability":[226],"be":[228],"\"encoded\"":[229],"transcriptomic":[232],"amputation.":[235]},"counts_by_year":[{"year":2026,"cited_by_count":2}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
