{"id":"https://openalex.org/W2153453980","doi":"https://doi.org/10.1371/journal.pcbi.1003734","title":"Epigenetic Landscapes Explain Partially Reprogrammed Cells and Identify Key Reprogramming Genes","display_name":"Epigenetic Landscapes Explain Partially Reprogrammed Cells and Identify Key Reprogramming Genes","publication_year":2014,"publication_date":"2014-08-14","ids":{"openalex":"https://openalex.org/W2153453980","doi":"https://doi.org/10.1371/journal.pcbi.1003734","mag":"2153453980","pmid":"https://pubmed.ncbi.nlm.nih.gov/25122086"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1003734","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003734","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003734&type=printable","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":["arxiv","crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003734&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5108197044","display_name":"Alex Lang","orcid":null},"institutions":[{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Alex H. Lang","raw_affiliation_strings":["Department of Physics, Boston University, Boston, Massachusetts, United States of America; Center for Regenerative Medicine, Boston University, Boston, Massachusetts, United States of America","Center for Regenerative Medicine, Boston University, Boston, Massachusetts, United States of America","Department of Physics, Boston University, Boston, Massachusetts, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Physics, Boston University, Boston, Massachusetts, United States of America; Center for Regenerative Medicine, Boston University, Boston, Massachusetts, United States of America","institution_ids":[]},{"raw_affiliation_string":"Center for Regenerative Medicine, Boston University, Boston, Massachusetts, United States of America","institution_ids":["https://openalex.org/I111088046"]},{"raw_affiliation_string":"Department of Physics, Boston University, Boston, Massachusetts, United States of America","institution_ids":["https://openalex.org/I111088046"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100444593","display_name":"Hu Li","orcid":"https://orcid.org/0000-0001-5957-5472"},"institutions":[{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hu Li","raw_affiliation_strings":["Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, United States of America","Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, United States of America","Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, United States of America","institution_ids":[]},{"raw_affiliation_string":"Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, United States of America","institution_ids":[]},{"raw_affiliation_string":"Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America","institution_ids":["https://openalex.org/I111088046"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065209470","display_name":"James J. Collins","orcid":"https://orcid.org/0000-0002-5560-8246"},"institutions":[{"id":"https://openalex.org/I1344073410","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90","country_code":"US","type":"facility","lineage":["https://openalex.org/I1344073410"]},{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James J. Collins","raw_affiliation_strings":["Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, United States of America; Howard Hughes Medical Institute, Boston, Massachusetts, United States of America; Center for BioDynamics, Boston University, Boston, Massachusetts, United States of America","Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America","Center for BioDynamics, Boston University, Boston, Massachusetts, United States of America","Howard Hughes Medical Institute, Boston, Massachusetts, United States of America","Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, United States of America; Howard Hughes Medical Institute, Boston, Massachusetts, United States of America; Center for BioDynamics, Boston University, Boston, Massachusetts, United States of America","institution_ids":[]},{"raw_affiliation_string":"Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America","institution_ids":["https://openalex.org/I111088046"]},{"raw_affiliation_string":"Center for BioDynamics, Boston University, Boston, Massachusetts, United States of America","institution_ids":["https://openalex.org/I111088046"]},{"raw_affiliation_string":"Howard Hughes Medical Institute, Boston, Massachusetts, United States of America","institution_ids":["https://openalex.org/I1344073410"]},{"raw_affiliation_string":"Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, United States of America","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5015366699","display_name":"Pankaj Mehta","orcid":"https://orcid.org/0000-0003-1290-5897"},"institutions":[{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Pankaj Mehta","raw_affiliation_strings":["Department of Physics, Boston University, Boston, Massachusetts, United States of America; Center for Regenerative Medicine, Boston University, Boston, Massachusetts, United States of America","Department of Physics, Boston University, Boston, Massachusetts, United States of America","Center for Regenerative Medicine, Boston University, Boston, Massachusetts, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Physics, Boston University, Boston, Massachusetts, United States of America; Center for Regenerative Medicine, Boston University, Boston, Massachusetts, United States of America","institution_ids":[]},{"raw_affiliation_string":"Department of Physics, Boston University, Boston, Massachusetts, United States of America","institution_ids":["https://openalex.org/I111088046"]},{"raw_affiliation_string":"Center for Regenerative Medicine, Boston University, Boston, Massachusetts, United States of America","institution_ids":["https://openalex.org/I111088046"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5015366699","https://openalex.org/A5108197044"],"corresponding_institution_ids":["https://openalex.org/I111088046"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":5.8471,"has_fulltext":true,"cited_by_count":125,"citation_normalized_percentile":{"value":0.97058556,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"10","issue":"8","first_page":"e1003734","last_page":"e1003734"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9986000061035156,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9986000061035156,"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/T10505","display_name":"Pluripotent Stem Cells Research","score":0.9965999722480774,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9948999881744385,"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/reprogramming","display_name":"Reprogramming","score":0.9449548721313477},{"id":"https://openalex.org/keywords/epigenetics","display_name":"Epigenetics","score":0.8232591152191162},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.7186204195022583},{"id":"https://openalex.org/keywords/cell-fate-determination","display_name":"Cell fate determination","score":0.5933255553245544},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.5237859487533569},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5226414203643799},{"id":"https://openalex.org/keywords/epigenesis","display_name":"Epigenesis","score":0.5001266002655029},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4672750234603882},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.44328102469444275},{"id":"https://openalex.org/keywords/dna-methylation","display_name":"DNA methylation","score":0.4086422324180603},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.378330796957016},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3372557759284973},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.2396152913570404}],"concepts":[{"id":"https://openalex.org/C77255625","wikidata":"https://www.wikidata.org/wiki/Q402093","display_name":"Reprogramming","level":3,"score":0.9449548721313477},{"id":"https://openalex.org/C41091548","wikidata":"https://www.wikidata.org/wiki/Q26939","display_name":"Epigenetics","level":3,"score":0.8232591152191162},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7186204195022583},{"id":"https://openalex.org/C163952510","wikidata":"https://www.wikidata.org/wiki/Q5058196","display_name":"Cell fate determination","level":4,"score":0.5933255553245544},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.5237859487533569},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5226414203643799},{"id":"https://openalex.org/C179463898","wikidata":"https://www.wikidata.org/wiki/Q10273301","display_name":"Epigenesis","level":5,"score":0.5001266002655029},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4672750234603882},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.44328102469444275},{"id":"https://openalex.org/C190727270","wikidata":"https://www.wikidata.org/wiki/Q874745","display_name":"DNA methylation","level":4,"score":0.4086422324180603},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.378330796957016},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3372557759284973},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.2396152913570404}],"mesh":[{"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":"D002478","descriptor_name":"Cells, Cultured","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002478","descriptor_name":"Cells, Cultured","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002478","descriptor_name":"Cells, Cultured","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":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013234","descriptor_name":"Stem Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013234","descriptor_name":"Stem Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013234","descriptor_name":"Stem Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018507","descriptor_name":"Gene Expression Regulation, Developmental","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D018507","descriptor_name":"Gene Expression Regulation, Developmental","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D018507","descriptor_name":"Gene Expression Regulation, Developmental","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D044127","descriptor_name":"Epigenesis, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D044127","descriptor_name":"Epigenesis, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D044127","descriptor_name":"Epigenesis, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D065150","descriptor_name":"Cellular Reprogramming","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D065150","descriptor_name":"Cellular Reprogramming","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D065150","descriptor_name":"Cellular Reprogramming","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":8,"locations":[{"id":"doi:10.1371/journal.pcbi.1003734","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003734","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003734&type=printable","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":"pmh:oai:arXiv.org:1211.3133","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1211.3133","pdf_url":"https://arxiv.org/pdf/1211.3133","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":null,"raw_type":"text"},{"id":"pmid:25122086","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25122086","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:dash.harvard.edu:1/12785891","is_oa":true,"landing_page_url":"http://nrs.harvard.edu/urn-3:HUL.InstRepos:12785891","pdf_url":null,"source":{"id":"https://openalex.org/S4306401540","display_name":"Digital Access to Scholarship at Harvard (DASH) (Harvard University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I136199984","host_organization_name":"Harvard University","host_organization_lineage":["https://openalex.org/I136199984"],"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":"","raw_type":"Journal Article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.726.1631","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.726.1631","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://physics.bu.edu/%7Epankajm/Papers/Landscapes.pdf","raw_type":"text"},{"id":"pmh:oai:doaj.org/article:8a4fd51465244b7eabf47a56bd2bd5d2","is_oa":true,"landing_page_url":"https://doaj.org/article/8a4fd51465244b7eabf47a56bd2bd5d2","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-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 10, Iss 8, p e1003734 (2014)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:3105985","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4133049","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:figshare.com:article/1140010","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/_Epigenetic_Landscapes_Explain_Partially_Reprogrammed_Cells_and_Identify_Key_Reprogramming_Genes_/1140010","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"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":"","raw_type":"Dataset"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1003734","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003734","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003734&type=printable","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":[{"score":0.5600000023841858,"id":"https://metadata.un.org/sdg/11","display_name":"Sustainable cities and communities"}],"awards":[{"id":"https://openalex.org/G3826294261","display_name":null,"funder_award_id":"DGE-1247312","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2153453980.pdf","grobid_xml":"https://content.openalex.org/works/W2153453980.grobid-xml"},"referenced_works_count":72,"referenced_works":["https://openalex.org/W134271320","https://openalex.org/W614012683","https://openalex.org/W936759852","https://openalex.org/W1591423336","https://openalex.org/W1643429854","https://openalex.org/W1884390770","https://openalex.org/W1962432205","https://openalex.org/W1967729506","https://openalex.org/W1969015262","https://openalex.org/W1970084119","https://openalex.org/W1970779075","https://openalex.org/W1971445167","https://openalex.org/W1972773888","https://openalex.org/W1974248456","https://openalex.org/W1979927933","https://openalex.org/W1983574866","https://openalex.org/W1983889411","https://openalex.org/W1986595047","https://openalex.org/W1989315333","https://openalex.org/W2002249792","https://openalex.org/W2008365696","https://openalex.org/W2014706477","https://openalex.org/W2016180314","https://openalex.org/W2017050785","https://openalex.org/W2017438799","https://openalex.org/W2017840637","https://openalex.org/W2027357228","https://openalex.org/W2029182425","https://openalex.org/W2029991507","https://openalex.org/W2031195065","https://openalex.org/W2038596854","https://openalex.org/W2050953282","https://openalex.org/W2051893135","https://openalex.org/W2056401732","https://openalex.org/W2057641653","https://openalex.org/W2063854986","https://openalex.org/W2069129925","https://openalex.org/W2072319015","https://openalex.org/W2075406901","https://openalex.org/W2076486071","https://openalex.org/W2081496349","https://openalex.org/W2091142825","https://openalex.org/W2098597036","https://openalex.org/W2099143970","https://openalex.org/W2108020239","https://openalex.org/W2112246162","https://openalex.org/W2117249342","https://openalex.org/W2123806948","https://openalex.org/W2124486107","https://openalex.org/W2125987139","https://openalex.org/W2128084896","https://openalex.org/W2132278571","https://openalex.org/W2134759932","https://openalex.org/W2136541538","https://openalex.org/W2141545875","https://openalex.org/W2143658931","https://openalex.org/W2147238273","https://openalex.org/W2147284744","https://openalex.org/W2155574792","https://openalex.org/W2161224111","https://openalex.org/W2167202160","https://openalex.org/W2167874626","https://openalex.org/W2169187183","https://openalex.org/W2171755502","https://openalex.org/W2177721432","https://openalex.org/W2331030820","https://openalex.org/W2504767107","https://openalex.org/W2962692602","https://openalex.org/W3022482973","https://openalex.org/W3122281318","https://openalex.org/W3147726452","https://openalex.org/W4298064144"],"related_works":["https://openalex.org/W2947488007","https://openalex.org/W2725308582","https://openalex.org/W2908970830","https://openalex.org/W2966780451","https://openalex.org/W4200563924","https://openalex.org/W2951567297","https://openalex.org/W2540215816","https://openalex.org/W2507652170","https://openalex.org/W2046783559","https://openalex.org/W193469126"],"abstract_inverted_index":{"A":[0],"common":[1],"metaphor":[2],"for":[3,30,110,123],"describing":[4],"development":[5],"is":[6,47],"a":[7,21,28,48,69,120],"rugged":[8],"\"epigenetic":[9],"landscape\"":[10],"where":[11],"cell":[12,45,89,114],"fates":[13],"are":[14,68,119],"represented":[15],"as":[16],"attracting":[17],"valleys":[18],"resulting":[19],"from":[20,41,87],"complex":[22],"regulatory":[23],"network.":[24],"Here,":[25],"we":[26],"introduce":[27],"framework":[29],"explicitly":[31],"constructing":[32],"epigenetic":[33,117],"landscapes":[34,118],"that":[35,64,77,84],"combines":[36],"genomic":[37],"data":[38],"with":[39],"techniques":[40],"spin-glass":[42],"physics.":[43],"Each":[44],"fate":[46,55],"dynamic":[49],"attractor,":[50],"yet":[51],"cells":[52,67,80],"can":[53],"change":[54],"in":[56],"response":[57],"to":[58,112],"external":[59],"signals.":[60],"Our":[61,99],"model":[62,100],"suggests":[63],"partially":[65,78],"reprogrammed":[66,79],"natural":[70],"consequence":[71],"of":[72],"high-dimensional":[73],"landscapes,":[74],"and":[75,105],"predicts":[76],"should":[81],"be":[82],"hybrids":[83],"co-express":[85],"genes":[86],"multiple":[88],"fates.":[90],"We":[91],"verify":[92],"this":[93],"prediction":[94],"by":[95],"reanalyzing":[96],"existing":[97],"datasets.":[98],"reproduces":[101],"known":[102],"reprogramming":[103,111],"protocols":[104],"identifies":[106],"candidate":[107],"transcription":[108],"factors":[109],"novel":[113],"fates,":[115],"suggesting":[116],"powerful":[121],"paradigm":[122],"understanding":[124],"cellular":[125],"identity.":[126]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":11},{"year":2022,"cited_by_count":11},{"year":2021,"cited_by_count":12},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":13},{"year":2018,"cited_by_count":14},{"year":2017,"cited_by_count":16},{"year":2016,"cited_by_count":14},{"year":2015,"cited_by_count":9},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":1}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
