{"id":"https://openalex.org/W2027539967","doi":"https://doi.org/10.1186/1471-2105-15-269","title":"Study of cell differentiation by phylogenetic analysis using histone modification data","display_name":"Study of cell differentiation by phylogenetic analysis using histone modification data","publication_year":2014,"publication_date":"2014-08-08","ids":{"openalex":"https://openalex.org/W2027539967","doi":"https://doi.org/10.1186/1471-2105-15-269","mag":"2027539967","pmid":"https://pubmed.ncbi.nlm.nih.gov/25104072"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-15-269","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-15-269","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-269","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-269","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5034496465","display_name":"Nishanth Ulhas Nair","orcid":"https://orcid.org/0000-0002-8832-0329"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I5124864","display_name":"\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne","ror":"https://ror.org/02s376052","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I5124864"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Nishanth Ulhas Nair","raw_affiliation_strings":["School of Computer and Communication Sciences, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL), EPFL IC IIF LCBB, INJ 211 (Batiment INJ), Station 14, CH-1015, Lausanne, Switzerland","Swiss Institute of Bioinformatics, Lausanne, Switzerland","School of Computer and Communication Sciences, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL), EPFL IC IIF LCBB, INJ 211 (Batiment INJ), Lausanne, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer and Communication Sciences, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL), EPFL IC IIF LCBB, INJ 211 (Batiment INJ), Station 14, CH-1015, Lausanne, Switzerland","institution_ids":["https://openalex.org/I5124864"]},{"raw_affiliation_string":"Swiss Institute of Bioinformatics, Lausanne, Switzerland","institution_ids":["https://openalex.org/I12708293"]},{"raw_affiliation_string":"School of Computer and Communication Sciences, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL), EPFL IC IIF LCBB, INJ 211 (Batiment INJ), Lausanne, Switzerland","institution_ids":["https://openalex.org/I5124864"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079714822","display_name":"Yu Lin","orcid":"https://orcid.org/0000-0001-6339-2644"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yu Lin","raw_affiliation_strings":["Department of Computer Science and Engineering, University of California, San Diego, San Diego, USA","Department of Computer Science and Engineering , University of California , San Diego, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, University of California, San Diego, San Diego, USA","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Department of Computer Science and Engineering , University of California , San Diego, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061755328","display_name":"Ana Manasovska","orcid":null},"institutions":[{"id":"https://openalex.org/I5124864","display_name":"\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne","ror":"https://ror.org/02s376052","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I5124864"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Ana Manasovska","raw_affiliation_strings":["School of Computer and Communication Sciences, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL), EPFL IC IIF LCBB, INJ 211 (Batiment INJ), Station 14, CH-1015, Lausanne, Switzerland","School of Computer and Communication Sciences, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL), EPFL IC IIF LCBB, INJ 211 (Batiment INJ), Lausanne, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer and Communication Sciences, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL), EPFL IC IIF LCBB, INJ 211 (Batiment INJ), Station 14, CH-1015, Lausanne, Switzerland","institution_ids":["https://openalex.org/I5124864"]},{"raw_affiliation_string":"School of Computer and Communication Sciences, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL), EPFL IC IIF LCBB, INJ 211 (Batiment INJ), Lausanne, Switzerland","institution_ids":["https://openalex.org/I5124864"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034030337","display_name":"Jelena Anti\u0107","orcid":null},"institutions":[{"id":"https://openalex.org/I5124864","display_name":"\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne","ror":"https://ror.org/02s376052","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I5124864"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Jelena Antic","raw_affiliation_strings":["School of Computer and Communication Sciences, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL), EPFL IC IIF LCBB, INJ 211 (Batiment INJ), Station 14, CH-1015, Lausanne, Switzerland","School of Computer and Communication Sciences, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL), EPFL IC IIF LCBB, INJ 211 (Batiment INJ), Lausanne, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer and Communication Sciences, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL), EPFL IC IIF LCBB, INJ 211 (Batiment INJ), Station 14, CH-1015, Lausanne, Switzerland","institution_ids":["https://openalex.org/I5124864"]},{"raw_affiliation_string":"School of Computer and Communication Sciences, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL), EPFL IC IIF LCBB, INJ 211 (Batiment INJ), Lausanne, Switzerland","institution_ids":["https://openalex.org/I5124864"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042906861","display_name":"Paulina Grnarova","orcid":null},"institutions":[{"id":"https://openalex.org/I5124864","display_name":"\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne","ror":"https://ror.org/02s376052","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I5124864"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Paulina Grnarova","raw_affiliation_strings":["School of Computer and Communication Sciences, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL), EPFL IC IIF LCBB, INJ 211 (Batiment INJ), Station 14, CH-1015, Lausanne, Switzerland","School of Computer and Communication Sciences, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL), EPFL IC IIF LCBB, INJ 211 (Batiment INJ), Lausanne, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer and Communication Sciences, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL), EPFL IC IIF LCBB, INJ 211 (Batiment INJ), Station 14, CH-1015, Lausanne, Switzerland","institution_ids":["https://openalex.org/I5124864"]},{"raw_affiliation_string":"School of Computer and Communication Sciences, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL), EPFL IC IIF LCBB, INJ 211 (Batiment INJ), Lausanne, Switzerland","institution_ids":["https://openalex.org/I5124864"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087641795","display_name":"Avinash Sahu","orcid":"https://orcid.org/0000-0002-2193-6276"},"institutions":[{"id":"https://openalex.org/I66946132","display_name":"University of Maryland, College Park","ror":"https://ror.org/047s2c258","country_code":"US","type":"education","lineage":["https://openalex.org/I66946132"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Avinash Das Sahu","raw_affiliation_strings":["Department of Computer Science, University of Maryland, College Park, Maryland, USA","Dept of Computer Science, University of Maryland, College Park, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Maryland, College Park, Maryland, USA","institution_ids":["https://openalex.org/I66946132"]},{"raw_affiliation_string":"Dept of Computer Science, University of Maryland, College Park, USA","institution_ids":["https://openalex.org/I66946132"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103270230","display_name":"Philipp B\u00fccher","orcid":"https://orcid.org/0000-0003-4824-885X"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I5124864","display_name":"\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne","ror":"https://ror.org/02s376052","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I5124864"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Philipp Bucher","raw_affiliation_strings":["School of Computer and Communication Sciences, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL), EPFL IC IIF LCBB, INJ 211 (Batiment INJ), Station 14, CH-1015 Lausanne, Switzerland. philipp.bucher@epfl.ch","School of Life Sciences, Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL), Lausanne, Switzerland","\u2021Swiss Institute of Bioinformatics, Lausanne, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer and Communication Sciences, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL), EPFL IC IIF LCBB, INJ 211 (Batiment INJ), Station 14, CH-1015 Lausanne, Switzerland. philipp.bucher@epfl.ch","institution_ids":["https://openalex.org/I5124864"]},{"raw_affiliation_string":"School of Life Sciences, Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL), Lausanne, Switzerland","institution_ids":["https://openalex.org/I5124864"]},{"raw_affiliation_string":"\u2021Swiss Institute of Bioinformatics, Lausanne, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5059287546","display_name":"Bernard M. E. Moret","orcid":"https://orcid.org/0000-0003-1549-4544"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I5124864","display_name":"\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne","ror":"https://ror.org/02s376052","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I5124864"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Bernard ME Moret","raw_affiliation_strings":["School of Computer and Communication Sciences, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL), EPFL IC IIF LCBB, INJ 211 (Batiment INJ), Station 14, CH-1015, Lausanne, Switzerland","Swiss Institute of Bioinformatics, Lausanne, Switzerland","School of Computer and Communication Sciences, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL), EPFL IC IIF LCBB, INJ 211 (Batiment INJ), Lausanne, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer and Communication Sciences, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL), EPFL IC IIF LCBB, INJ 211 (Batiment INJ), Station 14, CH-1015, Lausanne, Switzerland","institution_ids":["https://openalex.org/I5124864"]},{"raw_affiliation_string":"Swiss Institute of Bioinformatics, Lausanne, Switzerland","institution_ids":["https://openalex.org/I12708293"]},{"raw_affiliation_string":"School of Computer and Communication Sciences, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL), EPFL IC IIF LCBB, INJ 211 (Batiment INJ), Lausanne, Switzerland","institution_ids":["https://openalex.org/I5124864"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5059287546","https://openalex.org/A5103270230"],"corresponding_institution_ids":["https://openalex.org/I12708293","https://openalex.org/I5124864"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.9772,"has_fulltext":true,"cited_by_count":24,"citation_normalized_percentile":{"value":0.74386985,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"15","issue":"1","first_page":"269","last_page":"269"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.845300018787384,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.845300018787384,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.05570000037550926,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.013100000098347664,"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/histone","display_name":"Histone","score":0.7810821533203125},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6101155281066895},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5664933323860168},{"id":"https://openalex.org/keywords/cellular-differentiation","display_name":"Cellular differentiation","score":0.5510894060134888},{"id":"https://openalex.org/keywords/cell-type","display_name":"Cell type","score":0.5394777059555054},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.46178773045539856},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.4566236734390259},{"id":"https://openalex.org/keywords/epigenetics","display_name":"Epigenetics","score":0.43825194239616394},{"id":"https://openalex.org/keywords/biological-data","display_name":"Biological data","score":0.4355141818523407},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.42424076795578003},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4078948497772217},{"id":"https://openalex.org/keywords/cell","display_name":"Cell","score":0.3702763319015503},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.34597915410995483},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.20167222619056702},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.15863856673240662},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.14222407341003418}],"concepts":[{"id":"https://openalex.org/C64927066","wikidata":"https://www.wikidata.org/wiki/Q36293","display_name":"Histone","level":3,"score":0.7810821533203125},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6101155281066895},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5664933323860168},{"id":"https://openalex.org/C148738053","wikidata":"https://www.wikidata.org/wiki/Q210861","display_name":"Cellular differentiation","level":3,"score":0.5510894060134888},{"id":"https://openalex.org/C189014844","wikidata":"https://www.wikidata.org/wiki/Q189118","display_name":"Cell type","level":3,"score":0.5394777059555054},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.46178773045539856},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.4566236734390259},{"id":"https://openalex.org/C41091548","wikidata":"https://www.wikidata.org/wiki/Q26939","display_name":"Epigenetics","level":3,"score":0.43825194239616394},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.4355141818523407},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.42424076795578003},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4078948497772217},{"id":"https://openalex.org/C1491633281","wikidata":"https://www.wikidata.org/wiki/Q7868","display_name":"Cell","level":2,"score":0.3702763319015503},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.34597915410995483},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.20167222619056702},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.15863856673240662},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.14222407341003418}],"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":"D002454","descriptor_name":"Cell Differentiation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006657","descriptor_name":"Histones","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006657","descriptor_name":"Histones","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006657","descriptor_name":"Histones","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006657","descriptor_name":"Histones","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006657","descriptor_name":"Histones","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006657","descriptor_name":"Histones","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006657","descriptor_name":"Histones","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006657","descriptor_name":"Histones","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057890","descriptor_name":"Epigenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057890","descriptor_name":"Epigenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057890","descriptor_name":"Epigenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057890","descriptor_name":"Epigenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/1471-2105-15-269","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-15-269","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-269","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:25104072","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25104072","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:4138389","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4138389","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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:infoscience.epfl.ch:202426","is_oa":true,"landing_page_url":"http://infoscience.epfl.ch/record/202426","pdf_url":null,"source":{"id":"https://openalex.org/S4306400487","display_name":"Infoscience (Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:openresearch-repository.anu.edu.au:1885/153020","is_oa":false,"landing_page_url":"http://hdl.handle.net/1885/153020","pdf_url":null,"source":{"id":"https://openalex.org/S4306402539","display_name":"ANU Open Research (Australian National University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I118347636","host_organization_name":"Australian National University","host_organization_lineage":["https://openalex.org/I118347636"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Journal article"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-15-269","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-15-269","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-269","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320320924","display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","ror":"https://ror.org/00yjd3n13"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2027539967.pdf","grobid_xml":"https://content.openalex.org/works/W2027539967.grobid-xml"},"referenced_works_count":23,"referenced_works":["https://openalex.org/W33797842","https://openalex.org/W953729042","https://openalex.org/W1544691147","https://openalex.org/W1590074528","https://openalex.org/W1979594866","https://openalex.org/W1987055178","https://openalex.org/W1997437810","https://openalex.org/W2015416439","https://openalex.org/W2017840637","https://openalex.org/W2019229253","https://openalex.org/W2065579185","https://openalex.org/W2072977772","https://openalex.org/W2081942683","https://openalex.org/W2097706568","https://openalex.org/W2106179083","https://openalex.org/W2119885620","https://openalex.org/W2120819924","https://openalex.org/W2143027433","https://openalex.org/W2146734921","https://openalex.org/W2164819701","https://openalex.org/W2171808845","https://openalex.org/W2952900934","https://openalex.org/W3104066961"],"related_works":["https://openalex.org/W2415545834","https://openalex.org/W2069695727","https://openalex.org/W2416898748","https://openalex.org/W2150084125","https://openalex.org/W2118505788","https://openalex.org/W1802639773","https://openalex.org/W4239910696","https://openalex.org/W1975186375","https://openalex.org/W4225694350","https://openalex.org/W3192072182"],"abstract_inverted_index":{"BACKGROUND:":[0],"In":[1,44],"cell":[2,5,53,131,171,184,207,223],"differentiation,":[3],"a":[4,7,14,36,49,77,200],"of":[6,13,52,72,79,115,126,147,166,182,206,222],"less":[8],"specialized":[9,16],"type":[10,185],"becomes":[11],"one":[12],"more":[15],"type,":[17,150],"even":[18],"though":[19],"all":[20],"cells":[21,116,146],"have":[22],"the":[23,40,70,135,148,155,179,197,204,220],"same":[24,149],"genome.":[25],"Transcription":[26],"factors":[27],"and":[28,55,75,89,95,151,177],"epigenetic":[29],"marks":[30],"like":[31,163],"histone":[32,64,127,167,188],"modifications":[33,128],"can":[34,215],"play":[35],"significant":[37],"role":[38],"in":[39],"differentiation":[41,56,172],"process.":[42,173],"RESULTS:":[43],"this":[45],"paper,":[46],"we":[47,194],"present":[48],"simple":[50],"analysis":[51],"types":[54,114],"paths":[57],"using":[58,134],"phylogenetic":[59,101],"inference":[60,102],"based":[61],"on":[62,123],"ChIP-Seq":[63,93],"modification":[65,168,189],"data.":[66,190],"We":[67,83,119,153,175,209],"precisely":[68],"defined":[69],"notion":[71],"cell-type":[73,108,213],"trees":[74,109,186,214],"provided":[76],"procedure":[78],"building":[80],"such":[81],"trees.":[82],"propose":[84],"new":[85,201],"data":[86,94],"representation":[87],"techniques":[88],"distance":[90],"measures":[91],"for":[92,129],"use":[96,154],"these":[97],"together":[98],"with":[99],"standard":[100],"methods":[103],"to":[104,137,157,199,203,218],"build":[105],"biologically":[106],"meaningful":[107],"that":[110],"indicate":[111],"how":[112,212],"diverse":[113],"are":[117],"related.":[118],"demonstrate":[120],"our":[121],"approach":[122,202],"various":[124,130,139],"kinds":[125],"types,":[132],"also":[133,210],"datasets":[136],"explore":[138],"issues":[140],"surrounding":[141],"replicate":[142],"data,":[143],"variability":[144],"between":[145],"robustness.":[152],"results":[156,193],"get":[158],"some":[159],"interesting":[160],"biological":[161],"findings":[162],"important":[164],"patterns":[165],"changes":[169],"during":[170],"CONCLUSIONS:":[174],"introduced":[176],"studied":[178],"novel":[180],"problem":[181],"inferring":[183],"from":[187],"The":[191],"promising":[192],"obtain":[195],"point":[196],"way":[198],"study":[205,219],"differentiation.":[208],"discuss":[211],"be":[216],"used":[217],"evolution":[221],"types.":[224]},"counts_by_year":[{"year":2023,"cited_by_count":11},{"year":2022,"cited_by_count":2},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":1}],"updated_date":"2026-07-02T09:51:11.867554","created_date":"2025-10-10T00:00:00"}
