{"id":"https://openalex.org/W3207202060","doi":"https://doi.org/10.1093/bioinformatics/btab735","title":"Phylotranscriptomic patterns of network stochasticity and pathway dynamics during embryogenesis","display_name":"Phylotranscriptomic patterns of network stochasticity and pathway dynamics during embryogenesis","publication_year":2021,"publication_date":"2021-10-19","ids":{"openalex":"https://openalex.org/W3207202060","doi":"https://doi.org/10.1093/bioinformatics/btab735","mag":"3207202060","pmid":"https://pubmed.ncbi.nlm.nih.gov/34677580"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab735","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab735","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5016941402","display_name":"Kuei-Yueh Ko","orcid":"https://orcid.org/0000-0001-8564-8524"},"institutions":[{"id":"https://openalex.org/I16733864","display_name":"National Taiwan University","ror":"https://ror.org/05bqach95","country_code":"TW","type":"education","lineage":["https://openalex.org/I16733864"]},{"id":"https://openalex.org/I170897317","display_name":"Duke University","ror":"https://ror.org/00py81415","country_code":"US","type":"education","lineage":["https://openalex.org/I170897317"]}],"countries":["TW","US"],"is_corresponding":false,"raw_author_name":"Kuei-Yueh Ko","raw_affiliation_strings":["Computational Biology and Bioinformatics Program, Duke University , Durham, NC 27710, USA","Genome and Systems Biology Degree Program, National Taiwan University , Taipei 106, Taiwan"],"raw_orcid":"https://orcid.org/0000-0001-8564-8524","affiliations":[{"raw_affiliation_string":"Computational Biology and Bioinformatics Program, Duke University , Durham, NC 27710, USA","institution_ids":["https://openalex.org/I170897317"]},{"raw_affiliation_string":"Genome and Systems Biology Degree Program, National Taiwan University , Taipei 106, Taiwan","institution_ids":["https://openalex.org/I16733864"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047081427","display_name":"Cho-Yi Chen","orcid":"https://orcid.org/0000-0002-7915-7814"},"institutions":[{"id":"https://openalex.org/I148366613","display_name":"National Yang Ming Chiao Tung University","ror":"https://ror.org/00se2k293","country_code":"TW","type":"education","lineage":["https://openalex.org/I148366613"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Cho-Yi Chen","raw_affiliation_strings":["Institute of Biomedical Informatics, National Yang Ming Chiao Tung University , Taipei 112, Taiwan"],"raw_orcid":"https://orcid.org/0000-0002-7915-7814","affiliations":[{"raw_affiliation_string":"Institute of Biomedical Informatics, National Yang Ming Chiao Tung University , Taipei 112, Taiwan","institution_ids":["https://openalex.org/I148366613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052313712","display_name":"Hsueh\u2010Fen Juan","orcid":"https://orcid.org/0000-0003-4876-3309"},"institutions":[{"id":"https://openalex.org/I16733864","display_name":"National Taiwan University","ror":"https://ror.org/05bqach95","country_code":"TW","type":"education","lineage":["https://openalex.org/I16733864"]}],"countries":["TW"],"is_corresponding":true,"raw_author_name":"Hsueh-Fen Juan","raw_affiliation_strings":["Department of Life Science, Graduate Institute of Biomedical Electronics and Bioinformatics, Center for Computational and Systems Biology, National Taiwan University , Taipei 106, Taiwan","Genome and Systems Biology Degree Program, National Taiwan University , Taipei 106, Taiwan"],"raw_orcid":"https://orcid.org/0000-0003-4876-3309","affiliations":[{"raw_affiliation_string":"Department of Life Science, Graduate Institute of Biomedical Electronics and Bioinformatics, Center for Computational and Systems Biology, National Taiwan University , Taipei 106, Taiwan","institution_ids":["https://openalex.org/I16733864"]},{"raw_affiliation_string":"Genome and Systems Biology Degree Program, National Taiwan University , Taipei 106, Taiwan","institution_ids":["https://openalex.org/I16733864"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5049081893","display_name":"Hsuan\u2010Cheng Huang","orcid":"https://orcid.org/0000-0002-3386-0934"},"institutions":[{"id":"https://openalex.org/I148366613","display_name":"National Yang Ming Chiao Tung University","ror":"https://ror.org/00se2k293","country_code":"TW","type":"education","lineage":["https://openalex.org/I148366613"]}],"countries":["TW"],"is_corresponding":true,"raw_author_name":"Hsuan-Cheng Huang","raw_affiliation_strings":["Institute of Biomedical Informatics, National Yang Ming Chiao Tung University , Taipei 112, Taiwan"],"raw_orcid":"https://orcid.org/0000-0002-3386-0934","affiliations":[{"raw_affiliation_string":"Institute of Biomedical Informatics, National Yang Ming Chiao Tung University , Taipei 112, Taiwan","institution_ids":["https://openalex.org/I148366613"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5049081893","https://openalex.org/A5052313712"],"corresponding_institution_ids":["https://openalex.org/I148366613","https://openalex.org/I16733864"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.10115574,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":98},"biblio":{"volume":"38","issue":"3","first_page":"763","last_page":"769"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.6287999749183655,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.6287999749183655,"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/T12417","display_name":"Morphological variations and asymmetry","score":0.10909999907016754,"subfield":{"id":"https://openalex.org/subfields/2608","display_name":"Geometry and Topology"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10268","display_name":"Developmental Biology and Gene Regulation","score":0.0210999995470047,"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/dynamics","display_name":"Dynamics (music)","score":0.6758518815040588},{"id":"https://openalex.org/keywords/embryogenesis","display_name":"Embryogenesis","score":0.5233696699142456},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.47962889075279236},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3547084927558899},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2997041344642639},{"id":"https://openalex.org/keywords/embryo","display_name":"Embryo","score":0.25011759996414185},{"id":"https://openalex.org/keywords/cell-biology","display_name":"Cell biology","score":0.19960084557533264},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.07497543096542358}],"concepts":[{"id":"https://openalex.org/C145912823","wikidata":"https://www.wikidata.org/wiki/Q113558","display_name":"Dynamics (music)","level":2,"score":0.6758518815040588},{"id":"https://openalex.org/C87073359","wikidata":"https://www.wikidata.org/wiki/Q33196","display_name":"Embryogenesis","level":3,"score":0.5233696699142456},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.47962889075279236},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3547084927558899},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2997041344642639},{"id":"https://openalex.org/C196843134","wikidata":"https://www.wikidata.org/wiki/Q33196","display_name":"Embryo","level":2,"score":0.25011759996414185},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.19960084557533264},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.07497543096542358},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D047108","descriptor_name":"Embryonic Development","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D047108","descriptor_name":"Embryonic Development","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D047108","descriptor_name":"Embryonic Development","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btab735","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab735","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34677580","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34677580","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land","score":0.5799999833106995}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":44,"referenced_works":["https://openalex.org/W1768482373","https://openalex.org/W1863458465","https://openalex.org/W1964761197","https://openalex.org/W1977280998","https://openalex.org/W1982510939","https://openalex.org/W1992532041","https://openalex.org/W2001547980","https://openalex.org/W2002249792","https://openalex.org/W2005036862","https://openalex.org/W2013944141","https://openalex.org/W2016893462","https://openalex.org/W2026907845","https://openalex.org/W2046781332","https://openalex.org/W2052574531","https://openalex.org/W2056757171","https://openalex.org/W2062826759","https://openalex.org/W2064174293","https://openalex.org/W2074468058","https://openalex.org/W2076849630","https://openalex.org/W2080252585","https://openalex.org/W2081773126","https://openalex.org/W2083721700","https://openalex.org/W2106198931","https://openalex.org/W2128227526","https://openalex.org/W2133357256","https://openalex.org/W2140638448","https://openalex.org/W2159707944","https://openalex.org/W2161153002","https://openalex.org/W2161466790","https://openalex.org/W2170624222","https://openalex.org/W2283570988","https://openalex.org/W2320417950","https://openalex.org/W2782262419","https://openalex.org/W2888213668","https://openalex.org/W2950408703","https://openalex.org/W3041924726","https://openalex.org/W3099262248","https://openalex.org/W3104763962","https://openalex.org/W3122281318","https://openalex.org/W4237629094","https://openalex.org/W4242631111","https://openalex.org/W4247662742","https://openalex.org/W6637809728","https://openalex.org/W6753814428"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2478288626","https://openalex.org/W2350741829","https://openalex.org/W2530322880","https://openalex.org/W1596801655"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1],"hourglass":[2],"model":[3,8,43],"is":[4],"a":[5,18,74,166],"popular":[6],"evo-devo":[7],"depicting":[9],"that":[10,33,78,156,205],"the":[11,15,25,54,90,94,122,135,138,147,157,188,196,200,224],"developmental":[12,19,50,128,143,152,201],"constraints":[13,92],"in":[14,35,83,89,115,130,141,171],"middle":[16],"of":[17,112,124,174,190,211],"process":[20],"are":[21,27,63,221,231],"higher,":[22],"and":[23,37,57,76,102,164,203],"hence":[24],"phenotypes":[26],"evolutionarily":[28],"more":[29],"conserved,":[30],"than":[31],"those":[32],"occur":[34],"early":[36],"late":[38],"ontogeny":[39],"stages.":[40,216,226],"Although":[41],"this":[42,61,70],"has":[44],"been":[45],"supported":[46],"by":[47,133],"studies":[48],"analyzing":[49],"gene":[51],"expression":[52],"data,":[53],"evolutionary":[55],"explanation":[56],"molecular":[58],"mechanism":[59],"behind":[60],"phenomenon":[62],"not":[64],"fully":[65],"understood":[66],"yet.":[67],"To":[68,181],"approach":[69],"problem,":[71],"Raff":[72],"proposed":[73],"hypothesis":[75,170],"claimed":[77,114],"higher":[79,218],"interconnectivity":[80,113],"among":[81,127,176],"elements":[82],"an":[84,161],"organism":[85],"during":[86,179,187],"organogenesis":[87],"resulted":[88],"larger":[91],"at":[93,223,233],"mid-developmental":[95,225],"stage.":[96,144],"By":[97,145],"employing":[98],"stochastic":[99],"network":[100,125,140,148,158,191],"analysis":[101],"gene-set":[103],"pathway":[104,197],"analysis,":[105],"we":[106,154,193],"aim":[107],"to":[108],"demonstrate":[109],"such":[110,165],"changes":[111,123,173],"Raff's":[116,169],"hypothesis.":[117],"RESULTS:":[118],"We":[119],"first":[120],"compared":[121],"randomness":[126],"processes":[129,213],"different":[131,215],"species":[132,206],"measuring":[134],"stochasticity":[136,159],"within":[137],"biological":[139,177,184,212],"each":[142,151],"tracking":[146],"entropy":[149],"along":[150,199],"process,":[153],"found":[155,204,222],"follows":[160],"anti-hourglass":[162],"trajectory,":[163],"pattern":[167],"supports":[168],"dynamic":[172],"interconnections":[175],"modules":[178],"development.":[180],"understand":[182],"which":[183],"functions":[185],"change":[186],"transition":[189],"stochasticity,":[192],"sketched":[194],"out":[195],"dynamics":[198],"stages":[202],"may":[207],"activate":[208],"similar":[209],"groups":[210],"across":[214],"Moreover,":[217],"interspecies":[219],"correlations":[220],"SUPPLEMENTARY":[227],"INFORMATION:":[228],"Supplementary":[229],"data":[230],"available":[232],"Bioinformatics":[234],"online.":[235]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
