{"id":"https://openalex.org/W7213473111","doi":"https://doi.org/10.64898/2026.09.15.751584","title":"Enhancer Activity-informed Gap GEne Regulatory Network (EAGER) to model Drosophila gap gene expression on the entire anterior-posterior (A-P) axis","display_name":"Enhancer Activity-informed Gap GEne Regulatory Network (EAGER) to model Drosophila gap gene expression on the entire anterior-posterior (A-P) axis","publication_year":2026,"publication_date":"2026-09-17","ids":{"openalex":"https://openalex.org/W7213473111","doi":"https://doi.org/10.64898/2026.09.15.751584"},"language":"en","primary_location":{"id":"doi:10.64898/2026.09.15.751584","doi":"https://doi.org/10.64898/2026.09.15.751584","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.15.751584","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/17/2026.09.15.751584.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/17/2026.09.15.751584.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5043851140","display_name":"Razeen Shaikh","orcid":"https://orcid.org/0009-0006-5584-3402","observed_orcids":["https://orcid.org/0009-0006-5584-3402"]},"institutions":[{"id":"https://openalex.org/I91045830","display_name":"Texas A&M University","ror":"https://ror.org/01f5ytq51","country_code":"US","type":"education","lineage":["https://openalex.org/I91045830"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Razeen Shaikh","raw_affiliation_strings":["Texas A & M University;"],"raw_orcid":"https://orcid.org/0009-0006-5584-3402","affiliations":[{"raw_affiliation_string":"Texas A & M University;","institution_ids":["https://openalex.org/I91045830"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039636100","display_name":"Sebastiano Busato","orcid":"https://orcid.org/0000-0002-2542-3443","observed_orcids":["https://orcid.org/0000-0002-2542-3443"]},"institutions":[{"id":"https://openalex.org/I137902535","display_name":"North Carolina State University","ror":"https://ror.org/04tj63d06","country_code":"US","type":"education","lineage":["https://openalex.org/I137902535"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sebastiano Busato","raw_affiliation_strings":["North Carolina State University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"North Carolina State University","institution_ids":["https://openalex.org/I137902535"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5107154128","display_name":"Sadia Siddika Dima","orcid":"https://orcid.org/0009-0008-3558-9093","observed_orcids":["https://orcid.org/0009-0008-3558-9093"]},"institutions":[{"id":"https://openalex.org/I91045830","display_name":"Texas A&M University","ror":"https://ror.org/01f5ytq51","country_code":"US","type":"education","lineage":["https://openalex.org/I91045830"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sadia Siddika Dima","raw_affiliation_strings":["Texas A & M University;"],"raw_orcid":"https://orcid.org/0009-0008-3558-9093","affiliations":[{"raw_affiliation_string":"Texas A & M University;","institution_ids":["https://openalex.org/I91045830"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001212028","display_name":"Cranos Williams","orcid":"https://orcid.org/0000-0002-0477-9707","observed_orcids":["https://orcid.org/0000-0002-0477-9707"]},"institutions":[{"id":"https://openalex.org/I137902535","display_name":"North Carolina State University","ror":"https://ror.org/04tj63d06","country_code":"US","type":"education","lineage":["https://openalex.org/I137902535"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Cranos Williams","raw_affiliation_strings":["North Carolina State University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"North Carolina State University","institution_ids":["https://openalex.org/I137902535"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5012498470","display_name":"Gregory T. Reeves","orcid":"https://orcid.org/0000-0003-0836-7766","observed_orcids":["https://orcid.org/0000-0003-0836-7766"]},"institutions":[{"id":"https://openalex.org/I91045830","display_name":"Texas A&M University","ror":"https://ror.org/01f5ytq51","country_code":"US","type":"education","lineage":["https://openalex.org/I91045830"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Gregory T Reeves","raw_affiliation_strings":["Texas A & M University;"],"raw_orcid":"https://orcid.org/0000-0003-0836-7766","affiliations":[{"raw_affiliation_string":"Texas A & M University;","institution_ids":["https://openalex.org/I91045830"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5012498470"],"corresponding_institution_ids":["https://openalex.org/I91045830"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.5874000191688538,"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":0.5874000191688538,"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/T10268","display_name":"Developmental Biology and Gene Regulation","score":0.4032999873161316,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.004600000102072954,"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/drosophila-embryo","display_name":"Drosophila embryo","score":0.8330000042915344},{"id":"https://openalex.org/keywords/anteroposterior-axis","display_name":"anterior-posterior axis","score":0.9620000123977661},{"id":"https://openalex.org/keywords/enhancer-activity","display_name":"enhancer activity","score":0.9279999732971191},{"id":"https://openalex.org/keywords/gene-expression-modeling","display_name":"gene expression modeling","score":0.4399999976158142},{"id":"https://openalex.org/keywords/parameter-sensitivity-analysis","display_name":"parameter sensitivity analysis","score":0.7490000128746033},{"id":"https://openalex.org/keywords/identifiability-analysis","display_name":"identifiability analysis","score":0.8989999890327454}],"concepts":[{"id":"https://openalex.org/C184937244","wikidata":"https://www.wikidata.org/wiki/Q410820","display_name":"Gap gene","level":4,"score":0.9376000165939331},{"id":"https://openalex.org/C111936080","wikidata":"https://www.wikidata.org/wiki/Q913367","display_name":"Enhancer","level":4,"score":0.8406000137329102},{"id":"https://openalex.org/C2778386714","wikidata":"https://www.wikidata.org/wiki/Q417084","display_name":"Morphogen","level":3,"score":0.7965999841690063},{"id":"https://openalex.org/C98535976","wikidata":"https://www.wikidata.org/wiki/Q4088022","display_name":"Blastoderm","level":4,"score":0.739300012588501},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7174000144004822},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.6413999795913696},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.6401000022888184},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.620199978351593},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5153999924659729},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.48429998755455017},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4729999899864197},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.46309998631477356},{"id":"https://openalex.org/C33498276","wikidata":"https://www.wikidata.org/wiki/Q2138797","display_name":"Regulator gene","level":4,"score":0.4560000002384186},{"id":"https://openalex.org/C21592294","wikidata":"https://www.wikidata.org/wiki/Q3238407","display_name":"Regulatory sequence","level":4,"score":0.4311000108718872},{"id":"https://openalex.org/C2780104201","wikidata":"https://www.wikidata.org/wiki/Q130888","display_name":"Drosophila melanogaster","level":3,"score":0.41999998688697815},{"id":"https://openalex.org/C143065580","wikidata":"https://www.wikidata.org/wiki/Q3285695","display_name":"Mutant","level":3,"score":0.4156999886035919},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.3903999924659729},{"id":"https://openalex.org/C143211211","wikidata":"https://www.wikidata.org/wiki/Q1343064","display_name":"Enhancer trap","level":5,"score":0.34299999475479126},{"id":"https://openalex.org/C114009990","wikidata":"https://www.wikidata.org/wiki/Q7125117","display_name":"Pair-rule gene","level":5,"score":0.3319000005722046},{"id":"https://openalex.org/C2991772755","wikidata":"https://www.wikidata.org/wiki/Q751748","display_name":"Gene interaction","level":3,"score":0.3059000074863434},{"id":"https://openalex.org/C173396325","wikidata":"https://www.wikidata.org/wiki/Q1501275","display_name":"Gene knockdown","level":3,"score":0.3012999892234802},{"id":"https://openalex.org/C190796033","wikidata":"https://www.wikidata.org/wiki/Q1093165","display_name":"Cis-regulatory module","level":5,"score":0.28380000591278076},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.2671000063419342},{"id":"https://openalex.org/C2781435330","wikidata":"https://www.wikidata.org/wiki/Q6440544","display_name":"Kr\u00fcppel","level":4,"score":0.2639000117778778},{"id":"https://openalex.org/C27153228","wikidata":"https://www.wikidata.org/wiki/Q3787274","display_name":"Transcriptional regulation","level":4,"score":0.25769999623298645},{"id":"https://openalex.org/C6929976","wikidata":"https://www.wikidata.org/wiki/Q3771881","display_name":"Regulator","level":3,"score":0.2556000053882599},{"id":"https://openalex.org/C111829913","wikidata":"https://www.wikidata.org/wiki/Q211083","display_name":"Gene targeting","level":3,"score":0.25220000743865967}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.64898/2026.09.15.751584","doi":"https://doi.org/10.64898/2026.09.15.751584","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.15.751584","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/17/2026.09.15.751584.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.64898/2026.09.15.751584","doi":"https://doi.org/10.64898/2026.09.15.751584","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.15.751584","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/17/2026.09.15.751584.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7213473111.pdf","grobid_xml":"https://content.openalex.org/works/W7213473111.grobid-xml"},"referenced_works_count":22,"referenced_works":["https://openalex.org/W1509329028","https://openalex.org/W1883406310","https://openalex.org/W1963587334","https://openalex.org/W1973183687","https://openalex.org/W1990316414","https://openalex.org/W1991136044","https://openalex.org/W1999870633","https://openalex.org/W2002797053","https://openalex.org/W2022851401","https://openalex.org/W2077122170","https://openalex.org/W2087093185","https://openalex.org/W2117607492","https://openalex.org/W2135061355","https://openalex.org/W2135105208","https://openalex.org/W2137057693","https://openalex.org/W2145707773","https://openalex.org/W2153904514","https://openalex.org/W2161304688","https://openalex.org/W2166012954","https://openalex.org/W2171005709","https://openalex.org/W2949348481","https://openalex.org/W4381887893"],"related_works":["https://openalex.org/W2053076760","https://openalex.org/W2056680906","https://openalex.org/W7033522489","https://openalex.org/W2048013262","https://openalex.org/W2077122170","https://openalex.org/W2087755954","https://openalex.org/W2506581559","https://openalex.org/W2286169753","https://openalex.org/W2166012954","https://openalex.org/W2066238490"],"abstract_inverted_index":{"Across":[0],"metazoa,":[1],"morphogen":[2,27],"gradients":[3],"differentially":[4],"regulate":[5],"gene":[6,22,45,84,102,136,196],"expression":[7,46,89,103,137,208],"and":[8,87,153,159,171,191],"activate":[9],"a":[10,155,176,185],"spatially":[11],"distinct":[12,43],"program":[13],"to":[14,41,59,78,162],"specify":[15],"body":[16],"axis":[17,52],"development.":[18],"The":[19],"Drosophila":[20,57],"gap":[21,44,83,101,135,195],"network,":[23],"initiated":[24],"by":[25,210],"maternal":[26],"Bicoid,":[28],"is":[29],"one":[30],"of":[31,53,64,82,148,166,179,188,219],"the":[32,49,54,61,65,80,100,106,129,140,146,164,167,180,194,199,207],"most":[33],"well-studied":[34],"systems.":[35,92],"Several":[36,72],"regulatory":[37,85,189],"interactions":[38,190,197],"act":[39],"synergistically":[40],"produce":[42],"patterns":[47,138],"along":[48,128],"anterior-posterior":[50],"(AP)":[51],"blastoderm":[55],"stage":[56,70],"embryo":[58],"ensure":[60],"proper":[62],"segmentation":[63],"larval":[66],"and,":[67],"eventually,":[68],"adult":[69],"fly.":[71],"mathematical":[73],"models":[74,95,218],"have":[75,96],"been":[76],"proposed":[77],"summarize":[79],"interconnectivity":[81],"elements":[86],"predict":[88],"in":[90,217],"mutant":[91],"However,":[93],"these":[94],"not":[97],"successfully":[98,133,192],"predicted":[99],"profile":[104],"over":[105,139,198],"entire":[107,141,200],"AP":[108,130,142,201],"axis.":[109,143,202],"Here,":[110],"we":[111],"present":[112],"an":[113],"Enhancer":[114],"Activity-informed":[115],"Gap":[116],"GEne":[117],"Regulatory":[118],"network":[119],"(EAGER)":[120],"model":[121,169],"that":[122,206],"incorporates":[123],"enhancer":[124],"activity-driven":[125],"differential":[126],"regulation":[127],"axis,":[131],"which":[132,183],"summarizes":[134,193],"We":[144,173],"validated":[145],"predictions":[147],"EAGER":[149,168],"on":[150],"Kr":[151],"mutants":[152],"performed":[154],"comprehensive":[156],"parametric":[157],"sensitivity":[158],"identifiability":[160],"analysis":[161],"evaluate":[163],"robustness":[165],"fits":[170],"predictions.":[172],"also":[174],"propose":[175],"reduced":[177],"version":[178],"model,":[181],"rEAGER,":[182],"identifies":[184],"minimal":[186],"set":[187],"Our":[203],"results":[204],"suggest":[205],"driven":[209],"individual":[211],"enhancers":[212],"must":[213],"be":[214],"accounted":[215],"for":[216],"developmental":[220],"pattern":[221],"formation.":[222]},"counts_by_year":[],"updated_date":"2026-11-09T13:22:03.289127","created_date":"2026-09-17T00:00:00"}