{"id":"https://openalex.org/W4401966967","doi":"https://doi.org/10.1101/2024.08.27.609971","title":"Dissecting the regulatory logic of specification and differentiation during vertebrate embryogenesis","display_name":"Dissecting the regulatory logic of specification and differentiation during vertebrate embryogenesis","publication_year":2024,"publication_date":"2024-08-27","ids":{"openalex":"https://openalex.org/W4401966967","doi":"https://doi.org/10.1101/2024.08.27.609971","pmid":"https://pubmed.ncbi.nlm.nih.gov/39253514","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/11383055"},"language":"en","primary_location":{"id":"doi:10.1101/2024.08.27.609971","doi":"https://doi.org/10.1101/2024.08.27.609971","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2024.08.27.609971","pdf_url":null,"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":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.1101/2024.08.27.609971","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100456647","display_name":"Jialin Liu","orcid":"https://orcid.org/0000-0002-9883-0963","observed_orcids":["https://orcid.org/0000-0002-9883-0963"]},"institutions":[{"id":"https://openalex.org/I1850255","display_name":"University of Basel","ror":"https://ror.org/02s6k3f65","country_code":"CH","type":"education","lineage":["https://openalex.org/I1850255"]},{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["CH","US"],"is_corresponding":false,"raw_author_name":"Jialin Liu","raw_affiliation_strings":["Allen Discovery Center for Cell Lineage Tracing, University of Washington, Seattle, WA, 98195, USA","Biozentrum, University of Basel, Basel, 4056, Switzerland","Allen Discovery Center for Cell Lineage Tracing, University of Washington, Seattle, WA, 9895, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Allen Discovery Center for Cell Lineage Tracing, University of Washington, Seattle, WA, 98195, USA","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Biozentrum, University of Basel, Basel, 4056, Switzerland","institution_ids":["https://openalex.org/I1850255"]},{"raw_affiliation_string":"Allen Discovery Center for Cell Lineage Tracing, University of Washington, Seattle, WA, 9895, USA","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040747910","display_name":"Sebastian M. Castillo-Hair","orcid":"https://orcid.org/0000-0002-2384-3129","observed_orcids":["https://orcid.org/0000-0002-2384-3129"]},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sebastian M. Castillo-Hair","raw_affiliation_strings":["Department of Electrical & Computer Engineering, University of Washington, Seattle, WA, 98195, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical & Computer Engineering, University of Washington, Seattle, WA, 98195, USA","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001326617","display_name":"Lucia Y. Du","orcid":"https://orcid.org/0000-0003-0151-3783","observed_orcids":["https://orcid.org/0000-0003-0151-3783"]},"institutions":[{"id":"https://openalex.org/I1850255","display_name":"University of Basel","ror":"https://ror.org/02s6k3f65","country_code":"CH","type":"education","lineage":["https://openalex.org/I1850255"]},{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["CH","US"],"is_corresponding":false,"raw_author_name":"Lucia Y. Du","raw_affiliation_strings":["Allen Discovery Center for Cell Lineage Tracing, University of Washington, Seattle, WA, 98195, USA","Biozentrum, University of Basel, Basel, 4056, Switzerland","Allen Discovery Center for Cell Lineage Tracing, University of Washington, Seattle, WA, 9895, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Allen Discovery Center for Cell Lineage Tracing, University of Washington, Seattle, WA, 98195, USA","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Biozentrum, University of Basel, Basel, 4056, Switzerland","institution_ids":["https://openalex.org/I1850255"]},{"raw_affiliation_string":"Allen Discovery Center for Cell Lineage Tracing, University of Washington, Seattle, WA, 9895, USA","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Yiqun Wang","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I150209017","display_name":"Scripps Institution of Oceanography","ror":"https://ror.org/04v7hvq31","country_code":"US","type":"facility","lineage":["https://openalex.org/I150209017","https://openalex.org/I36258959"]},{"id":"https://openalex.org/I1850255","display_name":"University of Basel","ror":"https://ror.org/02s6k3f65","country_code":"CH","type":"education","lineage":["https://openalex.org/I1850255"]},{"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":["CH","US"],"is_corresponding":false,"raw_author_name":"Yiqun Wang","raw_affiliation_strings":["Biozentrum, University of Basel, Basel, 4056, Switzerland","Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, UCSD, La Jolla, CA, 92037, USA","Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, UCSD, La Jolla, CA, 9207, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biozentrum, University of Basel, Basel, 4056, Switzerland","institution_ids":["https://openalex.org/I1850255"]},{"raw_affiliation_string":"Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, UCSD, La Jolla, CA, 92037, USA","institution_ids":["https://openalex.org/I150209017","https://openalex.org/I36258959"]},{"raw_affiliation_string":"Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, UCSD, La Jolla, CA, 9207, USA","institution_ids":["https://openalex.org/I150209017","https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063941501","display_name":"Adam N. Carte","orcid":"https://orcid.org/0000-0002-3791-4872","observed_orcids":["https://orcid.org/0000-0002-3791-4872"]},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I1850255","display_name":"University of Basel","ror":"https://ror.org/02s6k3f65","country_code":"CH","type":"education","lineage":["https://openalex.org/I1850255"]}],"countries":["CH","US"],"is_corresponding":false,"raw_author_name":"Adam N. Carte","raw_affiliation_strings":["Biozentrum, University of Basel, Basel, 4056, Switzerland","Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, 02115, USA","Biozentrum, University of Basel, Basel, 056, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biozentrum, University of Basel, Basel, 4056, Switzerland","institution_ids":["https://openalex.org/I1850255"]},{"raw_affiliation_string":"Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, 02115, USA","institution_ids":["https://openalex.org/I136199984"]},{"raw_affiliation_string":"Biozentrum, University of Basel, Basel, 056, Switzerland","institution_ids":["https://openalex.org/I1850255"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036005142","display_name":"Mariona Colomer-Rosell","orcid":"https://orcid.org/0000-0002-3523-315X","observed_orcids":["https://orcid.org/0000-0002-3523-315X"]},"institutions":[{"id":"https://openalex.org/I1850255","display_name":"University of Basel","ror":"https://ror.org/02s6k3f65","country_code":"CH","type":"education","lineage":["https://openalex.org/I1850255"]},{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["CH","US"],"is_corresponding":false,"raw_author_name":"Mariona Colomer-Rosell","raw_affiliation_strings":["Allen Discovery Center for Cell Lineage Tracing, University of Washington, Seattle, WA, 98195, USA","Biozentrum, University of Basel, Basel, 4056, Switzerland","Allen Discovery Center for Cell Lineage Tracing, University of Washington, Seattle, WA, 9895, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Allen Discovery Center for Cell Lineage Tracing, University of Washington, Seattle, WA, 98195, USA","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Biozentrum, University of Basel, Basel, 4056, Switzerland","institution_ids":["https://openalex.org/I1850255"]},{"raw_affiliation_string":"Allen Discovery Center for Cell Lineage Tracing, University of Washington, Seattle, WA, 9895, USA","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083664145","display_name":"Christopher Yin","orcid":"https://orcid.org/0009-0005-5658-4097","observed_orcids":["https://orcid.org/0009-0005-5658-4097"]},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Christopher Yin","raw_affiliation_strings":["Department of Electrical & Computer Engineering, University of Washington, Seattle, WA, 98195, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical & Computer Engineering, University of Washington, Seattle, WA, 98195, USA","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021731745","display_name":"Georg Seelig","orcid":"https://orcid.org/0000-0002-3163-8782","observed_orcids":["https://orcid.org/0000-0002-3163-8782"]},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Georg Seelig","raw_affiliation_strings":["Department of Electrical & Computer Engineering, University of Washington, Seattle, WA, 98195, USA","Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, 98195, USA","Department of Electrical & Computer Engineering, University of Washington, Seattle, WA, 9819, USA","Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, 9819, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical & Computer Engineering, University of Washington, Seattle, WA, 98195, USA","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, 98195, USA","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Department of Electrical & Computer Engineering, University of Washington, Seattle, WA, 9819, USA","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, 9819, USA","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5066848145","display_name":"Alexander F. Schier","orcid":"https://orcid.org/0000-0001-7645-5325","observed_orcids":["https://orcid.org/0000-0001-7645-5325","https://orcid.org/0000-0002-5317-494X"]},"institutions":[{"id":"https://openalex.org/I1850255","display_name":"University of Basel","ror":"https://ror.org/02s6k3f65","country_code":"CH","type":"education","lineage":["https://openalex.org/I1850255"]},{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["CH","US"],"is_corresponding":true,"raw_author_name":"Alexander F. Schier","raw_affiliation_strings":["Allen Discovery Center for Cell Lineage Tracing, University of Washington, Seattle, WA, 98195, USA","Biozentrum, University of Basel, Basel, 4056, Switzerland","Allen Discovery Center for Cell Lineage Tracing, University of Washington, Seattle, WA, 9895, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Allen Discovery Center for Cell Lineage Tracing, University of Washington, Seattle, WA, 98195, USA","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Biozentrum, University of Basel, Basel, 4056, Switzerland","institution_ids":["https://openalex.org/I1850255"]},{"raw_affiliation_string":"Allen Discovery Center for Cell Lineage Tracing, University of Washington, Seattle, WA, 9895, USA","institution_ids":["https://openalex.org/I201448701"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5066848145"],"corresponding_institution_ids":["https://openalex.org/I1850255","https://openalex.org/I201448701"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":13,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.44359999895095825,"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":0.44359999895095825,"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":0.382099986076355,"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":0.12479999661445618,"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/vertebrate-embryonic-development","display_name":"vertebrate embryonic development","score":0.8100000023841858},{"id":"https://openalex.org/keywords/cell-type-specification","display_name":"cell specification","score":0.5540000200271606},{"id":"https://openalex.org/keywords/cell-differentiation","display_name":"cell differentiation","score":0.9589999914169312},{"id":"https://openalex.org/keywords/chromatin-accessibility","display_name":"chromatin accessibility","score":0.8510000109672546},{"id":"https://openalex.org/keywords/transcription-factors","display_name":"transcription factors","score":0.9269999861717224},{"id":"https://openalex.org/keywords/zebrafish-embryos","display_name":"zebrafish embryos","score":0.7350000143051147},{"id":"https://openalex.org/keywords/single-cell-multi-omics","display_name":"single-cell multi-omics","score":0.8059999942779541},{"id":"https://openalex.org/keywords/nanog","display_name":"Nanog","score":0.9670000076293945},{"id":"https://openalex.org/keywords/pluripotency","display_name":"pluripotency","score":0.8130000233650208},{"id":"https://openalex.org/keywords/mesendoderm","display_name":"mesendoderm","score":0.8379999995231628},{"id":"https://openalex.org/keywords/enhancer-accessibility","display_name":"enhancer accessibility","score":0.8460000157356262},{"id":"https://openalex.org/keywords/gene-regulatory-networks","display_name":"gene regulatory networks","score":0.7720000147819519}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.8008520603179932},{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.7399541735649109},{"id":"https://openalex.org/C111936080","wikidata":"https://www.wikidata.org/wiki/Q913367","display_name":"Enhancer","level":4,"score":0.649878978729248},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.5759097337722778},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.5397852659225464},{"id":"https://openalex.org/C148738053","wikidata":"https://www.wikidata.org/wiki/Q210861","display_name":"Cellular differentiation","level":3,"score":0.51959627866745},{"id":"https://openalex.org/C145103041","wikidata":"https://www.wikidata.org/wiki/Q1151519","display_name":"Embryonic stem cell","level":3,"score":0.5082008838653564},{"id":"https://openalex.org/C107459253","wikidata":"https://www.wikidata.org/wiki/Q674925","display_name":"Induced pluripotent stem cell","level":4,"score":0.48167717456817627},{"id":"https://openalex.org/C2776878037","wikidata":"https://www.wikidata.org/wiki/Q169444","display_name":"Zebrafish","level":3,"score":0.472195029258728},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.4700081944465637},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.4482290744781494},{"id":"https://openalex.org/C163952510","wikidata":"https://www.wikidata.org/wiki/Q5058196","display_name":"Cell fate determination","level":4,"score":0.43920302391052246},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4064677953720093},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.40383708477020264},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3646949231624603},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.3082541227340698}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1101/2024.08.27.609971","doi":"https://doi.org/10.1101/2024.08.27.609971","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2024.08.27.609971","pdf_url":null,"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":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},{"id":"pmid:39253514","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39253514","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,"listed_in":[],"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":"bioRxiv : the preprint server for biology","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:11383055","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11383055","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,"listed_in":[],"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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1101/2024.08.27.609971","doi":"https://doi.org/10.1101/2024.08.27.609971","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2024.08.27.609971","pdf_url":null,"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":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G7609225095","display_name":"Joint receptor and protein expression immunophenotyping through split-pool barcoding","funder_award_id":"R33CA255893","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":78,"referenced_works":["https://openalex.org/W1888475523","https://openalex.org/W1890963650","https://openalex.org/W1948230326","https://openalex.org/W1973492715","https://openalex.org/W1985999273","https://openalex.org/W1991655646","https://openalex.org/W2028689768","https://openalex.org/W2038254017","https://openalex.org/W2043056194","https://openalex.org/W2044911975","https://openalex.org/W2045362835","https://openalex.org/W2069089843","https://openalex.org/W2084036080","https://openalex.org/W2084984120","https://openalex.org/W2090160722","https://openalex.org/W2091152603","https://openalex.org/W2102619694","https://openalex.org/W2104065792","https://openalex.org/W2107575419","https://openalex.org/W2125349610","https://openalex.org/W2145055902","https://openalex.org/W2165737607","https://openalex.org/W2198606573","https://openalex.org/W2340897895","https://openalex.org/W2345512687","https://openalex.org/W2596915537","https://openalex.org/W2609558322","https://openalex.org/W2618851150","https://openalex.org/W2724521833","https://openalex.org/W2750049634","https://openalex.org/W2771926526","https://openalex.org/W2796674913","https://openalex.org/W2800028441","https://openalex.org/W2800912249","https://openalex.org/W2802302382","https://openalex.org/W2804905734","https://openalex.org/W2806844404","https://openalex.org/W2889236955","https://openalex.org/W2896103138","https://openalex.org/W2898981235","https://openalex.org/W2935703330","https://openalex.org/W2958554910","https://openalex.org/W2965417358","https://openalex.org/W2992957227","https://openalex.org/W3000545884","https://openalex.org/W3081371264","https://openalex.org/W3088687225","https://openalex.org/W3093858607","https://openalex.org/W3100453790","https://openalex.org/W3130819465","https://openalex.org/W3131634425","https://openalex.org/W3164692211","https://openalex.org/W3184729641","https://openalex.org/W3190721160","https://openalex.org/W3210860076","https://openalex.org/W4200382470","https://openalex.org/W4205345182","https://openalex.org/W4206037526","https://openalex.org/W4213292643","https://openalex.org/W4220985590","https://openalex.org/W4283789731","https://openalex.org/W4300862723","https://openalex.org/W4302010984","https://openalex.org/W4312211397","https://openalex.org/W4319591822","https://openalex.org/W4382022265","https://openalex.org/W4384198561","https://openalex.org/W4388694332","https://openalex.org/W4389613138","https://openalex.org/W4389613185","https://openalex.org/W4390828901","https://openalex.org/W4391171690","https://openalex.org/W4396729369","https://openalex.org/W4399855179","https://openalex.org/W4400423459","https://openalex.org/W4404706568","https://openalex.org/W4411025191","https://openalex.org/W7135049868"],"related_works":["https://openalex.org/W4391886120","https://openalex.org/W6945868482","https://openalex.org/W3012969293","https://openalex.org/W7140190448","https://openalex.org/W4205914585","https://openalex.org/W3155444987","https://openalex.org/W4400423459","https://openalex.org/W4205507169","https://openalex.org/W4403561159","https://openalex.org/W4400423248"],"abstract_inverted_index":{"The":[0],"interplay":[1],"between":[2],"transcription":[3,62,136,148],"factors":[4,63,137,149],"and":[5,34,55,108,171],"chromatin":[6,35,49,66],"accessibility":[7,36,50,84],"regulates":[8],"cell":[9],"type":[10],"diversification":[11],"during":[12,37],"vertebrate":[13],"embryogenesis.":[14,40],"To":[15],"systematically":[16],"decipher":[17],"the":[18,82,91,173],"gene":[19,113,169],"regulatory":[20,114,174],"logic":[21,175],"guiding":[22],"this":[23,118],"process,":[24],"we":[25,75,97],"generated":[26],"a":[27,43,58,77,123,132,163],"single-cell":[28],"multi-omics":[29],"atlas":[30],"of":[31,61,85,95,112,135,141,146,176],"RNA":[32],"expression":[33],"early":[38],"zebrafish":[39],"We":[41],"developed":[42],"deep":[44],"learning":[45],"model":[46],"to":[47,90,155],"predict":[48],"based":[51],"on":[52],"DNA":[53],"sequence":[54],"found":[56],"that":[57,117,138],"small":[59,133],"number":[60],"underlie":[64],"cell-type-specific":[65],"landscapes.":[67],"While":[68],"Nanog":[69],"is":[70,120,153],"well-established":[71],"in":[72,80,126,150],"promoting":[73],"pluripotency,":[74],"discovered":[76],"new":[78],"function":[79],"priming":[81],"enhancer":[83],"mesendodermal":[86],"genes.":[87,143],"In":[88],"addition":[89],"classical":[92],"stepwise":[93],"mode":[94],"differentiation,":[96,100],"describe":[98],"instant":[99,177],"where":[101],"pluripotent":[102,151],"cells":[103,152],"skip":[104],"intermediate":[105],"fate":[106],"transitions":[107],"terminally":[109],"differentiate.":[110],"Reconstruction":[111],"interactions":[115],"reveals":[116,172],"process":[119],"driven":[121],"by":[122],"shallow":[124],"network":[125],"which":[127],"maternally":[128],"deposited":[129],"regulators":[130],"activate":[131,157],"set":[134],"co-regulate":[139],"hundreds":[140],"differentiation":[142],"Notably,":[144],"misexpression":[145],"these":[147],"sufficient":[154],"ectopically":[156],"their":[158],"targets.":[159],"This":[160],"study":[161],"provides":[162],"rich":[164],"resource":[165],"for":[166],"analyzing":[167],"embryonic":[168],"regulation":[170],"differentiation.":[178]},"counts_by_year":[{"year":2026,"cited_by_count":7},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":4}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2024-08-29T00:00:00"}