{"id":"https://openalex.org/W4404301974","doi":"https://doi.org/10.1093/bib/bbae592","title":"Deciphering lineage-relevant gene regulatory networks during endoderm formation by InPheRNo-ChIP","display_name":"Deciphering lineage-relevant gene regulatory networks during endoderm formation by InPheRNo-ChIP","publication_year":2024,"publication_date":"2024-09-23","ids":{"openalex":"https://openalex.org/W4404301974","doi":"https://doi.org/10.1093/bib/bbae592","pmid":"https://pubmed.ncbi.nlm.nih.gov/39535258"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbae592","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae592","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/bib/bbae592","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5112109160","display_name":"Chen Su","orcid":"https://orcid.org/0000-0002-1873-7022"},"institutions":[{"id":"https://openalex.org/I5023651","display_name":"McGill University","ror":"https://ror.org/01pxwe438","country_code":"CA","type":"education","lineage":["https://openalex.org/I5023651"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Chen Su","raw_affiliation_strings":["Department of Electrical and Computer Engineering, McGill University , 845 Sherbrooke Street West, Montreal, Quebec H3A 0G4 ,"],"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, McGill University , 845 Sherbrooke Street West, Montreal, Quebec H3A 0G4 ,","institution_ids":["https://openalex.org/I5023651"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037086547","display_name":"William A. Pastor","orcid":"https://orcid.org/0000-0003-4176-5299"},"institutions":[{"id":"https://openalex.org/I2801345345","display_name":"Cancer Institute (WIA)","ror":"https://ror.org/01tc10z29","country_code":"IN","type":"healthcare","lineage":["https://openalex.org/I2801345345"]},{"id":"https://openalex.org/I5023651","display_name":"McGill University","ror":"https://ror.org/01pxwe438","country_code":"CA","type":"education","lineage":["https://openalex.org/I5023651"]}],"countries":["CA","IN"],"is_corresponding":false,"raw_author_name":"William A Pastor","raw_affiliation_strings":["Department of Biochemistry, McGill University , 845 Sherbrooke Street West, Montreal, Quebec H3A 0G4 ,","The Rosalind and Morris Goodman Cancer Institute , 1160 Pine Avenue, Montreal, Quebec H3A 1A3 ,"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, McGill University , 845 Sherbrooke Street West, Montreal, Quebec H3A 0G4 ,","institution_ids":["https://openalex.org/I5023651"]},{"raw_affiliation_string":"The Rosalind and Morris Goodman Cancer Institute , 1160 Pine Avenue, Montreal, Quebec H3A 1A3 ,","institution_ids":["https://openalex.org/I2801345345"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5009196285","display_name":"Amin Emad","orcid":"https://orcid.org/0000-0002-5108-4887"},"institutions":[{"id":"https://openalex.org/I4210164802","display_name":"Mila - Quebec Artificial Intelligence Institute","ror":"https://ror.org/05c22rx21","country_code":"CA","type":"facility","lineage":["https://openalex.org/I4210164802"]},{"id":"https://openalex.org/I2801345345","display_name":"Cancer Institute (WIA)","ror":"https://ror.org/01tc10z29","country_code":"IN","type":"healthcare","lineage":["https://openalex.org/I2801345345"]},{"id":"https://openalex.org/I5023651","display_name":"McGill University","ror":"https://ror.org/01pxwe438","country_code":"CA","type":"education","lineage":["https://openalex.org/I5023651"]}],"countries":["CA","IN"],"is_corresponding":false,"raw_author_name":"Amin Emad","raw_affiliation_strings":["Department of Electrical and Computer Engineering, McGill University , 845 Sherbrooke Street West, Montreal, Quebec H3A 0G4 ,","Mila, Quebec AI Institute , 6666 St-Urbain Street #200, Montreal, Quebec H2S 3H1 ,","The Rosalind and Morris Goodman Cancer Institute , 1160 Pine Avenue, Montreal, Quebec H3A 1A3 ,"],"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, McGill University , 845 Sherbrooke Street West, Montreal, Quebec H3A 0G4 ,","institution_ids":["https://openalex.org/I5023651"]},{"raw_affiliation_string":"Mila, Quebec AI Institute , 6666 St-Urbain Street #200, Montreal, Quebec H2S 3H1 ,","institution_ids":["https://openalex.org/I4210164802"]},{"raw_affiliation_string":"The Rosalind and Morris Goodman Cancer Institute , 1160 Pine Avenue, Montreal, Quebec H3A 1A3 ,","institution_ids":["https://openalex.org/I2801345345"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5112109160"],"corresponding_institution_ids":["https://openalex.org/I5023651"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.2361,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.59118984,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"25","issue":"6","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9976000189781189,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9976000189781189,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9948999881744385,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.994700014591217,"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/inference","display_name":"Inference","score":0.6654757261276245},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.658907413482666},{"id":"https://openalex.org/keywords/endoderm","display_name":"Endoderm","score":0.6559222936630249},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6073029637336731},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5878903865814209},{"id":"https://openalex.org/keywords/phenotype","display_name":"Phenotype","score":0.4909873306751251},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4481005370616913},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.4298897683620453},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.317302942276001},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.29282987117767334},{"id":"https://openalex.org/keywords/embryonic-stem-cell","display_name":"Embryonic stem cell","score":0.22857710719108582},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.20412227511405945},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.12589484453201294}],"concepts":[{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6654757261276245},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.658907413482666},{"id":"https://openalex.org/C2777164004","wikidata":"https://www.wikidata.org/wiki/Q331858","display_name":"Endoderm","level":4,"score":0.6559222936630249},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6073029637336731},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5878903865814209},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.4909873306751251},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4481005370616913},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.4298897683620453},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.317302942276001},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.29282987117767334},{"id":"https://openalex.org/C145103041","wikidata":"https://www.wikidata.org/wiki/Q1151519","display_name":"Embryonic stem cell","level":3,"score":0.22857710719108582},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.20412227511405945},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.12589484453201294},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000066449","descriptor_name":"Human Embryonic Stem Cells","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D000066449","descriptor_name":"Human Embryonic Stem Cells","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D000066449","descriptor_name":"Human Embryonic Stem Cells","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D000066449","descriptor_name":"Human Embryonic Stem Cells","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D000066449","descriptor_name":"Human Embryonic Stem Cells","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000066449","descriptor_name":"Human Embryonic Stem Cells","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000066449","descriptor_name":"Human Embryonic Stem Cells","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000066449","descriptor_name":"Human Embryonic Stem Cells","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":null,"qualifier_name":null,"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":"D002454","descriptor_name":"Cell Differentiation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004707","descriptor_name":"Endoderm","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":true},{"descriptor_ui":"D004707","descriptor_name":"Endoderm","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":true},{"descriptor_ui":"D004707","descriptor_name":"Endoderm","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":true},{"descriptor_ui":"D004707","descriptor_name":"Endoderm","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":true},{"descriptor_ui":"D004707","descriptor_name":"Endoderm","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D004707","descriptor_name":"Endoderm","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D004707","descriptor_name":"Endoderm","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D004707","descriptor_name":"Endoderm","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"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":"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":"D018507","descriptor_name":"Gene Expression Regulation, Developmental","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018507","descriptor_name":"Gene Expression Regulation, Developmental","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018507","descriptor_name":"Gene Expression Regulation, Developmental","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018507","descriptor_name":"Gene Expression Regulation, Developmental","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019070","descriptor_name":"Cell Lineage","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019070","descriptor_name":"Cell Lineage","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019070","descriptor_name":"Cell Lineage","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019070","descriptor_name":"Cell Lineage","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D051542","descriptor_name":"Hepatocyte Nuclear Factor 3-beta","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D051542","descriptor_name":"Hepatocyte Nuclear Factor 3-beta","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D051542","descriptor_name":"Hepatocyte Nuclear Factor 3-beta","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D051542","descriptor_name":"Hepatocyte Nuclear Factor 3-beta","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D051542","descriptor_name":"Hepatocyte Nuclear Factor 3-beta","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D051542","descriptor_name":"Hepatocyte Nuclear Factor 3-beta","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D051542","descriptor_name":"Hepatocyte Nuclear Factor 3-beta","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D051542","descriptor_name":"Hepatocyte Nuclear Factor 3-beta","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055760","descriptor_name":"SOXF Transcription Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055760","descriptor_name":"SOXF Transcription Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055760","descriptor_name":"SOXF Transcription Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055760","descriptor_name":"SOXF Transcription Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbae592","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae592","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:39535258","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39535258","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11558691","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11558691","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11558691/pdf/bbae592.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbae592","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae592","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1597412403","display_name":null,"funder_award_id":"RGPIN-","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G2165548363","display_name":null,"funder_award_id":"Canada","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G3216283581","display_name":null,"funder_award_id":"RGPIN-201","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G4450149547","display_name":null,"funder_award_id":"RGPIN-2019-04460","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G615757196","display_name":null,"funder_award_id":"2022-NC-300688","funder_id":"https://openalex.org/F4320334841","funder_display_name":"Fonds de recherche du Qu\u00e9bec \u2013 Nature et technologies"},{"id":"https://openalex.org/G6221715925","display_name":null,"funder_award_id":"RGPIN","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G7089305364","display_name":null,"funder_award_id":"Doctoral","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G8284766523","display_name":null,"funder_award_id":"(NSERC)","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G832689143","display_name":null,"funder_award_id":"RGPIN-2019","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"}],"funders":[{"id":"https://openalex.org/F4320331257","display_name":"Alliance de recherche num\u00e9rique du Canada","ror":"https://ror.org/010r6td27"},{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"},{"id":"https://openalex.org/F4320334618","display_name":"Fonds de Recherche du Qu\u00e9bec - Sant\u00e9","ror":"https://ror.org/02eqrsj93"},{"id":"https://openalex.org/F4320334841","display_name":"Fonds de recherche du Qu\u00e9bec \u2013 Nature et technologies","ror":"https://ror.org/00b9f9778"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":47,"referenced_works":["https://openalex.org/W1588334150","https://openalex.org/W1976194722","https://openalex.org/W1984827465","https://openalex.org/W2011961689","https://openalex.org/W2020672230","https://openalex.org/W2021593900","https://openalex.org/W2030094937","https://openalex.org/W2033551209","https://openalex.org/W2035809306","https://openalex.org/W2038063712","https://openalex.org/W2042203018","https://openalex.org/W2043861102","https://openalex.org/W2056760934","https://openalex.org/W2062984040","https://openalex.org/W2079181843","https://openalex.org/W2101007313","https://openalex.org/W2114104545","https://openalex.org/W2115664087","https://openalex.org/W2122097157","https://openalex.org/W2124514674","https://openalex.org/W2138309709","https://openalex.org/W2146512944","https://openalex.org/W2151870437","https://openalex.org/W2159675211","https://openalex.org/W2345356016","https://openalex.org/W2494631976","https://openalex.org/W2540716273","https://openalex.org/W2735132087","https://openalex.org/W2893014212","https://openalex.org/W2901292166","https://openalex.org/W2936506456","https://openalex.org/W2953622121","https://openalex.org/W2997831639","https://openalex.org/W3014872938","https://openalex.org/W3045962899","https://openalex.org/W3082292479","https://openalex.org/W3088521497","https://openalex.org/W3108286911","https://openalex.org/W3120280701","https://openalex.org/W3127975644","https://openalex.org/W3133393002","https://openalex.org/W3184607208","https://openalex.org/W3200158711","https://openalex.org/W4200437116","https://openalex.org/W4213111299","https://openalex.org/W4386373863","https://openalex.org/W4396895461"],"related_works":["https://openalex.org/W1564861386","https://openalex.org/W2006730050","https://openalex.org/W2063353254","https://openalex.org/W4249379514","https://openalex.org/W2034421461","https://openalex.org/W2950199998","https://openalex.org/W2560421304","https://openalex.org/W2951387065","https://openalex.org/W4385727351","https://openalex.org/W4306798985"],"abstract_inverted_index":{"Deciphering":[0],"the":[1,27,31,77,94,105,117,137,140,175,179,190,200],"underlying":[2],"gene":[3],"regulatory":[4,123,161],"networks":[5],"(GRNs)":[6],"that":[7,44,75,101],"govern":[8],"early":[9],"human":[10,143],"embryogenesis":[11],"is":[12,70],"critical":[13],"for":[14,205],"understanding":[15],"developmental":[16],"mechanisms":[17],"yet":[18],"remains":[19],"challenging":[20],"due":[21],"to":[22,57,87,104,135,159],"limited":[23],"sample":[24],"availability":[25],"and":[26,54,121,132,168,196],"inherent":[28],"complexity":[29],"of":[30,67,80,96,142,177,193,202],"biological":[32],"processes":[33],"involved.":[34],"To":[35],"address":[36],"this,":[37],"we":[38],"developed":[39],"InPheRNo-ChIP,":[40],"a":[41,71,89,152],"computational":[42],"framework":[43],"integrates":[45],"multimodal":[46,203],"data,":[47,198],"including":[48],"RNA-seq,":[49,195],"transcription":[50],"factor":[51],"(TF)-specific":[52],"ChIP-seq,":[53,194],"phenotypic":[55,91,106,111,180,197],"labels,":[56],"reconstruct":[58],"phenotype-relevant":[59,207],"GRNs":[60],"associated":[61],"with":[62],"endoderm":[63,164],"development.":[64],"The":[65],"core":[66],"this":[68],"method":[69],"probabilistic":[72],"graphical":[73],"model":[74],"models":[76],"simultaneous":[78],"effect":[79],"TFs":[81],"on":[82],"their":[83],"putative":[84],"target":[85],"genes":[86],"influence":[88],"particular":[90],"outcome.":[92],"Unlike":[93],"majority":[95],"existing":[97],"GRN":[98,114,138,208],"inference":[99],"methods":[100],"are":[102],"agnostic":[103],"outcomes,":[107],"InPheRNo-ChIP":[108,134],"directly":[109],"incorporates":[110],"information":[112],"during":[113,182],"inference,":[115],"enabling":[116],"distinction":[118],"between":[119],"lineage-specific":[120],"general":[122],"interactions.":[124],"We":[125],"integrated":[126],"data":[127],"from":[128],"three":[129],"experimental":[130],"studies":[131],"applied":[133],"infer":[136],"governing":[139],"differentiation":[141],"embryonic":[144],"stem":[145],"cells":[146],"into":[147],"definitive":[148],"endoderm.":[149],"Benchmarking":[150],"against":[151],"scRNA-seq":[153],"CRISPRi":[154],"study":[155,188],"demonstrated":[156],"InPheRNo-ChIP's":[157],"ability":[158],"identify":[160],"interactions":[162],"involving":[163],"markers":[165],"FOXA2,":[166],"SMAD2,":[167],"SOX17,":[169],"outperforming":[170],"other":[171],"methods.":[172],"This":[173],"highlights":[174],"importance":[176],"incorporating":[178],"context":[181],"network":[183],"inference.":[184],"Furthermore,":[185],"an":[186],"ablation":[187],"confirms":[189],"synergistic":[191],"contribution":[192],"highlighting":[199],"value":[201],"integration":[204],"accurate":[206],"reconstruction.":[209]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-03-25T14:56:36.534964","created_date":"2025-10-10T00:00:00"}