{"id":"https://openalex.org/W4417267341","doi":"https://doi.org/10.1093/bib/bbaf661","title":"Beyond metaphor: quantitative reconstruction of Waddington landscape and exploration of cellular behavior","display_name":"Beyond metaphor: quantitative reconstruction of Waddington landscape and exploration of cellular behavior","publication_year":2025,"publication_date":"2025-11-01","ids":{"openalex":"https://openalex.org/W4417267341","doi":"https://doi.org/10.1093/bib/bbaf661","pmid":"https://pubmed.ncbi.nlm.nih.gov/41370633"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf661","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf661","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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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/bbaf661","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5028660451","display_name":"Yourui Han","orcid":null},"institutions":[{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]},{"id":"https://openalex.org/I99418890","display_name":"Northwestern Polytechnic University","ror":"https://ror.org/05wn69s11","country_code":"US","type":"education","lineage":["https://openalex.org/I99418890"]}],"countries":["CN","US"],"is_corresponding":true,"raw_author_name":"Yourui Han","raw_affiliation_strings":["School of Computer Science , Northwestern Polytechnical University, 1 Dongxiang Road, Chang\u2019an District, Xi\u2019an 710072,"],"affiliations":[{"raw_affiliation_string":"School of Computer Science , Northwestern Polytechnical University, 1 Dongxiang Road, Chang\u2019an District, Xi\u2019an 710072,","institution_ids":["https://openalex.org/I17145004","https://openalex.org/I99418890"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100748642","display_name":"Bolin Chen","orcid":"https://orcid.org/0000-0001-5507-2288"},"institutions":[{"id":"https://openalex.org/I99418890","display_name":"Northwestern Polytechnic University","ror":"https://ror.org/05wn69s11","country_code":"US","type":"education","lineage":["https://openalex.org/I99418890"]},{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]},{"id":"https://openalex.org/I890469752","display_name":"Ministry of Industry and Information Technology","ror":"https://ror.org/0385nmy68","country_code":"CN","type":"government","lineage":["https://openalex.org/I890469752"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Bolin Chen","raw_affiliation_strings":["Key Laboratory of Big Data Storage and Management , Northwestern Polytechnical University, Ministry of Industry and Information Technology, 1 Dongxiang Road, Chang\u2019an District, Xi\u2019an 710072,","School of Computer Science , Northwestern Polytechnical University, 1 Dongxiang Road, Chang\u2019an District, Xi\u2019an 710072,"],"affiliations":[{"raw_affiliation_string":"Key Laboratory of Big Data Storage and Management , Northwestern Polytechnical University, Ministry of Industry and Information Technology, 1 Dongxiang Road, Chang\u2019an District, Xi\u2019an 710072,","institution_ids":["https://openalex.org/I17145004","https://openalex.org/I890469752"]},{"raw_affiliation_string":"School of Computer Science , Northwestern Polytechnical University, 1 Dongxiang Road, Chang\u2019an District, Xi\u2019an 710072,","institution_ids":["https://openalex.org/I17145004","https://openalex.org/I99418890"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072393490","display_name":"Jinlei Zhang","orcid":"https://orcid.org/0000-0003-0763-9344"},"institutions":[{"id":"https://openalex.org/I99418890","display_name":"Northwestern Polytechnic University","ror":"https://ror.org/05wn69s11","country_code":"US","type":"education","lineage":["https://openalex.org/I99418890"]},{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Jinlei Zhang","raw_affiliation_strings":["School of Computer Science , Northwestern Polytechnical University, 1 Dongxiang Road, Chang\u2019an District, Xi\u2019an 710072,"],"affiliations":[{"raw_affiliation_string":"School of Computer Science , Northwestern Polytechnical University, 1 Dongxiang Road, Chang\u2019an District, Xi\u2019an 710072,","institution_ids":["https://openalex.org/I17145004","https://openalex.org/I99418890"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5109723363","display_name":"Xuequn Shang","orcid":null},"institutions":[{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]},{"id":"https://openalex.org/I890469752","display_name":"Ministry of Industry and Information Technology","ror":"https://ror.org/0385nmy68","country_code":"CN","type":"government","lineage":["https://openalex.org/I890469752"]},{"id":"https://openalex.org/I99418890","display_name":"Northwestern Polytechnic University","ror":"https://ror.org/05wn69s11","country_code":"US","type":"education","lineage":["https://openalex.org/I99418890"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Xuequn Shang","raw_affiliation_strings":["Key Laboratory of Big Data Storage and Management , Northwestern Polytechnical University, Ministry of Industry and Information Technology, 1 Dongxiang Road, Chang\u2019an District, Xi\u2019an 710072,","School of Computer Science , Northwestern Polytechnical University, 1 Dongxiang Road, Chang\u2019an District, Xi\u2019an 710072,"],"affiliations":[{"raw_affiliation_string":"Key Laboratory of Big Data Storage and Management , Northwestern Polytechnical University, Ministry of Industry and Information Technology, 1 Dongxiang Road, Chang\u2019an District, Xi\u2019an 710072,","institution_ids":["https://openalex.org/I17145004","https://openalex.org/I890469752"]},{"raw_affiliation_string":"School of Computer Science , Northwestern Polytechnical University, 1 Dongxiang Road, Chang\u2019an District, Xi\u2019an 710072,","institution_ids":["https://openalex.org/I17145004","https://openalex.org/I99418890"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5028660451"],"corresponding_institution_ids":["https://openalex.org/I17145004","https://openalex.org/I99418890"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.8149,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.79430213,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"26","issue":"6","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":0.8037999868392944,"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":0.8037999868392944,"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":0.021900000050663948,"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":0.020099999383091927,"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/heuristic","display_name":"Heuristic","score":0.49149999022483826},{"id":"https://openalex.org/keywords/metaphor","display_name":"Metaphor","score":0.4896000027656555},{"id":"https://openalex.org/keywords/categorization","display_name":"Categorization","score":0.4471000134944916},{"id":"https://openalex.org/keywords/computational-model","display_name":"Computational model","score":0.3871000111103058},{"id":"https://openalex.org/keywords/conceptual-framework","display_name":"Conceptual framework","score":0.36160001158714294},{"id":"https://openalex.org/keywords/stability","display_name":"Stability (learning theory)","score":0.35600000619888306}],"concepts":[{"id":"https://openalex.org/C188147891","wikidata":"https://www.wikidata.org/wiki/Q147638","display_name":"Cognitive science","level":1,"score":0.5616000294685364},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5593000054359436},{"id":"https://openalex.org/C173801870","wikidata":"https://www.wikidata.org/wiki/Q201413","display_name":"Heuristic","level":2,"score":0.49149999022483826},{"id":"https://openalex.org/C2778311575","wikidata":"https://www.wikidata.org/wiki/Q18534","display_name":"Metaphor","level":2,"score":0.4896000027656555},{"id":"https://openalex.org/C94124525","wikidata":"https://www.wikidata.org/wiki/Q912550","display_name":"Categorization","level":2,"score":0.4471000134944916},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.41819998621940613},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.3871000111103058},{"id":"https://openalex.org/C14224292","wikidata":"https://www.wikidata.org/wiki/Q13600188","display_name":"Conceptual framework","level":2,"score":0.36160001158714294},{"id":"https://openalex.org/C112972136","wikidata":"https://www.wikidata.org/wiki/Q7595718","display_name":"Stability (learning theory)","level":2,"score":0.35600000619888306},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3521000146865845},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3395000100135803},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.3240000009536743},{"id":"https://openalex.org/C79379906","wikidata":"https://www.wikidata.org/wiki/Q3174497","display_name":"Dynamical systems theory","level":2,"score":0.31380000710487366},{"id":"https://openalex.org/C76969082","wikidata":"https://www.wikidata.org/wiki/Q486902","display_name":"Mathematical model","level":2,"score":0.3059999942779541},{"id":"https://openalex.org/C527412718","wikidata":"https://www.wikidata.org/wiki/Q855395","display_name":"Interpretation (philosophy)","level":2,"score":0.263700008392334}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbaf661","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf661","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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41370633","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41370633","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:12694459","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12694459/","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12694459/pdf/bbaf661.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbaf661","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf661","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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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/G1121271761","display_name":null,"funder_award_id":"Program","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G1231421488","display_name":null,"funder_award_id":"under","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2087396116","display_name":null,"funder_award_id":"China","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3317480652","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3825787491","display_name":null,"funder_award_id":"62433016","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5994120800","display_name":null,"funder_award_id":"Natural","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7178638761","display_name":null,"funder_award_id":"100040","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7726157001","display_name":null,"funder_award_id":"Grant No.","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":90,"referenced_works":["https://openalex.org/W1535321247","https://openalex.org/W1544150116","https://openalex.org/W1963712961","https://openalex.org/W1970779075","https://openalex.org/W1984263697","https://openalex.org/W1985506636","https://openalex.org/W1987910254","https://openalex.org/W1993287310","https://openalex.org/W2005207943","https://openalex.org/W2009390821","https://openalex.org/W2013305619","https://openalex.org/W2014719297","https://openalex.org/W2022247244","https://openalex.org/W2023183725","https://openalex.org/W2024626836","https://openalex.org/W2046451925","https://openalex.org/W2046537766","https://openalex.org/W2048800133","https://openalex.org/W2054251743","https://openalex.org/W2055047900","https://openalex.org/W2055214702","https://openalex.org/W2062029454","https://openalex.org/W2062784127","https://openalex.org/W2063854986","https://openalex.org/W2067439821","https://openalex.org/W2081848717","https://openalex.org/W2088430534","https://openalex.org/W2102216585","https://openalex.org/W2105998918","https://openalex.org/W2125987139","https://openalex.org/W2128084896","https://openalex.org/W2138710479","https://openalex.org/W2141545875","https://openalex.org/W2155221318","https://openalex.org/W2168221215","https://openalex.org/W2172790580","https://openalex.org/W2214074259","https://openalex.org/W2295450494","https://openalex.org/W2297701691","https://openalex.org/W2395347108","https://openalex.org/W2463090257","https://openalex.org/W2463855622","https://openalex.org/W2484685366","https://openalex.org/W2528005577","https://openalex.org/W2572662684","https://openalex.org/W2611346822","https://openalex.org/W2620676965","https://openalex.org/W2757339220","https://openalex.org/W2775251218","https://openalex.org/W2786672974","https://openalex.org/W2793477525","https://openalex.org/W2802722915","https://openalex.org/W2885673883","https://openalex.org/W2911279170","https://openalex.org/W2913658479","https://openalex.org/W2948209659","https://openalex.org/W2950222828","https://openalex.org/W2952840385","https://openalex.org/W2952938648","https://openalex.org/W2974067482","https://openalex.org/W2985979440","https://openalex.org/W3003192283","https://openalex.org/W3022585649","https://openalex.org/W3047141442","https://openalex.org/W3081464148","https://openalex.org/W3093858607","https://openalex.org/W3094630184","https://openalex.org/W3112600195","https://openalex.org/W3129293149","https://openalex.org/W3166328131","https://openalex.org/W3196649716","https://openalex.org/W3200674343","https://openalex.org/W3201007633","https://openalex.org/W4205394018","https://openalex.org/W4205496949","https://openalex.org/W4220765701","https://openalex.org/W4283079314","https://openalex.org/W4300862018","https://openalex.org/W4308687619","https://openalex.org/W4353041376","https://openalex.org/W4362597581","https://openalex.org/W4376641475","https://openalex.org/W4384341779","https://openalex.org/W4388490141","https://openalex.org/W4389166577","https://openalex.org/W4391971327","https://openalex.org/W4393026761","https://openalex.org/W4393518422","https://openalex.org/W4404531767","https://openalex.org/W4406142575"],"related_works":[],"abstract_inverted_index":{"Originally":[0],"proposed":[1],"as":[2],"a":[3,32,44,83],"conceptual":[4,34],"metaphor,":[5],"the":[6,13,20,28,74,92,96,106,113],"Waddington":[7,29,75,97,107],"landscape":[8,30,108],"was":[9],"used":[10],"to":[11],"illustrate":[12],"directional":[14],"nature":[15],"of":[16,23,73,95,119],"embryonic":[17],"development":[18],"and":[19,50,62,102,116,130],"relative":[21],"stability":[22],"distinct":[24],"developmental":[25,132],"states.":[26],"While":[27],"offers":[31],"valuable":[33],"framework":[35],"for":[36,105],"understanding":[37],"cellular":[38,124],"dynamics,":[39],"its":[40],"quantitative":[41,71],"reconstruction":[42,72],"remains":[43],"significant":[45],"challenge":[46],"in":[47,55,122],"systems":[48,65],"biology":[49],"biophysics.":[51],"Recent":[52],"methodological":[53],"advances":[54],"single-cell":[56],"omics":[57],"technologies,":[58],"computational":[59,101],"modeling":[60],"approaches,":[61],"nonlinear":[63],"dynamical":[64],"theory":[66],"have":[67],"facilitated":[68],"progress":[69],"toward":[70],"landscape,":[76,98],"thereby":[77],"transforming":[78],"this":[79,88],"heuristic":[80],"metaphor":[81],"into":[82],"predictive":[84],"theoretical":[85,93],"framework.":[86],"In":[87],"review,":[89],"we":[90,111],"summarize":[91],"foundations":[94],"categorize":[99],"current":[100],"mathematical":[103],"approaches":[104,121],"reconstruction.":[109],"Meanwhile,":[110],"highlight":[112],"potential":[114],"applications":[115],"inherent":[117],"limitations":[118],"these":[120],"characterizing":[123],"behaviors,":[125],"predicting":[126],"cell":[127],"fate":[128],"decisions,":[129],"modulating":[131],"trajectories.":[133]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-03-27T14:29:43.386196","created_date":"2025-12-11T00:00:00"}
