{"id":"https://openalex.org/W1999397355","doi":"https://doi.org/10.1186/1752-0509-3-122","title":"A computational approach to resolve cell level contributions to early glandular epithelial cancer progression","display_name":"A computational approach to resolve cell level contributions to early glandular epithelial cancer progression","publication_year":2009,"publication_date":"2009-12-01","ids":{"openalex":"https://openalex.org/W1999397355","doi":"https://doi.org/10.1186/1752-0509-3-122","mag":"1999397355","pmid":"https://pubmed.ncbi.nlm.nih.gov/20043854"},"language":"en","primary_location":{"id":"doi:10.1186/1752-0509-3-122","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-3-122","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-3-122","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-3-122","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5034771520","display_name":"Sean H. J. Kim","orcid":null},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Sean HJ Kim","raw_affiliation_strings":["UCSF/UC Berkeley Joint Graduate Group in Bioengineering, University of California, Berkeley, California 94720, USA. seanhjk@berkeley.edu","UCSF/UC Berkeley Joint Graduate Group in Bioengineering, University of California,Berkeley,USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UCSF/UC Berkeley Joint Graduate Group in Bioengineering, University of California, Berkeley, California 94720, USA. seanhjk@berkeley.edu","institution_ids":["https://openalex.org/I95457486"]},{"raw_affiliation_string":"UCSF/UC Berkeley Joint Graduate Group in Bioengineering, University of California,Berkeley,USA","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001716925","display_name":"Jayanta Debnath","orcid":"https://orcid.org/0000-0002-8745-4069"},"institutions":[{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jayanta Debnath","raw_affiliation_strings":["Department of Pathology, University of California, San Francisco, California, 94143, USA","Department of Pathology, University of California, San Francisco, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pathology, University of California, San Francisco, California, 94143, USA","institution_ids":["https://openalex.org/I180670191"]},{"raw_affiliation_string":"Department of Pathology, University of California, San Francisco, USA","institution_ids":["https://openalex.org/I180670191"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076973759","display_name":"Keith E. Mostov","orcid":"https://orcid.org/0000-0002-8123-6247"},"institutions":[{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Keith Mostov","raw_affiliation_strings":["Department of Anatomy, University of California, San Francisco, California, 94143, USA","Dept. of Anatomy, University of California, San Francisco, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Anatomy, University of California, San Francisco, California, 94143, USA","institution_ids":["https://openalex.org/I180670191"]},{"raw_affiliation_string":"Dept. of Anatomy, University of California, San Francisco, USA","institution_ids":["https://openalex.org/I180670191"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Sunwoo Park","orcid":null},"institutions":[{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sunwoo Park","raw_affiliation_strings":["Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California, 94143, USA","Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California, 94143, USA","institution_ids":["https://openalex.org/I180670191"]},{"raw_affiliation_string":"Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, USA","institution_ids":["https://openalex.org/I180670191"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5001335754","display_name":"C. Anthony Hunt","orcid":"https://orcid.org/0000-0001-9372-6860"},"institutions":[{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]},{"id":"https://openalex.org/I19620478","display_name":"Graduate Theological Union","ror":"https://ror.org/00xs48965","country_code":"US","type":"other","lineage":["https://openalex.org/I19620478"]},{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"C Anthony Hunt","raw_affiliation_strings":["Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California, 94143, USA","UCSF/UC Berkeley Joint Graduate Group in Bioengineering, University of California, Berkeley, California, 94720, USA","UCSF/UC Berkeley Joint Graduate Group in Bioengineering, University of California, Berkeley, USA","Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California, 94143, USA","institution_ids":["https://openalex.org/I180670191"]},{"raw_affiliation_string":"UCSF/UC Berkeley Joint Graduate Group in Bioengineering, University of California, Berkeley, California, 94720, USA","institution_ids":["https://openalex.org/I95457486"]},{"raw_affiliation_string":"UCSF/UC Berkeley Joint Graduate Group in Bioengineering, University of California, Berkeley, USA","institution_ids":["https://openalex.org/I19620478","https://openalex.org/I95457486"]},{"raw_affiliation_string":"Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, USA","institution_ids":["https://openalex.org/I180670191"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5034771520"],"corresponding_institution_ids":["https://openalex.org/I95457486"],"apc_list":null,"apc_paid":null,"fwci":2.8812,"has_fulltext":true,"cited_by_count":32,"citation_normalized_percentile":{"value":0.89395546,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"3","issue":"1","first_page":"122","last_page":"122"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11829","display_name":"Mathematical Biology Tumor Growth","score":0.9372000098228455,"subfield":{"id":"https://openalex.org/subfields/2611","display_name":"Modeling and Simulation"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11829","display_name":"Mathematical Biology Tumor Growth","score":0.9372000098228455,"subfield":{"id":"https://openalex.org/subfields/2611","display_name":"Modeling and Simulation"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10379","display_name":"Cellular Mechanics and Interactions","score":0.0052999998442828655,"subfield":{"id":"https://openalex.org/subfields/1307","display_name":"Cell 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/T10336","display_name":"Cancer Cells and Metastasis","score":0.005200000014156103,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.6862195730209351},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5060264468193054},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.46370843052864075},{"id":"https://openalex.org/keywords/modelling-biological-systems","display_name":"Modelling biological systems","score":0.41049087047576904},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.384219229221344}],"concepts":[{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.6862195730209351},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5060264468193054},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.46370843052864075},{"id":"https://openalex.org/C137866125","wikidata":"https://www.wikidata.org/wiki/Q4299308","display_name":"Modelling biological systems","level":3,"score":0.41049087047576904},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.384219229221344}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004195","descriptor_name":"Disease Models, Animal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004195","descriptor_name":"Disease Models, Animal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004195","descriptor_name":"Disease Models, Animal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004195","descriptor_name":"Disease Models, Animal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004285","descriptor_name":"Dogs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004285","descriptor_name":"Dogs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004285","descriptor_name":"Dogs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004285","descriptor_name":"Dogs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","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":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","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":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009375","descriptor_name":"Neoplasms, Glandular and Epithelial","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D009375","descriptor_name":"Neoplasms, Glandular and Epithelial","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D009375","descriptor_name":"Neoplasms, Glandular and Epithelial","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D009375","descriptor_name":"Neoplasms, Glandular and Epithelial","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D009375","descriptor_name":"Neoplasms, Glandular and Epithelial","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D009375","descriptor_name":"Neoplasms, Glandular and Epithelial","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D009375","descriptor_name":"Neoplasms, Glandular and Epithelial","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D009375","descriptor_name":"Neoplasms, Glandular and Epithelial","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017209","descriptor_name":"Apoptosis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017209","descriptor_name":"Apoptosis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017209","descriptor_name":"Apoptosis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017209","descriptor_name":"Apoptosis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018450","descriptor_name":"Disease Progression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018450","descriptor_name":"Disease Progression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018450","descriptor_name":"Disease Progression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018450","descriptor_name":"Disease Progression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018929","descriptor_name":"Cell Culture Techniques","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D018929","descriptor_name":"Cell Culture Techniques","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D018929","descriptor_name":"Cell Culture Techniques","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D018929","descriptor_name":"Cell Culture Techniques","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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D044127","descriptor_name":"Epigenesis, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D044127","descriptor_name":"Epigenesis, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D044127","descriptor_name":"Epigenesis, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D044127","descriptor_name":"Epigenesis, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems 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":false},{"descriptor_ui":"D049490","descriptor_name":"Systems 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":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/1752-0509-3-122","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-3-122","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-3-122","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},{"id":"pmid:20043854","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20043854","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":"BMC systems biology","raw_type":null},{"id":"pmh:ark:/13030/qt7p6874ps","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:escholarship.org/ark:/13030/qt7p6874ps","is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/7p6874ps","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC systems biology, vol 3, iss 1","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2814811","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2814811","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,"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":"BMC Syst Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1752-0509-3-122","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-3-122","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-3-122","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6794065192","display_name":null,"funder_award_id":"R01 DK074398","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320308813","display_name":"International Foundation for Ethical Research","ror":"https://ror.org/02by3t490"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1999397355.pdf","grobid_xml":"https://content.openalex.org/works/W1999397355.grobid-xml"},"referenced_works_count":55,"referenced_works":["https://openalex.org/W1964333640","https://openalex.org/W1971221092","https://openalex.org/W1978486653","https://openalex.org/W1981962653","https://openalex.org/W1984087468","https://openalex.org/W1986397618","https://openalex.org/W1989963027","https://openalex.org/W1994683536","https://openalex.org/W2006012747","https://openalex.org/W2006067863","https://openalex.org/W2008434851","https://openalex.org/W2008566763","https://openalex.org/W2012047089","https://openalex.org/W2016385245","https://openalex.org/W2019438752","https://openalex.org/W2020285793","https://openalex.org/W2024686059","https://openalex.org/W2025176241","https://openalex.org/W2028249595","https://openalex.org/W2029572691","https://openalex.org/W2032461554","https://openalex.org/W2034301798","https://openalex.org/W2038653804","https://openalex.org/W2051177925","https://openalex.org/W2058324879","https://openalex.org/W2062835218","https://openalex.org/W2090683259","https://openalex.org/W2093199237","https://openalex.org/W2099626566","https://openalex.org/W2105054044","https://openalex.org/W2106747948","https://openalex.org/W2110059498","https://openalex.org/W2120038224","https://openalex.org/W2124559417","https://openalex.org/W2128333867","https://openalex.org/W2131519618","https://openalex.org/W2144244247","https://openalex.org/W2145139438","https://openalex.org/W2147298213","https://openalex.org/W2154010000","https://openalex.org/W2154333296","https://openalex.org/W2157425630","https://openalex.org/W2162225090","https://openalex.org/W2165429151","https://openalex.org/W2166223265","https://openalex.org/W2169961781","https://openalex.org/W2171770404","https://openalex.org/W2171935083","https://openalex.org/W2185194229","https://openalex.org/W2267176325","https://openalex.org/W2330820039","https://openalex.org/W2331870214","https://openalex.org/W2593753358","https://openalex.org/W4241949168","https://openalex.org/W4243385699"],"related_works":["https://openalex.org/W4386563820","https://openalex.org/W631732704","https://openalex.org/W2155261113","https://openalex.org/W2064988479","https://openalex.org/W1748979965","https://openalex.org/W3199870583","https://openalex.org/W1593256703","https://openalex.org/W4254550161","https://openalex.org/W5284979","https://openalex.org/W4245853730"],"abstract_inverted_index":{"BACKGROUND:":[0],"Three-dimensional":[1],"(3D)":[2],"embedded":[3,145],"cell":[4,94,103,114,125,146,154,182],"cultures":[5],"provide":[6,255],"an":[7,64,70],"appropriate":[8],"physiological":[9],"environment":[10],"to":[11,37,47,159,194,254,259],"reconstruct":[12],"features":[13,79,107,162],"of":[14,23,51,53,80,88,100,112,124,139,150,165,198,228,269],"early":[15,59,241],"glandular":[16],"epithelial":[17,54,74,270],"cancer.":[18],"Although":[19],"these":[20],"are":[21,30,220,252],"orders":[22],"magnitude":[24],"simpler":[25],"than":[26],"tissues,":[27],"they":[28],"too":[29],"complex":[31],"systems":[32],"that":[33,136,185,215],"have":[34,209],"proven":[35],"challenging":[36],"understand.":[38],"We":[39,96],"used":[40],"agent-based,":[41],"discrete":[42],"event":[43],"simulation":[44],"modeling":[45],"methods":[46,263],"build":[48],"working":[49],"hypotheses":[50],"mechanisms":[52,227],"3D":[55,144],"culture":[56],"phenotype":[57],"and":[58,116,131,171,205,235,250,272],"cancer":[60,231,242,273],"progression.":[61,274],"Starting":[62],"with":[63],"earlier":[65],"software":[66],"analogue,":[67],"we":[68],"validated":[69],"improved":[71],"in":[72,142,166,174,187,216,229,261],"silico":[73],"analogue":[75],"(ISEA)":[76],"for":[77,240,264],"cardinal":[78],"a":[81,121,143,195,256],"normally":[82],"developed":[83],"MDCK":[84,140],"cyst.":[85],"A":[86],"set":[87,123],"axiomatic":[89],"operating":[90,126],"principles":[91],"defined":[92],"simulated":[93,102],"actions.":[95,104],"explored":[97],"selective":[98],"disruption":[99,149,192],"individual":[101],"New":[105],"framework":[106],"enabled":[108],"recording":[109],"detailed":[110],"measures":[111],"ISEA":[113,128,158,202,248],"activities":[115],"morphology.":[117],"RESULTS:":[118],"Enabled":[119],"by":[120],"small":[122],"principles,":[127],"cells":[129,141],"multiplied":[130],"self-organized":[132],"into":[133],"cyst-like":[134],"structures":[135],"mimicked":[137],"those":[138,164],"culture.":[147],"Selective":[148],"\"anoikis\"":[151],"or":[152,179,233],"directional":[153],"division":[155],"caused":[156],"the":[157,213,222,266],"develop":[160],"phenotypic":[161],"resembling":[163],"vitro":[167,218,230,262],"tumor":[168],"reconstruction":[169,232],"models":[170],"cancerous":[172],"tissues":[173],"vivo.":[175],"Disrupting":[176],"either":[177],"process,":[178],"both,":[180],"altered":[181],"activity":[183],"patterns":[184],"resulted":[186],"morphologically":[188],"similar":[189],"outcomes.":[190],"Increased":[191],"led":[193],"prolonged":[196],"presence":[197],"intraluminal":[199],"cells.":[200],"CONCLUSIONS:":[201],"mechanisms,":[203],"behaviors,":[204],"morphological":[206],"properties":[207],"may":[208],"biological":[210],"counterparts.":[211],"To":[212],"extent":[214],"silico-to-in":[217],"mappings":[219],"valid,":[221],"results":[223],"suggest":[224],"plausible,":[225],"additional":[226],"reversion,":[234],"raise":[236],"potentially":[237],"significant":[238],"implications":[239],"diagnosis":[243],"based":[244],"on":[245],"histology.":[246],"Further":[247],"development":[249],"use":[251],"expected":[253],"viable":[257],"platform":[258],"complement":[260],"unraveling":[265],"mechanistic":[267],"basis":[268],"morphogenesis":[271]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":4},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":2}],"updated_date":"2026-04-29T09:16:38.111599","created_date":"2025-10-10T00:00:00"}