{"id":"https://openalex.org/W2129708422","doi":"https://doi.org/10.1039/c0ib00092b","title":"Phenotypic transition maps of 3D breast acini obtained by imaging-guided agent-based modeling","display_name":"Phenotypic transition maps of 3D breast acini obtained by imaging-guided agent-based modeling","publication_year":2011,"publication_date":"2011-01-01","ids":{"openalex":"https://openalex.org/W2129708422","doi":"https://doi.org/10.1039/c0ib00092b","mag":"2129708422","pmid":"https://pubmed.ncbi.nlm.nih.gov/21373705","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/4009383"},"language":"en","primary_location":{"id":"doi:10.1039/c0ib00092b","doi":"https://doi.org/10.1039/c0ib00092b","is_oa":false,"landing_page_url":"https://doi.org/10.1039/c0ib00092b","pdf_url":null,"source":{"id":"https://openalex.org/S10577112","display_name":"Integrative Biology","issn_l":"1757-9694","issn":["1757-9694","1757-9708"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-c","jufo-1","medline","norway-1","poland-100","russia-white-list-2"],"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Integrative Biology","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4009383","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102006300","display_name":"Jonathan Tang","orcid":"https://orcid.org/0000-0002-8831-5976","observed_orcids":["https://orcid.org/0000-0002-8831-5976"]},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]},{"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":"Jonathan Tang","raw_affiliation_strings":["Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. jonathantang@lbl.gov","Bay Area Physical Sciences-Oncology Center,UC Berkeley,Berkeley","Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. jonathantang@lbl.gov","institution_ids":["https://openalex.org/I148283060"]},{"raw_affiliation_string":"Bay Area Physical Sciences-Oncology Center,UC Berkeley,Berkeley","institution_ids":["https://openalex.org/I95457486"]},{"raw_affiliation_string":"Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, USA","institution_ids":["https://openalex.org/I148283060"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014796235","display_name":"Heiko Enderling","orcid":"https://orcid.org/0000-0002-9696-6410","observed_orcids":["https://orcid.org/0000-0002-9696-6410"]},"institutions":[{"id":"https://openalex.org/I121934306","display_name":"Tufts University","ror":"https://ror.org/05wvpxv85","country_code":"US","type":"education","lineage":["https://openalex.org/I121934306"]},{"id":"https://openalex.org/I3018163063","display_name":"St. Elizabeth's Medical Center","ror":"https://ror.org/00cr15z55","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I3018163063"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Heiko Enderling","raw_affiliation_strings":["Center of Cancer Systems Biology, St Elizabeth's Medical Center, Tufts University School of Medicine, Boston, MA 02135, USA","Center of Cancer Systems Biology, St Elizabeth's Medical Center, Tufts University School of Medicine,Boston,USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center of Cancer Systems Biology, St Elizabeth's Medical Center, Tufts University School of Medicine, Boston, MA 02135, USA","institution_ids":["https://openalex.org/I121934306","https://openalex.org/I3018163063"]},{"raw_affiliation_string":"Center of Cancer Systems Biology, St Elizabeth's Medical Center, Tufts University School of Medicine,Boston,USA","institution_ids":["https://openalex.org/I121934306","https://openalex.org/I3018163063"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011011136","display_name":"Sabine Becker-Weimann","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]},{"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":"Sabine Becker-Weimann","raw_affiliation_strings":["Bay Area Physical Sciences-Oncology Center, UC Berkeley, Berkeley CA 94720","Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA","Bay Area Physical Sciences-Oncology Center,UC Berkeley,Berkeley","Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bay Area Physical Sciences-Oncology Center, UC Berkeley, Berkeley CA 94720","institution_ids":["https://openalex.org/I95457486"]},{"raw_affiliation_string":"Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA","institution_ids":["https://openalex.org/I148283060"]},{"raw_affiliation_string":"Bay Area Physical Sciences-Oncology Center,UC Berkeley,Berkeley","institution_ids":["https://openalex.org/I95457486"]},{"raw_affiliation_string":"Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, USA","institution_ids":["https://openalex.org/I148283060"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076424383","display_name":"Christopher J. Pham","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Christopher Pham","raw_affiliation_strings":["Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA","Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, USA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA","institution_ids":["https://openalex.org/I148283060"]},{"raw_affiliation_string":"Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, USA#TAB#","institution_ids":["https://openalex.org/I148283060"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090590141","display_name":"Aris A. Polyzos","orcid":"https://orcid.org/0000-0002-9542-5807","observed_orcids":["https://orcid.org/0000-0002-9542-5807"]},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Aris Polyzos","raw_affiliation_strings":["Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA","Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, USA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA","institution_ids":["https://openalex.org/I148283060"]},{"raw_affiliation_string":"Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, USA#TAB#","institution_ids":["https://openalex.org/I148283060"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060133536","display_name":"Chen-Yi Chen","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chen-Yi Chen","raw_affiliation_strings":["Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA","Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, USA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA","institution_ids":["https://openalex.org/I148283060"]},{"raw_affiliation_string":"Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, USA#TAB#","institution_ids":["https://openalex.org/I148283060"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5076358770","display_name":"Sylvain V. Costes","orcid":"https://orcid.org/0000-0002-8542-2389","observed_orcids":["https://orcid.org/0000-0002-8542-2389"]},"institutions":[{"id":"https://openalex.org/I121934306","display_name":"Tufts University","ror":"https://ror.org/05wvpxv85","country_code":"US","type":"education","lineage":["https://openalex.org/I121934306"]},{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]},{"id":"https://openalex.org/I3018163063","display_name":"St. Elizabeth's Medical Center","ror":"https://ror.org/00cr15z55","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I3018163063"]},{"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":"Sylvain V. Costes","raw_affiliation_strings":["Bay Area Physical Sciences-Oncology Center, UC Berkeley, Berkeley CA 94720","Center of Cancer Systems Biology, St Elizabeth's Medical Center, Tufts University School of Medicine, Boston, MA 02135, USA","Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA","Bay Area Physical Sciences-Oncology Center, UC Berkeley, Berkeley","Center of Cancer Systems Biology, St Elizabeth's Medical Center, Tufts University School of Medicine, Boston, USA","Life Sciences Division, Lawrence Berkeley National Laboratory,Berkeley,USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bay Area Physical Sciences-Oncology Center, UC Berkeley, Berkeley CA 94720","institution_ids":["https://openalex.org/I95457486"]},{"raw_affiliation_string":"Center of Cancer Systems Biology, St Elizabeth's Medical Center, Tufts University School of Medicine, Boston, MA 02135, USA","institution_ids":["https://openalex.org/I121934306","https://openalex.org/I3018163063"]},{"raw_affiliation_string":"Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA","institution_ids":["https://openalex.org/I148283060"]},{"raw_affiliation_string":"Bay Area Physical Sciences-Oncology Center, UC Berkeley, Berkeley","institution_ids":["https://openalex.org/I95457486"]},{"raw_affiliation_string":"Center of Cancer Systems Biology, St Elizabeth's Medical Center, Tufts University School of Medicine, Boston, USA","institution_ids":["https://openalex.org/I121934306","https://openalex.org/I3018163063"]},{"raw_affiliation_string":"Life Sciences Division, Lawrence Berkeley National Laboratory,Berkeley,USA","institution_ids":["https://openalex.org/I148283060"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5076358770","https://openalex.org/A5102006300"],"corresponding_institution_ids":["https://openalex.org/I121934306","https://openalex.org/I148283060","https://openalex.org/I3018163063","https://openalex.org/I95457486"],"apc_list":{"value":3522,"currency":"USD","value_usd":3522},"apc_paid":null,"fwci":5.7876,"has_fulltext":false,"cited_by_count":43,"citation_normalized_percentile":{"value":0.95186926,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":88,"max":99},"biblio":{"volume":"3","issue":"4","first_page":"408","last_page":"408"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11829","display_name":"Mathematical Biology Tumor Growth","score":0.9247999787330627,"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":0.9247999787330627,"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":0.03750000149011612,"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":0.020800000056624413,"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/epithelial-morphogenesis","display_name":"epithelial morphogenesis","score":0.8349999785423279},{"id":"https://openalex.org/keywords/agent-based-modeling","display_name":"agent-based modeling","score":0.8230000138282776},{"id":"https://openalex.org/keywords/apoptosis","display_name":"apoptosis","score":0.9300000071525574},{"id":"https://openalex.org/keywords/cell-proliferation","display_name":"cell proliferation","score":0.9700000286102295},{"id":"https://openalex.org/keywords/cell-polarization","display_name":"cell polarization","score":0.9829999804496765},{"id":"https://openalex.org/keywords/lumen-formation","display_name":"lumen formation","score":0.9440000057220459},{"id":"https://openalex.org/keywords/ductal-carcinoma-in-situ","display_name":"ductal carcinoma in situ","score":0.878000020980835},{"id":"https://openalex.org/keywords/mcf-10a-cells","display_name":"MCF10A cells","score":0.8730000257492065},{"id":"https://openalex.org/keywords/nuclear-density","display_name":"nuclear density","score":0.7730000019073486},{"id":"https://openalex.org/keywords/high-content-image-analysis","display_name":"high-content image analysis","score":0.5950000286102295}],"concepts":[{"id":"https://openalex.org/C2991948145","wikidata":"https://www.wikidata.org/wiki/Q16801175","display_name":"National laboratory","level":2,"score":0.6932845711708069},{"id":"https://openalex.org/C161191863","wikidata":"https://www.wikidata.org/wiki/Q199655","display_name":"Library science","level":1,"score":0.527616024017334},{"id":"https://openalex.org/C52119013","wikidata":"https://www.wikidata.org/wiki/Q50637","display_name":"Art history","level":1,"score":0.40286898612976074},{"id":"https://openalex.org/C74916050","wikidata":"https://www.wikidata.org/wiki/Q841090","display_name":"Classics","level":1,"score":0.3470245599746704},{"id":"https://openalex.org/C142362112","wikidata":"https://www.wikidata.org/wiki/Q735","display_name":"Art","level":0,"score":0.3147774338722229},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.24405935406684875},{"id":"https://openalex.org/C61696701","wikidata":"https://www.wikidata.org/wiki/Q770766","display_name":"Engineering physics","level":1,"score":0.15832209587097168},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.15252691507339478}],"mesh":[{"descriptor_ui":"D002452","descriptor_name":"Cell Count","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002460","descriptor_name":"Cell Line","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002461","descriptor_name":"Cell Line, Transformed","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":"D004847","descriptor_name":"Epithelial Cells","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D004847","descriptor_name":"Epithelial Cells","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","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":"D007091","descriptor_name":"Image Processing, Computer-Assisted","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":"D009024","descriptor_name":"Morphogenesis","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012985","descriptor_name":"Software Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016764","descriptor_name":"Cell Polarity","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D017209","descriptor_name":"Apoptosis","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D018929","descriptor_name":"Cell Culture Techniques","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D021621","descriptor_name":"Imaging, Three-Dimensional","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D042361","descriptor_name":"Mammary Glands, Human","qualifier_ui":"Q000033","qualifier_name":"anatomy & histology","is_major_topic":false},{"descriptor_ui":"D042361","descriptor_name":"Mammary Glands, Human","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D042361","descriptor_name":"Mammary Glands, Human","qualifier_ui":"Q000254","qualifier_name":"growth & development","is_major_topic":true},{"descriptor_ui":"D042361","descriptor_name":"Mammary Glands, Human","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D049109","descriptor_name":"Cell Proliferation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":8,"locations":[{"id":"doi:10.1039/c0ib00092b","doi":"https://doi.org/10.1039/c0ib00092b","is_oa":false,"landing_page_url":"https://doi.org/10.1039/c0ib00092b","pdf_url":null,"source":{"id":"https://openalex.org/S10577112","display_name":"Integrative Biology","issn_l":"1757-9694","issn":["1757-9694","1757-9708"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-c","jufo-1","medline","norway-1","poland-100","russia-white-list-2"],"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Integrative Biology","raw_type":"journal-article"},{"id":"pmid:21373705","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21373705","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":"Integrative biology : quantitative biosciences from nano to macro","raw_type":"Journal Article"},{"id":"pmh:oai:europepmc.org:2989702","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4009383","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:4009383","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4009383","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":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"Integr Biol (Camb)","raw_type":"Text"},{"id":"pmh:oai:osti.gov:1017062","doi":null,"is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1017062","pdf_url":"https://www.osti.gov/servlets/purl/1017062","source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:info:ark/67531/metadc836144","doi":null,"is_oa":false,"landing_page_url":"https://digital.library.unt.edu/ark:/67531/metadc836144/","pdf_url":null,"source":{"id":"https://openalex.org/S4306400792","display_name":"University of North Texas Digital Library (University of North Texas)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I123534392","host_organization_name":"University of North Texas","host_organization_lineage":["https://openalex.org/I123534392"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Integrative Biology","raw_type":"Article"},{"id":"pmh:oai:escholarship.org/ark:/13030/qt89g9n3tn","doi":null,"is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/89g9n3tn","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,"listed_in":[],"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":"","raw_type":"article"},{"id":"pmh:qt89g9n3tn","doi":null,"is_oa":false,"landing_page_url":"http://www.escholarship.org/uc/item/89g9n3tn","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,"listed_in":[],"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":"Tang, Jonathan. (2011). Phenotypic transition maps of 3D breast acini obtained by imaging-guided agent-based modeling. Lawrence Berkeley National Laboratory. doi: 10.1039/c0ib00092b. Lawrence Berkeley National Laboratory: Lawrence Berkeley National Laboratory. Retrieved from: http://www.escholarship.org/uc/item/89g9n3tn","raw_type":"article"}],"best_oa_location":{"id":"pmh:oai:europepmc.org:2989702","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4009383","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"Text"},"sustainable_development_goals":[{"score":0.5683000087738037,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"study_designs":[],"awards":[{"id":"https://openalex.org/G4692362935","display_name":"Fundamental Mechanobiology of Tumor Progression","funder_award_id":"U54CA143836","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G900793794","display_name":"Intercellular Interactions Modulate Carcinogenesis Course: A Dynamic System Study","funder_award_id":"U54CA149233","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2129708422.pdf","grobid_xml":"https://content.openalex.org/works/W2129708422.grobid-xml"},"referenced_works_count":53,"referenced_works":["https://openalex.org/W1525971636","https://openalex.org/W1604746898","https://openalex.org/W1748552538","https://openalex.org/W1906450972","https://openalex.org/W1980039397","https://openalex.org/W1981962653","https://openalex.org/W1987717176","https://openalex.org/W1988059443","https://openalex.org/W1989963027","https://openalex.org/W1994683536","https://openalex.org/W1994843494","https://openalex.org/W1999397355","https://openalex.org/W2000003193","https://openalex.org/W2001576206","https://openalex.org/W2003657279","https://openalex.org/W2004550343","https://openalex.org/W2008566763","https://openalex.org/W2024771744","https://openalex.org/W2026912481","https://openalex.org/W2029405376","https://openalex.org/W2036374135","https://openalex.org/W2040196588","https://openalex.org/W2042835353","https://openalex.org/W2044719035","https://openalex.org/W2045854741","https://openalex.org/W2066288526","https://openalex.org/W2070945559","https://openalex.org/W2071279332","https://openalex.org/W2071599428","https://openalex.org/W2075631796","https://openalex.org/W2081399416","https://openalex.org/W2082222204","https://openalex.org/W2086356330","https://openalex.org/W2086811477","https://openalex.org/W2087805577","https://openalex.org/W2090678178","https://openalex.org/W2093160601","https://openalex.org/W2107316538","https://openalex.org/W2109000871","https://openalex.org/W2110059498","https://openalex.org/W2112497627","https://openalex.org/W2120391834","https://openalex.org/W2124688359","https://openalex.org/W2133278361","https://openalex.org/W2142603939","https://openalex.org/W2151654304","https://openalex.org/W2153063790","https://openalex.org/W2156171664","https://openalex.org/W2156678998","https://openalex.org/W2159748585","https://openalex.org/W2165477530","https://openalex.org/W2166223265","https://openalex.org/W2167931729"],"related_works":["https://openalex.org/W2040196588","https://openalex.org/W206875627","https://openalex.org/W2068716083","https://openalex.org/W2136156049","https://openalex.org/W2001576206","https://openalex.org/W1998301679","https://openalex.org/W1994683536","https://openalex.org/W2061826779","https://openalex.org/W1988644010","https://openalex.org/W2362267832"],"abstract_inverted_index":{"We":[0],"introduce":[1],"an":[2],"agent-based":[3,47],"model":[4,48,143,221],"of":[5,24,32,58,123,162,240,251],"epithelial":[6],"cell":[7,68,92],"morphogenesis":[8,61],"to":[9,158,169,177],"explore":[10],"the":[11,21,95,121,142,154,160,214,228,238],"complex":[12],"interplay":[13],"between":[14,132],"apoptosis,":[15],"proliferation,":[16],"and":[17,34,42,51,71,85,103,134,185,243,257],"polarization.":[18],"By":[19],"varying":[20],"activity":[22],"levels":[23],"these":[25,209],"mechanisms":[26],"we":[27],"derived":[28],"phenotypic":[29],"transition":[30],"maps":[31,38],"normal":[33,114,149,202],"aberrant":[35],"morphogenesis.":[36],"These":[37],"identify":[39],"homeostatic":[40],"ranges":[41],"morphologic":[43],"stability":[44],"conditions.":[45],"The":[46,204,218],"was":[49,156,166],"parameterized":[50],"validated":[52],"using":[53],"novel":[54],"high-content":[55],"image":[56,191],"analysis":[57,192],"mammary":[59],"acini":[60,77,104,115,210],"in":[62,113,136,219,234],"vitro":[63],"with":[64,144,181],"focus":[65],"on":[66],"time-dependent":[67],"densities,":[69],"proliferation":[70,242],"death":[72],"rates,":[73],"as":[74,76],"well":[75],"morphologies.":[78],"Model":[79],"simulations":[80,107,128,247],"reveal":[81,129],"apoptosis":[82,135],"being":[83,94],"necessary":[84],"sufficient":[86],"for":[87,98,201],"initiating":[88],"lumen":[89],"formation,":[90],"but":[91],"polarization":[93,133],"pivotal":[96],"mechanism":[97],"maintaining":[99],"physiological":[100],"epithelium":[101],"morphology":[102],"sphericity.":[105],"Furthermore,":[106],"highlight":[108],"that":[109,208,231,249,262],"acinus":[110],"growth":[111,138,161,205],"arrest":[112],"can":[116,265],"be":[117],"achieved":[118],"by":[119],"controlling":[120],"fraction":[122],"proliferating":[124],"cells.":[125],"Interestingly,":[126],"our":[127],"a":[130,148,194],"synergism":[131],"enhancing":[137],"arrest.":[139],"After":[140],"validating":[141],"experimental":[145],"data":[146],"from":[147],"human":[150],"breast":[151],"line":[152],"(MCF10A),":[153],"system":[155],"challenged":[157],"predict":[159],"MCF10A":[163],"where":[164],"AKT-1":[165,252],"overexpressed,":[167],"leading":[168],"reduced":[170],"apoptosis.":[171,245],"As":[172],"previously":[173],"reported,":[174],"this":[175,225],"led":[176],"non":[178],"growth-arrested":[179],"acini,":[180],"very":[182],"large":[183],"sizes":[184],"partially":[186],"filled":[187],"lumen.":[188],"However,":[189],"surprisingly,":[190],"revealed":[193],"much":[195],"lower":[196],"nuclear":[197],"density":[198],"than":[199,213],"observed":[200],"acini.":[203],"kinetics":[206],"indicates":[207],"grew":[211],"faster":[212],"cells":[215],"comprising":[216],"it.":[217],"silico":[220],"could":[222],"not":[223],"replicate":[224],"behavior,":[226],"contradicting":[227],"classic":[229],"paradigm":[230],"ductal":[232],"carcinoma":[233],"situ":[235],"is":[236],"only":[237],"result":[239],"high":[241],"low":[244],"Our":[246],"suggest":[248],"overexpression":[250],"must":[253],"also":[254],"perturb":[255],"cell-cell":[256],"cell-ECM":[258],"communication,":[259],"reminding":[260],"us":[261],"extracellular":[263],"context":[264],"dictate":[266],"cellular":[267],"behavior.":[268]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":4},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":7},{"year":2012,"cited_by_count":5}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2016-06-24T00:00:00"}
