This page contains selected publications that used CompuCell3D. While we try to keep this page updated some publications might be missing. If you want your CompuCell3D-based publication to be displayed here, please e-mail us ( jsluka@iu.edu ) '''''For list of Ph.D. and Master theses completed using CC3D please click [[Theses|here]].''''' == How to cite CompuCell3D == [[http://www.sciencedirect.com/science/article/pii/B9780123884039000138|Multi-Scale Modeling of Tissues Using CompuCell3D]] – [[http://www.indiana.edu/~bioc/people/?p=staff|M. Swat]], [[http://www.if.ufrgs.br/pos/portugues/thomas.html|Gilberto L. Thomas]], Julio M. Belmonte, A. Shirinifard, D. Hmeljak, [[http://www.indiana.edu/~bioc/jglazier/|J. A. Glazier]], ''__Computational Methods in Cell Biology__, Methods in Cell Biology '''''110''': 325-366 (2012) == Publications == ==== 2022 ==== 1. [[https://onlinelibrary.wiley.com/doi/10.1002/cnm.3633|"The modeling study of the effect of morphological behaviors of extracellular matrix fibers on the dynamic interaction between tumor cells and antitumor immune response."]] Guanjie Jia, Hao Yang, Kaiqun Wang, Di Huang, Weiyi Chen, Yanhu Shan. International Journal for Numerical Methods in Biomedical Engineering. 2022: e3633. DOI: 10.1002/cnm.3633. 1. [[https://www.sciencedirect.com/science/article/abs/pii/S0022519322000261|"A mathematical model to study the impact of intra-tumour heterogeneity on anti-tumour CD8+ T cell immune response."]]. Leschiera, Emma, Tommaso Lorenzi, Shensi Shen, Luis Almeida, and Chloe Audebert. Journal of Theoretical Biology (2022): 111028. 1. [[https://doi.org/10.1101/2022.02.09.479678|Matrix-driven jamming dynamics mediates transition of ovarian cancer spheroids to stable morphologies]]. Tavishi Dutt, Jimpi Langthasa, U Monica, Prosenjit Sen, Ramray Bhat bioRxiv 2022.02.09.479678; doi:https://doi.org/10.1101/2022.02.09.479678 1. [[https://doi.org/10.1007/978-94-024-2101-9_5|Modelling Direct and Indirect Effects of Radiation: Experimental, Clinical and Environmental Implications]]. Brüningk, S.C., Powathil, G.G. (2022). In: Wood, M.D., Mothersill, C.E., Tsakanova, G., Cresswell, T., Woloschak, G.E. (eds) Biomarkers of Radiation in the Environment. NATO Science for Peace and Security Series A: Chemistry and Biology. Springer, Dordrecht. 1. [[https://www.sciencedirect.com/science/article/pii/S0378437121007846|Shape–velocity correlation defines polarization in migrating cell simulations]]. Fortuna, Gabriel C. Perrone, François Graner, Rita M.C. de Almeida. Physica A: Statistical Mechanics and its Applications, Volume 587, 2022, 126511, ISSN 0378-4371, https://doi.org/10.1016/j.physa.2021.126511. 1. [[https://doi.org/10.3390/v14030605|Multiscale Model of Antiviral Timing, Potency, and Heterogeneity Effects on an Epithelial Tissue Patch Infected by SARS-CoV-2]]. Ferrari Gianlupi, J.; Mapder, T.; Sego, T.J.; Sluka, J.P.; Quinney, S.K.; Craig, M.; Stratford, R.E., Jr.; Glazier, J.A. Viruses 2022, 14, 605. https://doi.org/10.3390/v14030605 1. [[https://www.biorxiv.org/content/10.1101/784496v3.full|Parameterized Computational Framework for the Description and Design of Genetic Circuits of Morphogenesis Based on Contact-Dependent Signaling and Changes in Cell–Cell Adhesion]]. Calvin Lam*, Sajeev Saluja, George Courcoubetis, Dottie Yu, Christian Chung, Josquin Courte, and Leonardo Morsut* Cite this: ACS Synth. Biol. 2022, 11, 4, 1417–1439 Publication Date:April 1, 2022 https://doi.org/10.1021/acssynbio.0c00369 ==== 2021 ==== 1. [[https://onlinelibrary.wiley.com/doi/full/10.1111/cpr.13187|A multiscale cell‐based model of tumor growth for chemotherapy assessment and tumor‐targeted therapy through a 3D computational approach]].Jafari Nivlouei, S., Soltani, M., Shirani, E., Salimpour, M. R., Travasso, R., & Carvalho, J. (2022). Cell proliferation, 55(3), e13187 1. [[https://aasldpubs.onlinelibrary.wiley.com/doi/10.1002/hep4.1848|Negative Feedback Loop and Transcription Factor Cooperation Regulate Zonal Gene Induction by 2, 3, 7, 8-Tetrachlorodibenzo-p-Dioxin in the Mouse Liver.]] Yang Y, Filipovic D, Bhattacharya S. Hepatol Commun. 2021 Nov 2. doi: 10.1002/hep4.1848. Epub ahead of print. PMID: 34726355. 1. [[https://doi.org/10.1016/j.jocs.2021.101421|Effects of combined chemotherapeutic drugs on the growth and survival of cancerous tumours– an in-silico study]] Prerna Kaura, Tanya Mishra, Nishith Verma, Indranil Saha Dalal, Vivek Sheraton. ''Journal of Computational Science'', 2021 '''54''', 2021, 101421, ISSN 1877-7503, https://doi.org/10.1016/j.jocs.2021.101421. 1. [[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8478073/|A multiscale multicellular spatiotemporal model of local influenza infection and immune response.]] Sego TJ, Mochan ED, Ermentrout GB, Glazier JA. J Theor Biol. 2021 Sep 27;532:110918. doi: 10.1016/j.jtbi.2021.110918. Epub ahead of print. PMID: 34592264; PMCID: PMC8478073. 1. [[https://www.sciencedirect.com/science/article/pii/S0378437121007846|Shape-velocity correlation defines polarization in migrating cell simulations]] Thomas GL, Fortuna I, Perrone GC, Graner F, de Almeida RMC. Physica A: Statistical Mechanics and its Applications. 2021 Oct 12; doi: 10.1016/j.physa.2021.126511. 1. [[https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-021-01115-z|Generation of multicellular spatiotemporal models of population dynamics from ordinary differential equations, with applications in viral infection]] Sego TJ, Aponte-Serrano JO, Gianlupi JF, Glazier JA. . BMC Biol. 2021 Sep 8;19(1):196. doi: 10.1186/s12915-021-01115-z. PMID: 34496857. 1. [[https://www.science.org/doi/10.1126/sciadv.abh2278|The environment topography alters the way to multicellularity in Myxococcus xanthus]] - Ramos CH, Rodríguez-Sánchez E, Del Angel JAA, Arzola AV, Benítez M, Escalante AE, Franci A, Volpe G, Rivera-Yoshida N. Sci Adv. 2021 Aug 25;7(35):eabh2278. doi: 10.1126/sciadv.abh2278. PMID: 34433567; PMCID: PMC8386931. 1. [[https://elifesciences.org/articles/61011|Cell-scale biophysical determinants of cell competition in epithelia]] - Daniel Gradeci, Anna Bove, Giulia Vallardi, Alan R Lowe, Shiladitya Banerjee, and Guillaume Charras. eLife. 2021; 10: e61011. Published online 2021 May 20. doi: 10.7554/eLife.61011 *[[https://journals-biologists-com.proxyiub.uits.iu.edu/jcs/article/134/7/jcs250225/238125/Combined-heterogeneity-in-cell-size-and|Combined heterogeneity in cell size and deformability promotes cancer invasiveness]] - Asadullah, Kumar S, Saxena N, Sarkar M, Barai A, Sen S. J Cell Sci. 2021 Apr 1;134(7):jcs250225. doi: 10.1242/jcs.250225. PMID: 33602741. *[[https://www.biorxiv.org/content/10.1101/2021.04.29.441921v2.full|Cluster Size Distribution of Cells Disseminating from a Primary Tumor]] - Mrinmoy Mukherjee, Herbert Levine. BioRxiv. doi: https://doi.org/10.1101/2021.04.29.441921 *[[https://www.biorxiv.org/content/10.1101/2021.02.09.430466v1.full|Supracellular organization confers directionality and mechanical potency to migrating pairs of cardiopharyngeal progenitor cells]] - Yelena Y. Bernadskaya, Haicen Yue, Calina Copos, Lionel Christiaen, Alex Mogilner. !BioRxiv. doi: https://doi.org/10.1101/2021.02.09.430466 *[[https://www-sciencedirect-com.proxyiub.uits.iu.edu/science/article/pii/S0022519320303428|A Cellular Potts energy-based approach to analyse the influence of the surface topography on single cell motility]] - Thenard T, Catapano A, Mesnard M, Allena R. J Theor Biol. 2021 Jan 21;509:110487. doi: 10.1016/j.jtbi.2020.110487. Epub 2020 Sep 16. PMID: 32949589. *[[https://www.biorxiv.org/content/10.1101/2020.01.14.905711v1|Computational Modelling of Nephron Progenitor Cell Movement and Aggregation during Kidney Organogenesis]] - Pauli Tikka, Moritz Mercker, Ilya Skovorodkin, Ulla Saarela, Seppo Vainio, Veli-Pekka Ronkainen, James P. Sluka, James A. Glazier, Anna Marciniak-Czochra, Franz Schaefer. BioRxiv. doi: https://doi.org/10.1101/2020.01.14.905711 *[[https://doi.org/10.1590/1806-9126-RBEF-2020-0400|Fenômenos estocásticos em migração celular: teoria, experimentos e simulações (Stochastic phenomena in single cell migration: theory, experiments, and simulations)]] - Rita M.C. de Almeida. Seção Especial • Rev. Bras. Ensino Fís. 43 (Suppl 1). 2021. *[[https://pubs.acs.org/doi/abs/10.1021/acscentsci.0c00601|Heterogeneity in 2,6-Linked Sialic Acids Potentiates Invasion of Breast Cancer Epithelia]] - Pally D, Pramanik D, Hussain S, Verma S, Srinivas A, Kumar RV, Everest-Dass A, Bhat R. ACS Cent Sci. 2021 Jan 27;7(1):110-125. doi: 10.1021/acscentsci.0c00601. Epub 2021 Jan 4. PMID: 33532574; PMCID: PMC7844859. *[[https://www.biorxiv.org/content/10.1101/2021.01.27.428527v1.full|The environment topography alters the transition from single-cell populations to multicellular structures in Myxococcus xanthus]] - Karla C. Hernández Ramos, Edna Rodríguez-Sánchez, Juan Antonio Arias del Angel, Alejandro V. Arzola, Mariana Benítez, Ana E. Escalante, Alessio Franci, Giovanni Volpe, Natsuko Rivera-Yoshida. !BioRxiv. doi: https://doi.org/10.1101/2021.01.27.428527 * A useful review of methods, including CC3D: [[https://link.springer.com/article/10.1007/s11831-021-09554-1|Computational Models and Simulations of Cancer Metastasis]] - Anvari, S., Nambiar, S., Pang, J. et al. Arch Computat Methods Eng (2021). https://doi-org.proxyiub.uits.iu.edu/10.1007/s11831-021-09554-1. *[[https://link.springer.com/article/10.1007/s00262-020-02790-7|Run for your life: an integrated virtual tissue platform for incorporating exercise oncology into immunotherapy]] - Serrano JA, Hagar A. Cancer Immunol Immunother. 2021 Jul;70(7):1951-1964. doi: 10.1007/s00262-020-02790-7. Epub 2021 Jan 8. PMID: 33416943. *[[https://link.springer.com/chapter/10.1007/978-3-030-58688-1_2|Position of the Kenzan Method in the Space-Time of Tissue Engineering]] - Moldovan N.I. (2021) In: Nakayama K. (eds) Kenzan Method for Scaffold-Free Biofabrication. Springer, Cham. https://doi-org.proxyiub.uits.iu.edu/10.1007/978-3-030-58688-1_2 *[[https://www-sciencedirect-com.proxyiub.uits.iu.edu/science/article/pii/S0022519321001557|Matrix adhesion and remodeling diversifies modes of cancer invasion across spatial scales]] - Pramanik D, Jolly MK, Bhat R. J Theor Biol. 2021 Sep 7;524:110733. doi: 10.1016/j.jtbi.2021.110733. Epub 2021 Apr 30. PMID: 33933478. *[[https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=9451315|Physical Forces Influence the Self-organization of the Leader Cell Formation During Collective Cell Migration]] - M. Pan, Y. Yang and L. Liu. 2021 IEEE 16th International Conference on Nano/Micro Engineered and Molecular Systems (NEMS), 2021, pp. 1923-1926, doi: 10.1109/NEMS51815.2021.9451315. *[[https://www-sciencedirect-com.proxyiub.uits.iu.edu/science/article/pii/S2452310021000251\|Multiscale modeling in disease]] - Ashlee N. !FordVersyp. Current Opinion in Systems Biology. In press. Available online 8 May 2021. https://doi.org/10.1016/j.coisb.2021.05.001. *[[https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1009081|Multiscale modeling of tumor growth and angiogenesis: Evaluation of tumor-targeted therapy]] - Jafari Nivlouei S, Soltani M, Carvalho J, Travasso R, Salimpour MR, Shirani E. PLoS Comput Biol. 2021 Jun 23;17(6):e1009081. doi: 10.1371/journal.pcbi.1009081. PMID: 34161319. *[[https://doi.org/10.1016/j.isci.2021.102317|A Mechanical Model of Early Somite Segmentation]] - Adhyapok, P., Piatkowska, A.M, Norman, M.J, Clendenon, S.G, Stern, C.D, Glazier, J.A, Belmonte, J.M, ISCIENCE (2021), in press. doi: [[https://doi.org/10.1016/j.isci.2021.102317|https://doi.org/10.1016/j.isci.2021.102317]]. * [[https://www.biorxiv.org/content/10.1101/2021.01.28.428647v1|Generating Agent-Based Multiscale Multicellular Spatiotemporal Models from Ordinary Differential Equations of Biological Systems, with Applications in Viral Infection]] - T.J. Sego, Josua Aponte-Serrano, Juliano Ferrari Gianlupi and James A. Glaizer, DOI: 10.1101/2021.01.28.428647. Jan 29, 2021. ''Preprint in bioRxiv''. * [[https://pubmed.ncbi.nlm.nih.gov/33498017/|Biofabrication of spheroids fusion-based tumor models: computational simulation of glucose effects]]. Bustamante DJ, Basile EJ, Hildreth BM, Browning NW, Jensen SA, Moldovan L, Petrache HI, Moldovan NI. Biofabrication. 2021 Jan 26. doi: 10.1088/1758-5090/abe025. Online ahead of print. PMID: 33498017 * [[https://pubmed.ncbi.nlm.nih.gov/33339019/|Development of a coupled simulation toolkit for computational radiation biology based on Geant4 and CompuCell3D]]. Liu R, Higley KA, Swat MH, Chaplain MAJ, Powathil GG, Glazier JA. Phys Med Biol. 2021 Feb 11;66(4):045026. doi: 10.1088/1361-6560/abd4f9. PMID: 33339019 ==== 2020 ==== 1. [[https://pubmed.ncbi.nlm.nih.gov/32407685/|CompuCell3D Simulations Reproduce Mesenchymal Cell Migration on Flat Substrates]]. Fortuna I, Perrone GC, Krug MS, Susin E, Belmonte JM, Thomas GL, Glazier JA, de Almeida RMC. Biophys J. 2020 Jun 2;118(11):2801-2815. doi: 10.1016/j.bpj.2020.04.024. Epub 2020 Apr 30. PMID: 32407685 * [[https://www.nature.com/articles/s41598-020-63506-6|Multiscale modelling of motility wave propagation in cell migration]] - Hamid Khataee, Andras Czirok, and Zoltan Neufeld, ''__Scientific Reports.__'' DOI: 10.1038/s41598-020-63506-6, (2020). * [[https://elifesciences.org/articles/61026|Dynamics of nevus development implicate cell cooperation in the growth arrest of transformed melanocytes]] - Ruiz-Vega, Rolando, et al., ''__Elife.__'' DOI: 10.7554/eLife.61026, (2020). * [[https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008451|A modular framework for multiscale, multicellular, spatiotemporal modeling of acute primary viral infection and immune response in epithelial tissues and its application to drug therapy timing and effectiveness]] - T.J. Sego, Josua Aponte-Serrano, Juliano Ferrari Gianlupi, Sam Heaps, Kira Breithaupt, Lutz Brusch, et al., ''__PLoS Computational Biology.__'' DOI: 10.1371/journal.pcbi.1008451, (2020). * [[https://royalsocietypublishing.org/doi/full/10.1098/rsif.2019.0739|Mechanisms of endothelial cell coverage by pericytes: computational modelling of cell wrapping and in vitro experiments]] – Kei Sugihara, et al., ''__Journal of the Royal Society Interface.__'' DOI: 10.1098/rsif.2019.0739, (2020). ==== 2019 ==== 1. [[https://aiche.onlinelibrary.wiley.com/doi/abs/10.1002/aic.16671|A hybrid discrete–continuous model of metastatic cancer cell migration through a remodeling extracellular matrix]] - Edalgo Nguyen, Yen T., Anya L. Zornes, and Ashlee N. Ford Versypt, ''__AIChE Journal.__'' DOI: 10.1002/aic.16671, (2019). * [[https://journals.plos.org/ploscompbiol/article?rev=2&id=10.1371/journal.pcbi.1007053|Metabolic reprogramming dynamics in tumor spheroids: Insights from a multicellular, multiscale model]] - Mahua Roy and Stacey D. Finley, ''__PLoS Computational Biology.__'' DOI: 10.1371/journal.pcbi.1007053S, (2019). * [[https://www.frontiersin.org/articles/10.3389/fimmu.2019.00230/full|Model-based assessment of the Role of Uneven Partitioning of Molecular Content on Heterogeneity and Regulation of Differentiation in CD8 T-cell Immune Responses]] – Simon Girel, et al, ''__Frontiers in immunology.__'' DOI: 10.3389/fimmu.2019.00230, (2019). * [[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6700745/|An Interplay Between Reaction-Diffusion and Cell-Matrix Adhesion Regulates Multiscale Invasion in Early Breast Carcinomatosis]] - Pally D, Pramanik D, Bhat R., ''__Front Physiol.__'' 2019 Aug 13;10:790. doi: 10.3389/fphys.2019.00790. eCollection 2019. * [[https://www.sciencedirect.com/science/article/pii/S0022519319303248?via=ihub|A multiscale in silico model of endothelial to mesenchymal transformation in a tumor microenvironment]]- Chowkwale M, Mahler GJ, Huang P, Murray BT., ''__J Theor Biol.__'' 2019 Nov 7;480:229-240. doi: 10.1016/j.jtbi.2019.08.012. Epub 2019 Aug 17. * [[https://link.springer.com/protocol/10.1007/978-1-4939-9224-9_1|Agent-Based Modelling to Delineate Spatiotemporal Control Mechanisms of the Stem Cell Niche]]" - Mines R, Chen KY, Shen X., ''__Methods Mol Biol.__'' 2019;1975:3-35. doi: 10.1007/978-1-4939-9224-9_1. PMID: 31062303 * [[https://link.springer.com/protocol/10.1007/978-1-4939-9021-4_19|Methods of Computational Analysis in Kidney Development]] - Tikka P, Schaefer F., ''__Methods Mol Biol.__'' 2019;1926:235-246. doi: 10.1007/978-1-4939-9021-4_19. * [[https://pubmed.ncbi.nlm.nih.gov/31456688/|An Interplay Between Reaction-Diffusion and Cell-Matrix Adhesion Regulates Multiscale Invasion in Early Breast Carcinomatosis]]. Pally D, Pramanik D, Bhat R. Front Physiol. 2019 Aug 13;10:790. doi: 10.3389/fphys.2019.00790. eCollection 2019. PMID: 31456688. * [[https://pubmed.ncbi.nlm.nih.gov/31430445/|A multiscale in silico model of endothelial to mesenchymal transformation in a tumor microenvironment]]. Chowkwale M, Mahler GJ, Huang P, Murray BT. J Theor Biol. 2019 Nov 7;480:229-240. doi: 10.1016/j.jtbi.2019.08.012. Epub 2019 Aug 17. PMID: 31430445 * [[https://pubmed.ncbi.nlm.nih.gov/30742276/|Methods of Computational Analysis in Kidney Development]]. Tikka P, Schaefer F. Methods Mol Biol. 2019;1926:235-246. doi: 10.1007/978-1-4939-9021-4_19. PMID: 30742276 ==== 2018 ==== 1. [[https://www.embopress.org/doi/full/10.15252/msb.20178174|Fibroblast state switching orchestrates dermal maturation and wound healing|target=_blank]] - Emanuel Rognoni, Angela Oliveira Pisco, Toru Hiratsuka, Kalle H Sipilä, Julio M Belmonte, Seyedeh Atefeh Mobasseri, Christina Philippeos, Rui Dilão, Fiona M Watt, ''__Mol Syst Biol__'' (2018)14:e8174, https://doi.org/10.15252/msb.20178174. * [[https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006455|Rotation of sex combs in Drosophila melanogaster requires precise and coordinated spatio-temporal dynamics from forces generated by epithelial cells]] - Ernest C. Y. Ho, Juan Nicolas, Abha Ahuja, Rama Singh ,Ellen Larsen, ''__PLoS Comp. Bio.__'', https://doi.org/10.1371/journal.pcbi.1006455, (2018). * [[https://pubs.rsc.org/en/content/articlelanding/2018/ib/c8ib00048d/|Computational model of wound healing: EGF secreted by fibroblasts promotes delayed re-epithelialization of epithelial keratinocytes]] - Vivi Andasari, Dongyuan Lü, Maciej Swat, Shiliang Feng, Fabian Spill, Li Chen, Xiangdong Luo, Muhammad Zaman, Mian Long, ''__Integrative Biology__'', DOI: 10.1039/C8IB00048D, (2018). * [[https://www.molbiolcell.org/doi/10.1091/mbc.E17-05-0313|Multicompartment cell-based modeling of confined migration: regulation by cell intrinsic and extrinsic factors]] - Sandeep Kumar, Alakesh Das and Shamik Sen, ''__Molecular Biology of the Cell__'', DOI:10.1091/mbc.E17-05-0313, (2018). ==== 2017 ==== 1. [[http://pubs.acs.org/doi/abs/10.1021/acs.chemrestox.6b00350|Computational Model of Secondary Palate Fusion and Disruption]] - M. Shane Hutson, Maxwell C.K. Leung, Nancy Baker, Richard M. Spencer, and Thomas B. Knudsen, ''__Chemical Research in Toxicology__'', DOI: 10.1021/acs.chemrestox.6b00350, (2017). * [[http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.702072|Mathematical modelling of the immune response to cancer]] - Tough, Iona Kirsten. PhD Thesis, University of Dundee, (2017). * [[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5536454/pdf/pcbi.1005635.pdf|Blood vessel tortuosity selects against evolution of aggressive tumor cells in confined tissue environments: A modeling approach]] - A. Szabó and R. M. H. Merks, __''PLOS Comput Biol''__, vol. 13, no. 7, p. e1005635, Jul. 2017. * [[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5283809/pdf/kccy-16-02-1241603.pdf|Shaping the cell fate]] - T. N. Sato and R. M. H. Merks, __''Cell Cycle''__, vol. 16, no. 2, pp. 149–150, Jan. 2017. * [[https://academic-oup-com.proxyiub.uits.iu.edu/biolreprod/article/97/3/365/4082285|Cell-based computational model of early ovarian development in mice]] - Wear HM, Eriksson A, Yao HH, Watanabe KH. Biol Reprod. 2017 Sep 1;97(3):365-377. doi: 10.1093/biolre/iox089. PMID: 29088396; PMCID: PMC6231088. ==== 2016 ==== 1. [[http://aip.scitation.org/doi/pdf/10.1063/1.4952106|Multi-scale modeling of the CD8 immune response.]] - Barbarroux, L., Michel, P., Adimy, M., Crauste, F. AIP Conference Proceedings 1738, 320002 (2016); doi: http://dx.doi.org/10.1063/1.4952106. * [[http://www.molbiolcell.org/content/27/22/3673.full|Virtual-Tissue Computer Simulations Define the Roles of Cell Adhesion and Proliferation in the Onset of Kidney Cystic Disease]] – Julio M. Belmonte, Sherry G. Clendenon, Guilherme M. Oliveira, Maciej H. Swat, Evan V. Greene, Srividhya Jeyaraman, James A. Glazier, and Robert L. Bacallao, ''__Molecular Biology of the Cell__'' '''27''': 3673-3685 (2016). * [[http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0161915|Spheroid Formation of Hepatocarcinoma Cells in Microwells: Experiments and Monte Carlo Simulations]] – Yan Wang, Myung Hee Kim, Seyed R. Tabaei, Jae Hyeok Park, Kyuhwan Na, Seok Chung, Vladimir P. Zhdanov, Nam-Joon Cho, ''__PLoS ONE__'' '''11'''(8): e0161915 (2016). * [[https://www.hindawi.com/journals/jdr/2016/2508381/|A Computational Model of Peripheral Photocoagulation for the Prevention of Progressive Diabetic Capillary Occlusion]] – Thomas J. Gast, Xiao Fu, John Scott Gens, James A. Glazier, ''__Journal of Diabetes Research__'' vol. 2016, Article ID 2508381, 13 pages (2016) doi:10.1155/2016/2508381. * [[http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0162428|A Liver-Centric Multiscale Modeling Framework for Xenobiotics]] – James P. Sluka , Xiao Fu, Maciej Swat, Julio M. Belmonte, Alin Cosmanescu, Sherry G. Clendenon, John F. Wambaugh, James A. Glazier, ''__PLoS ONE__'' '''11''': e0162428 (2016). * [[https://bmcsystbiol.biomedcentral.com/articles/10.1186/s12918-016-0323-y|IL-2 sensitivity and exogenous IL-2 concentration gradient tune the productive contact duration of CD8+ T cell-APC: a multiscale modeling study]] – Xuefeng Gao, Christophe Arpin, Jacqueline Marvel, Sotiris A. Prokopiou, Olivier Gandrillon, Fabien Crauste, ''__BMC Systems Biology__'' '''10''':77 (2016). * [[http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004952|Filopodial-Tension Model of Convergent-Extension of Tissues]] – Julio M. Belmonte, Maciej H. Swat, James A. Glazier, ''__PLoS Comput Biol__'' '''12''': e1004952 (2016). * [[http://www.nature.com/articles/ncomms11963|Memory of cell shape biases stochastic fate decision-making despite mitotic rounding]] – Takashi Akanuma, Cong Chen, Tetsuo Sato, Roeland M. H. Merks, Thomas N. Sato, ''__Nature Commun__'' '''7''': 11963 (2016). * [[http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004932|Progression of Diabetic Capillary Occlusion: A Model]] – Xiao Fu, John Scott Gens, James A. Glazier, Stephen A. Burns, Thomas J. Gast, ''__PLoS Comput Biol__'' '''12''': e1004932 (2016). * [[http://www.sciencedirect.com/science/article/pii/S1534580716302039|The Molecular Basis of Radial Intercalation during Tissue Spreading in Early Development]] – András Szabó, Isidoro Cobo, Sharif Omara, Sophie McLachlan, Ray Keller, Roberto Mayor, ''__Developmental Cell__'' '''37''': 213–225 (2016). * [[http://www.sciencedirect.com/science/article/pii/S0022519316300315|Bystander effects and their implications for clinical radiation therapy: Insights from multiscale in silico experiments]] – Gibin George Powathil, Alastair J Munro, Mark Chaplain, Maciej H. 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Steinkamp, Kimberly Kanigel Winner, Bridget S. Wilson, ''__Frontiers in Oncology__'' '''3''':97 (2013). * [[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002996#pcbi-1002996-g008|A Computational Model Predicting Disruption of Blood Vessel Development]] – Nicole Kleinstreuer, David Dix, Michael Rountree, Nancy Baker, Nisha Sipes, David Reif, Richard Spencer, Thomas Knudsen, ''__PLoS Comput Biol__'' '''9'''(4): e1002996 (2013). * [[http://journals.aps.org/pre/abstract/10.1103/PhysRevE.87.012725|Vascular Networks Due to Dynamically Arrested Crystalline Ordering of Elongated Cells]] – Margriet M. Palm, Roeland M. H. Merks,. ''__Phyiscal Review E__'' '''87''': 012725 (2013). * [[http://cancerres.aacrjournals.org/content/73/5/1481.long|Acute and Fractionated Irradiation Differentially Modulate Glioma Stem Cell Division Kinetics]] – Xuefeng Gao, J. Tyson McDonald, Lynn Hlatky, Heiko Enderling, ''__Cancer Res__'' March 1, 73; 1481 (2013). ==== 2012 ==== 1. 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Gens]], [[http://www.physics.emory.edu/faculty/family/|F. Family]], [[http://math.lanl.gov/~yi/|Y. Jiang]], [[http://www.eyecenter.emory.edu/faculty/grossniklaus.htm|Hans E. Grossniklaus]], ''__PLoS Comput Biol__ '''''7'''(10): e1002155 (2012) [ [[http://newsinfo.iu.edu/news/page/normal/22239.html|IU press release]], [[http://www.gsu.edu/news/60630.html|GSU press release]] ]. * [[http://download.springer.com/static/pdf/23/chp:10.1007/978-88-470-2571-4_11.pdf?auth66=1425576897_7d893eb62674aacd4a93b56f9090ddac&ext=.pdf|Hybrid cellular Potts model for solid tumor growth]] – M. Scianna, L. Preziosi, ''in'' M. Chaplain, J. Batzel, M. Bachar, Eds., ''__New Challenges for Cancer Systems Biomedicine__'', p.205-224, Springer, (2012). * [[http://ieeexplore.ieee.org/Xplore/defdeny.jsp?url=http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=6217251&denyReason=-134&arnumber=6217251&productsMatched=null&userType=inst|Searching a multicellular model to tame tumor-induced angiogenesis]] – Podgorski, G.J., Flann, N.S. Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), ''2012 IEEE Symposium on DOI: 10.1109/CIBCB.2012.6217251'' , pp. 349-354 (2012). * [[http://www.sciencedirect.com/science/article/pii/S0169260713001752|Epithelial to mesenchymal transition: The roles of cell morphology, labile adhesion and junctional coupling]] – Tariq Abdulla, Luis Luna-Zurita, José Luis De La Pompa, Jean-Marc Schleich, Ron Summers, ''__Computer Methods And Programs In Biomedicine__'' '''111''':435-446 (2012). * [[http://www.nature.com/nature/journal/v491/n7425_supp/full/491S62a.html#close|Modelling: Computing Cancer]] – N. Savage, ''__Nature__'' '''491''':S62–S63 (2012). * [[http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=6211560&abstractAccess=no&userType=inst|Multiscale modelling of Notch-mediated lateral induction]] – Abdulla T., Schleich, J., Summers, R., Biomedical and Health Informatics (BHI), IEEE-EMBS International Conference, p. 257 – 260 (2012). * [[http://www.sciencedirect.com/science/article/pii/B9780123884039000138|Multi-Scale Modeling of Tissues Using CompuCell3D]] – [[http://www.indiana.edu/~bioc/people/?p=staff|M. Swat]], [[http://www.if.ufrgs.br/pos/portugues/thomas.html|Gilberto L. Thomas]], Julio M. Belmonte, A. Shirinifard, [[http://www.indiana.edu/~iubphys/faculty/mitja.shtml|D.Hmeljak]], [[http://www.indiana.edu/~bioc/jglazier/|J. A. Glazier]], ''__Computational Methods in Cell Biology__, Methods in Cell Biology '''''110''': 325-366 (2012). * [[http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033726#pone-0033726-g014|Integrating Intracellular Dynamics Using CompuCell3D and Bionetsolver: Applications to Multiscale Modelling of Cancer Cell Growth and Invasion]] – Vivi Andasari, Ryan T. Roper, Maciej H. Swat, Mark A. J. Chaplain, ''__PLoS ONE__'' '''7'''(3): e33726 (2012). * [[http://dl.acm.org/citation.cfm?doid=1878537.1878635|Workflows for parameter studies of multi-cell modeling]] – Randy Heiland, Maciek Swat, Benjamin Zaitlen, James A. Glazier, Andrew Lumsdaine, ''__Proceedings of the 2010 Spring Simulation Multiconference__'' p. 94 (2012). * [[http://biovis.net/year/2012/papers/visualizing-cells-and-their-connectivity-graphs-compucell3d|Visualizing Cells and their Connectivity Graphs for CompuCell3D]] – R. Heiland, M. Swat, J. Sluka, B. Zaitlen, A. Shirinifard, G. Thomas, A. Lumsdaine, J. Glazier, ''__2nd IEEE Symposium on Biological Data Visualization__'' (2012). ==== 2011 ==== 1. [[https://hal.archives-ouvertes.fr/inserm-00745327/document|Computational modelling of epithelial to mesenchymal transition]] – T. Abdulla, R. Imms, J.-L. Dillenseger, J.-M. Schleich, R. Summers, __''IRBM''__, 32(5):306–310 (2011). * [[https://www.semanticscholar.org/paper/A-robust-in-silico-analogue-of-MDCK-cystogenesis-m-Engelberg-Datta/e90bb59358980c4a619261a0e079dc725c551252|A Robust in Silico Analogue of MDCK Cystogenesis Mimics Growth in Multiple Culture Conditions]] - Engelberg, J. A., Datta, A., Mostov, K. E. & Hunt, C. A. ADS ’11 Proc. 2011 Work. Agent-Directed Simul. 52–56 (2011). * [[https://www.academia.edu/13476031/Emergent_networks_A_slime_mold_simulation?auto|Emergent networks:A slime mold simulation]] - Semmler, N. Bachelors Thesis, June 24, 2011. * [[http://www.tandfonline.com/doi/pdf/10.1080/00051144.2011.11828403?needAccess=true|Progress with a Multiscale Systems Engineering Approach to Cardiac Development]] - Summers, R., Abdulla, T., Houyel, L. & Schleich, J.-M. Autom. Control. Meas. Electron. Comput. Commun. 52, 49–57 (2011). * [[https://link.springer.com/content/pdf/10.1007/978-3-642-23508-5_333.pdf|3D Simulation of an in vitro Epithelial to Mesenchymal Transition]] - Summers, R., Abdulla, T., Imms, R. a & Schleich, J.-M. 5th Eur. IFMBE Conf. IFMBE Proc. 37 1287–1290 (2011). doi:10.1007/978-3-642-23508-5_333. * [[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002155|A Multi-cell, Multi-scale Model of Vertebrate Segmentation and Somite Formation]] – Susan D. Hester, Julio M. Belmonte, J. Scott Gens, Sherry G. Clendenon, James A. Glazier, ''__PLoS Comput Biol__ '''''7'''(10): e1002155 (2011) [ [[Models/BelmonteHesterSomite|model]] and a [[Models/BelmonteHesterSomite|movie]] are available ]. * [[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002030|MDCK Cystogenesis Driven by Cell Stabilization within Computational Analogues]] – Jesse A. Engelberg, Anirban Datta, Keith E. Mostov, C. Anthony Hunt, ''__PLoS Comput Biol__ '''''7'''(4): e1002030 (2011). * [[http://www.ipcbee.com/vol5/12-X00022.pdf|A Multiscale Model for Hypoxia-induced Avascular Tumor Growth]] – Xuefeng Gao, Mark Tangney, Sabin Tabirca, __''Proceedings of 2011 International Conference on Bioscience''__, Biochemistry and Bioinformatics IPCBEE vol.5 (2011). * [[http://www.plosone.org/article/info:doi/10.1371/journal.pone.0024999|Computer Simulations of Cell Sorting Due to Differential Adhesion]] – Ying Zhang, Gilberto L. Thomas, Maciej Swat, Abbas Shirinifard, James A. Glazier, ''__PLoS ONE__'' '''6'''(10):e24999 (2011). * [[http://www.ncbi.nlm.nih.gov/pubmed/22254345|Towards multiscale systems modeling of endocardial to mesenchymal transition]] – Abdulla T, Imms, R., Schleich, J., Summers R., Engineering in Medicine and Biology Society, EMBC, 2011 Annual International Conference of the IEEE, p. 449 – 452 (2011). * [[http://www.plosone.org/article/info:doi/10.1371/journal.pone.0022700|Coordination of Cell Differentiation and Migration in Mathematical Models of Caudal Embryonic Axis Extension]] – Nigel C. Harrison, Ruth Diez del Corral, Bakhtier Vasiev, ''__PLoS ONE__'' '''6'''(7):e22700 (2011). ==== 2010 ==== 1. [[https://link.springer.com/protocol/10.1007/978-1-60761-842-3_19|Genetic Algorithms and Their Application to In Silico Evolution of Genetic Regulatory Networks]] - Knabe, J., Wegner, K., Nehaniv, C., Schilstra, M. Computational Biology, 2010, 673, 297-321. * [[http://www.plosone.org/article/info:doi/10.1371/journal.pone.0010571|Modeling Gastrulation in the Chick Embryo: Formation of the Primitive Streak]] – Bakhtier Vasiev, Ariel Balter, Mark Chaplain, James A. Glazier, Cornelis J. Weijer, ''__PLoS ONE__'' '''5'''(5):e10571 (2010). * [[http://www.plosone.org/article/info:doi/10.1371/journal.pone.0010641|Front Instabilities and Invasiveness of Simulated 3D Avascular Tumors]] – Nikodem J. Popławski, Abbas Shirinifard, Ubirajara Agero, J. Scott Gens, Maciej Swat, James A. Glazier, ''__PLoS ONE__'' '''5'''(5): e10641 (2010). * [[http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000841|A Computer Simulation of Long-Range Patterning in the Drosophila Pupal Eye]] – David Larson , Ruth Johnson, Maciej H. Swat, J. Cordero, James A. Glazier, Ross Cagan, ''__PLoS Comput Bio__'' '''6''': e1000841 (2010) doi:10.1371/journal.pcbi.1000841. ==== 2009 ==== 1. [[http://www.plosone.org/article/info:doi/10.1371/journal.pone.0007190#pone-0007190-g004|3D Multi-Cell Simulation of Tumor Growth and Angiogenesis]] – Abbas Shirinifard, J. Scott Gens, Benjamin L. Zaitlen, Nikodem J. Popławski, Maciej Swat, James A. Glazier, ''__PLoS ONE__'' '''4'''(10):e7190 (2009). * [[http://old.compucell3d.org/links/index.php?id=35|Mathematical modeling of the capillary-like pattern generated by adrenomedullin-treated human vascular endothelial cells in vitro]] – Diego Guidolin, Giovanna Albertin, Elisa Sorato, Barbara Oselladore, Alessandra Mascarin, Domenico Ribatti, ''__Dev Dyn__'' '''238'''(8):1951-63 (2009). ==== 2008 ==== 1. [[http://panmental.de/papers/FlagPottsGRNALife11.pdf|Evolution and morphogenesis of differentiated multicellular organisms: autonomously generated diffusion gradients for positional information]] – J. F. Knabe, C. L. Nehaniv, M. J. 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Izaguirre, ''__Computing in Science and Engineering__'' '''9''': 50-60 (2007). * [[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168394/|Adhesion Between Cells, Diffusion of Growth Factors, and Elasticity of the AER Produce the Paddle Shape of the Chick Limb]] – Nikodem J. Popławski, Maciej Swat, J. Scott Gens, James A. Glazier, ''__Physica A__ '''''373''': 521-532 (2007). * '''A Brief History of the Glazier-Graner-Hogeweg Model.''' Glazier J.A., Balter A., Popławski N.J. (2007) Magnetization to Morphogenesis: In: Anderson A.R.A., Chaplain M.A.J., Rejniak K.A. (eds) Single-Cell-Based Models in Biology and Medicine. Mathematics and Biosciences in Interaction. Birkhäuser Basel * '''The Glazier-Graner-Hogeweg Model: Extensions, Future Directions, and Opportunities for Further Study.''' Balter A., Merks R.M.H., Popławski N.J., Swat M., Glazier J.A. (2007) In: Anderson A.R.A., Chaplain M.A.J., Rejniak K.A. (eds) Single-Cell-Based Models in Biology and Medicine. 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E. Hentschel, S. A. Newman, J. A. Glazier, M. Alber, ''__J. R. Soc. Interface__ '''''2''': 237-253 (2005). * [[http://www.sciencedirect.com/science/article/pii/S0378437104016188|A Cell-Centered Approach to Developmental Biology]] – Roeland M.H. Merks, James A. Glazier, ''__Physica A__ '''''352''': 113-130 (2005). ==== 2004 ==== 1. [[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1691788/|Dynamical Mechanisms For Skeletal Pattern Formation in the Vertebrate Limb]] – H. G. E. Hentschel, T. Glimm, J. A. Glazier, Stuart A. Newman, ''__Proc Biol Sci__'' '''271'''(1549): 1713-1722'' ''(2004). * [[http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.87.9008|A Hybrid Discrete-Continuum Model for 3D Skeletogenesis of the Vertebrate Limb]] – R. Chaturvedi, C. Huang, J. A. Izaguirre, Stuart A. Newman, J. A. Glazier, ''__Lecture Notes in Computer Science__ '''''3305''': 543-552 (2004). * [[http://bioinformatics.oxfordjournals.org/content/20/7/1129.full.pdf|CompuCell, a Multi-Model Framework For Simulation of Morphogenesis]] – J. A. Izaguirre, R. Chaturvedi, C. Huang, T. Cickovski, J. Coffland, G. Thomas, G. Forgacs, M. Alber, G. Hentschel, S. A. Newman, and J. A. Glazier, ''__Bioinformatics__ '''''20''': 1129-1137'' ''(2004). ==== 1993 ==== 1. '''Simulation of the differential adhesion driven rearrangement of biological cells.''' Glazier JA, Graner F. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 1993 Mar;'''47'''(3):2128-2154. ==== 1992 ==== 1. '''Simulation of biological cell sorting using a two-dimensional extended Potts model.''' Graner F, Glazier JA. Phys Rev Lett. 1992 Sep 28;'''69'''(13):2013-2016.