Grantee Research Project Results
Publications Details for Grant Number R835001
Ontologies for Data & Models for Liver Toxicology
RFA:
Computational Toxicology: Biologically-Based Multi-Scale Modeling (2010)
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| Reference Type | Citation | Progress Report Year | Document Sources |
|---|---|---|---|
| Book Chapter | Swat MH, Thomas GL, Belmonte JM, Shirinifard A, Hmeljak D, Glazier JA. Multi-scale modeling of tissues using CompuCell3D. In: Asthagiri AR, Arkin AP, eds. Methods in Cell Biology, Volume 110: Computational Methods in Cell Biology. Waltham, MA: Academic Press, 2012, pp. 325-366. |
R835001 (Final) |
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| Journal Article | Andasari V, Roper RT, Swat MH, Chaplain MAJ. Integrating intracellular dynamics using CompuCell3D and BioNetSolver: applications to multiscale modelling of cancer cell growth and invasion. PLoS ONE 2012;7(3):e33726. |
R835001 (Final) |
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| Journal Article | Petersen BK, Ropella G, Hunt CA. Toward modular biological models: defining analog modules based on referent physiological mechanisms. BMC Systems Biology 2014;8:95. |
R835001 (Final) |
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| Journal Article | Sluka JP, Glazier JA, Swat M. Infrastructure requirements for moving multiscale modeling from research tools to the clinical and regulatory domains. VPH NoE Newsletter 2012;7:12. |
R835001 (Final) |
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| Journal Article | Sluka J, Shirinifard A, Swat M, Cosmanescu A, Heiland RW, Glazier J. The Cell Behavior Ontology: describing the intrinsic biological behaviors of real and model cells seen as active agents. Bioinformatics 2014;30(16):2367-2374. |
R835001 (Final) |
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| Journal Article | Wambaugh JF, Wetmore BA, Pearce R, Strope C, Goldsmith R, Sluka JP, Sedykh A, Tropsha A, Bosgra S, Shah I, Judson R, Thomas RS, Setzer RW. Toxicokinetic triage for environmental chemicals. Toxicological Sciences 2015;147(1):55-67. |
R835001 (Final) R835166 (2015) R835166 (2016) R835166 (Final) |
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| Journal Article | Wang Y, Lin Z, Liu Z, Harris S, Kelly R, Zhang J, Ge W, Chen M, Borlak J, Tong W. A unifying ontology to integrate histological and clinical observations for drug-induced liver injury. American Journal of Pathology 2013;182(4):1180-1187. |
R835001 (Final) |
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| Presentation | Belmonte J, Fu X, Sluka JP, Swat M, Glazier JA. Blood flow and oxygen distribution in a simulated 3D liver lobule. Poster presented at the lnteragency Modeling and Analysis Group-Multiscale Modeling Consortium meeting, Bethesda, MD, September 2013. |
R835001 (Final) |
not available |
| Presentation | Fu X. Flow modeling in simulated liver lobule. Presented at the European Conference on Mathematical and Theoretical Biology, Gothenburg, Sweden, June 15-19, 2014. |
R835001 (Final) |
not available |
| Presentation | Fu X. A simulation framework for modeling acetaminophen induced liver toxicity. Presented at the Stuttgart Research Center Systems Biology, University of Stuttgart, Stuttgart, Germany, June 25, 2014. |
R835001 (Final) |
not available |
| Presentation | Glazier JA. [Presentation]. Presented at the Cell Behavior Ontology (CBO) and Cell Behavior Markup Language (CBML) Workshop at the International Conference on Systems Biology (ICSB-2011), Heidelberg-Mannheim, Germany, August 28-September 1, 2011. |
R835001 (Final) |
not available |
| Presentation | Glazier JA, Swat M, Sluka JP. Challenges for multi-scale virtual tissues: where we are and where we need to go: computational component libraries and biological component libraries. Presented at the Interagency Modeling and Analysis Group-Multiscale Modeling Consortium meeting, Bethesda, MD, September 3-4, 2014. |
R835001 (Final) |
not available |
| Presentation | Glazier J. From molecules to tissues: multiscale modeling from a multicellular viewpoint. Presented at the Toward the 3D Virtual Cell Conference, University of California at San Diego, San Diego, CA, December 13-14, 2012 (invited). |
R835001 (Final) |
not available |
| Presentation | Hunt CA, Ropella G, Smith A. Explanatory, concrete insight Into location-dependent, multiscale aspects of APAP-induced liver injury. Poster presented at the lnteragency Modeling and Analysis Group-Multiscale Modeling Consortium meeting, Bethesda, MD, September 2013. |
R835001 (Final) |
not available |
| Presentation | Ropella G, Petersen B, Hunt CA. Exploring two modularity techniques for agent-based models. Poster presented at the Interagency Modeling and Analysis Group-Multiscale Modeling Consortium meeting, Bethesda, MD, September 3-4, 2014. |
R835001 (Final) |
not available |
| Presentation | Sluka JP, Cosmanescu A, Swat M, Glazier JA. From macro to micro dosimetry, pharmacology and toxicity: a multiscale modeling framework of xenobiotics using open source tools. Poster presented at the Interagency Modeling and Analysis Group-Multiscale Modeling Consortium Meeting, Bethesda MD, September 2012. |
R835001 (Final) |
not available |
| Presentation | Sluka JP, Fu X, Swat M, Glazier JA. Parameter sensitivities in a multiscale model of acetaminophen metabolism: from whole-body to subcellular reaction kinetics. Poster presented at the Interagency Modeling and Analysis Group-Multiscale Modeling Consortium meeting, Bethesda, MD, September 3-4, 2014. |
R835001 (Final) |
not available |
| Presentation | Sluka J. Optimizing model specification in cross-scale computational biology. Presented at the Toward the 3D Virtual Cell Conference, University of California at San Diego, San Diego, CA, December 13-14, 2012 (invited). |
R835001 (Final) |
not available |
| Presentation | Sluka J, Fu X, Belmonte J, Cosmanescu A, Swat M, Glazier JA. A multiscale in silica modeling framework of xenobiotics. Poster presented at the 53rd Annual Meeting & ToxExpo of the Society of Toxicology, Phoenix, AZ, March 23-27, 2014. |
R835001 (Final) |
not available |
| Presentation | Smith A, Ropella G, Hunt CA. Explaining complex phenomena by discovering, validating, and falsifying in silico mechanistic hypotheses: a demonstration focused on multiple features of acetaminophen hepatotoxicity. Poster presented at the Interagency Modeling and Analysis Group-Multiscale Modeling Consortium meeting, Bethesda, MD, September 3-4, 2014. |
R835001 (Final) |
not available |
| Presentation | Swat M. Multicell modelling using CompuCell3D. Presented at the Toward the 3D Virtual Cell Conference, University of California at San Diego, San Diego, CA, December 13-14, 2012 (invited). |
R835001 (Final) |
not available |
| Presentation | Wambaugh J, Strope C, Nicolas C, Pearce R, Judson R, Goldsmith R, El-Masri H, Wetmore B, Sluka J, Tropsha A, Bosgra S, Shah I, Thomas R, Setzer RW. High throughput pharmacokinetics for environmental chemicals. Poster presented at the 53rd Annual Meeting & ToxExpo of the Society of Toxicology, Phoenix, AZ, March 23-27, 2014. |
R835001 (Final) |
not available |
| Proceedings | Heiland R, Swat M, Sluka J, Zaitlen B, Shirinifard A, Thomas G, Lumsdaine A, Glazier J. Visualizing cells and their connectivity graphs for CompuCell3D. In:Proceedings of the IEEE Symposium on Biological Data Visualization 2012, Seattle, WA, October 14-19, 2012, pp.85-90. |
R835001 (Final) |
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| Proceedings | Smith A, Ropella G, Kaplowitz N, Ookhtens M, Hunt CA. Mechanistic agent-based damage and repair models as hypotheses for patterns of necrosis caused by drug induced liver injury. In: Proceedings of the 2014 Summer Simulation Multiconference, San Diego, CA, 2014, article no. 16. |
R835001 (Final) |
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The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Conclusions drawn by the principal investigators have not been reviewed by the Agency.