Publications

Selected Publications from the An-Cockrell Lab

2024

  • Laubenbacher R, Adler F, An G, Castiglione F, Eubank S, Fonseca LL, Glazier J, Helikar T, Jett-Tilton M, Kirschner D, Macklin P, Mehrad B, Moore B, Pasour V, Shmulevich I, Smith A, Voight I, Yankeelov TE, Ziemessen T. Towards mechanistic medical digital twins: some use cases in immunology. Front. Digit. Health, 06 March 2024 Sec. Health Informatics Volume 6 - 2024 DOI
  • Laubenbacher R, Adler F, An G, Castiglione F, Eubank S, Fonseca LL, Glazier J, Helikar T, Jett-Tilton M, Kirschner D, Macklin P, Mehrad B, Moore B, Pasour V, Shmulevich I, Smith A, Voight I, Yankeelov TE, Ziemessen T. Forum on immune digital twins: a meeting report. npj Syst Biol Appl 10, 19 (2024). DOI

2023

  • Feuerwerker S, Cockrell C, An G. Characterizing the crosstalk between programmed cell death pathways in cytokine storm with an agent-based model. Surg Infect (Larchmt). 2023 Oct 12. DOI
  • Marassi C, Socia D, Larie D, An G, Cockrell RC. Children are small adults (when properly normalized): Transferrable/generalizable sepsis prediction. Surg Open Sci. 2023 Sep 22. DOI
  • An, G, Cockrell C. Generating synthetic multi-dimensional molecular-mediator trajectories for machine learning: Considerations. Front. Sys. Bio., 29 June 2023. DOI

2022

  • Cockrell C, Larie D, An G. Preparing for the next Pandemic: Simulation-based Deep Reinforcement Learning to discover and test multimodal control of systemic inflammation using repurposed immunomodulatory agents. Front. Immunology, 2022 Nov 8. DOI
  • An G, Cockrell C. Drug Development Digital Twins for drug discovery, repurposing and testing: a schema for requirements and development. Front. Syst. Biol., 2022 June 2. DOI
  • An, G. Specialty Grand Challenge: What it Will Take to Cross the Valley of Death: Translational Systems Biology, “True” Precision Medicine, Medical Digital Twins, Artificial Intelligence and In Silico Clinical Trials. Front. Syst. Biol., 2022 April 28. DOI
  • Schumaker, G., Becker, A., An, G., Badylak, S., Johnson, S., Jiang, P., Vodovotz, Y., Cockrell, R.C. Optical Biopsy Using a Neural Network to Predict Gene Expression from Photos of Wounds. Journal of Surgical Research, Volume 270, February 2022. DOI

2019-2021

  • Larie, D., An, G., Cockrell, C. Artificial neural networks for disease trajectory prediction in the context of sepsis. Frontiers in Physiology: Computational Physiology and Medicine, 2021 October 14. DOI
  • Cockrell, C., An, G. Comparative Computational Modeling of the Bat and Human Immune Response to Viral Infection with the Comparative Biology Immune Agent Based Model. Viruses, 16 August 2021. DOI
  • Cockrell C, An G. Using Genetic Algorithms to reproduce the heterogeneity of clinical data through model refinement and rule discovery in a high-dimensional agent-based model of systemic inflammation. Frontiers in Physiology: Computational Physiology and Medicine, 2021 May 19. DOI
  • Cockrell C, Ozik J, Collier N, An G. Nested Active Learning for Efficient Model Contextualization and Parameterization: Pathway to generating simulated populations using multi-scale computational models. Simulation, 2019 May 21. DOI
  • Ozik, J, Collier, N, Heiland, R, An, G, Macklin, P. Learning-accelerated discovery of immune-tumour interactions. Molecular Systems Design and Engineering, 2019. DOI
  • Petersen BK, Yang, J, Grathwohl WS, Cockrell C, Santiago C, An G, Faissol DM. Deep Reinforcement Learning and Simulation as Path Towards Precision Medicine. Journal of Computational Biology, 25 Jan 2019. DOI

2016-2018

  • An, G. The Crisis of Reproducibility, the Denominator Problem and the Role of Multi-scale Modeling. Bulletin of Mathematical Biology, Dec 2018. DOI
  • Ozik J, Collier N, Wozniak JM, Macal C, Cockrell C, Friedman SH, Ghaffarizadeh A, Heiland R, An G, Macklin P. High-throughput cancer hypothesis testing with an integrated PhysiCell-EMEWS workflow. BMC Bioinformatics 2018. DOI
  • Day JD, Cockrell C, Namas R, Zamora R, An G, Vodovotz Y. Inflammation and Disease: Modelling and modulation of the inflammatory response to alleviate critical Illness. Curr Opin Syst Biol, Dec 2018. DOI
  • Ozik J, Collier NT, Wozniak JM, Macal C, An G. Extreme-scale Dynamic Exploration of a Distributed Agent-based Model with the EMEWS Framework. IEEE Trans Comput Soc Syst, Sep 2018. DOI
  • Cockrell C, An, G. Examining the controllability of sepsis using genetic algorithms on an agent-based model of systemic inflammation. PLoS Comput Biol, Feb 2018. DOI
  • Cockrell C, An G. Sepsis reconsidered: Identifying novel metrics for behavioral landscape characterization with a high-performance computing implementation of an agent-based model. J Theor Biol, Jul 2017. DOI
  • An G, Fitzpatrick, BG, Christley S, Federico P, Kanarek A, Miller Neilan R, Oremland M, Salinas R, Laubenbacher R, Lenhart S. Optimization and Control of Agent-based Models in Biology: A Perspective. Bull Math Biol, Nov 2016. DOI

2013-2015

  • An, G. Introduction of a framework for dynamic knowledge representation of the control structure of transplant immunology: employing the power of abstraction with a solid organ transplant agent-based model. Frontiers in Immunology, Nov 2015. DOI
  • Cockrell, C, Christley, S, Chang, E, An, G. Towards Anatomic Scale Agent-Based Modeling with a Massively Parallel Spatially Explicit General-purpose Model of Enteric Tissue (SEGMEnT_HPC). PLoS ONE, Mar 2015. DOI
  • Peer, X., An, G. Agent-based model of Fecal Microbial Transplant effect on Bile Acid Metabolism on suppressing Clostridium difficile infection: an example of agent-based modeling of intestinal bacterial infection. J Pharmacokinet Pharmacodyn, Oct 2014. DOI
  • An, G, Kulkarni, S. An agent-based modeling framework linking inflammation and cancer using evolutionary principles: description of a generative hierarchy for the hallmarks of cancer and developing a bridge between mechanism and epidemiological data Mathematical Biosciences, 2014. DOI
  • Uppal, A, Wightman, SC, Ganai, S, Weichselbaum, RR, An, G. Investigation of the Essential Role of Platelet-Tumor Cell Interactions in Metastasis Progression Using an Agent-based Model. Theor Biol Med Model, Apr 2014. DOI
  • Cockrell, C., Christley, S., An, G. Investigation of gut mucosal tissue patterning and inflammation using a Spatially Explicit General-purpose Model of Enteric Tissue (SEGMEnT). PLoS Comput Biol, Mar 2014. DOI
  • Gopalakrishnan, V., Kim, M., An, G. Using an agent-based model to examine the role of dynamic bacterial virulence in surgical site infection. Adv Wound Care, 2013. DOI
  • Chapa, J., Bourgo, R.J., Greene, G.L., Kulkarni, S., An, G. Examining the pathogenesis of breast cancer using a novel agent-based model of mammary ductal epithelium dynamics. PLoS One, May 2013. DOI
  • Christley, S., Emr, B., Ghosh, A., Satalin, J., Gatto, L., Vodovotz, Y., Nieman, G.F., An, G. Bayesian inference of the lung alveolar spatial model for the identification of alveolar mechanics associated with acute respiratory distress syndrome. Phys Biol, Apr 2013. DOI
  • Stern, J.R., Christley, S., Zaborina, O., Alverdy, J.C., An, G. Agent-based model of epithelial host-pathogen interactions in anastomotic leak. J Surg Res, Jan 2013. DOI

2011-2012

  • Christley, S., An, G. A proposal for augmenting biological model construction with a semi-intelligent computational modeling assistant. Comput Math Organ Theory, 2012. DOI
  • Stern, J.R., Christley, S., Zaborina, O., Alverdy, J.C., An, G. Integration of TGF-β and EGFR based signaling pathways using an agent-based modeling of epithelial restitution. Wound Repair Regen, 2012. DOI
  • Kim, M., Christley, S., Alverdy, J.C., Liu, D., An, G. Immature Oxidative Stress Management as a Unifying Hypothesis in the Pathogenesis of Necrotizing Enterocolitis: Insights from an Agent-based Model. Surg Infect, Feb 2012. DOI
    • Featured in Global Medical Discovery [ISSN 1929 8536] (http://globalmedicaldiscovery.com)
  • Seal, J.B., Alverdy, J.C., Zaborina, O., An, G. Agent-based dynamic knowledge representation of Pseudomonas aeruginosa virulence activation in the stressed gut: Towards characterizing host-pathogen interactions in gut-derived sepsis. Theor Biol Med Model, Sep 2011. DOI
  • An, G, Christley, S. Agent-based Modeling and Biomedical Ontologies: A Roadmap. Wiley Interdiscip Rev Comput Stat, Apr 2011. DOI
  • An, G., Bartels, J., Vodovotz, Y. In silico augmentation of the drug development pipeline: Examples from the study of acute inflammation. Drug Dev Res, Mar 2011. PMID

Prior to 2010

  • Mi, Q., Li, N.Y.K., Ziraldo, C., Ghuma,A., Mikheev, M., Squires, R., Okonkwo, D.O., Verdolini, K., Constantine, G., An, G., Vodovotz, Y. Translational Systems Biology of Inflammation: Applications to Personalized Medicine. Personalized Medicine, Sep 2010. DOI
  • An, G. Closing the scientific loop: Bridging correlation and causality in the petaflop age. Sci Transl Med, 2010. DOI
  • An, G., Mi, Q., Dutta-Moscato, J., Vodovotz, Y. Agent-based models in translational systems biology. Wiley Interdisciplinary Reviews: Systems Biology and Medicine., Sep-Oct 2009. PMID
  • Chau, T.A., McCully, M.L., Brintnell, W., An, G., Kasper, K.J., Haeryfar, S.M.M., McCormick, J.K., Cairns, E., Heinrichs, D.E. and Madrenas, J TLR2 Ligands on the Staphylococcal Cell Wall Down-regulate Superantigen-Induced T Cell Activation and Prevent Toxic Shock Syndrome Nat Med, 2009. DOI
  • An G., Faeder J.R. Detailed qualitative dynamic knowledge representation using a BioNetGen model of TLR-4 signaling and preconditioning. Math Biosci, 2009. PMID
  • An G. A model of TLR4 signaling and tolerance using a qualitative, particle event-based method: Introduction of Spatially Configured Stochastic Reaction Chambers (SCSRC) Math Biosci, 2009. PMID
  • An G. Introduction of an agent-based multi-scale modular architecture for dynamic knowledge representation of acute inflammation. Theor Biol Med Model, 2008. DOI
  • Vodovotz Y, Csete M, Bartels J, Chang S, An G. Translational Systems Biology of Inflammation. PLoS Comput Biol, 2008. DOI
  • An G, Faeder J, Vodovotz Y. A Review of Translational Systems Biology as applied to Inflammation: Introduction of an Engineering Approach to the Pathophysiology of the Burn Patient. J Burn Care Res, 2008. 29(2):277-285. PMID
  • Folcik VA, An G, Orosz CG. The Basic Immune Simulator: an agent-based model to study the interactions between innate and adaptive immunity. Theor Biol Med Model, 2007. DOI
  • An G. Concepts for developing a collaborative in-silico model of the acute inflammatory response using agent based modeling. J Crit Care, 2006. 21(1): 105-110. PMID
  • An G. In-silico experiments of existing and hypothetical cytokine-directed clinical trials using agent based modeling. Crit Care Med, 2004. 32(10): 2050-2060. PMID
  • An G. Agent-based computer simulation and SIRS: Building a bridge between basic science and clinical trials. Shock, 2001. 16(4): 266-273. PMID

Pre-Prints

  • Cockrell C, Schobel-McHugh S, Lisboa F, Vodovotz Y and An G. Generating synthetic data with a mechanism-based Critical Illness Digital Twin: Demonstration for Post Traumatic Acute Respiratory Distress Syndrome. 2022, November 24. bioRxiv DOI
  • Cockrell C, Christley S, An G. Facilitating automated conversion of scientific knowledge into scientific simulation models with the Machine Assisted Generation, Calibration, and Comparison (MAGCC) Framework. 2022, April 21 arXiv: 2204.10382v1 (cs.AI) DOI