A hybrid simulation model for studying acute inflammatory response. - Wayne W. Wakeland; Louis M. Macovsky; Gary An (SpringSim (2), 2007)

Translational Systems Biology of Inflammation. - Yoram Vodovotz; Márie Csete; John Bartels; Steven Chang; Gary An (PLoS Comput. Biol., 2008)

Computational disease modeling - fact or fiction? - Jesper Tegnér; Albert Compte; Charles Auffray; Gary An; Gunnar Cedersund; Gilles Clermont; Boris S. Gutkin; Zoltán N. Oltvai; Klaas Enno Stephan; Randy Thomas; Pablo Villoslada (BMC Syst. Biol., 2009)

Djangology: A Light-weight Web-based Tool for Distributed Collaborative Text Annotation. - Emilia Apostolova; Sean Neilan; Gary An; Noriko Tomuro; Steven L. Lytinen (LREC, 2010)

SPARK: A Framework for Multi-Scale Agent-Based Biomedical Modeling. - Alexey Solovyev; Maxim Mikheev; Leming Zhou; Joyeeta Dutta-Moscato; Cordelia Ziraldo; Gary An; Yoram Vodovotz; Qi Mi (Int. J. Agent Technol. Syst., 2010)

A proposed method for dynamic knowledge representation via agent-directed composition from biomedical and simulation ontologies: an example using gut mucus layer dynamics. - Scott Christley; Gary An (SpringSim (ADS), 2011)

A proposal for augmenting biological model construction with a semi-intelligent computational modeling assistant. - Scott Christley; Gary An (Comput. Math. Organ. Theory, 2012)

Data-parallel techniques for simulating a mega-scale agent-based model of systemic inflammatory response syndrome on graphics processing units. - Samuel Alberts; Michael K. Keenan; Roshan M. D'Souza; Gary An (Simul., 2012)

Examining the dynamics of epithelial metaplasia and pouchitis in an ileal pouch with a spatially-explicit computational multi-scale gut model (MSGM). - Chase Cockrell; Scott Christley; Gary An; Eugene Chang; Marc Ward (SpringSim (ADS), 2013)

A multiscale modeling approach to inflammation: A case study in human endotoxemia. - Jeremy D. Scheff; Panteleimon D. Mavroudis; Panagiota T. Foteinou; Gary An; Steve E. Calvano; John Doyle 001; Thomas E. Dick; Stephen F. Lowry; Yoram Vodovotz; Ioannis P. Androulakis (J. Comput. Phys., 2013)

Investigation of Inflammation and Tissue Patterning in the Gut Using a Spatially Explicit General-Purpose Model of Enteric Tissue (SEGMEnT). - Chase Cockrell; Scott Christley; Gary An (PLoS Comput. Biol., 2014)

Computational Studies of the Intestinal Host-Microbiota Interactome. - Scott Christley; Chase Cockrell; Gary An (Comput., 2015)

A Computational, Tissue-Realistic Model of Pressure Ulcer Formation in Individuals with Spinal Cord Injury. - Cordelia Ziraldo; Alexey Solovyev; Ana Allegretti; Shilpa Krishnan; M. Kristi Henzel; Gwendolyn A. Sowa; David M. Brienza; Gary An; Qi Mi; Yoram Vodovotz (PLoS Comput. Biol., 2015)

High-throughput cancer hypothesis testing with an integrated PhysiCell-EMEWS workflow. - Jonathan Ozik; Nicholson T. Collier; Justin M. Wozniak; Charles M. Macal; Chase Cockrell; Samuel H. Friedman; Ahmadreza Ghaffarizadeh; Randy W. Heiland; Gary An; Paul Macklin (BMC Bioinform., 2018)

Precision medicine as a control problem: Using simulation and deep reinforcement learning to discover adaptive, personalized multi-cytokine therapy for sepsis. - Brenden K. Petersen; Jiachen Yang; Will S. Grathwohl; Chase Cockrell; Claudio Santiago; Gary An; Daniel M. Faissol (CoRR, 2018)

Examining the controllability of sepsis using genetic algorithms on an agent-based model of systemic inflammation. - Chase Cockrell; Gary An (PLoS Comput. Biol., 2018)

Extreme-Scale Dynamic Exploration of a Distributed Agent-Based Model With the EMEWS Framework. - Jonathan Ozik; Nicholson T. Collier; Justin M. Wozniak; Charles M. Macal; Gary An (IEEE Trans. Comput. Soc. Syst., 2018)

Deep Reinforcement Learning and Simulation as a Path Toward Precision Medicine. - Brenden K. Petersen; Jiachen Yang; Will S. Grathwohl; Chase Cockrell; Claudio Santiago; Gary An; Daniel M. Faissol (J. Comput. Biol., 2019)

Nested active learning for efficient model contextualization and parameterization: pathway to generating simulated populations using multi-scale computational models. - Chase Cockrell; Jonathan Ozik; Nick Collier; Gary An (Simul., 2021)

Facilitating automated conversion of scientific knowledge into scientific simulation models with the Machine Assisted Generation, Calibration, and Comparison (MAGCC) Framework. - Chase Cockrell; Scott Christley; Gary An (CoRR, 2022)

Building digital twins of the human immune system: toward a roadmap. - Reinhard C. Laubenbacher; Anna Niarakis; Tomás Helikar; Gary An; B. Shapiro; Rahuman S. Malik-Sheriff; T. J. Sego; Adam C. Knapp; Paul Macklin; James A. Glazier (npj Digit. Medicine, 2022)

Generating synthetic multi-dimensional molecular-mediator time series data for artificial intelligence-based disease trajectory forecasting and drug development digital twins: Considerations. - Gary An; Chase Cockrell (CoRR, 2023)

Toward mechanistic medical digital twins: some use cases in immunology. - Reinhard C. Laubenbacher; Fred Adler; Gary An; Filippo Castiglione; Stephen Eubank 002; Luis L. Fonseca; James A. Glazier; Tomás Helikar; Marti Jett-Tilton; Denise Kirschner; Paul Macklin; Borna Mehrad; et al. (Frontiers Digit. Health, 2024)

Examining B-cell dynamics and responsiveness in different inflammatory milieus using an agent-based model. - Bryan Shin; Gary An; Chase Cockrell (PLoS Comput. Biol., 2024)