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James Sluka
Jim Sluka

Senior Scientist

Education

Affiliations

Bio

My primary interests are in multiscale modeling of biological systems. My current work at the Biocomplexity Institute includes the development of (1) modeling-language standards (e.g., the Cell Behavior Ontology), (2) multiscale vascular, liver and kidney simulations (3) coupling subcellular reaction kinetics and whole body ADME models to multicell models, (4) drug modeling such as toxicity and bioavailability issues and (5) models of viral infectdion and treatment. I was the lead scientist on a recently completed EPA grant for computational liver toxicology and was the co-lead project scientist on an NIH funded project to develop a multiscale model of liver toxicity. Currently, I am part of the team developing and maintaining CompuCell3D, a multiscale modeling package. I also have extensive experience in cheminformatics, bioinformatics and software development with emphasis on modeling and text mining tools. I was the lead developer of the Cell Behavior Ontology, which links biological concepts to their instantiation in computer models. I am currently involved in standards development projects, and I am a voting member of the International Organization for Standards (ISO) committee on data standards in biotechnology. My work most relevant to this proposal is the development of liver-centric multiscale models of metabolism and modeling of environmental toxins as well as modeling viral infections of the lungs and drug treatments. My models couple from the whole body scale down to subcellular metabolic and signaling pathways and include spatially accurate representations of relevant tissues. In addition, in 2020 I contributed to a rapid pivot to model development for COVID-19. I am a founding member of an IMAG/MSM working group on modeling for viral pandemics.

Preferred Pronouns

He/him/his

Personal Academic Website

Research/Topics of Interest

Agent-based models
Compartmental models
Health systems
Intra-host modeling
Machine learning models
New methods development
Science communication
Time-series models
Artificial Intelligence
pharmacokinetics
drug development

Pathogens/Diseases of Main Interest/Expertise

COVID-19
Respiratory diseases

Countries of Work/Collaboration

United States

Projects

Papers

Ferrari Gianlupi J, Mapder T, Sego TJ, Sluka JP, Quinney SK, Craig M, Stratford RE Jr., Glazier JA. (2022). Multiscale Model of Antiviral Timing, Potency, and Heterogeneity Effects on an Epithelial Tissue Patch Infected by SARS-CoV-2. Viruses, 14(3)

Toledo-Marín JQ, Fox G, Sluka JP, Glazier JA. (2021). Deep Learning Approaches to Surrogates for Solving the Diffusion Equation for Mechanistic Real-World Simulations. Frontiers in physiology, (12)

Laubenbacher R, Sluka JP, Glazier JA. (2021). Using digital twins in viral infection. Science (New York, N.Y.), 371(6534)

Dunn KW, Martinez MM, Wang Z, Mang HE, Clendenon SG, Sluka JP, Glazier JA, Klaunig JE. (2020). Mitochondrial depolarization and repolarization in the early stages of acetaminophen hepatotoxicity in mice. Toxicology, (439)

Adhyapok P, Fu X, Sluka JP, Clendenon SG, Sluka VD, Wang Z, Dunn K, Klaunig JE, Glazier JA. (2020). A computational model of liver tissue damage and repair. PloS one, 15(12)

Clendenon SG, Fu X, Von Hoene RA, Clendenon JL, Sluka JP, Winfree S, Mang H, Martinez M, Filson A, Klaunig JE, Glazier JA, Dunn KW. (2019). Spatial Temporal Analysis of Fieldwise Flow in Microvasculature. Journal of visualized experiments : JoVE, 153

Fu X, Sluka JP, Clendenon SG, Dunn KW, Wang Z, Klaunig JE, Glazier JA. (2018). Modeling of xenobiotic transport and metabolism in virtual hepatic lobule models. PloS one, 13(9)

Clendenon SG, Fu X, Von Hoene RA, Clendenon JL, Sluka JP, Winfree S, Mang H, Martinez M, Filson AJ, Klaunig JE, Glazier JA, Dunn KW. (2019). A simple automated method for continuous fieldwise measurement of microvascular hemodynamics. Microvascular research, (123)

Clancy CE, An G, Cannon WR, Liu Y, May EE, Ortoleva P, Popel AS, Sluka JP, Su J, Vicini P, Zhou X, Eckmann DM. (2016). Multiscale Modeling in the Clinic: Drug Design and Development. Annals of biomedical engineering, 44(9)

Sluka JP, Fu X, Swat M, Belmonte JM, Cosmanescu A, Clendenon SG, Wambaugh JF, Glazier JA. (2016). A Liver-Centric Multiscale Modeling Framework for Xenobiotics. PloS one, 11(9)

Somogyi E, Sluka JP, Glazier JA. (2016). Formalizing Knowledge in Multi-Scale Agent-Based Simulations. Model driven engineering languages and systems : ... International Conference, MoDELS ... : proceedings. MODELS (Conference), (16)

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. (2015). Toxicokinetic Triage for Environmental Chemicals. Toxicological sciences : an official journal of the Society of Toxicology, 147(1)

Sluka JP, Shirinifard A, Swat M, Cosmanescu A, Heiland RW, Glazier JA. (2014). The cell behavior ontology: describing the intrinsic biological behaviors of real and model cells seen as active agents. Bioinformatics (Oxford, England), 30(16)

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