Presentations » Laboratory for Systems Medicine » College of Medicine

2024

Fonseca, L.L., Joyner, CJ, Moreno, A., Barnwell, JW, Galinski, MR, and Voit, E.O. “Modeling Host-Parasite Interactions in Malaria Blood-Stage Infections in Rhesus Macaques” Poster presented at the EPI Research Day 2024 at the Reitz Union Grand Ballroom (UF), Gainesville, FL, US, February 15, 2024.
Grey, ST, Clark, V., Marek, G., Aranyos, A., Brantly, M., Khodayari, N., Moore, H. “Noninvasive predictors of liver disease associated with alpha-1 antitrypsin deficiency” Invited talk at Spring Southeastern Sectional Meeting of the AMS in Tallahassee, FL, 24 March 2024.
Brunson JC, Nord D, Langerude L, Moussa H, Machuca T, Rackauskas M, Sharma A, Lin C, Emtiazjoo A, Atkinson C. “Machine Learning Using Multi-Site Cytokine Levels is Predictive of Primary Graft Dysfunction Following Lung Transplantation”. Oral presentation at the 44th Annual Meeting & Scientific Sessions of the International Society for Heart and Lung Transplantation in Prague, Czechia, 2024 April 11.
Brunson JC, Jaber JF, Nandavaram S, Emtiazjoo A, Mehrad B, Patel DC, Gomez Manjarres DC. “The Hispanic Paradox in Lung Transplant Outcomes: Disentangling the Roles of Primary Diagnosis, Monitoring Period, Age, and Era”. Poster presentation in the Lung Transplant Thematic Session at the American Thoracic Society 2024 International Conference in San Diego, CA, 2024 May 20.
Brunson JC, Emtiazjoo A, Mehrad B, Gries C. “Computational Models of Chronic Lung Allograft Dysfunction Following Lung Transplantation: A Scoping Review”. Poster presentation in the Chronic Organ Rejection Section at the American Transplant Congress (ATC2024) in Philadelphia, PA, 2024 June 1.
Grey, ST, Clark, V., Marek, G., Aranyos, A., Brantly, M., Khodayari, N., Moore, H. “Noninvasive predictors of liver fibrosis associated with alpha-1 antitrypsin deficiency (AATD)” poster presented at Department of Medicine Celebration of Research, Gainesville, FL, 26 October 2024.
Sordo Vieira, L, Shick, A, Goddard, Y, Menezes A, Mehrad, B, “Does coagulopathy contribute to the morbidity and mortality of pulmonary aspergillosis” Poster Presentation at Gordon Research Conference on Hemostasis, Aug. 2024. (K25AI175668, R01AI135128))
Sordo Vieira, L, Qu, G, Lazarte, A, Goddard, Y Atkinson, C, Mehrad, B “Heme-induced complement activation in invasive aspergillosis.” Poster Presentation. Keystone Symposia on Fungal Pathogens, Feb. 2024 (K25AI17566, R01AI135128)
Sego, T.J. “Reproducibility of Stochastic Simulation Results”. Invited talk in the Cell Modeling Online Summer School and Hackathon, Center for Reproducible Biomedical Modeling, University of Washington, Seattle, WA, July 26, 2024.
Cruz, DA. “Topological data analysis of pattern formation in stem cell colonies.” Invited oral presentation at University of Texas at Arlington Math Bio Club, Arlington, TX, US, March 7, 2024.
Knapp, AC, Cruz, DA, Mehrad, B, and Laubenbacher, RC. “Data Assimilation in Medical Models and Digital Twins”. Invited oral presentation at the AMS Special Session on Diversity in Mathematical Biology, 2024 AMS Spring Southeastern Sectional Meeting, Tallahassee, FL, US, March 24, 2024.
Cruz, DA and Knapp, AC. “Data Assimilation in Medical Models and Digital Twins”. Invited oral presentation at University of Florida Biomathematics Seminar, Gainesville, FL, US, April 4, 2024.
Cruz, DA. “Topological data analysis of pattern formation in stem cell colonies.” Invited oral presentation at Columbia Undergraduate Mathematics Colloquium, New York, NY, US, April 25, 2024.
Park, E, Cruz, DA, Toppen, J, Dimitrova, ES, and Kemp, M. “Extraction of Transcriptional Network Within Human Induced Pluripotent Colonies Via Boolean Logic.” Invited oral presentation at the Minisymposium on Discrete Biological Network Models in Biology, 2024 Society for Industrial and Applied Mathematics Conference on the Life Sciences (LS24), Portland, OR, US, June 10, 2024.
Knapp, AC, Cruz, DA, Mehrad, B, and Laubenbacher, RC. “Data Assimilation in Medical Models and Digital Twins”. Invited oral presentation at the Minisymposium on Modeling Dynamics in Biological Systems, 2024 Society for Industrial and Applied Mathematics Annual Meeting (AN24), Spokane, WA, US, July 10, 2024.
Cruz, DA. “Topological data analysis of pattern formation in stem cell colonies.” Invited oral presentation at Purdue University Mathematical Biology Seminar, West Lafayette, IN, US, August 1, 2024.
Laubenbacher, RC. “Digital Twins in Medicine” Invited oral presentation at Argonne National Laboratory, Chicago, IL, September 11, 2024.
Laubenbacher, RC. “AI-enabled optimal control of medical digital twins” Invited oral presentation at NIAID Symposium on AI and Immunology, NIAID, Rockville, MD, May 29, 2024.

2023

Laubenbacher, RC. “The mathematics of medical digital twins” Plenary talk, Mathematical Opportunities in Digital Twins Workshop, George Mason University, Fairfax, VA, December 11, 2023.
Sego, T.J. “Multiscale Multicellular Modeling: Current Challenges and Future Directions”. Invited talk in the Center for Reproducible Biomedical Modeling Seminar Series, Seattle, WA, December 1, 2023.
Laubenbacher, RC. “Modular decomposition of discrete dynamical systems” Invited oral presentation at University of Connecticut, Storrs, CT, November 30.
Laubenbacher, RC. “Multi-scale modeling of the early immune response to respiratory infections“, plenary address, Predictive Modeling in Biology and Medicine Conference, University of California Riverside, Riverside, CA, November 18.
Fonseca, Luis L. Treatment Optimization in Medical Digital Twins, UF Pulmonary Research Conference Seminar Series, Gainesville, FL, 2023 Oct 25
Moore, H. How to Calculate an Optimal Drug Regimen, UF Pulmonary Research Conference Seminar Series, Gainesville, FL, 2023 Oct 18
Cruz, DA. “Topological data analysis of pattern formation in stem cell colonies.” Invited oral presentation at University of Massachusetts Amherst Mathematical and Computational Biology Seminar, Amherst, MA, US, Sep 25, 2023.
Sordo Vieira, Qu G, Lazarte, A, Goddard, Y, Atkinson, C, Mehrad, B Heme-induced complement activation in invasive aspergillosis. Oral Presentation. International Complement Workshop, September 2023. (R01AI135128)
Aghaee M, Ledzewicz U, Robbins M, Bezman N, Cho HJ, Moore H, SIAM Control and Its Applications Conference Minisymposium Talk, July 24, 2023
Hartsock, I, Park, E, Toppen, J, Bubenik, P, Dimitrova, ES, Kemp, ML, and Cruz, DA. “Topological data analysis of pattern formation in stem cell colonies.” Invited oral presentation at the Minisymposium on Data-driven, modeling, and topological techniques in cell and developmental biology, 2023 Society for Mathematical Biology Annual Meeting (SMB 2023), Columbus, OH, US, Jul 18, 2023.
Moore, H. UK QSP Network Workshop Talk, July 12, 2023
Laubenbacher, RC. “Modular design of multi-scale models: toward medical digital twin technology“, IMAG Meeting: Lessons From the Past that Guide the Future, NIH, Bethesda, June 29.
Sego, T.J., Sluka, J.P., Sauro, H.M., Glazier, J.A.. “Interactive Biological and Biophysics Simulation with Tissue Forge”, Poster at IMAG/MSM Consortium, National Institutes of Health, Bethesda, MD, Jun 28, 2023.
Laubenbacher RC. Alliance Discussion, Research!America, 2023 June 15.
Sego TJ. CompuCell3D: Overview and Applications in Complex Biological Systems Modeling. Building Immune Digital Twins Workshop, Institut Pascal, Paris, France, 2023 May 15–June 2
Sego, T.J. “CompuCell3D: Overview and Applications in Complex Biological Systems Modeling” Invited talk at the Building Immune Digital Twins Workshop, University of Paris-Saclay, Paris, France, May 26, 2023.
Laubenbacher, RC. “Is this the right time for building immune digital twins? Workshop on Building Immune Digital Twins, Institut Pascal, University Paris Saclay, Paris, France, May 15.
Wheeler, M, Goddard, Goddard, Y, Scindia, Y, Sordo Vieira, L, Whitten, S, Yang, N, Laubenbacher, R, and Mehrad, B. “Mathematical Modeling of Neutrophil Responses to Aspergillus”. Poster presentation at AAI Immunology 2023 in Washington D.C. on May 12, 2023.
Sordo Vieira L. Can Non-Hoarding Specific Markers of Problems in Mental Health Predict Populations at Risk of Compulsive Hoarding? Society of Biological Psychiatry Annual Meeting, San Diego CA, 2023 Apr 27–29.
Laubenbacher, RC. “Digital twins in medicine and in the life sciences, keynote address, Interdisciplinary Biological Sciences Symposium, Iowa State University, April 26.
Laubenbacher, RC. Structure and dynamics of Boolean networks, with applications to the concept of modularity in biology” Invited oral presentation at Department of Mathematical Sciences, Iowa State University.
Yu Dongmei, Jean-Gilles, M., Nutley, S., Firestone K., Sordo Vieira, L., Chang, Y., Mackin, S., Scharf, J., Mathews, C. “The Genetic Risk of Alzheimer’s Disorder is Associated with Decreased Risk of Hoarding Disorder “ Poster presentation at the Society of Biological Psychiatry Annual Meeting in San Diego, CA,
Sego, T.J. “Interactive Biological and Biophysics Simulation with Tissue Forge”. Talk at HARMONY 2023, University of Washington, Seattle, WA, April 24, 2023.
Sego, T.J.. “Cell State Dynamics in Multicellular Contexts: Current Capabilities and Future Directions”. Talk at HARMONY 2023, University of Washington, Seattle, WA, April 24, 2023.
Laubenbacher, RC. “Digital twins in the medical sciences” ” Invited oral presentation at National Academy of Engineering Regional Meeting, University of Central Florida, Orlando, FL, April 12.
Laubenbacher, RC. “Mathematics and computation for precision medicine” Invited oral presentation at Lake Nona Leadership Council, University of Florida, College of Pharmacy, Orlando, FL, March 28.
Moore, H. US Federal Interagency Modeling & Simulation Group (IMAG) Seminar Talk, March 10, 2023
Sego TJ. Enabling the Future of Biological and Biomedical Sciences with Advanced Modeling, Software and Computing. Mechanical and Energy Engineering Research Seminar Series, Purdue School of Engineering & Technology, Indiana University–Purdue University Indianapolis, 2023 Mar 2.
Fonseca LL. Modeling Host-Parasite Interactions in Malaria Blood-Stage Infections in Rhesus Macaques. Emerging Pathogens Institute Research Day, University of Florida, Gainesville, FL, 2023 Feb 16.
Cruz DA. Estimating the Long-term Behavior of Biologically Inspired Agent-based Models. Biomathematics Seminar, University of Florida, Gainesville, FL, 2023 Feb 16.
Cruz DA. Topological data analysis of pattern formation in stem cell colonies. Invited by Prof. Vincent Martinez. Mathematics Colloquium, Hunter College, New York, NY, 2023 Feb 16.
Laubenbacher, RC. “Medical digital twins” Invited oral presentation at Engineering Directorate, National Science Foundation, February 15.
Sego TJ. Introduction to Particle-based Modeling in Tissue Forge. Invited by Prof. Herbert Sauro. Center for Reproducible Biomedical Modeling Tutorial Series, Department of Bioengineering, University of Washington, Seattle, WA, 2023 Feb 8.
Cruz DA. Topological data analysis of pattern formation in stem cell colonies. Invited oral presentation, Cal Poly Mathematics Department Colloquium, San Luis Obispo, CA, US, 2023 Feb 3.
Laubenbacher, RC. “Digital twins in the biomedical sciences, opening plenary, Opportunities and Challenges for Digital Twins in the Biomedical Sciences – A Workshop, National Academies of Science, Engineering, and Medicine, January 30, virtual, https://www.nationalacademies.org/event/01-30-2023/opportunities-and-challenges-for-digital-twins-in-biomedical-sciences-a-workshop
Sego, TJ. Developing Software Tools in Computational Biology. Invited by Prof. Jared Ashcroft. Micro Nano Technology Education Center, Pasadena City College, Pasadena, CA. 2023 Jan 27.
Cruz, DA, Toppen, J, Park, E, Kemp, M, and Dimitrova, ES. “Estimating the Long-term Behavior of Biologically Inspired Agent-based Models.” Invited oral presentation at the AMS Special Session on Modeling Collective Behavior in Biology, 2023 Joint Mathematics Meetings (JMM 2023), Boston, MA, USA,January 4-7, 2023
Laubenbacher, RC. “COVID-associated pulmonary aspergillosis in immunocompetent patients” Invited oral presentation at Joint Mathematics Meetings, Boston, MA, January 6

2022

Fonseca, LL, and Laubenbacher, R. “Generating ODE Approximations of Agent Based Models for Control Purposes.” Invited oral presentation In the minisymposium “Boolean networks and related modeling frameworks – Part I: Model Design and Analysis” organized by Claus Kadelka (Iowa State University), 12^th European Conference on Mathematical and Theoretical Biology (ESMTB & SMB), Heidelberg, Germany, September 19-23, 2022. (GATASD, R01GM127909)
Fonseca, L.L. and Laubenbacher, RC. “Mathematical Tools for Discovery of Interventions and Therapeutics in Medicine Using Computational Models” Poster presented at the Medicine 2022 Celebration of Research (UF), Gainesville, FL, US, October 18, 2022.
Fonseca LL. Generating ODE Approximations of Agent Based Models for Control Purposes. Minisymposium on Boolean networks and related modeling frameworks at the 12th European Conference on Mathematical and Theoretical Biology (ECMTB 2022). Heidelberg, Germany, 2022 Sep 19.
Brunson JC. Toward Tidy Principles for Matrix-Decomposed Data. Invited panel on New Developments in Graphing Multivariate Data at the Joint Statistical Meetings. Washington, DC, 2022 Aug 8.
Laubenbacher, R. “Multiscale computational models of lung immunity”. Invited oral presentation, University of Idaho, November 1, 2022.
Laubennbacher R. Multiscale computational models of lung immunity. U.S. Food and Drug Administration (virtual), 2022 Oct 26.
Laubennbacher R. Boolean networks in systems biology. Max Planck Institute for Mathematics in the Natural Sciences, Leipzig, Germany, 2022 Sep 23.
Laubennbacher R. Mathematics in 21st century medicine: digital twins. Annual meeting of the Society for Mathematical Biology, Heidelberg, Germany, 2022 Sep 22.
Walker M. Implications of Disease Spread Due to Variability in Body Mass from Larval Stages in Aedes Aegypti. MS35: Advances in Epidemiology, 2022 SIAM Conference on the Life Sciences (hybrid), 2022 Jul 12.
Laubennbacher R. Multiscale computational models for lung immunity. Keynote Lecture, 30th Conference on Intelligent Systems for Molecular Biology, SYSMOD, Madison, WI, 2022 Jul 11.
Brunson JC. Toward a tidy package ecosystem for topological data analysis. Special session on Expanding Tidyverse at useR! 2022. Virtual, 2022 Jun 23.
Brunson JC. Post-Transplant Disparities Amongst Sarcoidosis-Indicated Lung Recipients. Mini-symposium on Advances in Pre- and Post-Lung Transplant Care: From Selection to CLAD at the American Thoracic Society International Conference. San Francisco, CA, 2022 May 18.
Cruz DA. Invited panelist, professional development panel. Undergraduate Mathematics Research Conference, Georgia Tech, Atlanta, GA, 2022 Apr 23.
Laubennbacher R. Medical digital twins: mathematics for 21st century medicine, Geller Lecture, Texas A&M University, College Station, TX, 2022 Apr 12.
Ribeiro, HAL. “Multiscale Mechanistic Modeling of host defense in invasive Aspergillosis reveals hemorrhage as the driver of infection outcome.” Invited oral presentation, Department of Mathematics and Statistics, American University, Washington DC, USA, Feb 11, 2022. (R01AI135128, U01EB024501)