News and Events

Workshop Presentation

CompuCell3D: Overview and Applications in Complex Biological Systems Modeling

T.J. Sego showcased CompuCell3D, his software package for modeling cellular dynamics using a variety of simulation techniques. His talk surveyed CompuCell3D features and previous applications relevant to spatial and multiscale modeling of viral infection and immune response.


Journal Article

Stability of linear Boolean networks

We characterize the stability of linear Boolean networks in terms of Derrida curves, phase transition thresholds, and formulae for the number of attractor states of a network and the number of bijective networks.



Interactive Biological and Biophysics Simulation with Tissue Forge

Tissue Forge is an open-source interactive software environment for particle-based physics, chemistry and biology modeling and simulation. Tissue Forge allows users to create, simulate and explore models and virtual experiments based on soft condensed matter physics at multiple scales, from the molecular to the multicellular, using a simple, consistent interface.

COMBINE 2023 - Fig - Tissue Forge


Chhavi Pokharna, shown on the right

The weekend of April 15-16, 2023, Chhavi Pokharna and her team from Orlando Science High School competed and placed 6th overall at the Mu Alpha Theta State Convention!

Bhavya's and Chhavi's Achievements

Additional News and Events

Achievement – Bhavya Kambara – The weekend of April 13-16, 2023, Bhavya Kambara placed 1st in the state in her event, Home Health Aide, at the State Leadership Conference for Health Occupations Students of America qualifying her for the International Leadership Conference in Dallas, Texas!

Symposium – STUDENT RESEARCH SYMPOSIUM – April 19, 2023 • 4:30 – 6:30 – Learn More

Award – Intersect Fellowship for Computational Scientists and Immunologists – The American Association of Immunologists awarded Borna Mehrad, Matthew Wheeler, and Reinhard Laubenbacher an Intersect Fellowship for their project “Modeling the neutrophil response to Aspergillus”. – Award Announcement

Invited Oral Presentation – Enabling the Future of Biological and Biomedical Sciences with Advanced Modeling, Software and Computing – T.J. Sego presented his work at the Mechanical and Energy Engineering Research Seminar Series at Indiana University–Purdue University Indianapolis. – Conference Website

Invited Oral Presentation – Estimating the Long-term Behavior of Biologically Inspired Agent-based Models – Daniel Cruz presented his work to the Biomathematics Seminar organized by the Department of Mathematics. – View Website

Poster Presentation – Modeling Host-Parasite Interactions in Malaria Blood-Stage Infections in Rhesus Macaques – Luis Lopes da Fonseca presented his work at the Emerging Pathogens Institute Research Day.

Invited Oral Presentation – Topological Data Analysis of Pattern Formation in Stem Cell Colonies – Daniel Cruz presented his work to the Mathematics Colloquium at Hunter College, on the invitation of Prof. Vincent Martinez. – Visit Website

Invited Presentation – Introduction to Particle-based Modeling in Tissue Forge – T.J. Sego presented his work at the Center for Reproducible Biomedical Modeling Tutorial Series at the University of Washington, on the invitation of Prof. Herbert Sauro. – Venue

Journal Article – Cell Modeling in Jupyter Notebook using CompuCell3D – This work develops CompuCell3D modeling and simulation support for Jupyter Notebooks, an interactive computational environment, which brings the benefits of interactive simulation visualization, reproducibility, portability, and self-documentation to spatial multicellular modeling. – View Publication

Journal Article – Cell Modeling in Jupyter Notebook using CompuCell3D – This work develops CompuCell3D modeling and simulation support for Jupyter Notebooks, an interactive computational environment, which brings the benefits of interactive simulation visualization, reproducibility, portability, and self-documentation to spatial multicellular modeling. – View Publication

Invited Oral Presentation – Topological data analysis of pattern formation in stem cell colonies – Daniel Cruz was presented his work at the Cal Poly Mathematics Department Colloquium in San Luis Obispo, on the invitation of Prof. Elena Dimitrova. – Visit Website

Recent Publication – Identifying psychiatric and neurological comorbidities associated with hoarding disorder through network analysis – The relationships between hoarding disorder (HD) and other neurological and psychiatric disorders remain largely unknown. Although psychiatric burden in those with HD is high, less is known about neurological disorders. – View Publication

Poster Presentation – Mathematical and Computational Sciences Poster Walk at the Thirteenth American Conference on Pharmacometrics (ACoP13) – Mahya Aghaee was one of two presenters selected for the Mathematical and Computational Sciences Poster Walk at the Thirteenth American Conference on Pharmacometrics (ACoP13). Her poster presentation was titled Mathematical Optimization of Combination Therapy for Patients with Multiple Myeloma, based on her work with Helen Moore. Conference Website

Oral Presentation Award – 2022 American Conference on Pharmacometrics (ACoP13) Trainee Communication Challenge – Mahya Aghaee was awarded a Best Presentation prize at the 2022 American Conference on Pharmacometrics (ACoP13) Trainee Communication Challenge in Aurora, Colorado. All participants gave 5-minute presentations of their research without using any slides. Dr. Aghaee presented her work with Helen Moore on Multiple myeloma therapy optimization. Conference Website

Professional Membership – Admission to Society of Biological Psychiatry – Luis Sordo Vieira has been accepted as a Regular Member of the Society of Biological Psychiatry (SOBP). Dr. Sordo Vieira was admitted based on his professional record and an endorsement from a current member. Visit Website

December 12, 2022 – Student Research Symposium – Agenda

Recent Publication – Biomarker Discovery for Meta-Classification of Melanoma Metastatic Progression Using Transfer Learning – Melanoma is considered to be the most serious and aggressive type of skin cancer, and metastasis appears to be the most important factor in its prognosis. View Publication

Recent Publication – MaHPIC malaria systems biology data from Plasmodium cynomolgi sporozoite longitudinal infections in macaques – Plasmodium cynomolgi causes zoonotic malarial infections in Southeast Asia and this parasite species is important as a model for Plasmodium vivax and Plasmodium ovale. Each of these species produces hypnozoites in the liver, which can cause relapsing infections in the blood. – View Publication

September 19, 2022 – Oral Presentation – Generating ODE Approximations of Agent Based Models for Control Purposes – Luis L. Fonseca presented in a minisymposium on Boolean networks and related modeling frameworks at the 12th European Conference on Mathematical and Theoretical Biology (ECMTB 2022). Conference Website

Recent Publication – Impact of Hoarding and Obsessive-Compulsive Disorder Symptomatology on Quality of Life and Their Interaction With Depression Symptomatology – Hoarding disorder (HD) is a psychiatric condition characterized by difficulty discarding items and accumulation of clutter. Although studies have established the negative impact of HD and compulsive hoarding behavior, fewer have examined the impact on quality of life (QoL) of hoarding behavior independent of obsessive-compulsive disorder (OCD). – View Publication

Recent Publication – Predictors of professional burnout and fulfilment in a longitudinal analysis on nurses and healthcare workers in the COVID-19 pandemic – To investigate the vulnerability of nurses to experiencing professional burnout and low fulfilment across 5 months of the COVID-19 pandemic. (2) To identify modifiable variables in hospital leadership and individual vulnerabilities that may mitigate these effects. – View Publication

Recent Publication – Plasmodium knowlesi Cytoadhesion Involves SICA Variant Proteins – Plasmodium knowlesi poses a health threat throughout Southeast Asian communities and currently causes most cases of malaria in Malaysia. This zoonotic parasite species has been studied in Macaca mulatta (rhesus monkeys) as a model for severe malarial infections, chronicity, and antigenic variation. – View Publication

Recent Publication – A feasibility study on yoga’s mechanism of action for chronic low back pain: psychological and neurophysiological changes, including global gene expression and DNA methylation, following a yoga intervention for chronic low back pain – Yoga has been shown to reduce pain and improve function in populations with chronic low back pain (cLBP)… – View Publication

August 8, 2022 – Oral Presentation – Toward Tidy Principles For Matrix-Decomposed Data – Cory Brunson will present as part of an invited panel on New Developments in Graphing Multivariate Data at the Joint Statistical Meetings in Washington DC. – Conference Website

July 11, 2022 – Keynote Presentation – Multiscale Computational Models For Lung Immunity – Reinhard Laubenbacher will present at the 30th Conference on Intelligent Systems for Molecular Biology of the International Society for Computational Biology in Madison, WI. – Conference Website

June 23, 2022 – Oral Presentation – Toward a tidy package ecosystem for topological data analysis – In a special session on Expanding Tidyverse, Cory Brunson will discuss an open-source R package collection for TDA at the all-virtual useR! 2022. Watch Presentation

May 29 – June 5, 2022 – Workshop at Banff – Decomposition Theories for Discrete Dynamical Systems: An Approach to Modularity of Biological Systems – The Banff International Research Station hosted this workshop. Reinhard Laubenbacher and Matt Wheeler joined collaborators for a to work on developing a mathematical foundation for a theory of modularity of biological systems and completed a manuscript on their work. More Information

Recent Publication – Evaluation Framework for Systems Models – Digital twins, customized simulation models pioneered in industry, are beginning to be deployed in medicine and healthcare, with some major successes, for instance in cardiovascular diagnostics and in insulin pump control. – View Publication

Recent Publication – Topological Data Analysis in Biomedicine: A Review – Significant technological advances made in recent years have shepherded a dramatic increase in utilization of digital technologies for biomedicine– everything from the widespread use of electronic health records to… – View Publication

May 18, 2022 – Oral Presentation – Post-Transplant Disparities Amongst Sarcoidosis-Indicated Lung Recipients – Cory Brunson will give an oral presentation in a mini-symposium on Advances in Pre- and Post-Lung Transplant Care: From Selection to CLAD at the American Thoracic Society International Conference in San Francisco, CA. – Conference Website

May 10, 2022 – Student Research Symposium – Agenda

Recent Publication – Self-reporting of psychiatric illness in an online patient registry is a good indicator of the existence of psychiatric illness – Online registries offer many advantages for research, including the ability to efficiently assess large numbers of individuals and identify potential participants for clinical trials and genetic studies. – View Publication

Recent Publication – Multi-scale mechanistic modelling of the host defence in invasive aspergillosis reveals leucocyte activation and iron acquisition as drivers of infection outcome – Aspergillus species are ubiquitous environmental moulds, with spores inhaled daily by most humans. – View Publication

April 12, 2022 – 2022 Sue Geller Undergraduate Lecture – Medical Digital Twins: Mathematics for 21st Century Medicine – Reinhard Laubenbacher will deliver the 2022 Sue Geller Undergraduate Lecture at Texas A&M University. – Event Link

April 11, 2022 – Colloquium – The Dynamics of Boolean Networks – Reinhard Laubenbacher will present to the Texas A&M University Mathematics colloquium. – Event Link

April 9, 2022 – `Oral Presentation – The innate immune response to respiratory fungal pathogens: A multi-scale modeling approach – Reinhard Laubenbacher will present a paper to the AMS Special Session on Current Advances in Computational Biomedicine at the Virtual 2022 Joint Mathematics Meetings. – Event Link

April 8, 2022 – AMS Special Session on Mathematical Models for Biomolecular and Cellular Interactions – More Information

Recent Publication – The Impact of ACEs on BMI: An Investigation of the Genotype-Environment Effects of BMI – Adverse Childhood Experiences are stressful and traumatic events occurring before the age of eighteen shown to cause mental and physical health problems, including increased risk of obesity. Obesity remains an ongoing national challenge with no predicted solution. We examine… – View Publication

Recent Publication – Aspergillus utilizes extracellular heme as an iron source during invasive pneumonia, driving infection severity – Depriving microbes of iron is critical to host defense. Hemeproteins, the largest source of iron within vertebrates, are abundant in infected tissues in aspergillosis due to hemorrhage, but Aspergillus species have been… – View Publication

Recent Publication – Medical Digital Twins: a New Frontier – Last year, a new product for the treatment of type-1 diabetes came on the market: a “digital twin” of the human pancreas. The patient is outfitted with a bloodstream sensor and an insulin pump. The sensor continuously sends data about insulin levels to a device that looks a bit like a cellphone and that runs a mathematical model of glucose metabolism. – Read More

Recent Presentation – Computational models in systems biology: standards, dissemination, and best practices – Mathematical and computational models are a key technology in systems biology. Progress in the field depends on the replicability and reproducibility of their properties and behavior. For this, an essential requirement is a set of clear… – View Publication

Recent Presentation – Steady Cell Phenotype: A web-based tool for the modeling of biological networks with ternary logic – We introduce Steady Cell Phenotype, a browser based interface for the analysis of ternary biological networks. It includes tools for deterministically finding all steady states of a network… – View Publication

Recent Publication – Evaluation Framework for Systems Models – As decisions in drug development increasingly rely on predictions from mechanistic systems models, assessing the predictive capability of such models is becoming more important. Several frameworks for the development of quantitative systems pharmacology (QSP) models have been proposed. In this paper… – View Publication

Seminar Presentation – Microbes and Human Health: A Computational Modeling Perspective – Reinhard Laubenbacher gave a talk on Microbes and human health: a computational modeling perspective in the Seminar Series of the UF College of Dental Medicine Oral Biology Department.

Recent Publication – Dramatic Transcriptomic Differences in Macaca Mulatta and Macaca Fascicularis with Plasmodium Knowlesi Infections – Plasmodium knowlesi, a model malaria parasite, is responsible for a significant portion of zoonotic malaria cases in Southeast Asia and must be controlled to avoid disease severity and fatalities. Read More

Recent Publication – Optimization of Agent-Based Models Through Coarse-Graining – Optimization and control are important objectives across biology and biomedicine, and mathematical models are a key enabling technology. This paper reports a computational study of model-based multi-objective optimization in the setting of microbial ecology, using agent-based models. Read More

Recent Publication – The Why and How of Manuscript Review: What Goes Around Comes Around – Aside from conducting research itself, communicating it to the broader mathematical sciences community—as well as the general public—is the most important task that a researcher must accomplish, for the sake of progress within both the mathematical sciences and one’s own career… Read More

Interview – Helen Moore Interview – Helen Moore was Associate Director of Quantitative Clinical Pharmacology, Bristol-Myers Squibb in Princeton, New Jersey and recently joined UF as an Associate Professor in the Laboratory for Systems Medicine. Read Interview

Presentation – IMAG/MSM – Reinhard Laubenbacher presented a talk at the weekly meeting of the multiscale modeling and viral pandemics working group. The title of his talk was “A modular computational framework for medical digital twins.” Watch The Meeting

Poster Presentation – American Thoracic Society – Luis Sordo Vieira presented a poster presentation at the American Thoracic Society Annual Meeting Titled Discerning the Division of Labor of Monocyte Derived Immune Cells in Invasive Aspergillosis. Learn More

Poster Presentation – Society for Biological Psychiatry – Luis Sordo Vieira presented a poster at the Society for Biological Psychiatry Annual Meeting titled “Comorbidity Patterns in Hoarding Disorder.”

Mini-Symposium – Society for Mathematical Biology – Luis Sordo Vieira co-organized a mini symposium centered around the leading mathematical models of pulmonary immune responses to pulmonary insults at the Society for Mathematical Biology Annual Meeting.

Mini-Symposium – Society for Mathematical Biology – Henrique de Assis Lopes Robeiro presented at talk at the “SMB Minisymposium: The pressing need for within-host models of the pulmonary immune response.” The title of his presentation was: “Computational Modeling Reveals the Role of Macrophages in Respiratory A. fumigatus Infection in Immunocompromised Hosts.”

Recent Publication – Featured Publication – “A Modular Computational Framework for Medical Digital Twins” – This paper presents a modular software design that will help implement precision medicine in the form of medical digital twins which are computational models of disease processes calibrated to individual patients. Read Story

May 27, 2021 – Grand Rounds – Grand Rounds – Department of Medicine – University of Florida – View Video

February, 2021 – Mini-Symposium – AAAS Scientific Symposium – The Mathematics of Homeostasis and Health – AAA Annual Meeting – View Video

Mini-Symposium – The Mathematics of Homeostasis and Health. View Video

Mini-Symposium – Working Group on Multiscale Modeling and Viral Pandemics. Learn More