About Me

Last updated: Oct 7, 2026

dcruz66 [at] calpoly [dot] edu

Pronouns: he/him/él

I have been an assistant professor at the Mathematics Department at Cal Poly, San Luis Obispo since 2025.

Please note: My email address has changed. My old address (daniel.cruz@medicine.ufl.edu) has been closed and will not forward to my current inbox.

Research Interests

I am interested in mathematical and computational models motivated by biological systems which connect local interactions with emergent, system-level properties. In particular, I study spatial, multiscale models in which local (e.g. intercellular and/or biomolecular) communication gives rise to observable, "macro-level" features (e.g. pattern formation and disease progression). My research falls under MSC codes 68 & 92, and the topics / tools which I employ include:

Agent-based and data-driven models incorporating spatial dynamics;
Mathematical formalisms for multiscale models (e.g. cellular automata); and
Topological data analysis and data assimilation techniques for model development, analysis, and forecasting

Naming Convention: My full name is Daniel Alejandro Cruz Ortega, but I do not use "Ortega" in any professional setting.
Profile Picture Credit: UF Health Communications Team (October 23, 2023).

Upcoming and Recent Activities

(May 23-27, 2027) I am co-organizing a Workshop Celebrating Diversity (WCD) Session on "Topological Methods for Complex Biological Systems" at the SIAM Conference on Applications of Dynamical System with Sarah Tymochko and Alexandria Volkening.
(Jan 12-15, 2027) I will be giving a talk on "Harnessing Discrete, Multiscale Modeling and Topological Data Analysis to Forecast Stem Cell Behavior" in the AMS Special Session on Algebraic, Combinatoric, and Stochastic Approaches in Mathematical Biology at the 2027 Joint Mathematics Meetings.
(Oct 2, 2026) My four undergraduate students presented posters on their research from our department's Summer Undergraduate Research Program! This summer program is possible in large part thanks to the Frost Fund.
- Saúl Bañuelos presented on "Simulating Particle Movement Using Cellular Automata"
- Olivia Boyes presented on "Access to Polling Sites in Arkansas: Determining Gaps in Coverage using Persistent Homology"
- Jessica Chu presented on "Finding Gaps in Emergency Room Coverage using Topological Data Analysis"
- Oliver Kolbet presented on "Simulation of 2-Dimensional Cellular Automata With Systems of Interactive Molecular Arrangements"
(Oct 1, 2026) Our review "Mathematical Modeling of the Complement System: a Scoping Review" has been published at the Bulletin of Mathematical Biology!
(Sep 24, 2026) Our perspective on "Modularity in Biological Systems: Toward a Formal Conceptual Foundation" has been accepted for publication at npj Systems Biology and Applications!
(Jul 13-17, 2026) I gave two talks at the 2026 European Conference on Mathematical & Theoretical Biology and moderated one panel discussion.
- I gave a talk on "Harnessing Discrete, Multiscale Modeling and Topological Data Analysis to Forecast Stem Cell Behavior" at the Minisymposium on State of the art methods in modeling for cell and developmental biology.
- I gave a talk on "Towards Complement-based Therapeutics: Opportunities for (Discrete) Mathematical Modeling" at the Minisymposium on Discrete frameworks for modeling biological systems.
- As chair of the Society of Mathematical Biology's (SMB's) Community, Inclusion, and Engagement (CIE) Committee, I moderated a panel discussion on "Training in Mathematical Biology".
(Jul 6-9, 2026) I was on the organizing committee for the SIAM Conference on the Life Sciences.
- I also gave a talk on "Data-Driven Extensions to An Ensemble Kalman Filter-Based Algorithm for Personalizing Agent-Based Models" at the Minisymposium on Data-Driven Discovery and Inference in Biological Systems.
(Jun - Aug 2026) I mentored four undergraduate students via our department's Summer Undergraduate Research Program on projects associated with "Inferring Holes in Resource Coverage using Topological Data Analysis" and "Agent-based Modeling of Biological Systems". This summer program is possible in large part thanks to the Frost Fund.
- The students were Saúl Bañuelos, Olivia Boyes, Jessica Chu, and Oliver Kolbet.
(Mar 31, 2026) I was featured on an episode of the Biology in Numbers podcast.
(Mar 7-8, 2026) I gave a talk on "Developing Data Assimilation Methods for Agent-based, Biomedical Models" in the Special Session on Modeling Complex Biological Systems on Multiple Scales at the 2026 Spring Western Sectional Meeting.
(Jan 4-7, 2026) I gave a talk on "Developing Data Assimilation Methods for Agent-based Models" in the AMS Special Session on Hispanic Voices in Applied Mathematics at the Joint Mathematics Meetings.
- I also gave a talk on "Topological Data Analysis for a Summer Research Experience (REU) on Quantitative Justice" and supported the undergraduate students who participated in MSRI-UP this year for their talks on Jan 5, 2026!

Previous News and Events

(Nov 17, 2025) I gave a talk at Arizona State University on "Personalizing agent-based models to construct medical digital twins" in the Computational and Applied Math / Data Science Seminar.
(Oct 26-29, 2025) I will be giving a talk at the 2025 INFORMS Annual Meeting on "Personalizing Computational Models to Construct Medical Digital Twins".
(Sept 11, 2025) I joined the Mathematics Department at Cal Poly, San Luis Obispo as a tenure-track assistant professor!
(Aug 11-14, 2025) I gave a talk at the NITMB MathBio Convergence Conference on "Personalizing Agent-Based Models to Construct Medical Digital Twins".
(Aug 1, 2025) I became the chair of the SMB Diversity, Equity and Inclusion (DEI) Committee!
(Jul 28 - Aug 1, 2025) I will be giving a talk at the Third Joint SIAM/CAIMS Annual Meetings in "Dynamics, Networks, and Complex Systems: A Minisymposium Celebrating Diversity in Mathematics".
- Update: Unfortunately, I could not attend this conference. However, my co-author Adam Knapp presented our work at the minisymposium in my place.
(Jul 2, 2025) Our paper on "Personalizing computational models to construct medical digital twins" has been published at the Journal of the Royal Society Interface!
(Jun 14 - Jul 27, 2025) I joined Omayra Ortega as the MSRI-UP postdoc for the Summer 2025 Program on Quantitative Justice!
(May 11-15, 2025) I was on the organizing committee for the 2025 SIAM Conference on Applications of Dynamical Systems.
- I also gave a talk in the Minisymposium on Data-driven Modeling and Topological Data Analysis for Complex Biological Systems.
(Apr 4, 2025) Our paper on "Topological data analysis of pattern formation of human induced pluripotent stem cell colonies" has been published in Scientific Reports!
(Feb 24-26, 2025) I was invited to attend the workshop on "Uncertainty Quantification Strategies for Multi-Physics Systems and Digital Twins" at Institute for Mathematical and Statistical Innovation (IMSI).
(Feb 17, 2025) I gave a talk on "Careful Modeling: Ethical Concerns in Biomathematics" to the Cambridge University Ethics in Mathematics Society.
(Jan 8-11, 2025) Anna Nelson and I organized an AMS Special Session on Diversity in Mathematical Biology at the 2025 Joint Mathematics Meetings being held in Seattle, WA.
(Nov 4-8, 2024) I was invited to attend the "Random Dynamical Systems, with Applications to Biology" workshop at the new NSF-Simons National Institute for Theory and Mathematics in Biology (NITMB).
(Aug 1, 2024) I visited Purdue University and gave a talk on "Topological data analysis of pattern formation in stem cell colonies" at the Mathematical Biology Seminar.
(Jul 8-12, 2024) I gave a talk at the SIAM Annual Meeting (AN24) in Spokane, WA on "Data Assimilation in Medical Models and Digital Twins".
(Jun 10-13, 2024) I gave a talk at the SIAM Conference on the Life Sciences (LS24) in Portland, OR on "Extraction of Transcriptional Network Within Human Induced Pluripotent Colonies Via Boolean Logic".
(Jun 10-14, 2024) Alexandria Volkening, Sarah Tymochko, and I organized a mini symposium on "Topological Data Analysis in Dynamical Systems" at Equadiff 2024.
(May 31, 2024) Our manuscript preprint "Ensemble Kalman filter methods for agent-based medical digital twins" is now live on bioRxiv: https://doi.org/10.1101/2024.05.31.596692
(May 7, 2024) Our manuscript preprint "Topological data analysis of pattern formation of human induced pluripotent stem cell colonies" is now live on bioRxiv: https://doi.org/10.1101/2024.05.07.592985
(Apr 25, 2024) I gave a talk at the Columbia Undergraduate Mathematics Colloquium on "Topological data analysis of pattern formation in stem cell colonies".
(Apr 4, 2024) I gave a talk at the UF Biomathematics Seminar on "Data Assimilation in Medical Models and Digital Twins".
(Mar 23-24, 2024) Skylar Grey and I organized an AMS Special Session on Diversity in Mathematical Biology at the 2024 AMS Spring Southeastern Sectional Meeting hosted at Florida State University. I gave a talk at this session on "Data Assimilation in Medical Models and Digital Twins" as well.
(Mar 7, 2024) I gave a talk at the UT Arlington Math Bio Club on "Topological data analysis of pattern formation in stem cell colonies".
(Feb 6, 2024) I was named a MGB-SIAM Early Career Fellow!
(Jan 3-6, 2024) I attended the 2024 Joint Mathematics Meetings in San Francisco, CA and served as a poster reviewer.
(Nov 18-19, 2023) I gave a talk at the 2023 Online Undergraduate Resource Fair for the Advancement and Alliance of Marginalized Mathematicians (OURFA2M2).
(Nov 3-5, 2023) I received a travel grant to attend the 16th Annual Symposium on BEER in Richmond, VA.
(Sep 25, 2023) I gave a talk at the Mathematical and Computational Biology Seminar on "Topological data analysis of pattern formation in stem cell colonies".
(Jul 16-21, 2023) Margherita Maria Ferrari and I organized a minisymposium on "Algebra, Combinatorics, and Topology in Modern Biology" at the 2023 Society for Mathematical Biology Annual Meeting.
- I also gave a talk on "Topological data analysis of pattern formation in stem cell colonies" at a minisymposium organized by Alexandria Volkening, Andreas Buttenschoen, and Veronica Ciocanel.
(May 30 - Jul 25, 2023) As a member of the Society for Mathematical Biology (SMB) Diversity, Equity and Inclusion (DEI) Committee, I helped organize a summer seminar series to highlight the diversity in research and researchers in mathematical biology! For information, read this post.
(Mar 18-19, 2023) Margherita Maria Ferrari and I organized an AMS Special Session on Diversity in Mathematical Biology at the 2023 AMS Spring Southeastern Sectional Meeting hosted at Georgia Tech.
(Feb 16, 2023) I gave a talk at the Hunter College Mathematics Colloquium on "Topological data analysis of pattern formation in stem cell colonies".
(Feb 16, 2023) I gave a talk at the UF Biomathematics Seminar on "Estimating the Long-term Behavior of Biologically Inspired Agent-based Models".
(Feb 3, 2023) I gave a talk at the Cal Poly Mathematics Department colloquium on "Topological data analysis of pattern formation in stem cell colonies".
(Jan 15, 2023) The first Lathisms scholarship is now open! Vanessa Sun and I have been working as the scholarship co-chairs for some months, and I happy to share this scholarship aimed at supported Hispanic/Latinx students interested in pursuing a career focused in the mathematical sciences!
(Jan 4-5, 2023) I gave a talk at the 2023 Joint Mathematics Meeting in an AMS Special Session on "Modeling collective behavior in biology" organized by Alexandria Volkening and Philip Maini.
(Sep 19-23, 2022) Veronica Ciocanel, Stacey Finely, Jesse Kreger, and I organized a panel on "Building Inclusive Graduate Programs in Mathematical Biology" at the 12th European Conference on Mathematical and Theoretical Biology (ECMTB 2022), which was held in Heidelberg, Germany.
(Jul 7-9, 2022) I attended the Latinx in the Mathematical Sciences Conference 2022 hosted by the Institute for Pure and Applied Mathematics (IPAM) at the UCLA.
(May 9-13, 2022) - I attended the 2022 SCMB Workshop on Discrete and Topological Models in Molecular Biology (DTMB) and the 26th International Conference on Developments in Language Theory.
(Apr 23, 2022) - I was part of a panel at an undergraduate mathematics research conference hosted at Georgia Tech. The panel focused on sharing experiences with and giving advice to undergraduate students considering graduate studies in the mathematical sciences.
(Apr 11, 2022) - I joined the Laboratory for Systems Medicine at the University of Florida as a postdoctoral associate!
(Apr 8, 2022) - Margherita Maria Ferrari and I organized an AMS Special Session on Mathematical Models for Biomolecular and Cellular Interactions at the 2022 Joint Mathematics Meeting, which was held virtually.
(Mar 26-27, 2022) - Invited talk ("Evaluating Reproducibility in Agent-based Models of Cellular Biology") at the AMS Spring Central Sectional Meeting, Special Session on Mathematics of Complex Systems in Biology.
(Feb 2, 2022) - Invited seminar talk ("Agent-based modeling of emergent patterning within stem cell colonies") at UC Merced's mathematical biology seminar.
(Nov 20, 2021) - Invited talk ("Boolean Network Modeling of FGF Signaling Within Pluripotent Stem Cell Colonies") at the AMS Fall Southeastern Sectional Meeting, Special Session on Algebra, Combinatorics, and Topology in Biological Structures.
(Oct 27, 2021) - I was featured on the a blog post of the Society for Mathematical Biology Subgroup on Cell and Developmental Biology: https://smb-celldevbio.github.io/2021-10-27-CruzBlog/
(Oct 27, 2021) - My review on "Hybrid computational modeling methods for systems biology" with Melissa Kemp is out now: https://doi.org/10.1088/2516-1091/ac2cdf
(Jun 17, 2021) - I won a poster prize at the 2021 Annual Society of Mathematical Biology Meeting in the Cell & Developmental Biology category for my work on the SCMB seed project with Elena Dimitrova and Melissa Kemp!
(Jun 17, 2021) - Margherita Maria Ferrari and I organized a mini-symposium on Algebra, Combinatorics, and Topology in Modern Biology at the 2021 Annual Society of Mathematical Biology Meeting.

Prior to joining Cal Poly, SLO:

I was the postdoc associated with the 2025 MSRI Undergraduate Program (MSRI-UP) on Quantitative Justice, working with Omayra Ortega.
I was a postdoc in the Laboratory for Systems Medicine (LSM) at the University of Florida (Department of Medicine) working with Reinhard Laubenbacher. My primary focus was on the personalization of spatial, multiscale models for the development of medical digital twins.
I was a visiting assistant professor at Georgia Tech in the School of Mathematics. There I was also affiliated with the Southeast Center for Mathematics and Biology, an NSF-Simons Research Center for Mathematics of Complex Biological Systems.

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