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Under low concentrations of antibiotics causing DNA damage, \textit{Escherichia coli} bacteria can trigger stochastically a stress response known as the SOS response. While the expression of this stress response can make individual cells…
Supermodeling is a modern, model-ensembling paradigm that integrates several self-synchronized imperfect sub-models by controlling a few meta-parameters to generate more accurate predictions of complex systems' dynamics. Continual…
Background: Analysing tumour architecture for metastatic potential usually focuses on phenotypic differences due to cellular morphology or specific genetic mutations, but often ignore the cell's position within the heterogeneous…
In order to increase the efficiency of the computer simulation of biological molecules, it is very common to impose holonomic constraints on the fastest degrees of freedom; normally bond lengths, but also possibly bond angles. However, as…
This work investigates how biodiversity is affected in a cyclic spatial May-Leonard model with hierarchical and non-hierarchical rules. Here we propose a generalization of the traditional rock-paper-scissors model by considering highly…
Phenotypic heterogeneity along the epithelial-mesenchymal (E-M) axis contributes to cancer metastasis and drug resistance. Recent experimental efforts have collated detailed time-course data on the emergence and dynamics of E-M…
We consider a reaction-diffusion model for a population structured in phenotype. We assume that the population lives in a heterogeneous periodic environment, so that a given phenotypic trait may be more or less fit according to the spatial…
Understanding how stochastic and non-linear deterministic processes interact is a major challenge in population dynamics theory. After a short review, we introduce a stochastic individual-centered particle model to describe the evolution in…
We study a stochastic phase-field model for tumor growth dynamics coupling a stochastic Cahn-Hilliard equation for the tumor phase parameter with a stochastic reaction-diffusion equation governing the nutrient proportion. We prove strong…
Cell competition is recognized to be instrumental to the dynamics and structure of the tumor-host interface in invasive cancers. In mild competition scenarios, the healthy tissue and cancer cells can coexist. When the competition is…
Statistical and mathematical modeling are crucial to describe, interpret, compare and predict the behavior of complex biological systems including the organization of hematopoietic stem and progenitor cells in the bone marrow environment.…
Strong experimental evidence has indicated that tumor growth belongs to the molecular beam epitaxy universality class. This type of growth is characterized by the constraint of cell proliferation to the tumor border, and surface diffusion…
Collective cell movement, characterized by multiple cells that are in contact for substantial periods of time and undergo correlated motion, plays a central role in cancer and embryogenesis. Recent imaging experiments have provided…
Molecular phenotypes are important links between genomic information and organismic functions, fitness, and evolution. Complex phenotypes, which are also called quantitative traits, often depend on multiple genomic loci. Their evolution…
The interplay between tumor cells and macrophages plays a central regulatory role in cancer progression. In this study, we developed a mathematical model that incorporates tumor cells, M1 type macrophages, M2 type macrophages and an M3 type…
Pan-omics, pan-cancer analysis has advanced our understanding of the molecular heterogeneity of cancer, expanding what was known from single-cancer or single-omics studies. However, pan-cancer, pan-omics analyses have been limited in their…
We built a novel Bayesian hierarchical survival model based on the somatic mutation profile of patients across 50 genes and 27 cancer types. The pan-cancer quality allows for the model to "borrow" information across cancer types, motivated…
Biological systems encode function not primarily in steady states, but in the structure of transient responses elicited by time-varying stimuli. Overshoots, biphasic dynamics, adaptation kinetics, fold-change detection, entrainment, and…
We classify two types of Hierarchical Bayesian Model found in the literature as Hierarchical Prior Model (HPM) and Hierarchical Stochastic Model (HSM). Then, we focus on studying the theoretical implications of the HSM. Using examples of…
Cell-cell adhesion is one the most fundamental mechanisms regulating collective cell migration during tissue development, homeostasis and repair, allowing cell populations to self-organize and eventually form and maintain complex tissue…