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We introduce a flexible framework for modeling dependent feature allocations. Our approach addresses limitations in traditional nonparametric methods by directly modeling the logit-probability surface of the feature paintbox, enabling the…
Constructing gene regulatory networks is a fundamental task in systems biology. We introduce a Gaussian reciprocal graphical model for inference about gene regulatory relationships by integrating mRNA gene expression and DNA level…
It is now generally assumed that the heterogeneity of most networks in nature probably arises via preferential attachment of some sort. However, the origin of various other topological features, such as degree-degree correlations and…
The original Hardenberg's model of biomass patterns in arid and semi-arid regions is revisited to extend it to more general non flat regions. It is proposed a technique to study these more generalized (non-flat) regions using both a…
Arabidopsis thaliana is a plant species widely utilized by scientists to estimate the impact of genetic differences in root morphological features. For this purpose, images of this plant after genetic modifications are taken to study…
The process of morphogenesis, which can be defined as an evolution of the form of an organism, is one of the most intriguing mysteries in the life sciences. It is clear, that gene expression patterns cannot explain the development of the…
The integration and transmission of information in the brain are dependent on the interplay between structural and dynamical properties. Implicit in any pursuit aimed at understanding neural dynamics from appropriate sets of mathematically…
Spatial extent is a complicating factor in mathematical biology. The possibility that an action at point A cannot immediately affect what happens at point B creates the opportunity for spatial nonuniformity. This nonuniformity must change…
A new model for biological growth is introduced that couples the geometry of an organism (or part of the organism) to the flow and deposition of material. The model has three dynamical variables (a) a Riemann metric tensor for the geometry,…
Spatial self-organization emerges in distributed systems exhibiting local interactions when nonlinearities and the appropriate propagation of signals are at work. These kinds of phenomena can be modeled with different frameworks, typically…
We present a theory of pattern formation in growing domains inspired by biological examples of tissue development. Gradients of signaling molecules regulate growth, while growth changes these graded chemical patterns by dilution and…
The investigation of plant transcriptional regulation constitutes a fundamental basis for crop breeding, where cis-regulatory elements (CREs), as the key factor determining gene expression, have become the focus of crop genetic improvement…
Developmental transcriptional networks in plants and animals operate in both space and time. To understand these transcriptional networks it is essential to obtain whole-genome expression data at high spatiotemporal resolution. Substantial…
The Gene Regulatory Network (GRN) of biological cells governs a number of key functionalities that enables them to adapt and survive through different environmental conditions. Close observation of the GRN shows that the structure and…
Multicellular rosettes are observed in different situations such as morphogenesis, wound healing, and cancer progression. While some molecular insights have been gained to explain the presence of these assemblies of five or more cells…
Biofilms are microbial collectives that occupy a diverse array of surfaces. The function and evolution of biofilms are strongly influenced by the spatial arrangement of different strains and species within them, but how spatiotemporal…
We present a mathematical model that describes how tumour heterogeneity evolves in a tissue slice that is oxygenated by a single blood vessel. Phenotype is identified with the stemness level of a cell, $s$, that determines its proliferative…
Theoretical understanding of evolutionary dynamics in spatially structured populations often relies on non-spatial models. Biofilms are among such populations where a more accurate understanding is of theoretical interest and can reveal new…
I revisit two theories of cell differentiation in multicellular organisms published a half-century ago, Stuart Kauffman's global gene regulatory dynamics (GGRD) model and Roy Britten's and Eric Davidson's modular gene regulatory network…
Based on a recently proposed non-equilibrium mechanism for spatial pattern formation [cond-mat/0312366] we study how morphogenesis can be controlled by locally coupled discrete dynamical networks, similar to gene regulation networks of…