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Stem cell regeneration is a vital biological process in self-renewing tissues, governing development and tissue homeostasis. Gene regulatory network dynamics are pivotal in controlling stem cell regeneration and cell type transitions.…
Phenotype transition takes place in many biological processes such as differentiation, and understanding how a cell reprograms its global gene expression profile is a problem of rate theories. A cell phenotype transition accompanies with…
Image-based crop growth modeling can substantially contribute to precision agriculture by revealing spatial crop development over time, which allows an early and location-specific estimation of relevant future plant traits, such as leaf…
One of the grand challenges of cell biology is inferring the gene regulatory network (GRN) which describes interactions between genes and their products that control gene expression and cellular function. We can treat this as a causal…
A crop can be represented as a biotechnical system in which components are either chosen (cultivar, management) or given (soil, climate) and whose combination generates highly variable stress patterns and yield responses. Here, we used…
Transcriptional activity has been shown to relate to the organization of chromosomes in the eukaryotic nucleus and in the bacterial nucleoid. In particular, highly transcribed genes, RNA polymerases and transcription factors gather into…
A tumor can be thought of as an ecosystem, which critically means that we cannot just consider it as a collection of mutated cells but more as a complex system of many interacting cellular and microenvironmental elements. At its simplest, a…
In evolution, the effects of a single deleterious mutation can sometimes be compensated for by a second mutation which recovers the original phenotype. Such epistatic interactions have implications for the structure of genome space -…
How genes affect tissue scale organization remains a longstanding biological puzzle. As experimental efforts aim to quantify gene expression, chromatin organization, cellular structure, and tissue structure, computational modeling lags…
Rapid advance of experimental techniques provides an unprecedented in-depth view into complex developmental processes. Still, little is known on how the complexity of multicellular organisms evolved by elaborating developmental programs and…
In this review we summarize our recent efforts in trying to understand the role of heterogeneity in cancer progression by using neural networks to characterise different aspects of the mapping from a cancer cells genotype and environment to…
In this paper we introduce a model of spatial network growth in which nodes are placed at randomly selected locations on a unit square in $\mathbb{R}^2$, forming new connections to old nodes subject to the constraint that edges do not…
Organismal phenotypes emerge from a complex set of genotypic interactions. While technological advances in sequencing provide a quantitative description of an organism's genotype, characterization of an organism's physical phenotype lags…
Phenotypical variability in the absence of genetic variation often reflects complex energetic landscapes associated with underlying gene regulatory networks (GRNs). In this view, different phenotypes are associated with alternative states…
In this work, we study a class of hybrid dynamical systems called hybrid gene regulatory networks (HGRNs) which was proposed to model gene regulatory networks. In HGRNs, there exist well-behaved trajectories that reach a fixed point or…
Understanding the influence of an environment on the evolution of its resident population is a major challenge in evolutionary biology. Great progress has been made in homogeneous population structures while heterogeneous structures have…
Multicellular organisms contain a wide variety of highly specialized cell types. The consistency and robustness of developmental trajectories suggest that complex gene regulatory networks effectively act as low-dimensional cell fate…
During the development of an organism, cells must coordinate and organize to generate the correct shape, structure, and spatial patterns of tissues and organs, a process known as morphogenesis. The morphogenesis of embryonic tissues is…
Experimental data regarding auxin and venation formation exist at both macroscopic and molecular scales, and we attempt to unify them into a comprehensive model for venation formation. We begin with a set of principles to guide an abstract…
A central problem of neuroscience involves uncovering the principles governing the organization of nervous systems which ensure robustness in brain development. The nematode Caenorhabditis elegans provides us with a model organism for…