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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…
Regulatory interactions between genes show a large amount of cross-species variability, even when the underlying functions are conserved: There are many ways to achieve the same function. Here we investigate the ability of regulatory…
A great part of the effort in the study of coarse grained models of transcription networks is directed to the analysis of their dynamical features. In this letter, we consider the \emph{equilibrium} properties of such systems, showing that…
Embryonic development relies on the formation of sharp, precise gene expression boundaries. In the fruit fly Drosophila melanogaster, boundary formation has been proposed to occur at a dynamical critical point. Yet, in the paradigmatic case…
During organogenesis, developmental programs governed by Gene Regulatory Networks (GRN) define the functionality, size and shape of the different constituents of living organisms. Robustness, thus, is an essential characteristic that GRNs…
For the canonical two-state model of transcription, we derive exact analytic expressions for the entropy production rate of transcription at steady state, and assess detailed balance breaking in transcription. Our analytics allow us to…
Many causal systems such as biological processes in cells can only be observed indirectly via measurements, such as gene expression. Causal representation learning -- the task of correctly mapping low-level observations to latent causal…
Segmentation in arthropod embryogenesis represents a well-known example of body plan diversity. Striped patterns of gene expression that lead to the future body segments appear simultaneously or sequentially in long and short germ-band…
We consider evolution of a large population, where fitness of each organism is defined by many phenotypical traits. These traits result from expression of many genes. We propose a new model of gene regulation, where gene expression is…
Transcription regulation is largely governed by the profile and the dynamics of transcription factors' binding to DNA. Stochastic effects are intrinsic to this dynamics and the binding to functional sites must be controled with a certain…
Modeling gene regulatory networks (GRNs) is an important topic in systems biology. Although there has been much work focusing on various specific systems, the generic behavior of GRNs with continuous variables is still elusive. In…
Evolution of gene regulation is crucial for our understanding of the phenotypic differences between species, populations and individuals. Sequence-specific binding of transcription factors to the regulatory regions on the DNA is a key…
Genes with similar transcriptional activation kinetics can display very different temporal mRNA profiles due to differences in transcription time, degradation rate and RNA processing kinetics. Recent studies have shown that a…
Biological functions are generated as a result of developmental dynamics that form phenotypes governed by genotypes. The dynamical system for development is shaped through genetic evolution following natural selection based on the fitness…
The proper functioning of multicellular organisms requires the robust establishment of precise proportions between distinct cell-types. This developmental differentiation process typically involves intracellular regulatory and stochastic…
In unicellular organisms such as bacteria the same acquired mutations beneficial in one environment can be restrictive in another. However, evolving Escherichia coli populations demonstrate remarkable flexibility in adaptation. The…
Transcription is a complex phenomenon that permits the conversion of genetic information into phenotype by means of an enzyme called RNA polymerase, which erratically moves along and scans the DNA template. We perform Bayesian inference…
The evolutionary origins of structural features in reconstructed gene-regulatory networks (GRNs) remain poorly understood, especially given the random aspects of gene expression. Here, we extend a classical model of GRN evolution to allow a…
Timely up- or down-regulation of gene expression is crucial for cellular differentiation and function. While gene upregulation via transcriptional activators has been extensively investigated, gene silencing remains understudied, especially…
Expression of cellular genes is regulated by binding of transcription factors to their promoter, either activating or inhibiting transcription of a gene. Particularly interesting is the case when the expressed protein regulates its own…