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The current pandemic has highlighted the need for methodologies that can quickly and reliably prioritize clinically approved compounds for their potential effectiveness for SARS-CoV-2 infections. In the past decade, network medicine has…
We investigate a quantitative network of gene expression dynamics describing the competence development in Bacillus subtilis. First, we introduce an Onsager-Machlup approach to quantify the most probable transition pathway for both…
Gene/protein interactions provide critical information for a thorough understanding of cellular processes. Recently, considerable interest and effort has been focused on the construction and analysis of genome-wide gene networks. The large…
Predicting gene functions is a challenge for biologists in the post genomic era. Interactions among genes and their products compose networks that can be used to infer gene functions. Most previous studies adopt a linkage assumption, i.e.,…
Signal transduction is an important and basic mechanism to cell life activities. The stochastic state transition of receptor induces the release of signaling molecular, which triggers the state transition of other receptors. It constructs a…
Two alternative views of an economy are combined and studied. The first view is that of technological evolution as a process of combinatorial innovation. Recently a simple mathematical model (TAP) was introduced to study such a…
We introduce and analyze an extension of the mixed feedback loop model of Fran\c{c}ois and Hakim. Our extension includes an additional promoter state and allows for reversible protein sequestration, which was absent from the original…
Transcription factors are proteins that regulate gene activity by activating or repressing gene transcription. A special class of transcriptional repressors operates via a short-range mechanism, making local DNA regions inaccessible to…
This paper proposes a workflow to identify genes that respond to specific treatments in plants. The workflow takes as input the RNA sequencing read counts and phenotypical data of different genotypes, measured under control and treatment…
We propose a revisited version of the in vivo model of the cyanobacterial circadian clock. Our aim is to address the lack of robustness predicted for the mutant cyanobacteria without transcriptional regulation of the original model. For…
Recent studies revealed an important interplay between the detailed structure of fibration symmetric circuits and the functionality of biological and non-biological networks within which they have be identified. The presence of these…
Allostery is a form of protein regulation, where ligands that bind sites located apart from the active site can modify the activity of the protein. The molecular mechanisms of allostery have been extensively studied, because allosteric…
The discovery of nucleic acids and the structure of DNA have brought considerable advances in the understanding of life. The development of next-generation sequencing technologies has led to a large-scale generation of data, for which…
The study of control mechanisms of biological systems allows for interesting applications in bioengineering and medicine, for instance in cell reprogramming or drug target identification. A control strategy often consists of a set of…
We prove that nested canalizing functions are the minimum-sensitivity Boolean functions for any given activity ratio and we characterize the sensitivity boundary which has a nontrivial fractal structure. We further observe, on an extensive…
Increased ability to predict protein structures is moving research focus towards understanding protein dynamics. A promising approach is to represent protein dynamics through networks and take advantage of well-developed methods from…
Despite their noted potential in polynomial-system solving, there are few concrete examples of Newton-Okounkov bodies arising from applications. Accordingly, in this paper, we introduce a new application of Newton-Okounkov body theory to…
Translating metabolic networks into dynamic models is difficult if kinetic constants are unknown. Structural Kinetic Modelling (SKM) replaces reaction elasticities by independent random numbers. Here I propose a variant that accounts for…
The inference of networks of dependencies by Gaussian Graphical models on high-throughput data is an open issue in modern molecular biology. In this paper we provide a comparative study of three methods to obtain small sample and high…
In this paper we investigate the homeostatic mechanism in two biologically motivated models: intracellular copper regulation and self immune recognition. The analysis is based on the notions of infinitesimal homeostasis and near-perfect…