分子网络
Connecting the dynamics of biomolecular networks to experimentally measurable cell phenotypes remains a central challenge in systems biology. Here we introduce a model-based definition of phenotype as a partial steady state that is…
On exposure to 1,2-propanediol (1,2-PD), Salmonella enterica serovar Typhimurium LT2 produces 1,2-PD utilization (Pdu) microcompartments (MCPs), nanoscale protein-bound shells that encapsulate metabolic enzymes. MCPs serve as a…
In vitro transcription (IVT) plays a critical role in the manufacture of mRNA vaccines and therapeutics. Optimizing mRNA yield and ensuring product quality, such as capping efficiency and integrity, are essential but mechanistically…
A wide range of applications and research has been done with genome-scale metabolic models. In this work we describe a methodology for comparing metabolic networks constructed from genome-scale metabolic models and how to apply this…
Background: Nowadays, the reconstruction of genome scale metabolic models is a non-automatized and interactive process based on decision taking. This lengthy process usually requires a full year of one person's work in order to satisfactory…
In this contribution, a design of a synthetic calibration genetic circuit to characterize the relative strength of different sensing promoters is proposed and its specifications and performance are analyzed via an effective mathematical…
For a biological system to grow and expand, mass must be transferred from the environment to the system and be assimilated into its reaction network. Here, I characterize the biomass transfer process for growing autocatalytic systems. By…
Control of transcription presides over a vast array of biological processes, including those mediated by gene regulatory circuits that exhibit multistability. Within these circuits, two- and three-gene network motifs are particularly…
Both natural and synthetic chemical systems not only exhibit a range of non-trivial dynamics, but also transition between qualitatively different dynamical behaviours as environmental parameters change. Such transitions are called…
Zero-one reaction networks are pivotal to cellular signaling, and establishing the equivalence of such networks represents a foundational computational challenge in the realm of chemical reaction network research. Herein, we propose a…
The BioModels database is one of the premier databases for computational models in systems biology. The database contains over 1000 curated models and an even larger number of non-curated models. All the models are stored in the…
Metabolic diseases such as type 2 diabetes and obesity represent a rapidly escalating global health burden, yet current therapeutic strategies largely target isolated symptoms or single molecular pathways. To this end, we developed an…
Perturbation screens hold the potential to systematically map regulatory processes at single-cell resolution, yet modeling and predicting transcriptome-wide responses to perturbations remains a major computational challenge. Existing…
The complexity of molecular and cellular processes forces experimental studies to focus on subsystems. To study the functioning of biological systems across levels of structural and functional organisation, we require tools to compose and…
Biochemical signaling cascades transmit intracellular information while dissipating energy under nonequilibrium conditions. We model a cascade as a code string and apply information-entropy ideas to quantify an optimal transmission rate. A…
G-protein-coupled receptors (GPCRs) are central to cellular information processing, yet the physical principles governing their switching behavior remain incompletely understood. We present a first principles theoretical framework, grounded…
Gene regulatory networks are typically modeled using ordinary differential equations (ODEs) with phenomenological Hill functions to represent transcriptional regulation. While computationally efficient, Hill functions lack mechanistic…
Cellular decision-making under stress involves rapid pathway selection despite energy scarcity. Here we demonstrate that thermodynamic constraints actively drive energy-efficient sporulation, where continuous metabolic sources enable system…
The ribosome flow model (RFM) is a phenomenological model for the unidirectional flow of particles along a 1D chain of $n$ sites. The RFM has been extensively used to study the dynamics of ribosome flow along a single mRNA molecule during…
A hallmark of aging is loss of information in gene regulatory networks. These networks are tightly connected, raising the question of whether information could be restored by perturbing single genes. We develop a simple theoretical…