Molecular Networks
There is an unmet need to develop medications or drug combinations which can stop advancement of NASH to liver cirrhosis and HCC. Therefore, identifying key biomarkers based on overall survival and the exploring biological processes…
Chronic Hepatitis B (CHB) is an independent risk factor for hepatocellular carcinoma (HCC) initiation without cirrhosis occurrence. Apart from the favorable effects of some antiviral drugs following tumor resection on the survival of HCC…
The last decade has witnessed a surge of theoretical and computational models to describe the dynamics of complex gene regulatory networks, and how these interactions can give rise to multistable and heterogeneous cell populations. As the…
To facilitate a rapid response to pandemic threats, this paper focuses on developing a mechanistic simulation model for in vitro transcription (IVT) process, a crucial step in mRNA vaccine manufacturing. To enhance production and support…
The BReast CAncer type 2 susceptibility protein (BRCA2) responds to DNA damage by participating in homology-directed repair. BRCA2 deficiency culminates in defective DNA damage repair (DDR) that when prolonged leads to the accumulation of…
RNA structure and functional dynamics play fundamental roles in controlling biological systems. Molecular dynamics simulation, which can characterize interactions at an atomistic level, can advance the understanding on new drug discovery,…
The stochastic kinetics of BRN are described by a chemical master equation (CME) and the underlying laws of mass action. The CME must be usually solved numerically by generating enough traces of random reaction events. The resulting…
External flows of energy, entropy, and matter can cause sudden transitions in the stability of biological and industrial systems, fundamentally altering their dynamical function. How might we control and design these transitions in chemical…
Compartmentalised biochemical reactions are a ubiquitous building block of biological systems. The interplay between chemical and compartmental dynamics can drive rich and complex dynamical behaviors that are difficult to analyse…
The issue of reproducibility of computational models and the related FAIR principles (findable, accessible, interoperable, and reusable) are examined in a specific test case. I analyze a computational model of the segment polarity network…
The Kauffman model is the archetypal model of genetic computation. It highlights the importance of criticality, at which many biological systems seem poised. In a series of advances, researchers have honed in on how the number of attractors…
Switch-like motifs are among the basic building blocks of biochemical networks. A common motif that can serve as an ultrasensitive switch consists of two enzymes acting antagonistically on a substrate, one making and the other removing a…
Cancer is a systemic heterogeneous disease involving complex molecular networks. Tumor formation involves epithelial-mesenchymal transition (EMT), which promotes both metastasis and plasticity of cancer cells. Recent experiments proposed…
The physical interpretation of the functioning of the adaptive immune system, which has been thoroughly characterized on genetic and molecular levels, provides a unique opportunity to define an adaptive self-organizing biological system in…
Protein-protein interactions (PPIs) are crucial in various biological processes and their study has significant implications for drug development and disease diagnosis. Existing deep learning methods suffer from significant performance…
Identifying potential drug targets using metabolic modeling requires integrating multiple modeling methods and heterogenous biological datasets, which can be challenging without sophisticated tools. We developed COMO, a user-friendly…
We consider a generic class of gene circuits affected by nonlinear extrinsic noise. To address this nonlinearity we introduce a general perturbative methodology based on assuming timescale separation between noise and genes dynamics, with…
Switch-like responses arising from bistability have been linked to cell signaling processes and memory. Revealing the shape and properties of the set of parameters that lead to bistability is necessary to understand the underlying…
Biological cells encode information about their environment through biochemical signaling networks that control their internal state and response. This information is often encoded in the dynamical patterns of the signaling molecules,…
Given the large size and complexity of most biochemical regulation and signaling networks, there is a non-trivial relationship between the micro-level logic of component interactions and the observed macro-dynamics. Here we address this…