Molecular Networks
Motivation: SBML is the most widespread language for the definition of biochemical models. Although dozens of SBML simulators are available, there is a general lack of support to the integration of SBML models within open-standard…
Gene regulation is an important fundamental biological process. The regulation of gene expression is managed through a variety of methods including epigenetic processes (e.g., DNA methylation). Understanding the role of epigenetic changes…
We review the development of thermodynamic protein hydropathic scaling theory, starting from backgrounds in mathematics and statistical mechanics, and leading to biomedical applications. Darwinian evolution has organized each protein family…
Prediction of node and graph labels are prominent network science tasks. Data analyzed in these tasks are sometimes related: entities represented by nodes in a higher-level (higher-scale) network can themselves be modeled as networks at a…
COVID-19 is an infection caused by SARS-CoV-2 (Severe Acute Respiratory Syndrome coronavirus 2), which has caused a global outbreak. Current research efforts are focused on the understanding of the molecular mechanisms involved in…
Homeostasis refers to a phenomenon whereby the output $x_o$ of a system is approximately constant on variation of an input $\mathcal{I}$. Homeostasis occurs frequently in biochemical networks and in other networks of interacting elements…
Biology offers many examples of large-scale, complex, concurrent systems: many processes take place in parallel, compete on resources and influence each other's behavior. The scalable modeling of biological systems continues to be a very…
Apoptosis is a mechanism of programmed cell death in which cells engage in a controlled demolition and prepare to be digested without damaging their environment. In normal conditions apoptosis is repressed, until it is irreversibly induced…
Protein structural classification (PSC) is a supervised problem of assigning proteins into pre-defined structural (e.g., CATH or SCOPe) classes based on the proteins' sequence or 3D structural features. We recently proposed PSC approaches…
MomentClosure.jl is a Julia package providing automated derivation of the time-evolution equations of the moments of molecule numbers for virtually any chemical reaction network using a wide range of moment closure approximations. It…
Chemical reaction networks (CRNs) are fundamental computational models used to study the behavior of chemical reactions in well-mixed solutions. They have been used extensively to model a broad range of biological systems, and are primarily…
Cold atmospheric plasma (CAP) and plasma-treated liquids (PTLs) have recently become a promising option for cancer treatment, but the underlying mechanisms of the anti-cancer effect are still to a large extent unknown. Although hydrogen…
Introduction: Crohn's disease and ulcerative colitis, both under the umbrella of inflammatory bowel diseases (IBD), involve many distinct molecular processes. The difference in their molecular processes is studied by using the different…
For many stochastic models of interest in systems biology, such as those describing biochemical reaction networks, exact quantification of parameter uncertainty through statistical inference is intractable. Likelihood-free computational…
A central goal of synthetic biology is the design of molecular controllers that can manipulate the dynamics of intracellular networks in a stable and accurate manner. To address the fact that detailed knowledge about intracellular networks…
Given the severity of the SARS-CoV-2 pandemic, a major challenge is to rapidly repurpose existing approved drugs for clinical interventions. While a number of data-driven and experimental approaches have been suggested in the context of…
Recently discovered simple quantitative relations, known as bacterial growth laws, hint on the existence of simple underlying principles at the heart of bacterial growth. In this work, we provide a unifying picture on how these known…
The critical role of energy consumption in biological systems including T cell discrimination process has been investigated in various ways. The kinetic proofreading(KPR) in T cell recognition involving different levels of energy…
Metabolic modeling strives to develop modeling approaches that are robust and highly predictive. To achieve this, various modeling designs, including hybrid models, and parameter estimation methods that define the type and number of…
Network analyses, such as of gene co-expression networks, metabolic networks and ecological networks have become a central approach for the systems-level study of biological data. Several software packages exist for generating and analyzing…