Molecular Networks
The Gillespie algorithm and its extensions are commonly used for the simulation of chemical reaction networks. A limitation of these algorithms is that they have to process and update the system after every reaction, requiring significant…
Antiterminators are essential components of bacterial transcriptional regulation, allowing the control of gene expression in response to fluctuating environmental conditions. Among them, RNA-binding antiterminator proteins play a major role…
Dynamic Flux Balance Analysis (dFBA) extends the capabilities of FBA to track changes in metabolite concentrations and fluxes over time in response to environmental conditions and cellular processes. The key idea of the method called…
The dynamics of gene regulatory networks is governed by the interaction between deterministic biochemical reactions and molecular noise. To understand how gene regulatory networks process information during cell state transitions, we study…
Deciphering complex gene-gene interactions remains challenging in transcriptomics as traditional methods often miss higher-order and nonlinear dependencies. This study introduces a quantum-inspired framework leveraging tensor networks (TNs)…
Competitive inhibitors can, paradoxically, stimulate an enzymatic reaction at low to moderate doses. Competitive inhibition of an enzyme occurs when an inhibitor binds to the enzyme's binding site and blocks the enzyme's target molecule…
miRNA mRNA relations are closely linked to several biological processes and disease mechanisms In a recent study we tested the performance of large language models LLMs on extracting miRNA mRNA relations from PubMed PubMedBERT achieved the…
Despite the thousands of genes implicated in age-related phenotypes, effective interventions for aging remain elusive, a lack of advance rooted in the multifactorial nature of longevity and the functional interconnectedness of the molecular…
Understanding the modular structure and central elements of complex biological networks is critical for uncovering system-level mechanisms in disease. Here, we constructed weighted gene co-expression networks from bulk RNA-seq data of…
Stochastic systems have a control-theoretic interpretation in which noise plays the role of control. In the weak-noise limit, relevant at low temperatures or in large populations, this leads to a precise mathematical mapping: the most…
Efficient information processing is crucial for both living organisms and engineered systems. The mutual information rate, a core concept of information theory, quantifies the amount of information shared between the trajectories of input…
We propose a direct optimization framework for learning reduced and sparse chemical reaction networks (CRNs) from time-series trajectory data. In contrast to widely used indirect methods-such as those based on sparse identification of…
Cancer research has traditionally focused on identifying driver genes, those with mutations that initiate tumorigenesis. The Cancer Driver Gene (CDG) paradigm, further supported by the observation of oncogene addiction in tumors, has…
Objective: To investigate the mechanism by which quercetin inhibits triple-negative breast cancer (TNBC) through regulating T-cell-related targets, providing a novel strategy for TNBC immunotherapy.Methods: Single-cell RNA sequencing…
Understanding the complex and stochastic nature of Gene Regulatory Networks (GRNs) remains a central challenge in systems biology. Existing modeling paradigms often struggle to effectively capture the intricate, multi-factor regulatory…
Biological organisms are simple at heart: cells, their basic units, perform a variety of behaviors by expressing proteins from DNA-encoded genes. Gene expression though depends on sets of often-convoluted regulatory interactions known as…
Cancer is recognized as a complex group of diseases, contributing to the highest global mortality rates, with increasing prevalence and a trend toward affecting younger populations. It is characterized by uncontrolled proliferation of…
Cell phenotype dynamic homeostasis contrasts with the inherent randomness of intracellular reactions. Although feedback control of master regulatory genes (MRG) is a key strategy for maintaining gene network expression ranges limited,…
Intellectual disability (ID) is defined by an IQ under 70, in addition to deficits in two or more adaptive behaviors that affect everyday living. Throughout history, individuals with ID have often been margin-alized from society and…
Understanding the molecular-level mechanisms underpinning Alzheimer's disease (AD) by studying crucial genes associated with the disease remains a challenge. Alzheimer's, being a multifactorial disease, requires understanding the gene-gene…