分子网络
Cells regulate fates and complex body plans using spatiotemporal signaling cascades that alter gene expression. Enhancers, short DNA sequences (50-150 base pairs), help coordinate these cascades by attracting regulatory proteins to enhance…
We introduce a new model of \emph{step} Chemical Reaction Networks (step CRNs), motivated by the step-wise addition of materials in standard lab procedures. Step CRNs have ordered reactants that transform into products via reaction rules…
To successfully navigate chemical gradients, microorganisms need to predict how the ligand concentration changes in space. Due to their limited size, they do not take a spatial derivative over their body length but rather a temporal…
Ordered distributive double phosphorylation is a recurrent motif in intracellular signaling and control. It is either sequential (where the site phosphorylated last is dephosphorylated first) or cyclic (where the site phosphorylated first…
The strategic induction of cell death serves as a crucial immune defense mechanism for the eradication of pathogenic infections within host cells. Investigating the molecular mechanisms underlying immunogenic cell pathways has significantly…
Stochastic oscillations in individual cells are usually characterized by a non-monotonic power spectrum with an oscillatory autocorrelation function. Here we develop an analytical approach of stochastic oscillations in a minimal hybrid…
Isolated sarcoplasmic reticulum vesicles in the presence of Mg(2+) and absence of Ca(2+) retain significant ATP hydrolytic activity that can be attributed to the Ca(2+)-ATPase protein. At neutral pH and the presence of 5 mM Mg(2+), the…
Sarcoplasmic reticulum vesicles and purified Ca$^{2+}$-ATPase hydrolyze acetyl phosphate both in the presence and absence of Ca$^{2+}$. The Ca$^{2+}$-independent activity was fully sensitive to vanadate, insensitive to thapsigargin, and…
The enormous diversity of life forms thriving in drastically different environmental milieus involves a complex interplay among constituent proteins interacting with each other. However, the organizational principles characterizing the…
Nearly all circadian clocks maintain a period that is insensitive to temperature changes, a phenomenon known as temperature compensation (TC). Yet, it is unclear whether there is any common feature among different systems that exhibit TC.…
We introduce a biologically detailed, stochastic model of gene expression describing the multiple rate-limiting steps of transcription, nuclear pre-mRNA processing, nuclear mRNA export, cytoplasmic mRNA degradation and translation of mRNA…
Gene expression levels carry information about signals that have functional significance for the organism. Using the gap gene network in the fruit fly embryo as an example, we show how this information can be decoded, building a dictionary…
Boolean networks have been widely used to explore aspects of gene regulation, traditionally with a single network. A modified form of the model to explore the effects of increasing the number of gene states has also recently been…
Correlation is not causation. As simple as this widely agreed-upon statement may seem, scientifically defining causality and using it to drive our modern biomedical research is immensely challenging. In this perspective, we attempt to…
Gene regulatory networks (GRNs) play a central role in cellular decision-making. Understanding their structure and how it impacts their dynamics constitutes thus a fundamental biological question. GRNs are frequently modeled as Boolean…
N6-methyladenosine (m6A) is the most abundant mRNA modification within mammalian cells, holding pivotal significance in the regulation of mRNA stability, translation, and splicing. Furthermore, it plays a critical role in the regulation of…
The metabolic network plays a crucial role in regulating bacterial metabolism and growth, but it is subject to inherent molecular stochasticity. Previous studies have utilized flux balance analysis and the maximum entropy method to predict…
During photoheterotrophic growth on organic substrates, purple nonsulfur photosynthetic bacteria like Rhodospirillum rubrum can acquire electrons by multiple means, including oxidation of organic substrates, oxidation of inorganic electron…
The method developed by Michaelis and Menten was foundational in the development of our understanding of biochemical reaction kinetics. Extended models of metabolism encapsulated by reaction rate theory, stochastic reaction models, and…
Molecular property prediction refers to the task of labeling molecules with some biochemical properties, playing a pivotal role in the drug discovery and design process. Recently, with the advancement of machine learning, deep…