Related papers: Dissecting the Specificity of Protein-Protein Inte…
Concurrent with advancements in molecular communication (MC), bacterial communication is emerging as a key area of interest. Given the frequent use of bacteria in various MC models, it is essential to have a thorough grasp of their…
Microorganisms are found in almost every environment, including the soil, water, air, and inside other organisms, like animals and plants. While some microorganisms cause diseases, most of them help in biological processes such as…
The exchange of small molecular signals within microbial populations is generally referred to as quorum sensing (QS). QS is ubiquitous in nature and enables microorganisms to respond to fluctuations in living environments by working…
Electrochemical communication is a mechanism that enables intercellular interaction among bacteria within communities. Bacteria achieves synchronization and coordinates collective actions at the population level through the utilization of…
Signalling pathways are abstractions that help life scientists structure the coordination of cellular activity. Cross-talk between pathways accounts for many of the complex behaviours exhibited by signalling pathways and is often critical…
Predicting the critical temperature $T_c$ of new superconductors is a notoriously difficult task, even for electron-phonon paired superconductors for which the theory is relatively well understood. Early attempts by McMillan and Allen and…
Protein interaction networks (PIN) are popular means to visualize the proteome. However, PIN datasets are known to be noisy, incomplete and biased by the experimental protocols used to detect protein interactions. This paper aims at…
The dynamics of many microbial ecosystems are driven by cross-feeding interactions, in which metabolites excreted by some species are metabolised further by others. The population dynamics of such ecosystems are governed by…
The evolutionary reason for the increase in gene length from archaea to prokaryotes to eukaryotes observed in large scale genome sequencing efforts has been unclear. We propose here that the increasing complexity of protein-protein…
Specific elements of viral genomes regulate interactions within host cells. Here, we calculated the secondary structure content of >2500 coronaviruses and computed >100000 human protein interactions with severe acute respiratory syndrome…
Protein-protein interactions (PPIs) are crucial in regulating numerous cellular functions, including signal transduction, transportation, and immune defense. As the accuracy of multi-chain protein complex structure prediction improves, the…
The interactions between DNA, RNA, and proteins are fundamental to biological processes, as illustrated by the central dogma of molecular biology. Although modern biological pre-trained models have achieved great success in analyzing these…
The native conformation of structured proteins is stabilized by a complex network of interactions. We analyzed the elementary patterns that constitute such network and ranked them according to their importance in shaping protein sequence…
Central to understanding membrane bound cell signaling is to quantify how the membrane ultra-structure consisting of transient spatial domains modulates signaling and how the signaling influences this ultra-structure. Yet, measuring the…
Recent research on predicting the binding affinity between drug molecules and proteins use representations learned, through unsupervised learning techniques, from large databases of molecule SMILES and protein sequences. While these…
Membrane proteins deform the surrounding lipid bilayer, which can lead to membrane-mediated interactions between neighboring proteins. Using the mechanosensitive channel of large conductance (MscL) as a model system, we demonstrate how the…
This paper studies a multiple-input multiple-output (MIMO) orthogonal frequency division multiplexing (OFDM) networked integrated sensing and communication (ISAC) system, in which multiple base stations (BSs) perform beam tracking to…
Understanding protein sequences is vital and urgent for biology, healthcare, and medicine. Labeling approaches are expensive yet time-consuming, while the amount of unlabeled data is increasing quite faster than that of the labeled data due…
A major part of membrane function is conducted by proteins, both integral and peripheral. Peripheral membrane proteins temporarily adhere to biological membranes, either to the lipid bilayer or to integral membrane proteins with…
Identifying causal relationships is a challenging yet crucial problem in many fields of science like epidemiology, climatology, ecology, genomics, economics and neuroscience, to mention only a few. Recent studies have demonstrated that…