Related papers: The Lipid Interactome: An interactive and open acc…
The protein-protein interaction (PPI) network provides an overview of the complex biological reactions vital to an organism's metabolism and survival. Even though in the past PPI network were compared across organisms in detail, there has…
Motivation: Protein-protein interactions (PPI) are critical to the function of proteins in both normal and diseased cells, and many critical protein functions are mediated by interactions.Knowledge of the nature of these interactions is…
Understanding how molecular alterations propagate across biological systems to drive disease remains a central challenge. Although high-throughput profiling enables comprehensive characterization of tumor states, most models neglect…
The study presents a novel approach for quantifying cellular interactions in digital pathology using deep learning-based image cytometry. Traditional methods struggle with the diversity and heterogeneity of cells within tissues. To address…
Motivation: Protein interactions are fundamental building blocks of biochemical reaction systems underlying cellular functions. The complexity and functionality of such systems emerge not from the protein interactions themselves but from…
Random lateral translocation of lipids and proteins is a universal process on membrane surfaces. Local aggregation or organization of lipids and proteins can be induced when this lateral random diffusion is mediated by the electrostatic…
Topological analysis of large scale protein-protein interaction networks (PINs) is important for understanding the organisational and functional principles of individual proteins. The number of interactions that a protein has in a PIN has…
Knowledge about protein-protein interactions is essential in understanding the biological processes such as metabolic pathways, DNA replication, and transcription etc. However, a majority of the existing Protein-Protein Interaction (PPI)…
Response of lipid bilayers to external mechanical stimuli is an active area of research with implications for fundamental and synthetic cell biology. However, there is a lack of tools for systematically imposing mechanical strains and…
Specific lipid environments are necessary for the establishment of protein signalling platforms in membranes, yet their origin has been highly debated. We present a continuum, exactly solvable model of protein induced local demixing of…
The organization of lipids in biological membranes is essential for cellular functions such as signal transduction and membrane trafficking. A major challenge is how to control lateral lipid composition in supported membranes which are…
Functional protein-protein interactions are crucial in most cellular processes. They enable multi-protein complexes to assemble and to remain stable, and they allow signal transduction in various pathways. Functional interactions between…
Water-phospholipid interactions at the lipid bilayer/water interfaces are of essential importance for the dynamics, stability and function of biological membrane, and are also strongly associated with numerous biological processes at the…
Proteins perform their functions usually by interacting with other proteins. Predicting which proteins interact is a fundamental problem. Experimental methods are slow, expensive, and have a high rate of error. Many computational methods…
Protein-peptide interactions play essential functional roles in living organisms and their structural characterization is a hot subject of current experimental and theoretical research. Computational modeling of the structure of…
Network theorists have developed methods to characterize the complex interactions in natural phenomena. The structure of the network of interactions between proteins is important in the field of proteomics, and has been subject to intensive…
Cellular function is widely believed to be organized in a modular fashion. On all scales and at all levels of complexity, relatively independent sub-units perform relatively independent sub-tasks of biological function. This functional…
Interactive visualization tools are highly desirable to biologist and cancer researchers to explore the complex structures, detect patterns and find out the relationships among bio-molecules responsible for a cancer type. A pathway contains…
Biological membranes are known to form various structural motifs, from lipid bilayers to tubular filaments and networks facilitating e.g. adhesion and cell-cell communication. To understand the biophysical processes underpinning lipid-lipid…
How do living cells achieve sufficient abundances of functional protein complexes while minimizing promiscuous non-functional interactions? Here we study this problem using a first-principle model of the cell whose phenotypic traits are…