Related papers: Centralized Modularity of N-Linked Glycosylation P…
Glycans are the most complex biological sequence, with monosaccharides forming extended, non-linear sequences. As post-translational modifications, they modulate protein structure, function, and interactions. Due to their diversity and…
A new approach to the modular, complex systems analysis of nonlinear dynamics in cell cycling network transformations involved in carcinogenesis is proposed. Carcinogenesis is a complex process that involves dynamically inter-connected…
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…
The colonic mucus layer is a dynamic and complex structure formed by secreted and transmembrane mucins, which are high-molecular-weight and heavily glycosylated proteins. Colonic mucus consists of a loose outer layer and a dense…
N-methyl-D-aspartate receptors (NMDARs) are glycoproteins in the brain central to learning and memory. The effects of glycosylation on the structure and dynamics of NMDARs are largely unknown. In this work, we use extensive molecular…
Glycans are tree-like polymers made up of sugar monomer building blocks. They are found on the surface of all living cells, and distinct glycan trees act as identity markers for distinct cell types. Proteins called GTase enzymes assemble…
Glycans are structurally diverse and flexible biomolecules that play key roles in many biological processes. Their conformational variability makes the modeling of their interactions with proteins particularly challenging. This chapter…
Cell signaling, gene expression, and metabolism are affected by cell-cell heterogeneity and random changes in the environment. The effects of such fluctuations on cell signaling and gene expression have recently been studied intensively…
Metabolic oscillations in single cells underlie the mechanisms behind cell synchronization and cell-cell communication. For example, glycolytic oscillations mediated by biochemical communication between cells may synchronize the pulsatile…
Proteins are the "work horses" in biological systems. In almost all functions specific proteins are involved. They control molecular transport processes, stabilize the cell structure, enzymatically catalyze chemical reactions; others act as…
Cell differentiation in multicellular organisms is a complex process whose mechanism can be understood by a reductionist approach, in which the individual processes that control the generation of different cell types are identified.…
Glycans are basic biomolecules and perform essential functions within living organisms. The rapid increase of functional glycan data provides a good opportunity for machine learning solutions to glycan understanding. However, there still…
Interconnected ensembles of biological entities are perhaps some of the most complex systems that modern science has encountered so far. In particular, scientists have concentrated on understanding how the complexity of the interacting…
The galactose network is a complex system responsible for galactose metabolism. It has been extensively studied experimentally and mathematically at the unicellular level to broaden our understanding of its regulatory mechanisms at higher…
The emerging field of immunometabolism has underscored the central role of metabolic pathways in orchestrating immune cell function. Far from being passive background processes, metabolic activities actively regulate key immune responses.…
The concept of control is crucial for effectively understanding and applying biological network models. Key structural features relate to control functions through gene regulation, signaling, or metabolic mechanisms, and computational…
Posttranslational modification of proteins is key in transmission of signals in cells. Many signaling pathways contain several layers of modification cycles that mediate and change the signal through the pathway. Here, we study a simple…
Introduction: To leverage functionality and clinical relevance into understanding systems biology, one needs to understand the pathway of the genetic effects on risk factors/disease through intermediate molecular levels, such as…
Biological organisms are composed of numerous interconnected biochemical processes. Diseases occur when normal functionality of these processes is disrupted. Thus, understanding these biochemical processes and their interrelationships is a…
Understanding the various properties of glycans with machine learning has shown some preliminary promise. However, previous methods mainly focused on modeling the backbone structure of glycans as graphs of monosaccharides (i.e., sugar…