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Two distinct families of pan-primate endogenous retroviruses, namely HERVL and HERVH, infected primates germline, colonized host genomes, and evolved into the global retroviral genomic regulatory dominion (GRD) operating during human…
We present a thorough inspection of the dynamical behavior of epidemic phenomena in populations with complex and heterogeneous connectivity patterns. We show that the growth of the epidemic prevalence is virtually instantaneous in all…
Living systems rely on coordinated molecular interactions, especially those related to gene expression and protein activity. The Unfolded Protein Response is a crucial mechanism in eukaryotic cells, activated when unfolded proteins exceed a…
During the last decade, network approaches became a powerful tool to describe protein structure and dynamics. Here, we describe first the protein structure networks of molecular chaperones, then characterize chaperone containing…
Viral hepatitis is the regularly found health problem throughout the world among other easily transmitted diseases, such as tuberculosis, human immune virus, malaria and so on. Among all hepatitis viruses, the uppermost numbers of deaths…
Understanding the dynamical behavior of complex systems from their underlying network architectures is a long-standing question in complexity theory. Therefore, many metrics have been devised to extract network features like motifs,…
Virus trafficking is fundamental for infection success and plasmid cytosolic trafficking is a key step of gene delivery. Based on the main physical properties of the cellular transport machinery such as microtubules, motor proteins, our…
We argue that immune system is an adaptive complex system. It is shown that it has emergent properties. Its network structure is of the small world network type. The network is of the threshold type, which helps in avoiding autoimmunity. It…
CoV2019 has evolved to be much more dangerous than CoV2003. Experiments suggest that structural rearrangements dramatically enhance CoV2019 activity. We identify a new first stage of infection that precedes structural rearrangements by…
A reaction network is a chemical system involving multiple reactions and chemical species. Stochastic models of such networks treat the system as a continuous time Markov chain on the number of molecules of each species with reactions as…
At most 1-2% of the global virome has been sampled to date. Recent work has shown that predicting which host-virus interactions are possible but undiscovered or unrealized is, fundamentally, a network science problem. Here, we develop a…
The understanding of molecular cell biology requires insight into the structure and dynamics of networks that are made up of thousands of interacting molecules of DNA, RNA, proteins, metabolites, and other components. One of the central…
Emerging evidence shows that the modular organization of the human brain allows for better and efficient cognitive performance. Many of these cognitive functions are very fast and occur in subsecond time scale such as the visual object…
Incorporating social factors into disease prevention and control efforts is an important undertaking of behavioral epidemiology. The interplay between disease transmission and human health behaviors, such as vaccine uptake, results in…
This paper describes a novel approach to modeling homphily, i.e. the tendency of nodes that share (or differ in) certain attributes to be linked; we consider dynamic networks in which nodes can be added over time but not removed. Our…
We numerically study a dynamical system model of an idiotypic immune network with a small number of degrees of freedom. The model was originally introduced by Varela et.al., and describes antibodies interacting in a body in order to prepare…
Cell signaling networks are complex and often incompletely characterized, making it difficult to obtain a comprehensive picture of the mechanisms they encode. Mathematical modeling of these networks provides important clues, but the models…
The ability of the adaptive immune system to respond to arbitrary pathogens stems from the broad diversity of immune cell surface receptors (TCRs). This diversity originates in a stochastic DNA editing process (VDJ recombination) that acts…
Recently there has been a lot of interest in identifying modules at the level of genetic and metabolic networks of organisms, as well as in identifying single genes and reactions that are essential for the organism. A goal of computational…
In complex systems, we often observe complex global behavior emerge from a collection of agents interacting with each other in their environment, with each individual agent acting only on locally available information, without knowing the…