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The repertoire of lymphocyte receptors in the adaptive immune system protects organisms from diverse pathogens. A well-adapted repertoire should be tuned to the pathogenic environment to reduce the cost of infections. We develop a general…
In order to target threatening pathogens, the adaptive immune system performs a continuous reorganization of its lymphocyte repertoire. Following an immune challenge, the B cell repertoire can evolve cells of increased specificity for the…
Prion and prion-like molecules are a type of self replicating aggregate protein that have been implicated in a variety of neurodegenerative diseases. Over recent decades the molecular dynamics of prions have been characterized both…
Microbiota contribute to many dimensions of host phenotype, including disease. To link specific microbes to specific phenotypes, microbiome-wide association studies compare microbial abundances between two groups of samples. Abundance…
Detection of protein-protein interactions (PPIs) plays a vital role in molecular biology. Particularly, infections are caused by the interactions of host and pathogen proteins. It is important to identify host-pathogen interactions (HPIs)…
Partner selection is an important process in many social interactions, permitting individuals to decrease the risks associated with cooperation. In large populations, defectors may escape punishment by roving from partner to partner, but…
Human pathogens transmitted through environmental pathways are subject to stress and pressures outside of the host. These pressures may cause pathogen pathovars to diverge in their environmental persistence and their infectivity on an…
Proteins participating in a protein-protein interaction network can be grouped into homology classes following their common ancestry. Proteins added to the network correspond to genes added to the classes, so that the dynamics of the two…
In light of the rise of malicious attacks on the Internet, and the various networks and applications attached to it, new approaches towards modeling predatory activity in networks could be useful. Past research has simulated networks…
Antagonistic coevolution between hosts and parasites can have a major impact on host population structures, and hence on the evolution of social traits. Using stochastic modelling techniques in the context of bacteria-virus interactions, we…
Higher-order phases are characterized by corner or hinge modes that arise due to the interesting interplay of localization mechanisms along two or more dimensions. In this work, we introduce and construct a novel class of "hybrid"…
In nature and human societies, the effects of homogeneous and heterogeneous characteristics on the evolution of collective behaviors are quite different from each other. It is of great importance to understand the underlying mechanisms of…
We study how the dynamic equilibrium of the reversible protein-protein binding network in yeast Saccharomyces cerevisiae responds to large changes in abundances of individual proteins. The magnitude of shifts between free and bound…
Homologous proteins have similar three-dimensional structures and biological functions that shape their sequences. The resulting coevolution-driven correlations underlie methods from Potts models to AlphaFold, which infer protein structure…
A hybrid phase transition (HPT) that exhibits properties of continuous and discontinuous phase transitions at the same transition point has been observed in diverse complex systems. Previous studies of the HPTs on complex networks mainly…
Biological and artificial networks routinely make reliable distinctions between similar inputs, and the rules for making these distinctions are learned. In some ways, self/nonself discrimination in the immune system is similar, being both…
More and more evidence shows that mating preference is a mechanism that may lead to a reproductive isolation event. In this paper, a haploid population living on two patches linked by migration is considered. Individuals are ecologically…
Phenotypic heterogeneity is a strategy commonly used by bacteria to rapidly adapt to changing environmental conditions. Here, we study the interplay between phenotypic heterogeneity and genetic diversity in spatially extended populations.…
We consider a predator-prey population model with prey gathering together for defense purposes. A transmissible unrecoverable disease affects the prey. We characterize the system behavior, establishing that ultimately either only the…
Anthropogenic activity threatens biodiversity through climate change, habitat fragmentation, and increasing frequency and scale of disturbance. Various theoretical studies have sought to shed light on how these factors could promote or…