Related papers: Extreme antagonism arising from gene-environment i…
Gene-environment interactions have important implications to elucidate the genetic basis of complex diseases beyond the joint function of multiple genetic factors and their interactions (or epistasis). In the past, G$\times$E interactions…
For complex diseases, the interactions between genetic and environmental risk factors can have important implications beyond the main effects. Many of the existing interaction analyses conduct marginal analysis and cannot accommodate the…
For complex diseases, beyond the main effects of genetic (G) and environmental (E) factors, gene-environment (G-E) interactions also play an important role. Many of the existing G-E interaction methods conduct marginal analysis, which may…
Epistasis describes the phenomenon that mutations at different loci do not have independent effects with regard to certain phenotypes. Understanding the global epistatic landscape is vital for many genetic and evolutionary theories. Current…
The contribution to an organism's phenotype from one genetic locus may depend upon the status of other loci. Such epistatic interactions among loci are now recognized as fundamental to shaping the process of adaptation in evolving…
Cognizance of gene-environment interactions may help prevent or detain the onset of complex diseases like cardiovascular disease, cancer, type2 diabetes, autism or asthma by adjustments to lifestyle. In this regard, we extend the Bayesian…
Beneficial reversals of dominance reduce the costs of genetic trade-offs and can enable selection to maintain genetic variation for fitness. Beneficial dominance reversals are characterized by the beneficial allele for a given context (e.g.…
Living organisms must respond to environmental changes. Generally, accurate and rapid responses are provided by simple, unidirectional networks that connect inputs with outputs. Besides accuracy and speed, biological responses should also…
Recent research shows that a faulty or sub-optimally operating metabolic network can often be rescued by the targeted removal of enzyme-coding genes--the exact opposite of what traditional gene therapy would suggest. Predictions go as far…
For many complex diseases, prognosis is of essential importance. It has been shown that, beyond the main effects of genetic (G) and environmental (E) risk factors, the gene-environment (G$\times$E) interactions also play a critical role. In…
Gene-knockout experiments on single-cell organisms have established that expression of a substantial fraction of genes is not needed for optimal growth. This problem acquired a new dimension with the recent discovery that environmental and…
For the etiology, progression, and treatment of complex diseases, gene-environment (G-E) interactions have important implications beyond the main G and E effects. G-E interaction analysis can be more challenging with the higher…
We consider a simple information-theoretic model of communication, in which two species of bacteria have the option of exchanging information about their environment, thereby improving their chances of survival. For this purpose, we model a…
Ecology and evolution under changing environments are important in many subfields of biology with implications for medicine. Here, we explore an example: the consequences of fluctuating environments on the emergence of antibiotic…
Biological evolution of a population is governed by the fitness landscape, which is a map from genotype to fitness. However, a fitness landscape depends on the organisms environment, and evolution in changing environments is still poorly…
Approaches to gene interactions based on sign epistasis have been highly influential in recent time. Sign epistasis is useful for relating local and global properties of fitness landscapes, as well as for analyzing evolutionary trajectories…
Adaptation is a central topic in theoretical biology, of practical importance for analyzing drug resistance mutations. Several authors have used arguments based on extreme value theory in their work on adaptation. There are complications…
Feedback in cellular processes is typically inferred through cellular responses to experimental perturbations. Modular response analysis provides a theoretical framework for translating specific perturbations into feedback sensitivities…
An organism that is newly introduced into an existing population has a survival probability that is dependent on both the population density of its environment and the competition it experiences with the members of that population.…
The statistical properties of an ecosystem composed of species interacting via pairwise, random interactions and deterministic, concentration limiting self-interaction are studied analytically with tools of equilibrium statistical mechanics…