Related papers: What Omicron Does, and How It Does It
Models of codon evolution are commonly used to identify positive selection. Positive selection is typically a heterogeneous process, i.e., it acts on some branches of the evolutionary tree and not others. Previous work on DNA models showed…
Voluntary vaccination is effective to prevent infectious diseases from spreading. Both vaccination behavior and cognition of the vaccination risk play important roles in individual vaccination decision making. However, it is not clear how…
Humans, domestic animals, orchard crops, and ornamental plants are commonly treated with antibiotics in response to bacterial infection. By curing infectious individuals, antibiotic therapy might limit the spread of contagious disease among…
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…
Computer modelling for evolutionary systems consists in: 1) to store in the memory the individual features of each member of a large population; and 2) to update the whole system repeatedly, as time goes by, according to some prescribed…
The interaction between natural selection and random mutation is frequently debated in recent years. Does similar dilemma also exist in the evolution of real networks such as biological networks? In this paper, we try to discuss this issue…
The evolution of many microbes and pathogens, including circulating viruses such as seasonal influenza, is driven by immune pressure from the host population. In turn, the immune systems of infected populations get updated, chasing viruses…
SARS-CoV-2, the highly contagious pathogen responsible for the COVID-19 pandemic, has persistent effects that begin four weeks after initial infection and last for an undetermined duration. These chronic effects are more harmful than acute…
With the unprecedented global vaccination campaign against SARS-CoV-2 attention has now turned to the potential impact of this large-scale intervention on the evolution of the virus. In this perspective we summarize what is currently known…
SARS-CoV-2, like any other virus, continues to mutate as it spreads, according to an evolutionary process. Unlike any other virus, the number of currently available sequences of SARS-CoV-2 in public databases such as GISAID is already…
We explore the inclusion of vaccination in compartmental epidemiological models concerning the delta and omicron variants of the SARS-CoV-2 virus that caused the COVID-19 pandemic. We expand on our earlier compartmental-model work by…
The origin of altruistic behavior, i.e. the behavior that is useful for a population or a species but goes at the expense of an altruistic individual, has long been a challenge for students of evolutionary biology. The populations with…
Mechanisms of immunity, and of the host-pathogen interactions in general are among the most fundamental problems of medicine, ecology, and evolution studies. Here, we present a microscopic, protein-level, sequence-based model of immune…
At the end of 2020, policy responses to the SARS-CoV-2 outbreak have been shaken by the emergence of virus variants, impacting public health and policy measures worldwide. The emergence of these strains suspected to be more contagious, more…
Influenza viruses undergo continual antigenic evolution allowing mutant viruses to evade host immunity acquired to previous virus strains. Antigenic phenotype is often assessed through pairwise measurement of cross-reactivity between…
According to the Baldwin Effect learning can guide evolution. This does not suppose that information about what has been learned is transferred back into the genetic code: in the Baldwin Effect complex multi-gene characteristics are…
The problem of the directionality of genome evolution is studied from the information-theoretic view. We propose that the function-coding information quantity of a genome always grows in the course of evolution through sequence duplication,…
In light of the continuing emergence of new SARS-CoV-2 variants and vaccines, we create a simulation framework for exploring possible infection trajectories under various scenarios. The situations of primary interest involve the interaction…
The evolution of complexity has been a central theme for Biology [2] and Artificial Life research [1]. It is generally agreed that complexity has increased in our universe, giving way to life, multi-cellularity, societies, and systems of…
There is overwhelming evidence that human intelligence is a product of Darwinian evolution. Investigating the consequences of self-modification, and more precisely, the consequences of utility function self-modification, leads to the…