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The vast majority of mutations are deleterious, and are eliminated by purifying selection. Yet in finite asexual populations, purifying selection cannot completely prevent the accumulation of deleterious mutations due to Muller's ratchet:…
Tumor development is an evolutionary process in which a heterogeneous population of cells with differential growth capabilities compete for resources in order to gain a proliferative advantage. What are the minimal ingredients needed to…
Predicting the adaptation of populations to a changing environment is crucial to assess the impact of human activities on biodiversity. Many theoretical studies have tackled this issue by modeling the evolution of quantitative traits…
This study presents the first global, 1 Mbp level analysis of patterns of nucleotide substitutions along the human lineage. The study is based on the analysis of a large amount of repetitive elements deposited into the human genome since…
Due to the asymmetric nature of the nucleotides, the extant informational biomolecule, DNA, is constrained to replicate unidirectionally on a template. As a product of molecular evolution that sought to maximize replicative potential, DNA's…
In classical evolutionary theory, genetic variation provides the source of heritable phenotypic variation on which natural selection acts. Against this classical view, several theories have emphasized that developmental variability and…
From the experimental data on odd-even staggering of masses, we have shown that variation of pairing as a function of neutron number plays an important role in many distinctive features like occurrence of new shell closures, shell erosion,…
The majority of cancer treatments end in failure due to Intra-Tumor Heterogeneity (ITH). ITH in cancer is represented by clonal evolution where different sub-clones compete with each other for resources under conditions of Darwinian natural…
Immunotherapy has recently shown important clinical successes in a substantial number of oncology indications. Additionally, the tumor somatic mutation load has been shown to associate with response to these therapeutic agents, and specific…
We examine neutrino evolution in astrophysical environments where the neutrino flux is very large, including core-collapse supernovae and neutron star mergers. In these environments, the neutrino-neutrino and neutrino-antineutrino…
BACKGROUND: Many of the mutations accumulated by naturally evolving proteins are neutral in the sense that they do not significantly alter a protein's ability to perform its primary biological function. However, new protein functions evolve…
A tumor can be thought of as an ecosystem, which critically means that we cannot just consider it as a collection of mutated cells but more as a complex system of many interacting cellular and microenvironmental elements. At its simplest, a…
Regulatory networks consist of interacting molecules with a high degree of mutual chemical specificity. How can these molecules evolve when their function depends on maintenance of interactions with cognate partners and simultaneous…
Majority of Artificial Neural Network (ANN) implementations in autonomous systems use a fixed/user-prescribed network topology, leading to sub-optimal performance and low portability. The existing neuro-evolution of augmenting topology or…
Most non-synonymous mutations are thought to be deleterious because of their effect on protein sequence. These polymorphisms are expected to be removed or kept at low frequency by the action of natural selection, and rare deleterious…
Positive selection distorts the structure of genealogies and hence alters patterns of genetic variation within a population. Most analyses of these distortions focus on the signatures of hitchhiking due to hard or soft selective sweeps at a…
Cells regulate fates and complex body plans using spatiotemporal signaling cascades that alter gene expression. Enhancers, short DNA sequences (50-150 base pairs), help coordinate these cascades by attracting regulatory proteins to enhance…
The ability to absorb mutations while retaining structure and function, or mutational robustness, is a remarkable property of natural proteins. In this Letter, we use a computational model of organismic evolution [Zeldovich et al, PLOS Comp…
We model and discuss advantages of pan-editing, the complex way of expressing mitochondrial genes in kinetoplastids. The rapid spread and preservation of pan-editing seems to be due to its concomitant fragment dispersal. Such dispersal…
In many biological systems, natural selection acts simultaneously on multiple levels of organization. This scenario typically presents an evolutionary conflict between the incentive of individuals to cheat and the collective incentive to…