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Individual expression profiles from EBV transformed cell lines are an emerging resource for genomic investigation. In this study we characterize the effects of age, sex, and genetic variation on gene expression by surveying public datasets…
Unraveling the evolutionary forces shaping bacterial diversity can today be tackled using a growing amount of genomic data. While the genome of eukaryotes is highly stable, bacterial genomes from cells of the same species highly vary in…
The question of what determines genetic diversity both between and within species has long remained unsolved by the modern evolutionary theory (MET). However, it has not deterred researchers from producing interpretations of genetic…
Commonly recognized evolutionarily relevant effects of sexual reproduction include increased diversity, accelerated adaptation, and constrained accumulation of deleterious mutations, along with a secondary effect of species genotype…
Phylogenetic mixtures model the inhomogeneous molecular evolution commonly observed in data. The performance of phylogenetic reconstruction methods where the underlying data is generated by a mixture model has stimulated considerable recent…
Variability is ubiquitous in nature and a fundamental feature of complex systems. Few studies, however, have investigated variance itself as a trait under genetic control. By focusing primarily on trait means and ignoring the effect of…
Questions on possible relationship between phenotypic plasticity and evolvability, as well as that between robustness and evolution have been addressed over decades in the field of evolution-development. By introducing an evolutionary…
The biological world, especially its majority microbial component, is strongly interacting and may be dominated by collective effects. In this review, we provide a brief introduction for statistical physicists of the way in which living…
Phenotypic variation is a hallmark of cellular physiology. Metabolic heterogeneity, in particular, underpins single-cell phenomena such as microbial drug tolerance and growth variability. Much research has focussed on transcriptomic and…
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…
Cells often exhibit different and stable phenotypes from the same DNA sequence. Robustness and plasticity of such cellular states are controlled by diverse transcriptional and epigenetic mechanisms, among them the modification of…
In the field of evolutionary robotics, choosing the correct encoding is very complicated, especially when robots evolve both behaviours and morphologies at the same time. With the objective of improving our understanding of the mapping…
Many genetic mutations adversely affect the structure and function of load-bearing soft tissues, with clinical sequelae often responsible for disability or death. Parallel advances in genetics and histomechanical characterization provide…
Supplemental data for "Stochastic Gene Expression in a Lentiviral Positive Feedback Loop: HIV-1 Tat Fluctuations Drive Phenotypic Diversity" [q-bio.MN/0608002, Cell. 2005 Jul 29;122(2):169-82].
The current theory of evolution is almost the one Darwin and Wallace proposed two centuries ago and the following discoveries e.g., Mendelian genetics and neutral mutation theory have not made significant modifications. The current…
Chromosomal rearrangements, which shuffle DNA throughout the genome, are an important source of divergence across taxa. Using a paired-end read approach with Illumina sequence data for archaic humans, I identify changes in genome structure…
Heterozygote disadvantage is potentially a potent driver of population genetic divergence. Also referred to as underdominance, this phenomena describes a situation where a genetic heterozygote has a lower overall fitness than either…
In this short communication, we shall explore a nonlinear discrete dynamical system that naturally occurs in population systems to describe a transmission of a trait from parents to their offspring. We consider a Mendelian inheritance for a…
Development combines three basic processes asymmetric --- cell division, signaling and gene regulation --- in a multitude of ways to create an overwhelming diversity of multicellular life-forms. Here, we attempt to chart this diversity…
In the past decade, Genome-Wide Association Studies (GWAS) have delivered an increasingly broad view of the genetic basis of human phenotypic variation. One of the major developments from GWAS is polygenic scores, a genetic predictor of an…