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Supergenes are genomic regions containing sets of tightly linked loci that control multi-trait phenotypic polymorphisms under balancing selection. Recent advances in genomics have uncovered significant variation in both the genomic…
An approach for approximately calculating the number of genes in a genome is presented, which takes into account the average protein length expected for the species. A number of virus, bacterial and eukaryotic genomes are scrutinized.…
Despite recent advances in population-based structural health monitoring (PBSHM), knowledge transfer between highly-disparate structures (i.e., heterogeneous populations) remains a challenge. The current work proposes that heterogeneous…
In recent times whole-genome gene expression analysis has turned out to be a highly important tool to study the coordinated function of a very large number of genes within their corresponding cellular environment, especially in relation to…
We consider neutral evolution of a large population subject to changes in its population size. For a population with a time-variable carrying capacity we have computed the distributions of the total branch lengths of its sample genealogies.…
The human connectome represents a network map of the brain's wiring diagram and the pattern into which its connections are organized is thought to play an important role in cognitive function. The generative rules that shape the topology of…
Hierarchical Bayesian methods enable information sharing across multiple related regression problems. While standard practice is to model regression parameters (effects) as (1) exchangeable across datasets and (2) correlated to differing…
Understanding the relationship between genomic variation and variation in phenotypes for quantitative traits such as physiology, yield, fitness or behavior, will provide important insights for both predicting adaptive evolution and for…
Models of bacterial growth tend to be `irreversible', allowing for the number of bacteria in a colony to increase but not to decrease. By contrast, models of molecular self-assembly are usually `reversible', allowing for addition and…
1) Micro-evolutionary predictions are complicated by ecological feedbacks like density dependence, while ecological predictions can be complicated by evolutionary change. A widely used approach in micro-evolution, quantitative genetics,…
Infectious disease dynamics operate across multiple biological scales, with within-host viral dynamics being a key driver of between-host transmission. However, while models that explicitly link these scales exist, none have been developed…
We introduce several axioms which may or may not hold for any given subgraph of the directed graph of all organisms (past, present and future) where edges represent biological parenthood, with the simplifying background assumption that life…
The mapping between biological genotypes and phenotypes is central to the study of biological evolution. Here we introduce a rich, intuitive, and biologically realistic genotype-phenotype (GP) map, that serves as a model of self-assembling…
A previous report claimed no evidence of transgenerational epigenetic inheritance in a mouse model of in utero environmental exposure, based on the observation that gene expression changes observed in the germ cells of G1 and G2 male fetus…
We identify a set of 575 human genes that are expressed in all conditions tested in a publicly available database of microarray results. Based on this common occurrence, the set is expected to be rich in "housekeeping" genes, showing…
A taxonomy is a standardized framework to classify and organize items into categories. Hierarchical taxonomies are ubiquitous, ranging from the classification of organisms to the file system on a computer. Characterizing the typical…
Phylogenetic analyses of gene expression have great potential for addressing a wide range of questions. These analyses will, for example, identify genes that have evolutionary shifts in expression that are correlated with evolutionary…
Aging is a universal consequence of life, yet researchers have identified no universal theme. This manuscript considers aging from the perspective of entropy, wherein things fall apart. We first examine biological information change as a…
Although many phenotypic traits are determined by a large number of genetic variants, how a polygenic trait adapts in response to the changes in the environment is still poorly understood. Here we study the adaptation dynamics of a…
High-throughput genetic and epigenetic data are often screened for associations with an observed phenotype. For example, one may wish to test hundreds of thousands of genetic variants, or DNA methylation sites, for an association with…