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The evolutionary dynamics of HIV during the chronic phase of infection is driven by the host immune response and by selective pressures exerted through drug treatment. To understand and model the evolution of HIV quantitatively, the…
A key goal in studies of ecology and evolution is understanding the causes of phenotypic diversity in nature. Most traits of interest, such as those relating to morphology, life-history, immunity and behaviour are quantitative, and…
Genotype networks are a method used in systems biology to study the "innovability" of a set of genotypes having the same phenotype. In the past they have been applied to determine the genetic heterogeneity, and stability to mutations, of…
For families, kinship coefficients are quantifications of the amount of genetic sharing between a pair of individuals. These coefficients are critical for understanding the breeding habits and genetic diversity of diploid populations.…
Quantitatively predicting phenotype variables by the expression changes in a set of candidate genes is of great interest in molecular biology but it is also a challenging task for several reasons. First, the collected biological…
Probabilistic Graphical Models (PGM) are very useful in the fields of machine learning and data mining. The crucial limitation of those models,however, is the scalability. The Bayesian Network, which is one of the most common PGMs used in…
In ecology and population dynamics, gene-flow refers to the transfer of a trait from one population to another. This phenomenon appears in studying the evolution of social features, such as languages. From the mathematical point of view,…
We study a data-driven approach to the bee identification problem for DNA strands. The bee-identification problem, introduced by Tandon et al. (2019), requires one to identify $M$ bees, each tagged by a unique barcode, via a set of $M$…
The analysis of the leukemia data from Whitehead/MIT group is a discriminant analysis (also called a supervised learning). Among thousands of genes whose expression levels are measured, not all are needed for discriminant analysis: a gene…
A great deal of effort has been devoted to discovering a particular genetic disorder, but its classification across a broad spectrum of disorder classes and types remains elusive. Early diagnosis of genetic disorders enables timely…
The evolutionary significance of hybridization and subsequent introgression has long been appreciated, but evaluation of the genome-wide effects of these phenomena has only recently become possible. Crop-wild study systems represent ideal…
Risk evaluation to identify individuals who are at greater risk of cancer as a result of heritable pathogenic variants is a valuable component of individualized clinical management. Using principles of Mendelian genetics, Bayesian…
We present a novel classification-based method for learning to predict gene regulatory response. Our approach is motivated by the hypothesis that in simple organisms such as Saccharomyces cerevisiae, we can learn a decision rule for…
We study a family of selection-mutation models of a sexual population structured by a phenotypical trait. The main feature of these models is the asymmetric trait heredity or fecundity between the parents : we assume that each individual…
Experimental corn hybrids are created in plant breeding programs by crossing two parents, so-called inbred and tester, together. Identification of best parent combinations for crossing is challenging since the total number of possible cross…
Heritable differences in gene expression between individuals are an important source of phenotypic variation. The question of how closely the effects of genetic variation on protein levels mirror those on mRNA levels remains open. Here, we…
A probabilistic reconstruction of genealogies in a polyploid population (from 2x to 4x) is investigated, by considering genetic data analyzed as the probability of allele presence in a given genotype. Based on the likelihood of all possible…
Several studies question the adaptive value of female preferences for older males. Theory and evidence show that older males carry more deleterious mutations in their sperm than younger males carry. These mutations are not visible to…
The complex dynamics of gene expression in living cells can be well-approximated using Boolean networks. The average sensitivity is a natural measure of stability in these systems: values below one indicate typically stable dynamics…
Over the last decade, wireless networks have experienced an impressive growth and now play a main role in many telecommunications systems. As a consequence, scarce radio resources, such as frequencies, became congested and the need for…