Related papers: The dissection of expression quantitative trait lo…
In this paper, we study an integro-differential equation which describes the evolutionary dynamics of a population structured by a phenotypic trait. This population undergoes asexual reproduction, competition, selection, and mutation. We…
Clustering of gene expression time series gives insight into which genes may be coregulated, allowing us to discern the activity of pathways in a given microarray experiment. Of particular interest is how a given group of genes varies with…
Both genetic drift and natural selection cause the frequencies of alleles in a population to vary over time. Discriminating between these two evolutionary forces, based on a time series of samples from a population, remains an outstanding…
We consider resequencing studies of associated loci and the problem of prioritizing sequence variants for functional follow-up. Working within the multivariate linear regression framework helps us to account for correlation across variants,…
Admixture mapping is a popular tool to identify regions of the genome associated with traits in a recently admixed population. Existing methods have been developed primarily for identification of a single locus influencing a dichotomous…
We propose a quantitative method to estimate the statistical properties of sets of genes for which expression data are available and co-registered to a reference atlas of the brain. It is based on graph-theoretic properties of co-expression…
Bulk gene expression experiments relied on aggregations of thousands of cells to measure the average expression in an organism. Advances in microfluidic and droplet sequencing now permit expression profiling in single cells. This study of…
Molecular phenotypes link genomic information with organismic functions, fitness, and evolution. Quantitative traits are complex phenotypes that depend on multiple genomic loci. In this paper, we study the adaptive evolution of a…
During bouts of evolutionary diversification, such as adaptive radiations, the emerging species cluster around different locations in phenotype space, How such multimodal patterns in phenotype space can emerge from a single ancestral…
Understanding patterns of selectively neutral genetic variation is essential in order to model deviations from neutrality, caused for example by different forms of selection. Best understood is neutral genetic variation at a single locus,…
We consider a population subdivided into two demes connected by migration in which selection acts in opposite direction. We explore the effects of recombination and migration on the maintenance of multilocus polymorphism, on local…
Large Language Models (LLMs) are known to exhibit social, demographic, and gender biases, often as a consequence of the data on which they are trained. In this work, we adopt a mechanistic interpretability approach to analyze how such…
We give a simple statistical proof of a binomial identity, by evaluating the Laplace transform of the maximum of n independent exponential random variables in two different ways. As a by product, we obtain a simple proof of an interesting…
Representations from large language models are highly effective at predicting BOLD fMRI responses to language stimuli. However, these representations are largely opaque: it is unclear what features of the language stimulus drive the…
A model of mutation rate evolution for multiple loci under arbitrary selection is analyzed. Results are obtained using techniques from Karlin (1982) that overcome the weak selection constraints needed for tractability in prior studies of…
We consider the problem of testing the significance of features in high-dimensional settings. In particular, we test for differentially-expressed genes in a microarray experiment. We wish to identify genes that are associated with some type…
Multiplex networks are a powerful framework for representing systems with multiple types of interactions among a common set of entities. Understanding their structure requires statistical tools capturing higher-order cross-layer…
How do genes affect cognitive ability or other human quantitative traits such as height or disease risk? Progress on this challenging question is likely to be significant in the near future. I begin with a brief review of psychometric…
We present a new combinatorial model for identifying regulatory modules in gene co-expression data using a decomposition into weighted cliques. To capture complex interaction effects, we generalize the previously-studied weighted edge…
One of the most popular tools for large scale gene expression studies are high-density oligonucleotide (GeneChip(R)) arrays. These currently have 16-20 small probe cells (``features'') for evaluating the transcript abundance of each gene.…