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Standing genetic variation provides a rich reservoir of potentially useful mutations facilitating the adaptation to novel environments. Experimental evolution studies have demonstrated that rapid and strong phenotypic responses to selection…
Next-generation sequencing technologies provide a revolutionary tool for generating gene expression data. Starting with a fixed RNA sample, they construct a library of millions of differentially abundant short sequence tags or "reads",…
In phylogenomics, species-tree methods must contend with two major sources of noise; stochastic gene-tree variation under the multispecies coalescent model (MSC) and finite-sequence substitutional noise. Fast agglomerative methods such as…
DNA is subject to large deformations in a wide range of biological processes. Two key examples illustrate how such deformations influence the readout of the genetic information: the sequestering of eukaryotic genes by nucleosomes, and DNA…
Modern biological science produces vast amounts of genomic sequence data. This is fuelling the need for efficient algorithms for sequence compression and analysis. Data compression and the associated techniques coming from information…
Quantitative methods for studying biodiversity have been traditionally rooted in the classical theory of finite frequency tables analysis. However, with the help of modern experimental tools, like high throughput sequencing, we now begin to…
When performing an analysis on a collection of molecular sequences, it can be convenient to reduce the number of sequences under consideration while maintaining some characteristic of a larger collection of sequences. For example, one may…
Mutation rate variation across loci is well known to cause difficulties, notably identifiability issues, in the reconstruction of evolutionary trees from molecular sequences. Here we introduce a new approach for estimating general…
Recently developed spatial capture-recapture (SCR) models represent a major advance over traditional capture-recapture (CR) models because they yield explicit estimates of animal density instead of population size within an unknown area.…
The paper describes an algorithm to compute a consensus sequence from a set of DNA sequences of approximatively identical length generated by 3rd sequencing generation technologies. Its purpose targets DNA storage and is guided by specific…
Sequence-based place recognition methods for all-weather navigation are well-known for producing state-of-the-art results under challenging day-night or summer-winter transitions. These systems, however, rely on complex handcrafted…
We propose a new measure of support (the number of occur- rences of a pattern), in which instances are more important if they occur with a certain frequency and close after each other in the stream of trans- actions. We will explain this…
Because biological processes can make different loci have different evolutionary histories, species tree estimation requires multiple loci from across the genome. While many processes can result in discord between gene trees and species…
In evolutionary biology, genetic sequences carry with them a trace of the underlying tree that describes their evolution from a common ancestral sequence. The question of how many sequence sites are required to recover this evolutionary…
Frequencies of $k$-mers in sequences are sometimes used as a basis for inferring phylogenetic trees without first obtaining a multiple sequence alignment. We show that a standard approach of using the squared-Euclidean distance between…
Risk prediction that capitalizes on emerging genetic findings holds great promise for improving public health and clinical care. However, recent risk prediction research has shown that predictive tests formed on existing common genetic…
The advent of "next-generation" DNA sequencing (NGS) technologies has meant that collections of hundreds of millions of DNA sequences are now commonplace in bioinformatics. Knowing the longest common prefix array (LCP) of such a collection…
RNA sequencing (RNA-seq) enables characterization and quantification of individual transcriptomes as well as detection of patterns of allelic expression and alternative splicing. Current RNA-seq protocols depend on high-throughput…
Drone detection has become an essential task in object detection as drone costs have decreased and drone technology has improved. It is, however, difficult to detect distant drones when there is weak contrast, long range, and low…
Statistical consistency in phylogenetics has traditionally referred to the accuracy of estimating phylogenetic parameters for a fixed number of species as we increase the number of characters. However, as sequences are often of fixed length…