Related papers: Sample Size for Concurrent Species Detection in a …
The quality of the inferences we make from pathogen sequence data is determined by the number and composition of pathogen sequences that make up the sample used to drive that inference. However, there remains limited guidance on how to best…
One of the first successes of neutral ecology was to predict realistically-broad distributions of rare and abundant species. However, it has remained an outstanding theoretical challenge to describe how this distribution of abundances…
In classification problems, the purpose of feature selection is to identify a small, highly discriminative subset of the original feature set. In many applications, the dataset may have thousands of features and only a few dozens of samples…
Source-sink systems are metapopulations of patches that can be of variable habitat quality. They can be seen as graphs, where vertices represent the patches, and the weighted oriented edges give the probability of dispersal from one patch…
Botanical specimens are shared as long-term consultable research objects in a global network of specimen repositories. Multiple specimens are generated from a shared field collection event; generated specimens are then managed individually…
We examine the problem of family size statistics (the number of individuals carrying the same surname, or the same DNA sequence) in a given size subsample of an exponentially growing population. We approach the problem from two directions.…
The interpretation of count data originating from the current generation of DNA sequencing platforms requires special attention. In particular, the per-sample library sizes often vary by orders of magnitude from the same sequencing run, and…
Global species richness is a key biodiversity metric. Despite recent efforts to estimate global species richness, the resulting estimates have been highly uncertain and often logically inconsistent. Estimates lower down either the taxonomic…
Insects play such a crucial role in ecosystems that a shift in demography of just a few species can have devastating consequences at environmental, social and economic levels. Despite this, evaluation of insect demography is strongly…
By creating networks of biochemical pathways, communities of micro-organisms are able to modulate the properties of their environment and even the metabolic processes within their hosts. Next-generation high-throughput sequencing has led to…
Phylodynamics seeks to estimate effective population size fluctuations from molecular sequences of individuals sampled from a population of interest. One way to accomplish this task formulates an observed sequence data likelihood exploiting…
Frequency-dependent selection reflects the interaction between different species as they battle for limited resources in their environment. In a stochastic evolutionary game the species relative fitnesses guides the evolutionary dynamics…
The NBSS (normalized biomass size spectrum) is a common, intuitive approach for the study of natural ecosystems. However, very few studies have been dedicated to verifying possible flaws and paradoxes in this widely used method. Evident…
We describe a simple model of evolution which incorporates the branching and extinction of species lines, and also includes abiotic influences. A first principles approach is taken in which the probability for speciation and extinction are…
In ecology we may find scenarios where the same phenomenon (species occurrence, species abundance, etc.) is observed using two different types of samplers. For instance, species data can be collected from scientific sampling with a…
Ancestral sequence reconstruction is a key task in computational biology. It consists in inferring a molecular sequence at an ancestral species of a known phylogeny, given descendant sequences at the tip of the tree. In addition to its many…
Mixture models combine multiple components into a single probability density function. They are a natural statistical model for many situations in astronomy, such as surveys containing multiple types of objects, cluster analysis in various…
This paper concerns the modeling and numerical simulation of the process of speciation. In particular, given conditions for which one or more speciation events within an ecosystem occur, our aim is to develop the necessary modeling and…
The relationship between microscopic observations and macroscopic behavior is a fundamental open question in biophysical systems. Here, we develop a unified approach that---in contrast with existing methods---predicts cell type from…
Metagenomics sequencing is routinely applied to quantify bacterial abundances in microbiome studies, where the bacterial composition is estimated based on the sequencing read counts. Due to limited sequencing depth and DNA dropouts, many…