Related papers: Locating recombination hot spots in genomic sequen…
Certain retroviruses, including HIV, insert their DNA in a non-random fraction of the host genome via poorly understood selection mechanisms. Here, we develop a biophysical model for retroviral integrations as stochastic and…
Selective sweeps are typically associated with a local reduction of genetic diversity around the adaptive site. However, selective sweeps can also quickly carry neutral mutations to observable population frequencies if they arise early in a…
Site-specific recombination on supercoiled circular DNA molecules can yield a variety of knots and catenanes. Twist knots are some of the most common conformations of these products and they can act as substrates for further rounds of…
Understanding genetic variation, e.g., through mutations, in organisms is crucial to unravel their effects on the environment and human health. A fundamental characterization can be obtained by solving the haplotype assembly problem, which…
Mapper algorithm can be used to build graph-based representations of high-dimensional data capturing structurally interesting features such as loops, flares or clusters. The graph can be further annotated with additional colouring of…
We now need more than ever to make genome analysis more intelligent. We need to read, analyze, and interpret our genomes not only quickly, but also accurately and efficiently enough to scale the analysis to population level. There currently…
This study proposes a data condensation method for multivariate kernel density estimation by genetic algorithm. First, our proposed algorithm generates multiple subsamples of a given size with replacement from the original sample. The…
Computing the dispersion relation for two-dimensional photonic crystals is a notoriously challenging task: It involves solving parameterized Helmholtz eigenvalue problems with high-contrast coefficients. To resolve the challenge, we propose…
Within-host genetic sequencing from samples collected over time provides a dynamic view of how viruses evade host immunity. Immune-driven mutations might stimulate neutralization breadth by selecting antibodies adapted to cycles of immune…
Motivation: Computational methods are essential to extract actionable information from raw sequencing data, and to thus fulfill the promise of next-generation sequencing technology. Unfortunately, computational tools developed to call…
In this article we show that the reconstructions of semiconductor surfaces can be determined using a genetic procedure. Coupled with highly optimized interatomic potentials, the present approach represents an efficient tool for finding and…
Understanding and extracting the patterns of microscopy images has been a major challenge in the biomedical field. Although trained scientists can locate the proteins of interest within a human cell, this procedure is not efficient and…
We present a new method for exploring cancer gene expression data based on tools from algebraic topology. Our method selects a small relevant subset from tens of thousands of genes while simultaneously identifying nontrivial higher order…
A topological multiple testing approach to peak detection is proposed for the problem of detecting transcription factor binding sites in ChIP-Seq data. After kernel smoothing of the tag counts over the genome, the presence of a peak is…
Singular points detection is one of the most classical and important problem in the field of fingerprint recognition. However, current detection rates of singular points are still unsatisfactory, especially for low-quality fingerprints.…
Cellular populations are typically heterogenous collections of cells at different points in their respective cell cycles, each with a cell cycle time that varies from individual to individual. As a result, true single-cell behavior,…
When estimating a phylogeny from a multiple sequence alignment, researchers often assume the absence of recombination. However, if recombination is present, then tree estimation and all downstream analyses will be impacted, because…
There are many instances in genetics in which we wish to determine whether two candidate populations are distinguishable on the basis of their genetic structure. Examples include populations which are geographically separated, case--control…
Cre-lox and other systems are used as genetic tools to control site-specific recombination (SSR) events in genomic DNA. If multiple recombination sites are organized in a compact cluster within the same genome, a series of random…
We consider the problem of estimating overlapping community memberships in a network, where each node can belong to multiple communities. More than a few communities per node are difficult to both estimate and interpret, so we focus on…