Related papers: Finding easy regions for short-read variant callin…
Whole-genome sequencing (WGS) has revealed numerous non-coding short variants whose functional impacts remain poorly understood. Despite recent advances in deep-learning genomic approaches, accurately predicting and prioritizing clinically…
We consider models for which it is important, early in processing, to estimate some variables with high precision, but perhaps at relatively low rates of recall. If some variables can be identified with near certainty, then they can be…
Several biological problems require the identification of regions in a sequence where some feature occurs within a target density range: examples including the location of GC-rich regions, identification of CpG islands, and sequence…
In real-time trajectory planning for unmanned vehicles, on-board sensors, radars and other instruments are used to collect information on possible obstacles to be avoided and pathways to be followed. Since, in practice, observations of the…
Second-generation sequencing technologies have replaced array-based technologies and become the default method for genomics and epigenomics analysis. Second-generation sequencing technologies sequence tens of millions of DNA/cDNA fragments…
High throughput sequencing is a technology that allows for the generation of millions of reads of genomic data regarding a study of interest, and data from high throughput sequencing platforms are usually count compositions. Subsequent…
Many methods for machine learning rely on approximate inference from intractable probability distributions. Variational inference approximates such distributions by tractable models that can be subsequently used for approximate inference.…
This article studies the achievable guarantees on the error rates of certain learning algorithms, with particular focus on refining logarithmic factors. Many of the results are based on a general technique for obtaining bounds on the error…
Described are two algorithms to find long approximate palindromes in a string, for example a DNA sequence. A simple algorithm requires O(n)-space and almost always runs in $O(k.n)$-time where n is the length of the string and k is the…
In the last decade a number of algorithms and associated software have been developed to align next generation sequencing (NGS) reads with relevant reference genomes. The accuracy of these programs may vary significantly, especially when…
High-throughput biological assays such as microarrays let us ask very detailed questions about how diseases operate, and promise to let us personalize therapy. Data processing, however, is often not described well enough to allow for exact…
Statistical inference on the cancer-site specificities of collective ultra-rare whole genome somatic mutations is an open problem. Traditional statistical methods cannot handle whole-genome mutation data due to their…
The application of machine learning models can be significantly impeded by the occurrence of distributional shifts, as the assumption of homogeneity between the population of training and testing samples in machine learning and statistics…
Variant calling is a fundamental task in genomic research, essential for detecting genetic variations such as single nucleotide polymorphisms (SNPs) and insertions or deletions (indels). This paper presents an enhancement to DeepChem, a…
We present a novel Bayesian approach to analysing multiple time-series with the aim of detecting abnormal regions. These are regions where the properties of the data change from some normal or baseline behaviour. We allow for the…
RNA sequencing (RNA-seq) is the conventional genome-scale approach used to capture the expression levels of all detectable genes in a biological sample. This is now regularly used for population-based studies designed to identify genetic…
The tremdendous advances in high-throughput sequencing technologies have made population-scale sequencing as performed in the 1000 Genomes project and the Genome of the Netherlands project possible. Next-generation sequencing has allowed…
Several processes in the cell, such as gene regulation, start when key proteins recognise and bind to short DNA sequences. However, as these sequences can be hundreds of million times shorter than the genome, they are hard to find by simple…
Meta-analyses of diagnostic test accuracy (DTA) studies have been gathering attention in research in clinical epidemiology and health technology development, and bivariate random-effects model is becoming a standard tool. However, standard…
Genome sequencing is the basis for many modern biological and medicinal studies. With recent technological advances, metagenomics has become a problem of interest. This problem entails the analysis and reconstruction of multiple DNA…