Related papers: Misassembly Detection using Paired-End Sequence Re…
Genome sequence analysis plays a pivotal role in enabling many medical and scientific advancements in personalized medicine, outbreak tracing, and forensics. However, the analysis of genome sequencing data is currently bottlenecked by the…
In a corpus of data, outliers are either errors: mistakes in the data that are counterproductive, or are unique: informative samples that improve model robustness. Identifying outliers can lead to better datasets by (1) removing noise in…
Designing components that can robustly self-assemble into structures with biological complexity is a grand challenge for material science. Proofreading and error correction is required to improve assembly yield beyond equilibrium limits,…
The single nucleotide polymorphism (SNP) is the most widely studied type of genetic variation. A haplotype is defined as the sequence of alleles at SNP sites on each haploid chromosome. Haplotype information is essential in unravelling the…
When digitizing a print bilingual dictionary, whether via optical character recognition or manual entry, it is inevitable that errors are introduced into the electronic version that is created. We investigate automating the process of…
Currently, third-generation sequencing techniques, which allow to obtain much longer DNA reads compared to the next-generation sequencing technologies, are becoming more and more popular. There are many possibilities to combine data from…
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…
Motivation: Open-source bacterial genome assembly remains inaccessible to many biologists due to its complexity. Few software solutions exist that are capable of automating all steps in the process of de novo genome assembly from Illumina…
Despite the recent progress in genome sequencing and assembly, many of the currently available assembled genomes come in a draft form. Such draft genomes consist of a large number of genomic fragments (scaffolds), whose order and/or…
In human microbiome studies, sequencing reads data are often summarized as counts of bacterial taxa at various taxonomic levels specified by a taxonomic tree. This paper considers the problem of analyzing two repeated measurements of…
Down-sampling training data has long been shown to improve the generalization performance of a wide range of machine learning systems. Recently, down-sampling has proved effective in genetic programming (GP) runs that utilize the lexicase…
Emerging integrative analysis of genomic and anatomical imaging data which has not been well developed, provides invaluable information for the holistic discovery of the genomic structure of disease and has the potential to open a new…
Motivation: Illumina DNA sequencing is now the predominant source of raw genomic data, and data volumes are growing rapidly. Bioinformatic analysis pipelines are having trouble keeping pace. A common bottleneck in such pipelines is the…
We address key points for an efficient implementation of likelihood codes for modern weak lensing large-scale structure surveys. Specifically, we focus on the joint weak lensing convergence power spectrum-bispectrum probe and we tackle the…
Nanopore sequencing technology has the potential to render other sequencing technologies obsolete with its ability to generate long reads and provide portability. However, high error rates of the technology pose a challenge while generating…
We show that textual analysis of microbial genomes reveal telling footprints of the early evolution of the genomes. The frequencies of word occurrence of random DNA sequences considered as texts in their four nucleotides are expected to…
This is a review of a set of recent papers with some new data added. After a brief biological introduction a visualization scheme of the string composition of long DNA sequences, in particular, of bacterial complete genomes, will be…
Algorithms for causal discovery have recently undergone rapid advances and increasingly draw on flexible nonparametric methods to process complex data. With these advances comes a need for adequate empirical validation of the causal…
This paper examines the joint problem of detection and identification of a sudden and unobservable change in the probability distribution function (pdf) of a sequence of independent and identically distributed (i.i.d.) random variables to…
Metagenomics characterizes the taxonomic diversity of microbial communities by sequencing DNA directly from an environmental sample. One of the main challenges in metagenomics data analysis is the binning step, where each sequenced read is…