Related papers: Minimum error correction-based haplotype assembly:…
A critical problem in the emerging high-throughput genotyping protocols is to minimize the number of polymerase chain reaction (PCR) primers required to amplify the single nucleotide polymorphism loci of interest. In this paper we study PCR…
The Constrained Minimal Supersymmetric Standard Model (CMSSM) is one of the simplest and most widely-studied supersymmetric extensions to the standard model of particle physics. Nevertheless, current data do not sufficiently constrain the…
Short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) are two kinds of commonly used markers in Y chromosome studies of forensic and population genetics. There has been increasing interest in the cost saving strategy by…
Synthetic DNA can in principle be used for the archival storage of arbitrary data. Because errors are introduced during DNA synthesis, storage, and sequencing, an error-correcting code (ECC) is necessary for error-free recovery of the data.…
Segmental duplications (SDs), or low-copy repeats (LCR), are segments of DNA greater than 1 Kbp with high sequence identity that are copied to other regions of the genome. SDs are among the most important sources of evolution, a common…
Motivation: Genome-Wide Association Studies (GWAS) seek to identify causal genomic variants associated with rare human diseases. The classical statistical approach for detecting these variants is based on univariate hypothesis testing, with…
Motivation: Next generation methods of DNA sequencing produce relatively high rate of reading errors, which interfere with de novo genome assembly of newly sequenced organisms and particularly affect the quality of SNP detection important…
In this work we present a flexible, probabilistic and reference-free method of error correction for high throughput DNA sequencing data. The key is to exploit the high coverage of sequencing data and model short sequence outputs as…
New long read sequencing technologies, like PacBio SMRT and Oxford NanoPore, can produce sequencing reads up to 50,000 bp long but with an error rate of at least 15%. Reducing the error rate is necessary for subsequent utilisation of the…
Sparse coding (Sc) has been studied very well as a powerful data representation method. It attempts to represent the feature vector of a data sample by reconstructing it as the sparse linear combination of some basic elements, and a $L_2$…
The widely used genetic pleiotropic analysis of multiple phenotypes are often designed for examining the relationship between common variants and a few phenotypes. They are not suited for both high dimensional phenotypes and high…
Despite much progress over the past decade, current Single Nucleotide Polymorphism (SNP) genotyping technologies still offer an insufficient degree of multiplexing when required to handle user-selected sets of SNPs. In this paper we propose…
We propose masked particle modeling (MPM) as a self-supervised method for learning generic, transferable, and reusable representations on unordered sets of inputs for use in high energy physics (HEP) scientific data. This work provides a…
Computing haplotypes from sequencing data, i.e. haplotype assembly, is an important component of molecular and population genetics problems, including interpreting the effects of genetic variation on complex traits and reconstructing…
Accurate identification of haplotypes in sequenced human genomes can provide invaluable information about population demography and fine-scale correlations along the genome, thus empowering both population genomic and medical association…
Analysis of genomic segments shared identical-by-descent (IBD) between individuals is fundamental to many genetic applications, from demographic inference to estimating the heritability of diseases, but IBD detection accuracy in…
Sparse autoencoders (SAEs) are widely used for interpreting language model activations. A key evaluation metric is the increase in cross-entropy loss between the original model logits and the reconstructed model logits when replacing model…
The prevalent technique for DNA sequencing consists of two main steps: shotgun sequencing, where many randomly located fragments, called reads, are extracted from the overall sequence, followed by an assembly algorithm that aims to…
Statistically resolving the underlying haplotype pair for a genotype measurement is an important intermediate step in gene mapping studies, and has received much attention recently. Consequently, a variety of methods for this problem have…
Error correction of sequenced reads remains a difficult task, especially in single-cell sequencing projects with extremely non-uniform coverage. While existing error correction tools designed for standard (multi-cell) sequencing data…