Related papers: Even better correction of genome sequencing data

Motivation: With the development of third-generation sequencing technologies, people are able to obtain DNA sequences with lengths from 10s to 100s of kb. These long reads allow protein domain annotation without assembly, thus can produce…

A variety of genome-wide profiling techniques are available to probe complementary aspects of genome structure and function. Integrative analysis of heterogeneous data sources can reveal higher-level interactions that cannot be detected…

Genome-to-genome comparisons require designating anchor points, which are given by Maximum Exact Matches (MEMs) between their sequences. For large genomes this is a challenging problem and the performance of existing solutions, even in…

High read depth can be used to assemble short sequence repeats. The existing genome assemblers fail in repetitive regions of longer than average read. I propose a new algorithm for a DNA assembly which uses the relative frequency of reads…

We propose a new compression scheme for genomic data given as sequence fragments called reads. The scheme uses a reference genome at the decoder side only, freeing the encoder from the burdens of storing references and performing…

String kernels are typically used to compare genome-scale sequences whose length makes alignment impractical, yet their computation is based on data structures that are either space-inefficient, or incur large slowdowns. We show that a…

The high throughput and cost-effectiveness afforded by short-read sequencing technologies, in principle, enable researchers to perform 16S rRNA profiling of complex microbial communities at unprecedented depth and resolution. Existing…

Frequencies of $k$-mers in sequences are sometimes used as a basis for inferring phylogenetic trees without first obtaining a multiple sequence alignment. We show that a standard approach of using the squared-Euclidean distance between…

Aligning millions of short DNA or RNA reads, of 75 to 250 base pairs each, to a reference genome is a significant computation problem in bioinformatics. We present a flexible and fast FPGA-based short read alignment tool. Our aligner makes…

We present the GeneScore, a concept of feature reduction for Machine Learning analysis of biomedical data. Using expert knowledge, the GeneScore integrates different molecular data types into a single score. We show that the GeneScore is…

Deep shotgun sequencing and analysis of genomes, transcriptomes, amplified single-cell genomes, and metagenomes has enabled investigation of a wide range of organisms and ecosystems. However, sampling variation in short-read data sets and…

Large language models (LLMs) have recently shown strong progress on scientific reasoning, yet two major bottlenecks remain. First, explicit retrieval fragments reasoning, imposing a hidden "tool tax" of extra tokens and steps. Second,…

Kernel methods are an important class of techniques in machine learning. To be effective, good feature maps are crucial for mapping non-linearly separable input data into a higher dimensional (feature) space, thus allowing the data to be…

Genetic information is encoded in a linear sequence of nucleotides, represented by letters ranging from thousands to billions. Mutations refer to changes in the DNA or RNA nucleotide sequence. Thus, mutation detection is vital in all areas…

DNA sequences encode critical genetic information, yet their variable length and discrete nature impede direct utilization in deep learning models. Existing DNA representation schemes convert sequences into numerical vectors but fail to…

Mitigation and calibration schemes are central to maximize the computational reach of today's Noisy Intermediate Scale Quantum (NISQ) hardware, but these schemes are often specialized to exclusively address either coherent or decoherent…

Repetitive DNA sequences underpin genome architecture and evolutionary processes, yet they remain challenging to classify accurately. Terrier is a deep learning model designed to overcome these challenges by classifying repetitive DNA…

This article is focused on some variations of Reed-Muller codes that yield improvements to the rate for a prescribed decoding performance under the Berlekamp-Massey-Sakata algorithm with majority voting. Explicit formulas for the…

Modern high-throughput sequencing assays efficiently capture not only gene expression and different levels of gene regulation but also a multitude of genome variants. Focused analysis of alternative alleles of variable sites at homologous…

Nanopore sequencing can read substantially longer sequences of nucleic acid molecules, called reads, than other sequencing methods, which has led to advances in genomic analysis such as the gapless human genome assembly. By analyzing the…