Related papers: Bam-readcount -- rapid generation of basepair-reso…

Generating radiology reports automatically reduces the workload of radiologists and helps the diagnoses of specific diseases. Many existing methods take this task as modality transfer process. However, since the key information related to…

Machine learning (ML) interpretability techniques can reveal undesirable patterns in data that models exploit to make predictions--potentially causing harms once deployed. However, how to take action to address these patterns is not always…

AMRScan is a hybrid bioinformatics toolkit implemented in both R and [Nextflow](https://www.nextflow.io/) for the rapid and reproducible detection of antimicrobial resistance (AMR) genes from next-generation sequencing (NGS) data. The…

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…

Reducing the cost of sequencing genomes provided by next-generation sequencing technologies has greatly increased the number of genomic projects. As a result, there is a growing need for better assembly and assembly validation methods. One…

Massively parallel sequencing techniques have revolutionized biological and medical sciences by providing unprecedented insight into the genomes of humans, animals, and microbes. Modern sequencing platforms generate enormous amounts of…

Short-read DNA sequencing instruments can yield over 1e+12 bases per run, typically composed of reads 150 bases long. Despite this high throughput, de novo assembly algorithms have difficulty reconstructing contiguous genome sequences using…

The genome sequence contains the blueprint for governing cellular processes. While the availability of genomes has vastly increased over the last decades, experimental annotation of the various functional, non-coding and regulatory elements…

Most pattern recognition models are developed on pre-proce\-ssed data. In computer vision, for instance, RGB images processed through image signal processing (ISP) pipelines designed to cater to human perception are the most frequent input…

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…

Motivation: Seed location filtering is critical in DNA read mapping, a process where billions of DNA fragments (reads) sampled from a donor are mapped onto a reference genome to identify genomic variants of the donor. State-of-the-art read…

RNA sequencing (RNA-seq) has been rapidly adopted for the profiling of transcriptomes in many areas of biology, including studies into gene regulation, development and disease. Of particular interest is the discovery of differentially…

Next-generation sequencing technologies provide a revolutionary tool for generating gene expression data. Starting with a fixed RNA sample, they construct a library of millions of differentially abundant short sequence tags or "reads",…

RNA-sequencing (RNA-seq) has become an exemplar technology in modern biology and clinical applications over the past decade. It has gained immense popularity in the recent years driven by continuous efforts of the bioinformatics community…

Command-line bioinformatics tools remain essential for genomic analysis, yet their diversity in syntax and parameterization presents a persistent barrier to productive research. We present oxo-call, a Rust-based command-line assistant that…

As a powerful all-weather Earth observation tool, synthetic aperture radar (SAR) remote sensing enables critical military reconnaissance, maritime surveillance, and infrastructure monitoring. Although Vision language models (VLMs) have made…

Motivation: Next-generation sequencing tools have enabled producing of huge amount of genomic information at low cost. Unfortunately, presence of sequencing errors in such data affects quality of downstream analyzes. Accuracy of them can be…

In recent years, multimodal multidomain fake news detection has garnered increasing attention. Nevertheless, this direction presents two significant challenges: (1) Failure to Capture Cross-Instance Narrative Consistency: existing models…

For extended periods of time, sequence generation models rely on beam search algorithm to generate output sequence. However, the correctness of beam search degrades when the a model is over-confident about a suboptimal prediction. In this…

Linked-Reads technologies, such as 10x Genomics, combine both the high-quality and low cost of short-reads sequencing and a long-range information, through the use of barcodes able to tag reads which originate from a common long DNA…