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Transfer learning for T-cell response prediction
We study the prediction of T-cell response for specific given peptides, which could, among other applications, be a crucial step towards the development of personalized cancer vaccines. It is a challenging task due to limited, …
Read PDFClinical scientist in clinical bioinformatics - the under-implemented recommendation of the Topol Review?
One of the recommendations of the Topol Review was the 'expansion of Higher Specialist Scientist Training (HSST) for clinical bioinformaticians'. Freedom of Information requests show that there has been little uptake of bioinformatics trainees, both …
Read PDFKG-bench: benchmarking graph neural network algorithms for drug repurposing
<h4>Motivation</h4>Drug repurposing leverages existing drugs for new indications, accelerating drug development. Computational methods integrating diverse biological and chemical data can systematically prioritize repurposing candidates, but standardized benchmarks for deep learning evaluation are lacking. We present …
Read PDFSingletrack: an algorithm for improving memory consumption and performance of gap-affine sequence alignment
<h4>Motivation</h4>Advances in DNA sequencing have outpaced advances in computation, making sequence alignment a major bottleneck in genome data analyses. Classical dynamic programming (DP) algorithms are particularly memory-intensive, especially when computing gap-affine and dual gap-affine alignments. …
Read PDFBiochef: a client-side WebAssembly-based workflow builder for genomic data analysis
<h4>Background</h4>Genomics analyses often rely on command-line tools executed via remote servers, imposing usability barriers for non-technical users and raising privacy concerns. WebAssembly (WASM) enables native-code execution directly in web browsers, eliminating installations and data transfers.<h4>Results</h4>We …
Read PDFET-Pfam: ensemble transfer learning for protein family prediction
<h4>Motivation</h4>Due to the rapid growth of sequence generation, which has surpassed the expert curators ability to manually review and annotate them, the computational annotation of proteins remains a significant challenge in bioinformatics nowadays. The Pfam …
Read PDFIdentification, design, and <i>in vivo</i> proof of concept of a shared APC neoantigen delivered via a self-amplifying RNA containing virus-like nanoparticle for cancer vaccination
Colorectal Cancer (CRC) accounts for the second highest number of cancer-related mortalities rate worldwide, and its incidence and mortality is expected to continue to increase in the coming years. Over 80% of CRC cases are …
Read PDFCorrection: Shared immune-inflammatory gene networks and drug prediction in polycystic ovary syndrome and type 2 diabetes mellitus: a bioinformatics and experimental validation study
[This corrects the article DOI: 10.3389/fendo.2026.1747045.].
Read PDFDecoding causal m6A: a bioinformatics roadmap for psychiatric disorders
N 6-methyladenosine (m6A), the most prevalent internal RNA modification, is an emerging key regulator of gene expression in the central nervous system, and its dysregulation is connected to psychiatric disorders. However, disentangling the causal links …
Read PDFAn integrated bioinformatics analysis identifying ALOX15 as a novel pharmacological target for retinitis pigmentosa and diabetic retinopathy
This study aimed to find shared gene signatures, molecular processes, and potential pharmacological targets in retinitis pigmentosa (RP) and diabetic retinopathy (DR) through integrated bioinformatics analysis. Two datasets were downloaded from the Gene Expression Omnibus …
Read PDFMycobacteria Amplicon Sequencing Tool: automated resistance prediction and lineage classification for <i>Mycobacterium tuberculosis</i>
The Mycobacteria Amplicon Sequencing Tool (https://github.com/guthrielab/MAST) is a modular Nextflow pipeline for antimicrobial resistance prediction and lineage classification of <i>Mycobacterium tuberculosis</i> from amplicon or whole-genome sequencing data sets. The workflow automates read processing, variant calling, …
Read PDFNovel cuproptosis related long non-coding RNA signature in oral squamous cell carcinoma prognosis and immunotherapy
Cuproptosis, a recently identified copper-dependent regulated cell death, is increasingly recognized for its relevance in cancer biology. In their study, Kong L et al. have developed a four long non-coding RNA (lncRNA) cuproptosis-related prognostic signature …
Read PDFGeneral-purpose topology-aware embedding of tumor phylogenetic trees with graph neural networks
<h4>Motivation</h4>Phylogenetic trees are tree-like data structures commonly adopted to mathematically represent cancer clonal evolution. The information encoded by phylogenetic trees is important for clinical outcomes, but the automatic extraction of such information is still hard, …
Read PDFCelebrating 25 years of briefings in bioinformatics: a comprehensive bibliometric analysis
Over the past 25 years, Briefings in Bioinformatics (BIB) has been the leading journal in the bioinformatics field. To commemorate this milestone and trace the journal's academic trajectory, we conducted a comprehensive bibliometric analysis of …
Read PDFIdentification of monotonically classifying pairs of genes for ordinal disease outcomes
<h4>Summary</h4>We extend an existing classification method for identifying pairs of genes whose joint expression is associated with binary outcomes to ordinal multi-class outcomes, such as overall survival or disease progression. Our approach, called <b>multi-class bivariate …
Read PDFA framework to infer de novo exonic variants when parental genotypes are missing enhances association studies of autism
<h4>Motivation</h4>Gene-damaging mutations are highly informative for studies seeking to discover genes underlying developmental disorders. Traditionally, these de novo variants are recognized by evaluating high-quality DNA sequence from affected offspring and parents. However, when parental sequence …
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