Bioinformatics (Oxford, England)
May 6, 2025
MOTIVATION: Molecular property prediction with deep learning has accelerated drug discovery and retrosynthesis. However, the shortage of labeled molecular data and the challenge of generalizing across the vast chemical spaces pose significant hurdles...
Bioinformatics (Oxford, England)
May 6, 2025
MOTIVATION: Integrating Large Language Models (LLMs) with research tools presents technical and reproducibility challenges for biomedical research. While commercial artificial intelligence (AI) systems are easy to adopt, they obscure data provenance,...
Bioinformatics (Oxford, England)
May 6, 2025
SUMMARY: The Ontology Lookup Service (OLS) is an open source search engine for ontologies which is used extensively in the bioinformatics and chemistry communities to annotate biological and biomedical data with ontology terms. Recently, there has be...
Bioinformatics (Oxford, England)
May 6, 2025
MOTIVATION: Omics features, often measured by high-throughput technologies, combined with clinical features, significantly impact the understanding of many complex human diseases. Integrating key omics biomarkers with clinical risk factors is essenti...
Bioinformatics (Oxford, England)
May 6, 2025
SUMMARY: Currently available and frequently used tools for annotating antibiotic resistance genes (ARGs) in genomes and metagenomes provide results using inconsistent nomenclature. This makes the comparison of different ARG annotation outputs challen...
Bioinformatics (Oxford, England)
May 6, 2025
MOTIVATION: Understanding the protein sequence-function relationship is essential for advancing protein biology and engineering. However, <1% of known protein sequences have human-verified functions. While deep-learning methods have demonstrated prom...
Bioinformatics (Oxford, England)
May 6, 2025
MOTIVATION: Unraveling the human interactome to uncover disease-specific patterns and discover drug targets hinges on accurate protein-protein interaction (PPI) predictions. However, challenges persist in machine learning (ML) models due to a scarcit...
Bioinformatics (Oxford, England)
May 6, 2025
MOTIVATION: Enhancers and promoters, as regulatory DNA elements, play pivotal roles in gene expression, homeostasis, and disease development across various biological processes. With advancing research, it has been uncovered that distal enhancers may...
Bioinformatics (Oxford, England)
May 6, 2025
MOTIVATION: Predicting the binding affinity between antigens and antibodies accurately is crucial for assessing therapeutic antibody effectiveness and enhancing antibody engineering and vaccine design. Traditional machine learning methods have been w...
Briefings in bioinformatics
May 3, 2025
Antibody-drug conjugates (ADCs) have revolutionized the field of cancer treatment in the era of precision medicine due to their ability to precisely target cancer cells and release highly effective drugs. Nevertheless, the rational design and discove...