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,...
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...
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...
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...
MOTIVATION: Single-cell RNA sequencing (scRNA-seq) analysis relies heavily on effective clustering to facilitate numerous downstream applications. Although several machine learning methods have been developed to enhance single-cell clustering, most a...
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...
We introduce brain2print, a web-based application that converts T1-weighted MRI scans into 3D printable models. By leveraging artificial intelligence (AI), brain2print performs all computations directly on the user's device, preserving privacy while ...
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...
Antibody-antigen interactions (AAIs) are a pervasive phenomenon in the natural and are instrumental in the design of antibody-based drugs. Despite the emergence of various deep learning-based methods aimed at enhancing the accuracy of AAIs prediction...
Single-cell ribonucleic acid (RNA) sequencing (scRNA-seq) produces vast amounts of individual cell profiling data. Its analysis presents a significant challenge in accurately annotating cell types and their associated biomarkers. Different pipelines ...
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