Bioinformatics (Oxford, England)
Mar 4, 2025
MOTIVATION: Identifying bacteriophages (phages) within metagenomic sequences is essential for understanding microbial community dynamics. Transformer-based foundation models have been successfully employed to address various biological challenges. Ho...
Bioinformatics (Oxford, England)
Mar 4, 2025
MOTIVATION: Single-cell RNA sequencing (scRNA-seq) enables high-throughput transcriptomic profiling at single-cell resolution. The inherent spatial location is crucial for understanding how single cells orchestrate multicellular functions and drive d...
Bioinformatics (Oxford, England)
Mar 4, 2025
MOTIVATION: Enabling clinicians and researchers to directly interact with global genomic data resources by removing technological barriers is vital for medical genomics. AskBeacon enables large language models (LLMs) to be applied to securely shared ...
Bioinformatics (Oxford, England)
Mar 4, 2025
MOTIVATION: S-sulfhydration, a crucial post-translational protein modification, is pivotal in cellular recognition, signaling processes, and the development and progression of cardiovascular and neurological disorders, so identifying S-sulfhydration ...
Bioinformatics (Oxford, England)
Mar 4, 2025
MOTIVATION: Plasmids play an essential role in horizontal gene transfer, aiding their host bacteria in acquiring beneficial traits like antibiotic and metal resistance. There exist some plasmids that can transfer, replicate, or persist in multiple or...
Bioinformatics (Oxford, England)
Mar 4, 2025
MOTIVATION: Computational analyses of bulk and single-cell omics provide translational insights into complex diseases, such as COVID-19, by revealing molecules, cellular phenotypes, and signalling patterns that contribute to unfavourable clinical out...
Bioinformatics (Oxford, England)
Mar 4, 2025
MOTIVATION: Progress in sequencing technology has led to determination of large numbers of protein sequences, and large enzyme databases are now available. Although many computational tools for enzyme annotation were developed, sequence information i...
Bioinformatics (Oxford, England)
Mar 4, 2025
MOTIVATION: As the biological roles and disease implications of non-coding RNAs continue to emerge, the need to thoroughly characterize previously unexplored non-coding RNAs becomes increasingly urgent. These molecules hold potential as biomarkers an...
Bioinformatics (Oxford, England)
Feb 4, 2025
SUMMARY: Polygenic risk scores (PRSs) hold promise for early disease diagnosis and personalized treatment, but their overall discriminative power remains limited for many diseases in the general population. As a result, numerous novel PRS modeling te...
Bioinformatics (Oxford, England)
Feb 4, 2025
MOTIVATION: Accurately identifying and predicting molecular properties is a crucial task in molecular machine learning, and the key lies in how to extract effective molecular representations. Contrastive learning opens new avenues for representation ...