MOTIVATION: Topologically associated domains (TADs) play a key role in the 3D organization and function of genomes, and accurate detection of TADs is essential for revealing the relationship between genomic structure and function. Most current method...
Accurate cancer survival prediction remains a critical challenge in clinical oncology, largely due to the complex and multi-omics nature of cancer data. Existing methods often struggle to capture the comprehensive range of informative features requir...
RNA biomarkers enable early and precise disease diagnosis, monitoring, and prognosis, facilitating personalized medicine and targeted therapeutic strategies. However, identification of RNA biomarkers is hindered by the challenge of analyzing relative...
Even with the significant advances of AlphaFold-Multimer (AF-Multimer) and AlphaFold3 (AF3) in protein complex structure prediction, their accuracy is still not comparable with monomer structure prediction. Efficient and effective quality assessment ...
Spatial transcriptomics (ST) technology provides gene expression profiles with spatial context, offering critical insights into cellular interactions and tissue architecture. A core task in ST is spatial domain identification, which involves detectin...
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...
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...
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 ...
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...
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...
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