Genomics
Cancer exhibits diverse and complex phenotypes driven by multifaceted molecular interactions. Recent biomedical research has emphasized the comprehensive study of such diseases by integrating multi-omics datasets (genome, proteome,…
Data visualization is a fundamental tool in genomics research, enabling the exploration, interpretation, and communication of complex genomic features. While machine learning models show promise for transforming data into insightful…
Genome-resolved metagenomics has contributed largely to discovering prokaryotic genomes. When applied to microscopic eukaryotes, challenges such as the high number of introns and repeat regions found in nuclear genomes have hampered the…
Molecular sequence analysis is crucial for comprehending several biological processes, including protein-protein interactions, functional annotation, and disease classification. The large number of sequences and the inherently complicated…
Identifying cancer driver genes (CDGs) is essential for understanding cancer mechanisms and developing targeted therapies. Graph neural networks (GNNs) have recently been employed to identify CDGs by capturing patterns in biological…
Nanopore sequencing technologies continue to advance rapidly, offering critical benefits such as real-time analysis, the ability to sequence extremely long DNA fragments (up to millions of bases in a single read), and the option to…
Gene expression data is essential for understanding how genes are regulated and interact within biological systems, providing insights into disease pathways and potential therapeutic targets. Gene knockout has proven to be a fundamental…
Medulloblastoma is a malignant pediatric brain cancer, and the discovery of molecular subgroups is enabling personalized treatment strategies. In 2019, a consensus identified eight novel subtypes within Groups 3 and 4, each displaying…
Single-cell RNA sequencing (scRNA-seq) reveals cell heterogeneity, with cell clustering playing a key role in identifying cell types and marker genes. Recent advances, especially graph neural networks (GNNs)-based methods, have…
Epilepsy is a chronic neurological condition characterized by recurrent seizures, with global prevalence estimated at 50 million people worldwide. While progress in high-throughput sequencing has allowed for broad-based transcriptomic…
Background: Large foundation models have revolutionized single-cell analysis, yet no kidney-specific model currently exists, and it remains unclear whether organ-focused models can outperform generalized models. The kidney's complex…
Distinguishing the rare "driver" mutations that fuel cancer progression from the vast background of "passenger" mutations in the non-coding genome is a fundamental challenge in cancer biology. A primary mechanism that non-coding driver…
Gene enhancers control when and where genes switch on, yet their sequence diversity and tissue specificity make them hard to pinpoint in colorectal cancer. We take a sequence-only route and fine-tune DNABERT-2, a transformer genomic…
Large language models (LLMs) have shown strong ability in generating rich representations across domains such as natural language processing and generation, computer vision, and multimodal learning. However, their application in biomedical…
Background: Structural variants (SVs) are genomic differences $\ge$50 bp in length. They remain challenging to detect even with long sequence reads, and the sources of these difficulties are not well quantified. Results: We identified 35.4…
DNA language models have revolutionized our ability to understand and design DNA sequences--the fundamental language of life--with unprecedented precision, enabling transformative applications in therapeutics, synthetic biology, and gene…
Background: While benchmarks on short-read variant calling suggest low error rate below 0.5%, they are only applicable to predefined confident regions. For a human sample without such regions, the error rate could be 10 times higher.…
Motivation: Spliced alignment refers to the alignment of messenger RNA (mRNA) or protein sequences to eukaryotic genomes. It plays a critical role in gene annotation and the study of gene functions. Accurate spliced alignment demands…
Small interfering RNA (siRNA) is a short double-stranded RNA molecule (about 21-23 nucleotides) with the potential to cure diseases by silencing the function of target genes. Due to its well-understood mechanism, many siRNA-based drugs have…
Understanding disease similarity is critical for advancing diagnostics, drug discovery, and personalized treatment strategies. We present PhenoGnet, a novel graph-based contrastive learning framework designed to predict disease similarity…