In the field of genomics, understanding the spatial organization of the genome is crucial for uncovering gene regulatory mechanisms. Hi-C technology, as a genome-wide chromosome conformation capture technique, can reveal the three-dimensional structure of the genome, particularly the key role of chromatin loops in gene regulation. However, existing...
Non-coding RNAs (ncRNAs) play critical roles in cellular processes and disease development. Although genome sequencing projects have revealed a vast number of non-coding genes, the functional classification of ncRNAs remains a complex and challenging issue. The diversity, complexity, and functionality of ncRNAs make them important subjects in biome...
Privacy-Preserving Framework for Genomic Analysis: A Study Based on Multi-Key Homomorphic Encryption Academic Background With the reduction in the cost of genome sequencing, the widespread availability of genomic data has opened up new possibilities for personalized medicine (also known as genomic medicine). However, genomic data contains a vast am...
T-cell receptors (TCRs) play a crucial role in the adaptive immune system by recognizing pathogens through binding to specific antigen epitopes. Understanding the interactions between TCRs and epitopes is essential for uncovering the biological mechanisms of immune responses and developing T cell-mediated immunotherapies. However, although the impo...
Academic Background With the rapid advancement of sequencing technology, scientists have been able to obtain a vast amount of protein sequence data, including many enzyme sequences. However, despite the establishment of large enzyme databases such as the Kyoto Encyclopedia of Genes and Genomes (KEGG) and BRENDA, sequence information for many enzyme...
Plasmids are small, circular, double-stranded DNA molecules that exist independently of chromosomal DNA in bacteria. They facilitate horizontal gene transfer, enabling host bacteria to acquire beneficial traits such as antibiotic resistance and metal resistance. Some plasmids can transfer, replicate, or persist in multiple microorganisms, and these...
Academic Background DNA sequence alignment is a core task in genomics, aiming to map short DNA fragments (reads) to the most probable locations on a reference genome. Traditional methods typically involve two steps: first, indexing the genome, followed by efficient searching to locate potential positions for the reads. However, with the exponential...
During tumor development, copy number alterations (CNAs) are key drivers of tumor heterogeneity and evolution. Understanding these variations is crucial for developing personalized cancer diagnostics and therapies. Single-cell sequencing technology offers the highest resolution for copy number analysis, down to the individual cell level. However, l...
The three-dimensional structure of a protein is determined by its amino acid sequence, and the function of the protein is highly dependent on its three-dimensional structure. The side-chain conformations of proteins play a crucial role in protein folding, protein-protein interactions, and de novo protein design. Accurate prediction of protein side-...
Academic Background Cryogenic Electron Microscopy (Cryo-EM) is a crucial experimental technique for determining the structures of macromolecules such as proteins. However, the effectiveness of Cryo-EM is often hindered by noise and missing density values caused by experimental conditions such as low contrast and conformational heterogeneity. Althou...