Decoding DNA methylation sites through nanopore sequencing has emerged as a cutting-edge technology in the field of DNA methylation research, as it enables direct sequencing of native DNA molecules without the need for prior enzymatic or chemical tre...
The efficient analysis and interpretation of biological sequence data remain major challenges in bioinformatics. Graphical representation, as an emerging and effective visualization technique, offers a more intuitive method for analyzing DNA sequence...
DNBSEQ employs a patterned array to facilitate massively parallel sequencing of DNA nanoballs (DNBs), leading to a considerable boost in throughput. By employing the ultra-high-density (UHD) array with an increased density of DNB binding sites, the t...
International journal of molecular sciences
39519295
Enhancers are cis-regulatory DNA sequences that are widely distributed throughout the genome. They can precisely regulate the expression of target genes. Since the features of enhancer segments are difficult to detect, we propose DeepDualEnhancer, a ...
Identification of body fluid stain at crime scene is one of the important tasks of forensic evidence analysis. Currently, body fluid-specific CpGs detected by DNA methylation microarray screening, have been widely studied for forensic body fluid iden...
BACKGROUND: Accurate prediction of copy number variations (CNVs) from targeted capture next-generation sequencing (NGS) data relies on effective normalization of read coverage profiles. The normalization process is particularly challenging due to hid...
Neural networks : the official journal of the International Neural Network Society
39709643
Accurate modeling of DNA sequences requires capturing distant semantic relationships between the nucleotide acid bases. Most existing deep neural network models face two challenges: (1) they are limited to short DNA fragments and cannot capture long-...
The human microbiome, the community of microorganisms that reside on and inside the human body, is critically important for health and disease. However, it is influenced by various factors and may vary among individuals residing in distinct geographi...
Neural networks : the official journal of the International Neural Network Society
39667220
Self-supervised Learning (SSL) has been recognized as a method to enhance prediction accuracy in various downstream tasks. However, its efficacy for DNA sequences remains somewhat constrained. This limitation stems primarily from the fact that most e...
The critical stage of every de novo genome assembler is identifying paths in assembly graphs that correspond to the reconstructed genomic sequences. The existing algorithmic methods struggle with this, primarily due to repetitive regions causing comp...