IEEE transactions on nanobioscience
Jan 2, 2025
Traditional DNA storage technologies rely on passive filtering methods for error correction during synthesis and sequencing, which result in redundancy and inadequate error correction. Addressing this, the Low Quality Sequence Filter (LQSF) was intro...
Small methods
Dec 29, 2024
As one main form of multimedia data, images play a critical role in various applications. In this paper, a representation-based architecture is proposed which takes advantage of the outstanding representation and image-generation abilities of deep le...
Neural networks : the official journal of the International Neural Network Society
Dec 19, 2024
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-...
IEEE/ACM transactions on computational biology and bioinformatics
Dec 10, 2024
DNA N-methyladenine (6mA) is an important epigenetic modification that plays a vital role in various cellular processes. Accurate identification of the 6mA sites is fundamental to elucidate the biological functions and mechanisms of modification. How...
Neural networks : the official journal of the International Neural Network Society
Dec 7, 2024
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...
Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology
Dec 5, 2024
This short paper presents an educational approach to teaching three popular methods for encoding DNA sequences: one-hot encoding, binary encoding, and integer encoding. Aimed at bioinformatics and computational biology students, our learning interven...
Astrobiology
Nov 29, 2024
Life on Earth relies on mechanisms to store heritable information and translate this information into cellular machinery required for biological activity. In all known life, storage, regulation, and translation are provided by DNA, RNA, and ribosomes...
Technology and health care : official journal of the European Society for Engineering and Medicine
Nov 20, 2024
BackgroundDeep learning excels at processing raw data because it automatically extracts and classifies high-level features. Despite biology's low popularity in data analysis, incorporating computer technology can improve biological research.Objective...
International journal of biological macromolecules
Nov 19, 2024
CRISPR/Cas9 technology is widely used for gene editing, but off-targeting still remains a major concern in therapeutic applications. Although Cas9 variants with better mismatch discrimination have been developed, they have significantly lower rates o...
Nature communications
Nov 16, 2024
Understanding how genetic variants affect the epigenome is key to interpreting GWAS, yet profiling these effects across the non-coding genome remains challenging due to experimental scalability. This necessitates accurate computational models. Existi...