Advances in three-dimensional (3D) genomics have revealed the spatial characteristics of chromatin interactions in gene expression regulation, which is crucial for understanding molecular mechanisms in biological processes. High-throughput technologi...
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...
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-...
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...
Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology
39633594
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...
BACKGROUND/OBJECTIVES: Predicting the effects of protein and DNA mutations on the binding free energy of protein-DNA complexes is crucial for understanding how DNA variants impact wild-type cellular function. As many cellular interactions involve pro...
The journal of physical chemistry letters
39849911
Surface-enhanced Raman spectroscopy (SERS) has become an indispensable tool for biomolecular analysis, yet the detection of DNA signals remains hindered by spectral interference from citrate ions, which overlap with key DNA features. This study intro...
Artificially synthesized DNA holds significant promise in addressing fundamental biochemical questions and driving advancements in biotechnology, genetics, and DNA digital data storage. Rapid and precise electric identification of these artificial DN...
Promoters are essential DNA sequences that initiate transcription and regulate gene expression. Precisely identifying promoter sites is crucial for deciphering gene expression patterns and the roles of gene regulatory networks. Recent advancements in...
Gene regulation is inherently multiscale, but scale-adaptive machine learning methods that fully exploit this property in single-nucleus accessibility data are still lacking. Here, we develop ChromatinHD, a pair of scale-adaptive models that uses the...