Physical chemistry chemical physics : PCCP
Dec 21, 2023
Biological processes such as transcription, repair, and regulation require interactions between DNA and proteins. To unravel their functions, it is imperative to determine the high-resolution structures of DNA-protein complexes. However, experimental...
Nature
Dec 13, 2023
Gene expression is regulated by transcription factors that work together to read cis-regulatory DNA sequences. The 'cis-regulatory code' - how cells interpret DNA sequences to determine when, where and how much genes should be expressed - has proven ...
Science robotics
Dec 6, 2023
Nanoscale industrial robots have potential as manufacturing platforms and are capable of automatically performing repetitive tasks to handle and produce nanomaterials with consistent precision and accuracy. We demonstrate a DNA industrial nanorobot t...
Neural networks : the official journal of the International Neural Network Society
Dec 2, 2023
DNA molecules commonly exhibit wide interactions between the nucleobases. Modeling the interactions is important for obtaining accurate sequence-based inference. Although many deep learning methods have recently been developed for modeling DNA sequen...
Nature genetics
Nov 30, 2023
Deep learning methods have recently become the state of the art in a variety of regulatory genomic tasks, including the prediction of gene expression from genomic DNA. As such, these methods promise to serve as important tools in interpreting the ful...
PloS one
Oct 19, 2023
DNA has been discussed as a potential medium for data storage. Potentially it could be denser, could consume less energy, and could be more durable than conventional storage media such as hard drives, solid-state storage, and optical media. However, ...
Nature communications
Oct 17, 2023
Single-molecule experiments have changed the way we explore the physical world, yet data analysis remains time-consuming and prone to human bias. Here, we introduce Deep-LASI (Deep-Learning Assisted Single-molecule Imaging analysis), a software suite...
Journal of molecular biology
Oct 16, 2023
Enhancers are DNA regions that are responsible for controlling the expression of genes. Enhancers are usually found upstream or downstream of a gene, or even inside a gene's intron region, but are normally located at a distant location from the genes...
Journal of translational medicine
Oct 16, 2023
This paper addresses the crucial task of identifying DNA/RNA binding sites, which has implications in drug/vaccine design, protein engineering, and cancer research. Existing methods utilize complex neural network structures, diverse input types, and ...
International journal of molecular sciences
Oct 11, 2023
Data obtained with the use of massive parallel sequencing (MPS) can be valuable in population genetics studies. In particular, such data harbor the potential for distinguishing samples from different populations, especially from those coming from adj...