2'-O-methylation (2OM) is the most common post-transcriptional modification of RNA. It plays a crucial role in RNA splicing, RNA stability and innate immunity. Despite advances in high-throughput detection, the chemical stability of 2OM makes it diff...
Neural networks : the official journal of the International Neural Network Society
38150872
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...
i-Motifs (iMs), are secondary structures formed in cytosine-rich DNA sequences and are involved in multiple functions in the genome. Although putative iM forming sequences are widely distributed in the human genome, the folding status and strength of...
Journal of chemical information and modeling
38648189
It is now known that RNAs play more active roles in cellular pathways beyond simply serving as transcription templates. These biological mechanisms might be mediated by higher RNA stereo conformations, triggering the need to understand RNA secondary ...
Journal of chemical information and modeling
38739914
Owing to the value of DNA-wrapped single-walled carbon nanotube (SWNT)-based sensors for chemically specific imaging in biology, we explore machine learning (ML) predictions DNA-SWNT serotonin sensor responsivity as a function of DNA sequence based o...
Cell-type-specific regulatory elements, cataloged through extensive experiments and bioinformatics in large-scale consortiums, have enabled enrichment analyses of genetic associations that primarily utilize positional information of the regulatory el...
Chromatin interactions create spatial proximity between distal regulatory elements and target genes in the genome, which has an important impact on gene expression, transcriptional regulation, and phenotypic traits. To date, several methods have been...
Language models, especially transformer-based ones, have achieved colossal success in natural language processing. To be precise, studies like BERT for natural language understanding and works like GPT-3 for natural language generation are very impor...
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-...
Riboswitches are a class of noncoding RNA structures that interact with target ligands to cause a conformational change that can then execute some regulatory purpose within the cell. Riboswitches are ubiquitous and well characterized in bacteria and ...