IEEE/ACM transactions on computational biology and bioinformatics
Oct 7, 2021
The rapid development of high-throughput sequencing technology provides unique opportunities for studying of transcription factor binding sites, but also brings new computational challenges. Recently, a series of discriminative motif discovery (DMD) ...
How noncoding DNA determines gene expression in different cell types is a major unsolved problem, and critical downstream applications in human genetics depend on improved solutions. Here, we report substantially improved gene expression prediction a...
As a key component of gene regulation, transcription factors (TFs) play an important role in a number of biological processes. To fully understand the underlying mechanism of TF-mediated gene regulation, it is therefore critical to accurately identif...
Protein-DNA interactions play an important role in biological progress, such as DNA replication, repair, and modification processes. In order to have a better understanding of its functions, the one of the most important steps is the identification o...
Prime editing is a revolutionary genome-editing technology that can make a wide range of precise edits in DNA. However, designing highly efficient prime editors (PEs) remains challenging. We develop Easy-Prime, a machine learning-based program traine...
Promoter is a region of DNA that determines the transcription of a particular gene. There are several σ factors in the RNA polymerase, which has the function of identifying the promoter and facilitating the binding of the RNA polymerase to the promot...
Enhancers are regulatory elements involved in gene expression.It is a part of DNA, which can enhance the transcription rate of gene. However, the identification of enhancer by biological experimental methods is time-consuming and expensive. Therefore...
Journal of the American Chemical Society
Aug 4, 2021
An arrayed host:guest fluorescence sensor system can discriminate among and classify multiple different noncanonical DNA structures by exploiting selective molecular recognition. The sensor is highly selective and can discriminate between folds as si...
Journal of bioinformatics and computational biology
Jul 21, 2021
Accurate detection of N6-methyladenine (6mA) sites by biochemical experiments will help to reveal their biological functions, still, these wet experiments are laborious and expensive. Therefore, it is necessary to introduce a powerful computational m...
Targeted high-throughput DNA sequencing is a primary approach for genomics and molecular diagnostics, and more recently as a readout for DNA information storage. Oligonucleotide probes used to enrich gene loci of interest have different hybridization...