Proceedings of the National Academy of Sciences of the United States of America
Apr 6, 2023
Discovering DNA regulatory sequence motifs and their relative positions is vital to understanding the mechanisms of gene expression regulation. Although deep convolutional neural networks (CNNs) have achieved great success in predicting cis-regulator...
IEEE/ACM transactions on computational biology and bioinformatics
Feb 3, 2023
A DNA motif is a sequence pattern shared by the DNA sequence segments that bind to a specific protein. Discovering motifs in a given DNA sequence dataset plays a vital role in studying gene expression regulation. As an important attribute of the DNA ...
It is well-established that neural networks can predict or identify structural motifs of non-coding RNAs (ncRNAs). Yet, the neural network based identification of RNA structural motifs is limited by the availability of training data that are often in...
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...
BACKGROUND: Cis-regulatory elements (CREs) are DNA sequence segments that regulate gene expression. Among CREs are promoters, enhancers, Boundary Elements (BEs) and Polycomb Response Elements (PREs), all of which are enriched in specific sequence mot...
ChIP-seq is one of the core experimental resources available to understand genome-wide epigenetic interactions and identify the functional elements associated with diseases. The analysis of ChIP-seq data is important but poses a difficult computation...
The biology of bacterial cells is, in general, based on information encoded on circular chromosomes. Regulation of chromosome replication is an essential process that mostly takes place at the origin of replication (oriC), a locus unique per chromoso...
There is increasing interest in developing diagnostics that discriminate individual mutagenic mechanisms in a range of applications that include identifying population-specific mutagenesis and resolving distinct mutation signatures in cancer samples....
Deep learning has become a powerful paradigm to analyze the binding sites of regulatory factors including RNA-binding proteins (RBPs), owing to its strength to learn complex features from possibly multiple sources of raw data. However, the interpreta...
BACKGROUND: There are many different types of microRNAs (miRNAs) and elucidating their functions is still under intensive research. A fundamental step in functional annotation of a new miRNA is to classify it into characterized miRNA families, such a...
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