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Background: Small interfering RNA (siRNA) is a promising therapeutic agent due to its ability to silence disease-related genes via RNA interference. While traditional machine learning and early deep learning methods have made progress in…
Both short interfering RNAs (siRNAs) and microRNAs (miRNAs) mediate the repression of specific sequences of mRNA through the RNA interference pathway. In the last years several experiments have supported the hypothesis that siRNAs and…
Saliency maps are increasingly used as design guidance in siRNA efficacy prediction, yet attribution methods are rarely validated before motivating sequence edits. We introduce a pre-synthesis gate: a protocol for counterfactual sensitivity…
According to the `ceRNA hypothesis', microRNAs (miRNAs) may act as mediators of an effective positive interaction between long coding or non-coding RNA molecules, carrying significant potential implications for a variety of biological…
MicroRNAs (miRNAs) are small non-coding RNAs that control gene expression at the post-transcriptional level through complementary base pairing with the target mRNA, leading to mRNA degradation and blocking translation process. Any…
The pharmaceutical Research and development (R&D) process is lengthy and costly, taking nearly a decade to bring a new drug to the market. However, advancements in biotechnology, computational methods, and machine learning algorithms have…
MicroRNAs (miRNAs) are short sequences of ribonucleic acids that control the expression of target messenger RNAs (mRNAs) by binding them. Robust prediction of miRNA-mRNA pairs is of utmost importance in deciphering gene regulations but has…
Small regulatory RNAs (sRNAs) are short non-coding RNAs in bacteria capable of post-transcriptional regulation. sRNAs have recently gained attention as tools in basic and applied sciences for example to fine-tune genetic circuits or…
MicroRNAs (miRNAs) play crucial roles in multifarious biological processes associated with human diseases. Identifying potential miRNA-disease associations contributes to understanding the molecular mechanisms of miRNA-related diseases.…
MicroRNAs (miRNAs) are a class of small noncoding RNAs that can regulate many genes by base pairing to sites in mRNAs. The functionality of miRNAs overlaps that of short interfering RNAs (siRNAs), and many features of miRNA targeting have…
MicroRNA (miRNA) are small non-coding RNAs that regulates the gene expression at the post-transcriptional level. Determining whether a sequence segment is miRNA is experimentally challenging. Also, experimental results are sensitive to the…
We build a simple model for feedback systems involving small RNA (sRNA) molecules based on the iron metabolism system in the bacterium E. coli, and compare it with the corresponding system in H. pylori which uses purely transcriptional…
Infrared small target detection based on deep learning offers unique advantages in separating small targets from complex and dynamic backgrounds. However, the features of infrared small targets gradually weaken as the depth of convolutional…
Sequential recommender systems (SRSs) aim to predict the subsequent items which may interest users via comprehensively modeling users' complex preference embedded in the sequence of user-item interactions. However, most of existing SRSs…
Functional or non-coding RNAs are attracting more attention as they are now potentially considered valuable resources in the development of new drugs intended to cure several human diseases. The identification of drugs targeting the…
Solving the RNA inverse folding problem is a critical prerequisite to RNA design, an emerging field in bioengineering with a broad range of applications from reaction catalysis to cancer therapy. Although significant progress has been made…
MicroRNAs (miRNAs) are endogenous small non-coding RNAs that play an important role in post-transcriptional gene regulation. However, the experimental determination of miRNA sequence and structure is both expensive and time-consuming.…
RNA/protein interactions play crucial roles in controlling gene expression. They are becoming important targets for pharmaceutical applications. Due to RNA flexibility and to the strength of electrostatic interactions, standard docking…
Since microRNAs (miRNAs) play a crucial role in post-transcriptional gene regulation, miRNA identification is one of the most essential problems in computational biology. miRNAs are usually short in length ranging between 20 and 23 base…
Bacteria reside in constantly changing environments and require rapid and precise adjustments of gene expression to ensure survival. Small regulatory RNAs (sRNAs) are a crucial element that bacteria utilize to achieve this. sRNAs are short…