Related papers: Long non-coding RNAs as a source of new peptides

The RNA inverse folding problem, a key challenge in RNA design, involves identifying nucleotide sequences that can fold into desired secondary structures, which are critical for ensuring molecular stability and function. The inherent…

Cancer is one of the leading causes of human death. Many efforts have made to understand its mechanism and have further identified many proteins and DNA sequence variations as suspected targets for therapy. However, drugs targeting these…

Convolutional neural networks (CNN) have led to many state-of-the-art results spanning through various fields. However, a clear and profound theoretical understanding of the forward pass, the core algorithm of CNN, is still lacking. In…

Learning latent representations from long text sequences is an important first step in many natural language processing applications. Recurrent Neural Networks (RNNs) have become a cornerstone for this challenging task. However, the quality…

Isoforms are mRNAs produced from the same gene site in the phenomenon called Alternative Splicing. Studies have shown that more than 95% of human multi-exon genes have undergone alternative splicing. Although there are few changes in mRNA…

Transcription factors are proteins that regulate gene activity by activating or repressing gene transcription. A special class of transcriptional repressors operates via a short-range mechanism, making local DNA regions inaccessible to…

Fast radio bursts (FRBs) are millisecond-duration radio flashes of extragalactic origin, with magnetars implicated as viable central engines. Yet their triggering and radiation mechanisms remain unknown. Radio telescopes inevitably record…

A transversal topic of my research has been the development and application of computational methods for DNA sequence analysis. The methods I have been developing aim at improving our understanding of the regulation processes happening in…

microRNAs (miRNAs) regulate gene expression at post-transcriptional level by repressing target RNA molecules. Competition to bind miRNAs tends in turn to correlate their targets, establishing effective RNA-RNA interactions that can…

The work in this paper aims at determining the evolution and possible co-evolution of radio-loud active galactic nuclei (AGNs) and their cores via their radio luminosity functions (i.e., total and core RLF respectively). Using a large…

The DNA storage channel is considered, in which a codeword is comprised of $M$ unordered DNA molecules. At reading time, $N$ molecules are sampled with replacement, and then each molecule is sequenced. A coded-index concatenated-coding…

Ultra-reliable low-latency communications (URLLC) demand decoding algorithms that simultaneously offer high reliability and low complexity under stringent latency constraints. While iterative decoding schemes for LDPC and Polar codes offer…

Recurrent Neural Networks (RNNs), and specifically a variant with Long Short-Term Memory (LSTM), are enjoying renewed interest as a result of successful applications in a wide range of machine learning problems that involve sequential data.…

Background. Non-specific Lipid Transfer Proteins (nsLTPs) are widely distributed in the plant kingdom and constitute a superfamily of related proteins. More than 800 different sequences have been characterized so far, but their biological…

In order to survive, reproduce and (in multicellular organisms) differentiate, cells must control the concentrations of the myriad different proteins that are encoded in the genome. The precision of this control is limited by the inevitable…

The interactions between DNA, RNA, and proteins are fundamental to biological processes, as illustrated by the central dogma of molecular biology. Although modern biological pre-trained models have achieved great success in analyzing these…

Long short-term memory (LSTM) recurrent neural networks (RNNs) have been shown to give state-of-the-art performance on many speech recognition tasks, as they are able to provide the learned dynamically changing contextual window of all…

Our work is concerned with the generation and targeted design of RNA, a type of genetic macromolecule that can adopt complex structures which influence their cellular activities and functions. The design of large scale and complex…

Background: The evolution of microRNA regulation in metazoans is a mysterious process: MicroRNA sequences are highly conserved among distal organisms, but on the other hand, there is no evident conservation of their targets. Results: We…

Large language models (LLMs) have shown promise in various natural language processing tasks, including their application to proteomics data to classify protein fragments. In this study, we curated a limited mass spectrometry dataset with…