Related papers: RNAmountAlign: efficient software for local, globa…

RNA folding prediction remains challenging, but can be also studied using a topological mathematical approach. In the present paper, the mathematical method to compute the topological classification of RNA structures and based on matrix…

Recurrent Neural Networks (RNNs) are important tools for processing sequential data such as time-series or video. Interpretability is defined as the ability to be understood by a person and is different from explainability, which is the…

Conformational entropy for atomic-level, three dimensional biomolecules is known experimentally to play an important role in protein-ligand discrimination, yet reliable computation of entropy remains a difficult problem. Here we describe…

Proteins are essential biological macromolecules that execute life functions. Local structural motifs, such as active sites, are the most critical components for linking structure to function and are key to understanding protein evolution…

Accurate segmentation and classification of nuclei in histology images is critical but challenging due to nuclei heterogeneity, staining variations, and tissue complexity. Existing methods often struggle with limited dataset variability,…

Accurate prediction of RNA three-dimensional (3D) structure remains an unsolved challenge. Determining RNA 3D structures is crucial for understanding their functions and informing RNA-targeting drug development and synthetic biology design.…

Computational RNA design tasks are often posed as inverse problems, where sequences are designed based on adopting a single desired secondary structure without considering 3D conformational diversity. We introduce gRNAde, a geometric RNA…

It has been proven that the accessibility of the target sites has a critical influence for miRNA and siRNA. In this paper, we present a program, rip2.0, not only the energetically most favorable targets site based on the hybrid-probability,…

Biological network alignment aims to identify similar regions between networks of different species. Existing methods compute node "similarities" to rapidly identify from possible alignments the "high-scoring" alignments with respect to the…

Increasing test-time computation has emerged as a promising direction for improving language model performance, particularly in scenarios where model finetuning is impractical or impossible due to computational constraints or private model…

Calculating the similarities between a pair of genomic sequences is one of the most fundamental computational steps in genomic analysis. This step -- called sequence alignment -- is the computational bottleneck because: (1) it is…

Structural prediction has long been considered critical in RNA research, especially following the success of AlphaFold2 in protein studies, which has drawn significant attention to the field. While recent advances in machine learning and…

RNA design aims to identify RNA sequences that fold into a target secondary structure. This task is challenging in terms of computational efficiency. Most existing methods focus on either minimum free energy (MFE)-based or ensemble-based…

Sequence alignments are fundamental to bioinformatics which has resulted in a variety of optimized implementations. Unfortunately, the vast majority of them are hand-tuned and specific to certain architectures and execution models. This not…

We propose a modified MSA algorithm on quantum annealers with applications in areas of bioinformatics and genetic sequencing. To understand the human genome, researchers compare extensive sets of these genetic sequences -- or their protein…

Algorithmic sequence alignment identifies similar segments shared between pairs of documents, and is fundamental to many NLP tasks. But it is difficult to recognize similarities between distant versions of narratives such as translations…

Short Read Alignment Mapping Metrics (SRAMM): is an efficient and versatile command line tool providing additional short read mapping metrics, filtering, and graphs. Short read aligners report MAPing Quality (MAPQ), but these methods…

Motivation: Non-coding RNAs (ncRNAs) express their functions by adopting molecular structures. Specifically, RNA secondary structures serve as a relatively stable intermediate step before tertiary structures, offering a reliable signature…

Pattern matching is a fundamental process in almost every scientific domain. The problem involves finding the positions of a given pattern (usually of short length) in a reference stream of data (usually of large length). The matching can…

We present a novel approach to RNA-Seq quantification that is near optimal in speed and accuracy. Software implementing the approach, called kallisto, can be used to analyze 30 million unaligned paired-end RNA-Seq reads in less than 5…