Genomics
There has been a growing acknowledgement of the involvement of the gut microbiome - the collection of microbes that reside in our gut - in regulating our mood and behaviour. This phenomenon is referred to as the microbiome-gut-brain axis.…
Advances in gene sequencing have enabled in silico analyses of microbial genomes and have led to the revision of concepts of microbial taxonomy and evolution. We explore deficiencies in existing multiple sequence global alignment algorithms…
The intra- and inter-species genetic diversity of bacteria and the absence of 'reference', or the most representative, sequences of individual species present a significant challenge for sequence-based identification. The aims of this study…
The aim of this study was to develop a method that would identify the cluster centroids and the optimal number of clusters for a given sensitivity level and could work equally well for the different sequence datasets. A novel method that…
The translation of comparative genomics into clinical decision support tools often depends on the quality of sequence alignments. However, currently used methods of multiple sequence alignments suffer from significant biases and problems…
Single-cell multi-view clustering enables the exploration of cellular heterogeneity within the same cell from different views. Despite the development of several multi-view clustering methods, two primary challenges persist. Firstly, most…
The package mvlearnR and accompanying Shiny App is intended for integrating data from multiple sources or views or modalities (e.g. genomics, proteomics, clinical and demographic data). Most existing software packages for multiview learning…
Splice sites play a crucial role in gene expression, and accurate prediction of these sites in DNA sequences is essential for diagnosing and treating genetic disorders. We address the challenge of splice site prediction by introducing…
Given the increasing availability of RNA-seq data and its complex and heterogeneous nature, there has been growing interest in applying AI/machine learning methodologies to work with such data modalities. However, because omics data is…
Given several number sequences, determining the longest common subsequence is a classical problem in computer science. This problem has applications in bioinformatics, especially determining transposable genes. Nevertheless, related works…
A genome read data set can be quickly and efficiently remapped from one reference to another similar reference (e.g., between two reference versions or two similar species) using a variety of tools, e.g., the commonly-used CrossMap tool.…
Massively parallel sequencing techniques have revolutionized biological and medical sciences by providing unprecedented insight into the genomes of humans, animals, and microbes. Modern sequencing platforms generate enormous amounts of…
Motivation: We introduce SneakySnake, a highly parallel and highly accurate pre-alignment filter that remarkably reduces the need for computationally costly sequence alignment. The key idea of SneakySnake is to reduce the approximate string…
Given a flow network, the Minimum Flow Decomposition (MFD) problem is finding the smallest possible set of weighted paths whose superposition equals the flow. It is a classical, strongly NP-hard problem that is proven to be useful in RNA…
Human aging is a process controlled by both genetics and environment. Many studies have been conducted to identify a subset of genes related to aging from the human genome. Biologists implicitly categorize age-related genes into genes that…
Human genetic diseases often arise from point mutations, emphasizing the critical need for precise genome editing techniques. Among these, base editing stands out as it allows targeted alterations at the single nucleotide level. However,…
In the rapidly evolving landscape of genomics, deep learning has emerged as a useful tool for tackling complex computational challenges. This review focuses on the transformative role of Large Language Models (LLMs), which are mostly based…
The human genome encodes a family of editing enzymes known as APOBEC3 (apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3). Several family members, such as APO-BEC3G, APOBEC3F, and APOBEC3H haplotype II, exhibit activity…
Clinical variant classification of pathogenic versus benign genetic variants remains a pivotal challenge in clinical genetics. Recently, the proposition of protein language models has improved the generic variant effect prediction (VEP)…
Biological functions stem from coordinated interactions among proteins, nucleic acids and small molecules. Mass spectrometry technologies for reliable, high throughput single-cell proteomics will add a new modality to genomics and enable…