The Ribosomal Operon Database (ROD): A full-length rDNA operon database extracted from genome assemblies

Current rDNA reference sequence databases are tailored towards shorter DNA markers, such as parts of the 16/18S marker or the ITS region.

MotifScope: a multi-sample motif discovery and visualization tool for tandem repeats

Tandem repeats (TRs) constitute a significant portion of the human genome, exhibiting high levels of polymorphism due to variations in size and motif composition.

Direction-aware functional class scoring enrichment analysis of Infinium DNA methylation data

Infinium Methylation BeadChip arrays remain one of the most popular platforms for epigenome-wide association studies, but tools for downstream pathway analysis have their limitations.

Large language models improve annotation of prokaryotic viral proteins - Nature Microbiology

Ocean viral proteome annotations are expanded by a machine learning approach that is not reliant on sequence homology and can annotate sequences not homologous to those seen in training.

Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy - Nature Biotechnology

Nature Biotechnology - Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy

Robust, scalable, and informative clustering for diverse biological networks - Genome Biology

Clustering molecular data into informative groups is a primary step in extracting robust conclusions from big data.

FindAPhD : Pathogens and Host Defences Doctoral Training Partnership PhD Studentships at University of Sussex

Apply for a PhD: Pathogens and Host Defences Doctoral Training Partnership PhD Studentships at University of Sussex

Ongoing shuffling of protein fragments diversifies core viral functions linked to interactions with bacterial hosts - Nature Communications

Proteins are composed of distinct functional domains, each serving a specific role. Here, Smug et al. show that phages are able to shuffle fragments of their proteins and this predominantly occurs in proteins involved in bacterial host interactions.

Postdoctoral Fellow in Phylogenomics/Bioinformatics

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PhD position in viral evolution and diversity

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Remarkably high repeat content in the genomes of sparrows: the importance of genome assembly completeness for transposable element discovery.

Transposable elements (TE) play critical roles in shaping genome evolution. However, the highly repetitive sequence content of TEs is a major source of assembly gaps.

Universal signatures of transposable element compartmentalization across eukaryotic genes

The evolutionary mechanisms shaping the origins of genome architecture remain poorly understood but can now be assessed with unprecedented power due to the abundance of genome assemblies spanning phylogenetic diversity.

Systematic identification of cargo-carrying genetic elements reveals new dimensions of eukaryotic diversity

Cargo-carrying mobile elements (CCEs) are genetic entities that transpose diverse protein coding sequences. Although common in bacteria, we know little about the biology of eukaryotic CCEs because no appropriate tools exist for their annotation.

Long-read-based genome assembly reveals numerous endogenous viral elements in the green algal bacterivore Cymbomonas tetramitiformis

Abstract. The marine tetraflagellate Cymbomonas tetramitiformis has drawn attention as an early diverging green alga that uses a phago-mixotrophic mode of nutri

CRAN - Package phylter

ERGA BioGenome Analysis and Applications Seminars

The ERGA BioGenome Analysis and Applications Seminars represent a joint endeavor of the ERGA Data Analysis Committee (DAC) and the Biodiversity Genomics Europe Work Package 11 - Genome Applications.

Bacterial histones unveiled - Nature Microbiology

Computational, molecular and structural analyses reveal the presence of bacterial histones that bind DNA to form dense, DNA-enveloping fibres in Bdellovibrio bacteriovorus.

Polinton-like Viruses Associated with Entomopoxviruses Provide Insight into Replicon Evolution

Polinton-like viruses (PLVs) are a diverse group of small integrative dsDNA viruses that infect diverse eukaryotic hosts. Many PLVs are hypothesized to parasitize viruses in the phylum Nucleocytoviricota for their own propagation and spread.

Robert M. Waterhouse

Waterhouse Group Arthropoda Assembly Assessment Catalogue | DrosOMA Orthology Database | GO-Figure! Gene Ontology Visualisation

Revisiting genomes of non-model species with long reads yields new insights into their biology and evolution

High-quality genomes obtained using long-read data allow not only for a better understanding of heterozygosity levels, repeat content, and more accurate gene annotation, and prediction when compared to those obtained with short-read technologies, but…

Automated Bioinformatics Analysis via AutoBA

With the fast-growing and evolving omics data, the demand for streamlined and adaptable tools to handle the analysis continues to grow.

Redirecting

Phage-plasmids promote genetic exchanges between phages and plasmids and create novel ones.

Phages and plasmids have key roles in bacterial evolution and are usually very different. Yet, they must recombine, since they sometimes carry nearly identical accessory genes.

Major data analysis errors invalidate cancer microbiome findings

We re-analyzed the data from a recent large-scale study that reported strong correlations between microbial organisms and 33 different cancer types, and that created machine learning predictors with near-perfect accuracy at distinguishing among cance…

Building trees with SKA

SKA is a tool for comparing small and highly similar genomes using split k-mers. This guide will explain how to use SKA to build a phylogenetic tree for different Escherichia coli lineages in a few minutes.

PhD Researcher in Bioinformatics: Investigating protein evolution using machine learning

Three new genome assemblies of blue mussel lineages: North and South European Mytilus edulis and Mediterranean Mytilus galloprovincialis

The blue mussel species complex ( Mytilus edulls ) is of particular interest both as model species in population genetics and ecology, but also as an economic resource in many regions.

Unraveling the tangled evolution of figs

Containing more than 850 species, fig trees are one of the most diverse groups of plants in the world.

miniBUSCO: a faster and more accurate reimplementation of BUSCO

Motivation Assembly completeness evaluation of genome assembly is a critical assessment of the accuracy and reliability of genomic data. An incomplete assembly can lead to errors in gene predictions, annotation, and other downstream analyses.

Empirical Evidence That Complexity Limits Horizontal Gene Transfer

Abstract. Horizontal gene transfer (HGT) is a major contributor to bacterial genome evolution, generating phenotypic diversity, driving the expansion of protein

Built Into the Genome of the Microbes – Scientists Uncover Over 30,000 “Hidden” Viruses

Unveiled within the DNA of unicellular organisms lie thousands of enigmatic viruses. Researchers at the University of Innsbruck, utilizing the high-performance computing cluster known as "Leo," have identified more than 30,000 new viruses embedded wi…

Mobile element variation contributes to population-specific genome diversification, gene regulation and disease risk - Nature Genetics

MEGAnE is a new tool to detect and genotype mobile element variants (MEVs) from short-read whole-genome sequencing datasets. Genetic analyses implicate MEVs as population-specific drivers of gene expression variation and disease risk.

Every base everywhere all at once: pangenomics comes of age

Multi-genome assemblies called pangenomes can capture genetic diversity in a species, but researchers are still working out how best to build and explore them.