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.

JASPER: A fast genome polishing tool that improves accuracy of genome assemblies

Advances in long-read sequencing technologies have dramatically improved the contiguity and completeness of genome assemblies.

NGenomeSyn: an easy-to-use and flexible tool for publication-ready visualization of syntenic relationships across multiple genomes

AbstractSummary. Large-scale comparative genomic studies have provided important insights into species evolution and diversity, but also lead to a great challen

Linking prokaryotic genome size variation to metabolic potential and environment - ISME Communications

ISME Communications - Linking prokaryotic genome size variation to metabolic potential and environment

The methanogen core and pangenome: conservation and variability across biology’s growth temperature extremes

Abstract. Temperature is a key variable in biological processes. However, a complete understanding of biological temperature adaptation is lacking, in part beca

Scaling of Protein Function Across the Tree of Life

Scaling laws are a powerful way to compare genomes because they put all organisms onto a single curve and reveal non-trivial generalities as genomes change in size.

Regulatory dissection of the severe COVID-19 risk locus introgressed by Neanderthals

Key functional variants, discovered using Massively Parallel Reporter Assay (MPRA) and reporter assays in the context of SARS-CoV-2 infection, support the importance of two critical chemokine receptor genes CCR1 and CCR5 in severe Covid-19 illness.

NCBI Minute: Using BLAST Well

Presented October 3, 2018. In this webinar, the NCBI BLAST team lead will show you how to be more effective with NCBI’s standalone BLAST applications. You wi...

Decades-old crustaceans coaxed from lake mud give up genetic secrets revealing evolution in action

Human actions are changing the environment at an unprecedented rate. Plant and animal populations must try to keep up with these human-accelerated changes, often by trying to rapidly evolve tolerance to changing conditions.

Quantifying the local adaptive landscape of a nascent bacterial community - Nature Communications

Fitness landscapes largely shape the dynamics of evolution, but it is unclear how they shift upon ecological diversification. By engineering genome-wide knockout libraries of a nascent bacterial community, Ascensao et al.

Giant Transposons in Eukaryotes: Is Bigger Better?

Abstract. Transposable elements (TEs) are ubiquitous in both prokaryotes and eukaryotes, and the dynamic character of their interaction with host genomes brings

Current advances in primate genomics: novel approaches for understanding evolution and disease - Nature Reviews Genetics

In this Review, the authors describe how advances in comparative primate genomics — complemented by multi-layered omic resources and primate cell systems — are providing insights into the evolution of primates and the genetic underpinnings of key tra…

Ten things you should know about transposable elements - Genome Biology

Transposable elements (TEs) are major components of eukaryotic genomes. However, the extent of their impact on genome evolution, function, and disease remain a matter of intense interrogation.