Text editor for your terminal: easy, powerful and fast - sinelaw/fresh

A guide to making visualizations that accurately reflect the data, tell a story, and look professional.

Genomic structural variation is an important component of genetic variation in natural populations. By assembling and analyzing multiple high-quality genomes within a species or clade, pangenomes capture variation that can be missed by reference-based genomics at both the sequence and the genic levels. Although pangenomes are nascent tools for animals compared with other taxa, they have already unveiled novel insights into genome evolution, adaptation, the genomic basis of organismal traits, and conservation genomics. We highlight the rapid progress and unique ecological and evolutionary discoveries emerging from applying pangenome tools to diverse natural populations. We conclude that pangenomes are fundamentally shifting the field by revealing structural variants as a key source of adaptive potential and genomic diversity previously missed by single-reference methods.

Elevate your scripting game with these must-know Bash variables.

Development and application of the integrated linkage disequilibrium score (iLDS) reveals both selective pressures impacting the human gut microbiome and the mechanisms by which gut bacteria adapt to ...

A combination of genome-wide functional screening, imaging and chromatin profiling identifies a new class of highly prevalent genomic elements that help retain extrachromosomal DNA copies in dividing ...

Ctyper is a genotyping method for copy number variation and complex genes that produces sequence-resolved genotypes by directly comparing sequencing reads to pangenome haplotypes, achieving increased ...

A newly compiled atlas of species-wide structural variants and gene-based and graph pangenomes derived from highly complete assemblies of genomes from 1,086 natural isolates enable integrative genome-...

FUGAsseM predicts protein function in microbiomes using coexpression patterns from metatranscriptomes and diverse community-wide data.

Genome-wide approaches have uncovered the vast microbial and viral diversity across ecosystems. This Review explores advances in metagenomics, single-cell sequencing and functional profiling to elucid...

These notes serve as an introduction to R, but certainly is not comprehensive. The intention is to teach students enough to be able to work with data frames and make graphs using ggplot2. I also cover...

Optimized long-read sequencing constructs megabase-scale genome assemblies from complex soil samples.

LexicMap uses a fixed set of probes to efficiently query gene sequences for fast and low-memory alignment.

This blog post will give R users an overview of what Julia is and why they might want to use it, introduce some data processing Julia packages, and show how they can incorporate Julia into existing R ...

Standardized analysis pipelines contribute to making data bioinformatics research compliant with the paradigm of Findability, Accessibility, Interoperability, and Reusability (FAIR), and facilitate co...

Quarto extension to create a PDF document that renders a specially formatted list of topics, along a pre-defined span of days, allowing you to select the recurring days of the week for the topics. ...

Nature Reviews Microbiology, Published online: 11 July 2025; doi:10.1038/s41579-025-01200-yIn this Review, Franco and colleagues explore the structural and functional diversity of antimicrobial peptides (AMPs), their mechanism of action, recent advances in AMP design and optimization, and their potential to address antimicrobial resistance.

If you're looking to add a bit of Gemini AI productivity to your Linux command line workflow, you'll be surprised at how easy it is to install and use.

Protein homologs in large databases are rapidly identified with an alignment-free pipeline.

In this Review, Mondo and Grigoriev explore the central role of omics approaches to investigate the biology and evolution of fungi and understand phylogeny and how traits evolved over time within the ...

He and colleagues develop LucaOne, a biological foundation model pre-trained on nucleic acid and protein sequences from 169,861 species. It shows an emerging understanding of molecular biology’s centr...

In this Tutorial, we provide guidelines for the use of ML models to mine genomes and proteomes for the discovery of antimicrobial peptides, discussing the various stages of the ML workflow, recent advances in ML models and how to experimentally validate the computational predictions.

Nature Reviews Microbiology, Published online: 23 May 2025; doi:10.1038/s41579-025-01192-9This Genome Watch highlights the advantages and limitations of k-mer approaches versus standard alignment-based methods for analysing metagenomic data, assisting microbial species identification, microbial abundance estimation and their application in pathogen genomic epidemiology.