Most bioinformatics tools put software first and data second. GLUE does the opposite. In this blog post (link in reply), I provide a plain-language explanation of its data-oriented philosophy, and why that matters for reproducible virology. gluetools.substack.com/p/data-orien...

Genomics has a data rot problem. Pipelines change. Alignments are regenerated. Assumptions disappear. Context is lost. This post explains why GLUE was built around data immutability and durable scientific objects. gluetools.substack.com/p/data-immut...

Comparative genomics generates results fast - but preserving the context needed to understand them over time is much harder. I’ve written a perspective on GLUE as a long-lived, data-oriented knowledge base: projects as persistent scientific objects rather than disposable pipelines. sl1nk.com/Y0O4H

Studying immune gene evolution is rarely about a lack of data, it’s about keeping data, biology, and interpretation aligned as everything changes. New GLUE Genomics post: from viral genomes to immune genes, using interferon lambda as a case study. gluetools.substack.com/p/glue-resou...

Recovery of viral RNA from centuries old human tissue is genuinely exciting. This changes the horizons for recovery of ancient virus genomes.

Studying immune gene evolution is rarely about a lack of data, it’s about keeping data, biology, and interpretation aligned as everything changes. New GLUE Genomics post: from viral genomes to immune genes, using interferon lambda as a case study. gluetools.substack.com/p/glue-resou...

I’ve just published a new Substack post explaining how MLCA genotyping works in GLUE, and how to run it yourself locally using Docker. It covers the evolutionary logic behind MLCA and the practical workflow for using it. gluetools.substack.com/p/how-mlca-g...

Great read! Congratulations @katarinazimmer.bsky.social on your insightful @knowablemag.bsky.social piece exploring the remarkable biology of the Aedes aegypti #mosquito knowablemagazine.org/content/arti...

As virus discovery accelerates, integrating new sequences meaningfully is becoming a central challenge. Flavivirus-GLUE provides an open framework for multi-scale comparative genomic analyses of flaviviruses. gluetools.substack.com/p/flavivirus...

HCV-GLUE is best known as a web-based tool for HCV genotyping and drug resistance analysis. Less well known is that the same analysis can be run entirely offline and integrated into pipelines. I’ve written a short guide on running HCV-GLUE offline using Docker and GLUE scripts. shorturl.at/bvm3d

HCV-GLUE is best known as a web-based tool for HCV genotyping and drug resistance analysis. Less well known is that the same analysis can be run entirely offline and integrated into pipelines. I’ve written a short guide on running HCV-GLUE offline using Docker and GLUE scripts. shorturl.at/bvm3d

Virus taxonomy increasingly rests on phylogenetic hypotheses, but the trees, alignments, and assumptions behind them are often ephemeral. This post explores what it might look like to make that phylogenetic basis transparent and reproducible, using retroviruses as a case study. shorturl.at/s9aft

The translational potential of bat immune traits is wildly overstated. These aren’t modular switches we can port into humans; They’re parts of tightly integrated systems that don’t travel. www.sciencedirect.com/science/arti...

Gardening in the Viral Genome Wilderness: Why virus genomics needs structure, not pipelines. gluetools.substack.com/p/the-sequen...

Stellenbosch University Botanical Garden

This article by Linda Geddes reproduces every structural flaw I described in my recent Substack essay. Every narrative device, every logical inconsistency, and every evidentiary shortcut that sustains the ‘bat specialness’ story. www.gavi.org/vaccineswork...

Most viral workflows are fragile pipelines. GLUE turns them into structured, shareable projects: curated sequences, alignments, features, phylogenies, metadata & scripts all in one reproducible environment. gluetools.substack.com/p/glue-a-fle...

Introducing the GLUE Genomics Blog: gluetools.substack.com/p/welcome-to...

"The hyperreal bat: more vivid, more coherent, and more narratively satisfying than any bat in nature." Why does the idea of bats as special viral reservoirs endure? New Substack post: robertjgifford.substack.com/p/bats-and-v...

Grounded and thought-provoking reflections on LLMs.

Complete ape genomes! 🦍🦧 Our closest relatives get the deluxe sequencing treatment, resolving the most complex & often most interesting parts of the genome. Happy to make a tiny contribution alongside @panpan100.bsky.social to awesome teamwork & fantastic resource. www.nature.com/articles/s41...

Macduff, Scotland

The Ghost in the Culture Flask: Did Cold War virologists accidentally alter the evolution of a ubiquitous virus? shorturl.at/HSke3

The Ghost in the Culture Flask: Did Cold War virologists accidentally alter the evolution of a ubiquitous virus? shorturl.at/HSke3

Discover GLUE: a versatile framework for virus genomics and beyond. Explore adaptable tools, resources, and projects developed in our lab using GLUE: github.com/giffordlabcv... #Genomics #Bioinformatics #OpenScience

I've been comparing annual publication trends across different viruses The vast difference in the number of publications for SARS-CoV-2 compared to other viruses like Ebola, Dengue, and Influenza A is striking.

Personally, I have a lot of sympathy for Jens Kuhn. He's dealing with a fundamental and increasingly pressing issue in virology, one that might otherwise be neglected without the intense dedication of someone so earnestly committed to the cause.

Introducing HMPV-GLUE: a comprehensive, open-source resource for human metapneumovirus (HMPV) research. With the recent rise in HMPV cases in China, this tool offers timely support for the scientific community. github.com/giffordlabcv...