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Robert J. Gifford

@robjgifford.bsky.social
325 followers 554 following 62 posts

I carry out research into the evolution of viruses and their impact on host species. Open science.

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Robert J. Gifford @robjgifford.bsky.social · 22/02/2026
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...
gluetools.substack.com
Data-Oriented Virology
GLUE’s Philosophy in Plain Language
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Robert J. Gifford @robjgifford.bsky.social · 11/02/2026
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...
gluetools.substack.com
Data Immutability and Longevity in GLUE
A Design for Durable Host-Virus Genomics
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Robert J. Gifford @robjgifford.bsky.social · 05/02/2026
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
gluetools.substack.com
A Long-Lived, Data-Oriented Knowledge Base for Comparative Genomics
From Viral Genomes to Rapidly Evolving Host Genes
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Reposted by Robert J. Gifford
Robert J. Gifford @robjgifford.bsky.social · 01/02/2026
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...
gluetools.substack.com
GLUE Resources for Gene Families
Comparative Genomics Across the Host–Pathogen Interface
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Robert J. Gifford @robjgifford.bsky.social · 02/02/2026
Recovery of viral RNA from centuries old human tissue is genuinely exciting. This changes the horizons for recovery of ancient virus genomes.
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Robert J. Gifford @robjgifford.bsky.social · 01/02/2026
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...
gluetools.substack.com
GLUE Resources for Gene Families
Comparative Genomics Across the Host–Pathogen Interface
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Robert J. Gifford @robjgifford.bsky.social · 26/01/2026
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...
gluetools.substack.com
How MLCA Genotyping Works in GLUE
And How You Can Run It Yourself
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Reposted by Robert J. Gifford
The Lambrechts Lab @lambrechtslab.bsky.social · 19/01/2026
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...
knowablemagazine.org
Beating back the Aedes aegypti mosquito
Scientists are taking a multipronged approach to tackle this dangerous carrier of dengue, yellow fever and other noxious viruses
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Robert J. Gifford @robjgifford.bsky.social · 19/01/2026
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...
gluetools.substack.com
Flavivirus-GLUE
Comparative Genomics Across Evolutionary Scales
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Reposted by Robert J. Gifford
Robert J. Gifford @robjgifford.bsky.social · 11/01/2026
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
shorturl.at
Running HCV-GLUE Offline
Using HCV-GLUE in Automated Bioinformatics Pipelines
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Robert J. Gifford @robjgifford.bsky.social · 11/01/2026
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
shorturl.at
Running HCV-GLUE Offline
Using HCV-GLUE in Automated Bioinformatics Pipelines
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Robert J. Gifford @robjgifford.bsky.social · 05/01/2026
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
shorturl.at
Making Phylogeny-backed Virus Taxonomy Reproducible
A Retrovirus Case Study Using GLUE
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Robert J. Gifford @robjgifford.bsky.social · 08/12/2025
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...
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Robert J. Gifford @robjgifford.bsky.social · 04/12/2025
Gardening in the Viral Genome Wilderness: Why virus genomics needs structure, not pipelines. gluetools.substack.com/p/the-sequen...
gluetools.substack.com
Gardening in the Viral Genome Wilderness
Why virus genomics needs structure, not pipelines.
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Robert J. Gifford @robjgifford.bsky.social · 04/12/2025
Stellenbosch University Botanical Garden
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Robert J. Gifford @robjgifford.bsky.social · 04/12/2025
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...
gavi.org
The bat paradox: what nature’s night flyers could teach us about pandemics – and ourselves
Bats carry many deadly viruses, yet rarely fall ill themselves. Rather than fearing them, scientists say we should study and protect them, to safeguard our own health.
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Robert J. Gifford @robjgifford.bsky.social · 03/12/2025
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...
gluetools.substack.com
GLUE: A Flexible Software System for Virus Genomics
A General Solution to the Repeated Problems of Virus Genomics
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Robert J. Gifford @robjgifford.bsky.social · 03/12/2025
Introducing the GLUE Genomics Blog: gluetools.substack.com/p/welcome-to...
gluetools.substack.com
Welcome to the GLUE Blog
Technical support for virus genomics workflows
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Robert J. Gifford @robjgifford.bsky.social · 25/11/2025
"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...
robertjgifford.substack.com
Bats and Viruses: Rumour, Intrigue, Deception, and Spectacle
Bats as Hyperreal Reservoirs of Viral Disease
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Robert J. Gifford @robjgifford.bsky.social · 09/11/2025
Grounded and thought-provoking reflections on LLMs.
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Reposted by Robert J. Gifford
Cedric Feschotte @cedricfeschotte.bsky.social · 08/05/2025
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...
Complete genome sequences for 6 apes species
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Robert J. Gifford @robjgifford.bsky.social · 06/04/2025
Macduff, Scotland
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Reposted by Robert J. Gifford
Robert J. Gifford @robjgifford.bsky.social · 31/03/2025
The Ghost in the Culture Flask: Did Cold War virologists accidentally alter the evolution of a ubiquitous virus? shorturl.at/HSke3
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Robert J. Gifford @robjgifford.bsky.social · 31/03/2025
The Ghost in the Culture Flask: Did Cold War virologists accidentally alter the evolution of a ubiquitous virus? shorturl.at/HSke3
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Robert J. Gifford @robjgifford.bsky.social · 16/01/2025
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
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Robert J. Gifford @robjgifford.bsky.social · 13/01/2025
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.
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Robert J. Gifford @robjgifford.bsky.social · 11/01/2025
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.
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Robert J. Gifford @robjgifford.bsky.social · 09/01/2025
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...
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