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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
MLCA genotyping in GLUE is currently available for a range of viruses, including: HCV, HBV, HEV, dengue, chikungunya, West Nile virus, yellow fever virus, rabies virus, and lentiviruses (SRLVs, EIAV).
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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 · 06/12/2025
The Guardian frames a timing change for very low-risk infants as “limiting” vaccines. ACIP didn’t restrict access or question safety, it shifted a universal 24-hour rule to shared decision-making. When public-health advocates misstate the facts, it doesn’t protect trust. It erodes it.
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Robert J. Gifford @robjgifford.bsky.social · 06/12/2025
These scary numbers appear to come from a maximalist population model, based on delaying the birth dose to exactly 2 months for all infants. ACIP did not recommend: - eliminating the vaccine - delaying until 2 months - delaying universally - denying the birth dose to parents who want it
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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
- Presents a false paradox - Recycles unsupported, unfalsifiable bat immunology narratives - Conflates association with causation in outbreaks - Relies on a small circle of experts - Omits massive negative evidence - Treats rumour as fact - Applies mythic spectacle (bats as villains and saviours)
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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
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 · 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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Robert J. Gifford @robjgifford.bsky.social · 21/08/2025
Do you think that would also be the case here? Weekly symptoms of infection doesn't sound particularly appealing to me. www.newscientist.com/article/2492...
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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 · 10/04/2025
There is currently no approved vaccine for scarlet fever.
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Robert J. Gifford @robjgifford.bsky.social · 10/04/2025
It appears my error was in devoting decades to virology rather than mastering Victorian literature and kitchen remedies. A humbling revelation—thank you for your service to science.
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Robert J. Gifford @robjgifford.bsky.social · 09/04/2025
I don't think you're capable of a reasonable discussion. Bye!!!
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Robert J. Gifford @robjgifford.bsky.social · 09/04/2025
Read what I wrote.
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Robert J. Gifford @robjgifford.bsky.social · 09/04/2025
And why do you need a 2000 year timeline to make your point? Is it because a shorter timeline would show child mortality dropping precipitously prior to mass vaccination? It's not anti-vax to expect more honesty and clarity in public health messaging.
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Robert J. Gifford @robjgifford.bsky.social · 09/04/2025
I'm sorry to have to say it, but if this is meant to persuade vaccine skeptics, I think it's disingenuous and probably counterproductive. Why are you conflating water systems with vaccines? Who's against clean water?
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Robert J. Gifford @robjgifford.bsky.social · 07/04/2025
What starts as a critique of healthcare policy becomes an argument for a new moral regime in which science is moralised, and politics is medicalised.
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Robert J. Gifford @robjgifford.bsky.social · 07/04/2025
Scottish-American. 😉
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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 · 14/01/2025
Interest in non-primate lentiviruses also seems to be declining. This may impact efforts to manage the diseases caused by these viruses.
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Robert J. Gifford @robjgifford.bsky.social · 14/01/2025
OK. Not sure how this is relevant but fine.
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Robert J. Gifford @robjgifford.bsky.social · 13/01/2025
I wouldn't say it reflects infection rate. Otherwise there might be a million Torquetenovirus publications a year. It is reflective of global impact, but reaction was part of the impact.
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Robert J. Gifford @robjgifford.bsky.social · 13/01/2025
It also emphasises the need for a more equitable and sustained approach to addressing all major viral threats, not just those that capture immediate global attention.
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Robert J. Gifford @robjgifford.bsky.social · 13/01/2025
To me, this massive publication disparity illustrates how research priorities are shaped by societal and economic factors rather than inherent scientific value. I think it shows the reactive nature of scientific funding and research focus, which seem to be tied to immediate perceived crises.
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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 · 12/01/2025
Oh come along Professor Simmonds, now you're just being mean. 😉
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Robert J. Gifford @robjgifford.bsky.social · 12/01/2025
The tree I posted was not intended to suggest that Latin binomials are replacing common names but to show in context the contrast between using the traditional names versus the binomials.
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Robert J. Gifford @robjgifford.bsky.social · 12/01/2025
The application of rank-based scientific classification and Latin binomials to virus species is distinct, but obviously it impacts how how viruses are referred to - which is presumably what has made it controversial.
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Robert J. Gifford @robjgifford.bsky.social · 12/01/2025
The naming process has inevitably changed due to vastly increased rates of discovery, as well as greater awareness of the potential sensitivities associated with virus names.
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Robert J. Gifford @robjgifford.bsky.social · 12/01/2025
My comments were more generally about the changes in virus nomenclature that have occurred in recent times, with regard to both how viruses are named, and how they are referred to.
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