Robert J. Gifford
@robjgifford.bsky.social
I carry out research into the evolution of viruses and their impact on host species. Open science.
Pinned
Bats and Viruses: Rumour, Intrigue, Deception, and Spectacle
Bats as Hyperreal Reservoirs of Viral Disease
robertjgifford.substack.com
"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...
Why does the idea of bats as special viral reservoirs endure?
New Substack post:
robertjgifford.substack.com/p/bats-and-v...
Reposted by Robert J. Gifford
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...
New GLUE Genomics post: from viral genomes to immune genes, using interferon lambda as a case study.
gluetools.substack.com/p/glue-resou...
GLUE Resources for Gene Families
Comparative Genomics Across the Host–Pathogen Interface
gluetools.substack.com
February 1, 2026 at 3:35 PM
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...
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.
This changes the horizons for recovery of ancient virus genomes.
Excited to share our work on #AncientRNA from alcohol-preserved lungs, recovering the oldest human RNA virus genome (an 18th-century rhinovirus). Our study shows that viral RNA remnants persist in centuries-old tissue, opening new ways to study virus evolution and historical disease #Paleovirology🫁🦠
www.biorxiv.org
February 2, 2026 at 10:10 AM
Recovery of viral RNA from centuries old human tissue is genuinely exciting.
This changes the horizons for recovery of ancient virus genomes.
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...
New GLUE Genomics post: from viral genomes to immune genes, using interferon lambda as a case study.
gluetools.substack.com/p/glue-resou...
GLUE Resources for Gene Families
Comparative Genomics Across the Host–Pathogen Interface
gluetools.substack.com
February 1, 2026 at 3:35 PM
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...
New GLUE Genomics post: from viral genomes to immune genes, using interferon lambda as a case study.
gluetools.substack.com/p/glue-resou...
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).
HCV, HBV, HEV, dengue, chikungunya, West Nile virus, yellow fever virus, rabies virus, and lentiviruses (SRLVs, EIAV).
January 26, 2026 at 6:36 PM
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).
HCV, HBV, HEV, dengue, chikungunya, West Nile virus, yellow fever virus, rabies virus, and lentiviruses (SRLVs, EIAV).
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...
It covers the evolutionary logic behind MLCA and the practical workflow for using it.
gluetools.substack.com/p/how-mlca-g...
How MLCA Genotyping Works in GLUE
And How You Can Run It Yourself
gluetools.substack.com
January 26, 2026 at 6:35 PM
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...
It covers the evolutionary logic behind MLCA and the practical workflow for using it.
gluetools.substack.com/p/how-mlca-g...
Reposted by Robert J. Gifford
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...
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
knowablemagazine.org
January 19, 2026 at 4:47 PM
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...
Flavivirus-GLUE provides an open framework for multi-scale comparative genomic analyses of flaviviruses.
gluetools.substack.com/p/flavivirus...
Flavivirus-GLUE
Comparative Genomics Across Evolutionary Scales
gluetools.substack.com
January 19, 2026 at 2:39 PM
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...
Flavivirus-GLUE provides an open framework for multi-scale comparative genomic analyses of flaviviruses.
gluetools.substack.com/p/flavivirus...
Reposted by Robert J. Gifford
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
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
Running HCV-GLUE Offline
Using HCV-GLUE in Automated Bioinformatics Pipelines
shorturl.at
January 11, 2026 at 3:42 PM
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
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
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
Running HCV-GLUE Offline
Using HCV-GLUE in Automated Bioinformatics Pipelines
shorturl.at
January 11, 2026 at 3:42 PM
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
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
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
Making Phylogeny-backed Virus Taxonomy Reproducible
A Retrovirus Case Study Using GLUE
shorturl.at
January 5, 2026 at 12:45 PM
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
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...
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...
December 8, 2025 at 3:50 AM
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...
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...
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.
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.
December 6, 2025 at 5:04 PM
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.
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.
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
ACIP did not recommend:
- eliminating the vaccine
- delaying until 2 months
- delaying universally
- denying the birth dose to parents who want it
December 6, 2025 at 4:59 PM
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
ACIP did not recommend:
- eliminating the vaccine
- delaying until 2 months
- delaying universally
- denying the birth dose to parents who want it
Gardening in the Viral Genome Wilderness:
Why virus genomics needs structure, not pipelines.
gluetools.substack.com/p/the-sequen...
Why virus genomics needs structure, not pipelines.
gluetools.substack.com/p/the-sequen...
Gardening in the Viral Genome Wilderness
Why virus genomics needs structure, not pipelines.
gluetools.substack.com
December 4, 2025 at 3:06 PM
Gardening in the Viral Genome Wilderness:
Why virus genomics needs structure, not pipelines.
gluetools.substack.com/p/the-sequen...
Why virus genomics needs structure, not pipelines.
gluetools.substack.com/p/the-sequen...
Stellenbosch University Botanical Garden
December 4, 2025 at 2:14 PM
Stellenbosch University Botanical Garden
- 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)
- 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)
December 4, 2025 at 2:06 PM
- 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)
- 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)
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...
Every narrative device, every logical inconsistency, and every evidentiary shortcut that sustains the ‘bat specialness’ story.
www.gavi.org/vaccineswork...
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.
www.gavi.org
December 4, 2025 at 2:06 PM
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...
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...
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...
GLUE: A Flexible Software System for Virus Genomics
A General Solution to the Repeated Problems of Virus Genomics
gluetools.substack.com
December 3, 2025 at 1:04 PM
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...
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...
Welcome to the GLUE Blog
Technical support for virus genomics workflows
gluetools.substack.com
December 3, 2025 at 12:06 AM
"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...
Why does the idea of bats as special viral reservoirs endure?
New Substack post:
robertjgifford.substack.com/p/bats-and-v...
Bats and Viruses: Rumour, Intrigue, Deception, and Spectacle
Bats as Hyperreal Reservoirs of Viral Disease
robertjgifford.substack.com
November 25, 2025 at 3:35 PM
"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...
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.
I am genuinely impressed by large language models - they can absorb disparate components of text into some consolidated view, they can produce extremely good language and - with the right model - translate pretty well between languages and they are an excellent text based UI for humans to use. But..
November 9, 2025 at 9:52 AM
Grounded and thought-provoking reflections on LLMs.
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...
Weekly symptoms of infection doesn't sound particularly appealing to me.
www.newscientist.com/article/2492...
August 21, 2025 at 5:41 AM
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...
Weekly symptoms of infection doesn't sound particularly appealing to me.
www.newscientist.com/article/2492...
Reposted by Robert J. Gifford
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...
Happy to make a tiny contribution alongside @panpan100.bsky.social to awesome teamwork & fantastic resource.
www.nature.com/articles/s41...
May 8, 2025 at 7:47 AM
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...
Happy to make a tiny contribution alongside @panpan100.bsky.social to awesome teamwork & fantastic resource.
www.nature.com/articles/s41...
There is currently no approved vaccine for scarlet fever.
April 10, 2025 at 1:24 PM
There is currently no approved vaccine for scarlet fever.