Joseph Hughes
@bljog.bsky.social
https://bioinformatics.cvr.ac.uk/people/joseph-hughes/
Bioinformatics, phylogenetics, open science, bikes and cycling, ranting.
Views my own.
Bioinformatics, phylogenetics, open science, bikes and cycling, ranting.
Views my own.
Reposted by Joseph Hughes
📢 New preprint is out on bioRxiv 📢:
How much does virome prep influence our view of the human gut virome?
Short answer: a lot.
Long answer:
doi.org/10.1101/2025...
Different methods lead to distinct community structures, richness, and major virus-host abundance patterns.
🧵 1/5
How much does virome prep influence our view of the human gut virome?
Short answer: a lot.
Long answer:
doi.org/10.1101/2025...
Different methods lead to distinct community structures, richness, and major virus-host abundance patterns.
🧵 1/5
November 27, 2025 at 8:44 PM
📢 New preprint is out on bioRxiv 📢:
How much does virome prep influence our view of the human gut virome?
Short answer: a lot.
Long answer:
doi.org/10.1101/2025...
Different methods lead to distinct community structures, richness, and major virus-host abundance patterns.
🧵 1/5
How much does virome prep influence our view of the human gut virome?
Short answer: a lot.
Long answer:
doi.org/10.1101/2025...
Different methods lead to distinct community structures, richness, and major virus-host abundance patterns.
🧵 1/5
Reposted by Joseph Hughes
Are you fascinated by viruses? Would you like to design your own original research project in the UK's largest virology centre? Why not come and do a PhD @cvrinfo.bsky.social - application deadline 6th Jan 2026 (1/1): www.findaphd.com/phds/program...
FindAPhD : The MRC-University of Glasgow Centre for Virus Research (CVR) PhD Funded Programme at University of Glasgow
Apply for a PhD: The MRC-University of Glasgow Centre for Virus Research (CVR) PhD Funded Programme at University of Glasgow
www.findaphd.com
November 27, 2025 at 1:26 PM
Are you fascinated by viruses? Would you like to design your own original research project in the UK's largest virology centre? Why not come and do a PhD @cvrinfo.bsky.social - application deadline 6th Jan 2026 (1/1): www.findaphd.com/phds/program...
Reposted by Joseph Hughes
What makes bird flu spill over to humans? 4y funded PhD in the genomics and molecular virology behind zoonosis of avian influenza A virus, working with @tompeacock.bsky.social and others between Liverpool, Pirbright, and Uppsala!
open to applications until next week!
open to applications until next week!
November 28, 2025 at 2:34 PM
What makes bird flu spill over to humans? 4y funded PhD in the genomics and molecular virology behind zoonosis of avian influenza A virus, working with @tompeacock.bsky.social and others between Liverpool, Pirbright, and Uppsala!
open to applications until next week!
open to applications until next week!
Reposted by Joseph Hughes
I think more studies need to be done in humans as it seems likely that antipyretics do more harm than good in some situations. Lowering body temperature could be neutralising a powerful antiviral defence.
Thanks for reading this thread.
Thanks for reading this thread.
November 27, 2025 at 7:55 PM
I think more studies need to be done in humans as it seems likely that antipyretics do more harm than good in some situations. Lowering body temperature could be neutralising a powerful antiviral defence.
Thanks for reading this thread.
Thanks for reading this thread.
Reposted by Joseph Hughes
How does fever work?
Our new Science paper shows how elevated body temperature can protect against severe influenza and that avian-origin viruses escape this defence.
This is likely one reason why bird flus and some pandemic influenzas can be so severe.🧵
www.science.org/doi/10.1126/...
Our new Science paper shows how elevated body temperature can protect against severe influenza and that avian-origin viruses escape this defence.
This is likely one reason why bird flus and some pandemic influenzas can be so severe.🧵
www.science.org/doi/10.1126/...
Avian-origin influenza A viruses tolerate elevated pyrexic temperatures in mammals
Host body temperature can define a virus’s replicative profile—influenza A viruses (IAVs) adapted to 40° to 42°C in birds are less temperature sensitive in vitro compared with human isolates adapted t...
www.science.org
November 27, 2025 at 7:55 PM
How does fever work?
Our new Science paper shows how elevated body temperature can protect against severe influenza and that avian-origin viruses escape this defence.
This is likely one reason why bird flus and some pandemic influenzas can be so severe.🧵
www.science.org/doi/10.1126/...
Our new Science paper shows how elevated body temperature can protect against severe influenza and that avian-origin viruses escape this defence.
This is likely one reason why bird flus and some pandemic influenzas can be so severe.🧵
www.science.org/doi/10.1126/...
Reposted by Joseph Hughes
PhD position (Glasgow, UK)
Build lightweight AI tools supporting One Health decision-making.
with @kirstynbrunker.bsky.social @bljog.bsky.social @jakelever.bsky.social
at @sbohvm.gla.ac.uk
More details: http://iddjobs.org/jobs/2420
Build lightweight AI tools supporting One Health decision-making.
with @kirstynbrunker.bsky.social @bljog.bsky.social @jakelever.bsky.social
at @sbohvm.gla.ac.uk
More details: http://iddjobs.org/jobs/2420
November 21, 2025 at 9:15 PM
PhD position (Glasgow, UK)
Build lightweight AI tools supporting One Health decision-making.
with @kirstynbrunker.bsky.social @bljog.bsky.social @jakelever.bsky.social
at @sbohvm.gla.ac.uk
More details: http://iddjobs.org/jobs/2420
Build lightweight AI tools supporting One Health decision-making.
with @kirstynbrunker.bsky.social @bljog.bsky.social @jakelever.bsky.social
at @sbohvm.gla.ac.uk
More details: http://iddjobs.org/jobs/2420
Reposted by Joseph Hughes
New exciting resource published!! The Viro3D paper is out, describing our comprehensive database of predicted virus protein structures! 💻🧬
Work with @ulad-litvin.bsky.social , @grovearmada.bsky.social , Alex Jack, @bljog.bsky.social , @davidlrobertson.bsky.social
www.embopress.org/doi/full/10....
Work with @ulad-litvin.bsky.social , @grovearmada.bsky.social , Alex Jack, @bljog.bsky.social , @davidlrobertson.bsky.social
www.embopress.org/doi/full/10....
Viro3D: a comprehensive database of virus protein structure predictions | Molecular Systems Biology
imageimageViro3D provides proteome-level, high confidence AI-protein structure predictions for
>4,400 viruses, allowing mapping of form and function across the human and animal
virosphere. Viro3D i...
www.embopress.org
September 28, 2025 at 5:39 AM
New exciting resource published!! The Viro3D paper is out, describing our comprehensive database of predicted virus protein structures! 💻🧬
Work with @ulad-litvin.bsky.social , @grovearmada.bsky.social , Alex Jack, @bljog.bsky.social , @davidlrobertson.bsky.social
www.embopress.org/doi/full/10....
Work with @ulad-litvin.bsky.social , @grovearmada.bsky.social , Alex Jack, @bljog.bsky.social , @davidlrobertson.bsky.social
www.embopress.org/doi/full/10....
Reposted by Joseph Hughes
Team effort from @uofgmvls.bsky.social @cvrinfo.bsky.social
Science: @ulad-litvin.bsky.social @spyroslytras.bsky.social @davidlrobertson.bsky.social and @bljog.bsky.social
Website: Alexander Jack
Funding: @medresfdn.bsky.social @ukri.org @wellcometrust.bsky.social @royalsociety.org
Science: @ulad-litvin.bsky.social @spyroslytras.bsky.social @davidlrobertson.bsky.social and @bljog.bsky.social
Website: Alexander Jack
Funding: @medresfdn.bsky.social @ukri.org @wellcometrust.bsky.social @royalsociety.org
September 26, 2025 at 11:36 AM
Team effort from @uofgmvls.bsky.social @cvrinfo.bsky.social
Science: @ulad-litvin.bsky.social @spyroslytras.bsky.social @davidlrobertson.bsky.social and @bljog.bsky.social
Website: Alexander Jack
Funding: @medresfdn.bsky.social @ukri.org @wellcometrust.bsky.social @royalsociety.org
Science: @ulad-litvin.bsky.social @spyroslytras.bsky.social @davidlrobertson.bsky.social and @bljog.bsky.social
Website: Alexander Jack
Funding: @medresfdn.bsky.social @ukri.org @wellcometrust.bsky.social @royalsociety.org
Kieran Lamb from @davidlrobertson.bsky.social gets best poster prize at EVBC meeting in Lisboa
May 15, 2025 at 3:13 PM
Kieran Lamb from @davidlrobertson.bsky.social gets best poster prize at EVBC meeting in Lisboa
Reposted by Joseph Hughes
📄 NEW | Genetic Study shows that Wildlife Trade sparked COVID-19 Virus Emergence in Humans
SARS-CoV-2 arrived in Wuhan too quickly for bat hosts to have carried it there.
cell.com/cell/fulltex...
gla.ac.uk/research/az/...
@davidlrobertson.bsky.social
@spyroslytras.bsky.social
@bljog.bsky.social
SARS-CoV-2 arrived in Wuhan too quickly for bat hosts to have carried it there.
cell.com/cell/fulltex...
gla.ac.uk/research/az/...
@davidlrobertson.bsky.social
@spyroslytras.bsky.social
@bljog.bsky.social
The recency and geographical origins of the bat viruses ancestral to SARS-CoV and SARS-CoV-2
Recombination-aware evolutionary analyses of the entire genomes of SARS-CoV-1-like
and SARS-CoV-2-like viruses indicate that SARS-CoV-1 and SARS-CoV-2 descend from bat
coronaviruses that circulated as...
cell.com
May 8, 2025 at 9:49 AM
📄 NEW | Genetic Study shows that Wildlife Trade sparked COVID-19 Virus Emergence in Humans
SARS-CoV-2 arrived in Wuhan too quickly for bat hosts to have carried it there.
cell.com/cell/fulltex...
gla.ac.uk/research/az/...
@davidlrobertson.bsky.social
@spyroslytras.bsky.social
@bljog.bsky.social
SARS-CoV-2 arrived in Wuhan too quickly for bat hosts to have carried it there.
cell.com/cell/fulltex...
gla.ac.uk/research/az/...
@davidlrobertson.bsky.social
@spyroslytras.bsky.social
@bljog.bsky.social
Reposted by Joseph Hughes
For the US to side with Russia and North Korea to oppose a UN resolution condemning the illegal invasion of Ukraine defies all common sense and adds insult to the countless injuries suffered by the brave Ukrainian people. edition.cnn.com/2025/02/24/p...
US joins Russia to vote against UN resolution condemning Russia’s war against Ukraine | CNN Politics
The United States joined Russia to vote against a UN General Assembly resolution condemning Russia’s war against Ukraine Monday in a stunning shift from years of US policy.
edition.cnn.com
February 25, 2025 at 9:29 AM
For the US to side with Russia and North Korea to oppose a UN resolution condemning the illegal invasion of Ukraine defies all common sense and adds insult to the countless injuries suffered by the brave Ukrainian people. edition.cnn.com/2025/02/24/p...
Reposted by Joseph Hughes
‘I do not want a fellowship that can include such actions.’
Elon Musk's fellowship is undermining the purpose of the Royal Society, writes resigning fellow @andrewmillar.bsky.social.
In this piece, he tells us why he feels enough is enough.
www.researchprofessionalnews.com/rr-news-uk-v...
Elon Musk's fellowship is undermining the purpose of the Royal Society, writes resigning fellow @andrewmillar.bsky.social.
In this piece, he tells us why he feels enough is enough.
www.researchprofessionalnews.com/rr-news-uk-v...
February 13, 2025 at 12:05 PM
‘I do not want a fellowship that can include such actions.’
Elon Musk's fellowship is undermining the purpose of the Royal Society, writes resigning fellow @andrewmillar.bsky.social.
In this piece, he tells us why he feels enough is enough.
www.researchprofessionalnews.com/rr-news-uk-v...
Elon Musk's fellowship is undermining the purpose of the Royal Society, writes resigning fellow @andrewmillar.bsky.social.
In this piece, he tells us why he feels enough is enough.
www.researchprofessionalnews.com/rr-news-uk-v...
Reposted by Joseph Hughes
Recently we have been doing lots of work on how modern #AI methods can be applied to studying virus evolution, so it felt like great timing to write a perspective about it!
Very happy to see our paper as editor's pick in JVI!🥳🥳
doi.org/10.1128/jvi....
Very happy to see our paper as editor's pick in JVI!🥳🥳
doi.org/10.1128/jvi....
Pathogen genomic surveillance and the AI revolution | Journal of Virology
Genomic pathogen sequencing during the COVID-19 pandemic highlighted the critical
role of surveillance in understanding the persistence of SARS-CoV-2 in the human population
despite high levels of pro...
doi.org
February 4, 2025 at 1:32 PM
Recently we have been doing lots of work on how modern #AI methods can be applied to studying virus evolution, so it felt like great timing to write a perspective about it!
Very happy to see our paper as editor's pick in JVI!🥳🥳
doi.org/10.1128/jvi....
Very happy to see our paper as editor's pick in JVI!🥳🥳
doi.org/10.1128/jvi....
Reposted by Joseph Hughes
🎺 PhD studentship available at @lshtm.bsky.social and RVC! @influenzal.bsky.social and I are advertising for a project to investigate the unexpected phenomenon that mutagenic antiviral drugs can give rise to viruses with hundreds of mutations which are still viable. 🧵
www.lshtm.ac.uk/study/fees-a...
www.lshtm.ac.uk/study/fees-a...
2025-26 Bloomsbury Colleges PhD Studentships | LSHTM
The Bloomsbury Colleges group was set up in 2004 and consists of five institutions: Birkbeck, London School of Hygiene & Tropical Medicine (LSHTM), the Royal Veterinary College (RVC), the School of Or...
www.lshtm.ac.uk
January 22, 2025 at 12:04 PM
🎺 PhD studentship available at @lshtm.bsky.social and RVC! @influenzal.bsky.social and I are advertising for a project to investigate the unexpected phenomenon that mutagenic antiviral drugs can give rise to viruses with hundreds of mutations which are still viable. 🧵
www.lshtm.ac.uk/study/fees-a...
www.lshtm.ac.uk/study/fees-a...
Reposted by Joseph Hughes
This paper has been a side project for quite a few years now, so I'm extra happy to see it published!!
big thanks to co-lead Sej Modha as well as @bljog.bsky.social and Richard Orton + all the experts who gave valuable feedback at conferences and over the internet! 😁😁
big thanks to co-lead Sej Modha as well as @bljog.bsky.social and Richard Orton + all the experts who gave valuable feedback at conferences and over the internet! 😁😁
January 22, 2025 at 9:51 AM
This paper has been a side project for quite a few years now, so I'm extra happy to see it published!!
big thanks to co-lead Sej Modha as well as @bljog.bsky.social and Richard Orton + all the experts who gave valuable feedback at conferences and over the internet! 😁😁
big thanks to co-lead Sej Modha as well as @bljog.bsky.social and Richard Orton + all the experts who gave valuable feedback at conferences and over the internet! 😁😁
As a WOAH Collaborating Centre, we’re excited to announce our 8th annual Viral #Bioinformatics & #Genomics training course from 16th - 20th June 2025! 🧬
@cvrinfo.bsky.social
📅 Register by 30 April:
👉 bit.ly/VBGCourse2025
📲 Or scan the QR code to join.
@cvrinfo.bsky.social
📅 Register by 30 April:
👉 bit.ly/VBGCourse2025
📲 Or scan the QR code to join.
January 17, 2025 at 2:15 PM
As a WOAH Collaborating Centre, we’re excited to announce our 8th annual Viral #Bioinformatics & #Genomics training course from 16th - 20th June 2025! 🧬
@cvrinfo.bsky.social
📅 Register by 30 April:
👉 bit.ly/VBGCourse2025
📲 Or scan the QR code to join.
@cvrinfo.bsky.social
📅 Register by 30 April:
👉 bit.ly/VBGCourse2025
📲 Or scan the QR code to join.
Reposted by Joseph Hughes
Another human rabies death in the US:
Person dies from rabies in Northern Kentucky, first rabies death in state since 1996
The victim, a resident of Northern Kentucky, succumbed to the disease after receiving medical treatment in both Kentucky and Ohio.
local12.com
December 28, 2024 at 5:22 PM
Another human rabies death in the US:
Reposted by Joseph Hughes
Another virus outbreak (Severe Fever with Thrombocytopenia Syndrome Virus -SFTSV) associated with fur farming. It needs to stop. www.tandfonline.com/doi/full/10....
Concurrent Severe Fever with Thrombocytopenia Syndrome Virus Outbreaks on Multiple Fox Farms, China, 2023
The role of farmed animals in the viral spillover from wild animals to humans is of growing importance. Between July and September of 2023 infectious disease outbreaks were reported on six Arctic f...
www.tandfonline.com
December 29, 2024 at 1:57 AM
Another virus outbreak (Severe Fever with Thrombocytopenia Syndrome Virus -SFTSV) associated with fur farming. It needs to stop. www.tandfonline.com/doi/full/10....
Reposted by Joseph Hughes
Not sure of the original source of this, but the depiction with the final domino set to crush the pusher is devastatingly accurate.
December 28, 2024 at 6:11 PM
Not sure of the original source of this, but the depiction with the final domino set to crush the pusher is devastatingly accurate.
Reposted by Joseph Hughes
“Many Swedish cities, including Stockholm, prioritize snow clearance very differently. They now clear walkways & bike paths first, especially those near bus stops & primary schools. Next, they clear local roads, & then, finally, highways.” Via @usa.streetsblog.org
usa.streetsblog.org/2018/01/24/w...
usa.streetsblog.org/2018/01/24/w...
Why Sweden Clears Snow-Covered Walkways Before Roads — Streetsblog USA
It's part of "gender-balanced" policy that reflects the fact that women walk more than men.
usa.streetsblog.org
December 28, 2024 at 6:06 PM
“Many Swedish cities, including Stockholm, prioritize snow clearance very differently. They now clear walkways & bike paths first, especially those near bus stops & primary schools. Next, they clear local roads, & then, finally, highways.” Via @usa.streetsblog.org
usa.streetsblog.org/2018/01/24/w...
usa.streetsblog.org/2018/01/24/w...
Reposted by Joseph Hughes
An exciting resource we put together with Ulad Litvin, @grovearmada.bsky.social Alexander Jack, @davidlrobertson.bsky.social and @bljog.bsky.social bsky.app/profile/grov...
🎁 Early Xmas present from your friends at the MRC-University of Glasgow Centre for Virus Research @cvrinfo.bsky.social
We're thrilled to unwrap Viro3D - a comprehensive database of virus protein structures: >85,000 predicted structures from 4,400 human & animal viruses! 🦠
viro3d.cvr.gla.ac.uk
We're thrilled to unwrap Viro3D - a comprehensive database of virus protein structures: >85,000 predicted structures from 4,400 human & animal viruses! 🦠
viro3d.cvr.gla.ac.uk
Viro3D
viro3d.cvr.gla.ac.uk
December 21, 2024 at 2:45 PM
An exciting resource we put together with Ulad Litvin, @grovearmada.bsky.social Alexander Jack, @davidlrobertson.bsky.social and @bljog.bsky.social bsky.app/profile/grov...
Reposted by Joseph Hughes
✨ This was a huge team effort by Ulad Litvin, @spyroslytras.bsky.social, Alexander Jack, David Robertson and @bljog.bsky.social
Thank you to our funders MRC @ukri.org , @medresfdn.bsky.social, @wellcometrust.bsky.social.
We can't wait to see what discoveries you'll make with Viro3D in 2025! 🚀
Thank you to our funders MRC @ukri.org , @medresfdn.bsky.social, @wellcometrust.bsky.social.
We can't wait to see what discoveries you'll make with Viro3D in 2025! 🚀
December 20, 2024 at 5:51 PM
✨ This was a huge team effort by Ulad Litvin, @spyroslytras.bsky.social, Alexander Jack, David Robertson and @bljog.bsky.social
Thank you to our funders MRC @ukri.org , @medresfdn.bsky.social, @wellcometrust.bsky.social.
We can't wait to see what discoveries you'll make with Viro3D in 2025! 🚀
Thank you to our funders MRC @ukri.org , @medresfdn.bsky.social, @wellcometrust.bsky.social.
We can't wait to see what discoveries you'll make with Viro3D in 2025! 🚀
Reposted by Joseph Hughes
NEW Publication!😄
Here, we show how #PhyKIT — a broadly applicable toolkit for #phylogenomics — can be used to construct phylogenomic data matrices (& quantify biases therein), detect anomalies in predicted orthology, calculate gene-gene coevolution, & more!
🔗: tinyurl.com/yc5ja4xz
Here, we show how #PhyKIT — a broadly applicable toolkit for #phylogenomics — can be used to construct phylogenomic data matrices (& quantify biases therein), detect anomalies in predicted orthology, calculate gene-gene coevolution, & more!
🔗: tinyurl.com/yc5ja4xz
November 25, 2024 at 5:25 PM
NEW Publication!😄
Here, we show how #PhyKIT — a broadly applicable toolkit for #phylogenomics — can be used to construct phylogenomic data matrices (& quantify biases therein), detect anomalies in predicted orthology, calculate gene-gene coevolution, & more!
🔗: tinyurl.com/yc5ja4xz
Here, we show how #PhyKIT — a broadly applicable toolkit for #phylogenomics — can be used to construct phylogenomic data matrices (& quantify biases therein), detect anomalies in predicted orthology, calculate gene-gene coevolution, & more!
🔗: tinyurl.com/yc5ja4xz
So happy to see that there are still people with a moral compass
November 25, 2024 at 4:18 PM
So happy to see that there are still people with a moral compass
Reposted by Joseph Hughes
New blogpost:
deevybee.blogspot.com/2024/11/why-...
deevybee.blogspot.com/2024/11/why-...
Why I have resigned from the Royal Society
The Royal Society is a venerable institution founded in 1660, whose original members included such eminent men as Christopher Wren, Robert H...
deevybee.blogspot.com
November 25, 2024 at 7:49 AM
New blogpost:
deevybee.blogspot.com/2024/11/why-...
deevybee.blogspot.com/2024/11/why-...