Josie Bryant
@josiebryant.bsky.social
Group Leader at Wellcome Sanger Institute. Using omics to understand chronic lung infections and lung microbiomes in disease
Reposted by Josie Bryant
New 🧬✂️ pre-print! We show that paired prime editing can efficiently generate large deletions — even >1 Mb — with high precision and at scale. We use this to perform the first pooled prime deletion screen across the human genome.
🔗 biorxiv.org/content/10.1...
A short thread (by Juliane Weller)👇
🔗 biorxiv.org/content/10.1...
A short thread (by Juliane Weller)👇
Generating long deletions across the genome with pooled paired prime editing screens
Engineered deletions are a powerful probe for studying genome architecture, function, and regulation. Yet, the lack of effective methods to create them in large numbers and at multi-kilobase scale has...
biorxiv.org
November 5, 2025 at 2:17 PM
New 🧬✂️ pre-print! We show that paired prime editing can efficiently generate large deletions — even >1 Mb — with high precision and at scale. We use this to perform the first pooled prime deletion screen across the human genome.
🔗 biorxiv.org/content/10.1...
A short thread (by Juliane Weller)👇
🔗 biorxiv.org/content/10.1...
A short thread (by Juliane Weller)👇
Reposted by Josie Bryant
Showcase advances in infection and respiratory immunology at our 2026 conference!
Share your insights on respiratory infection, host-microbiome interactions, and immune cell dynamics with field leaders.
🗓️ #AIR2026 dates: 11-13 February
📩 Submit an abstract by 17 November
📎 bit.ly/46T6uJB
Share your insights on respiratory infection, host-microbiome interactions, and immune cell dynamics with field leaders.
🗓️ #AIR2026 dates: 11-13 February
📩 Submit an abstract by 17 November
📎 bit.ly/46T6uJB
October 2, 2025 at 7:00 AM
Showcase advances in infection and respiratory immunology at our 2026 conference!
Share your insights on respiratory infection, host-microbiome interactions, and immune cell dynamics with field leaders.
🗓️ #AIR2026 dates: 11-13 February
📩 Submit an abstract by 17 November
📎 bit.ly/46T6uJB
Share your insights on respiratory infection, host-microbiome interactions, and immune cell dynamics with field leaders.
🗓️ #AIR2026 dates: 11-13 February
📩 Submit an abstract by 17 November
📎 bit.ly/46T6uJB
Reposted by Josie Bryant
Interested in respiratory infections? who isn't! Then register for this fab conference with a fantastic line-up of speakers and sessions @sangerinstitute.bsky.social Abstract submission open until 17th Nov!! @eventswcs.bsky.social
coursesandconferences.wellcomeconnectingscience.org/event/air-20...
coursesandconferences.wellcomeconnectingscience.org/event/air-20...
October 8, 2025 at 12:12 PM
Interested in respiratory infections? who isn't! Then register for this fab conference with a fantastic line-up of speakers and sessions @sangerinstitute.bsky.social Abstract submission open until 17th Nov!! @eventswcs.bsky.social
coursesandconferences.wellcomeconnectingscience.org/event/air-20...
coursesandconferences.wellcomeconnectingscience.org/event/air-20...
New respiratory 🫁 infection and microbiomes conference in Hinxton with stellar line up of speakers.
🚨 Submit your abstracts now! 🚨
Please RT
coursesandconferences.wellcomeconnectingscience.org/event/air-20...
🚨 Submit your abstracts now! 🚨
Please RT
coursesandconferences.wellcomeconnectingscience.org/event/air-20...
AIR 2026: Genomic and Systems Approaches to Respiratory Infection, Microbiomes and Immunity — 20260211
Course exploring how genomics, microbiome profiling, and systems biology reshape our understanding of respiratory infections and immune dynamics.
coursesandconferences.wellcomeconnectingscience.org
October 8, 2025 at 2:48 PM
New respiratory 🫁 infection and microbiomes conference in Hinxton with stellar line up of speakers.
🚨 Submit your abstracts now! 🚨
Please RT
coursesandconferences.wellcomeconnectingscience.org/event/air-20...
🚨 Submit your abstracts now! 🚨
Please RT
coursesandconferences.wellcomeconnectingscience.org/event/air-20...
Reposted by Josie Bryant
After being with the journal since its very inception, the time has come for me to step back from Microbial Genomics. This is a wonderful opportunity to have a leadership role in one of the leading journals for microbial genomics research
microbiologysociety.org/news/society...
microbiologysociety.org/news/society...
<i>Microbial Genomics </i> Deputy Editor-in-Chief: Call for Expressions of interest
microbiologysociety.org
October 7, 2025 at 8:44 AM
After being with the journal since its very inception, the time has come for me to step back from Microbial Genomics. This is a wonderful opportunity to have a leadership role in one of the leading journals for microbial genomics research
microbiologysociety.org/news/society...
microbiologysociety.org/news/society...
Reposted by Josie Bryant
RIP Jane Goodall, by all accounts a wonderful woman who loved this Far Side cartoon
October 1, 2025 at 6:09 PM
RIP Jane Goodall, by all accounts a wonderful woman who loved this Far Side cartoon
Reposted by Josie Bryant
BBSRC Fellowships 2025 Triage Outcome Decisions were today. 277 applications, 42 put through to peer review and interview. A fellow I was supporting didn't get selected and BBSRC now offer *no feedback*.
Months of work and not a single iota of feedback for the applicant. Honestly, disgraceful.
Months of work and not a single iota of feedback for the applicant. Honestly, disgraceful.
October 1, 2025 at 1:28 PM
BBSRC Fellowships 2025 Triage Outcome Decisions were today. 277 applications, 42 put through to peer review and interview. A fellow I was supporting didn't get selected and BBSRC now offer *no feedback*.
Months of work and not a single iota of feedback for the applicant. Honestly, disgraceful.
Months of work and not a single iota of feedback for the applicant. Honestly, disgraceful.
Proud to see my lab's work on M. tuberculosis and P. aeruginosa highlighted in this blog post
October 1, 2025 at 11:29 AM
Proud to see my lab's work on M. tuberculosis and P. aeruginosa highlighted in this blog post
Reposted by Josie Bryant
Now published, our tool to run (almost) all biological models interactively in your web browser
Paper: academic.oup.com/bioinformati...
Website: biomodels.bacpop.org
Code: github.com/bacpop/SBMLt...
Paper: academic.oup.com/bioinformati...
Website: biomodels.bacpop.org
Code: github.com/bacpop/SBMLt...
September 29, 2025 at 9:49 AM
Now published, our tool to run (almost) all biological models interactively in your web browser
Paper: academic.oup.com/bioinformati...
Website: biomodels.bacpop.org
Code: github.com/bacpop/SBMLt...
Paper: academic.oup.com/bioinformati...
Website: biomodels.bacpop.org
Code: github.com/bacpop/SBMLt...
Reposted by Josie Bryant
Synthetic lethal TN-seq! #microsky 🦠
Dual transposon sequencing profiles the genetic interaction landscape in bacteria | Science www.science.org/doi/10.1126/...
Dual transposon sequencing profiles the genetic interaction landscape in bacteria
Gene redundancy complicates systematic characterization of gene function as single-gene deletions may not produce discernible phenotypes. We report dual transposon sequencing (dual Tn-seq), a platform...
www.science.org
September 26, 2025 at 5:10 AM
Synthetic lethal TN-seq! #microsky 🦠
Reposted by Josie Bryant
Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols.
Thread 1/n
Thread 1/n
September 25, 2025 at 9:29 PM
Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols.
Thread 1/n
Thread 1/n
Reposted by Josie Bryant
It's that time of the year again... Soon the applications for 12 PhD positions at @sangerinstitute.bsky.social will open. Interested in genomics and thinking about doing a PhD? Join us at Sanger. www.sanger.ac.uk/about/study/...
4-Year PhD Programme
The Wellcome Sanger Institute have a 4-year PhD programme and a Clinical PhD programme in genomics and genetics, registered with the University of Cambridge, which are open to UK and overseas applican...
www.sanger.ac.uk
September 18, 2025 at 3:04 PM
It's that time of the year again... Soon the applications for 12 PhD positions at @sangerinstitute.bsky.social will open. Interested in genomics and thinking about doing a PhD? Join us at Sanger. www.sanger.ac.uk/about/study/...
Reposted by Josie Bryant
Excited to share our @cp-cellhostmicrobe.bsky.social led by Magda showing how Bif has co-evolved with different animal hosts 🐒🐭🐷🐦
Key takeaways:
🔹 Host ancestry + diet shape Bif evolution
🔹 Mammals enriched for carb-busting enzymes
🔹 Untapped diversity in non-human hosts = new probiotic potential
Key takeaways:
🔹 Host ancestry + diet shape Bif evolution
🔹 Mammals enriched for carb-busting enzymes
🔹 Untapped diversity in non-human hosts = new probiotic potential
Bifido adaptations across hosts
@halllab.bsky.social survey insects, reptiles, birds & mammals to uncover how Bifidobacterium adapts to hosts. Bifidobacterium & host exhibit strong co-phylogenetic associations, driven by vertical transmission & dietary selection
www.cell.com/cell-host-mi...
@halllab.bsky.social survey insects, reptiles, birds & mammals to uncover how Bifidobacterium adapts to hosts. Bifidobacterium & host exhibit strong co-phylogenetic associations, driven by vertical transmission & dietary selection
www.cell.com/cell-host-mi...
Host-specific microbiome and genomic signatures in Bifidobacterium reveal co-evolutionary and functional adaptations across diverse animal hosts
Bifidobacterium are beneficial members of the microbiota across animal hosts. Kujawska
et al. demonstrate that bifidobacteria have likely co-evolved more closely with mammals,
particularly primates, a...
www.cell.com
September 11, 2025 at 2:49 PM
Excited to share our @cp-cellhostmicrobe.bsky.social led by Magda showing how Bif has co-evolved with different animal hosts 🐒🐭🐷🐦
Key takeaways:
🔹 Host ancestry + diet shape Bif evolution
🔹 Mammals enriched for carb-busting enzymes
🔹 Untapped diversity in non-human hosts = new probiotic potential
Key takeaways:
🔹 Host ancestry + diet shape Bif evolution
🔹 Mammals enriched for carb-busting enzymes
🔹 Untapped diversity in non-human hosts = new probiotic potential
Closing soon. Great opportunity to do spatial transcriptomics on pre-antibiotic TB
⭐ Excellence fellowships accepting applications ⭐ for Black ECRs who have a degree from the UK. sanger.wd103.myworkdayjobs.com/en-US/Wellco...
I have an amazing spatial transcriptomics project available on the world's most important pathogen, TB: www.sanger.ac.uk/wp-content/u...
Please reach out!
I have an amazing spatial transcriptomics project available on the world's most important pathogen, TB: www.sanger.ac.uk/wp-content/u...
Please reach out!
www.sanger.ac.uk
August 20, 2025 at 1:48 PM
Closing soon. Great opportunity to do spatial transcriptomics on pre-antibiotic TB
Reposted by Josie Bryant
Was great to put the dream team back together for a commentary on this with @alisonmather.bsky.social very cool study on AMR flow through food production chains in Europe www.nature.com/articles/s41...
July 31, 2025 at 10:26 AM
Was great to put the dream team back together for a commentary on this with @alisonmather.bsky.social very cool study on AMR flow through food production chains in Europe www.nature.com/articles/s41...
Reposted by Josie Bryant
Super interesting. Does it work for NTM?
Nature research paper: SuFEx-based antitubercular compound irreversibly inhibits Pks13
go.nature.com/40JdOnN
go.nature.com/40JdOnN
SuFEx-based antitubercular compound irreversibly inhibits Pks13 - Nature
A preclinical covalent compound, CMX410, contains a aryl fluorosulfate warhead that targets the acyltransferase domain of Mtb Pks13, an essential enzyme in cell-wall biosynthesis, making it a promising candidate for tuberculosis treatment regimens.
go.nature.com
July 31, 2025 at 8:17 AM
Super interesting. Does it work for NTM?
Reposted by Josie Bryant
Be thAIR or be squAIR
(My second entry into the organising committee pun competition. A winner there I think).
(My second entry into the organising committee pun competition. A winner there I think).
July 21, 2025 at 3:21 PM
Be thAIR or be squAIR
(My second entry into the organising committee pun competition. A winner there I think).
(My second entry into the organising committee pun competition. A winner there I think).
Reposted by Josie Bryant
Early notice of NEW Wellcome Conference -
AIR 2026: Genomic and Systems Approaches to Respiratory Infection, Microbiomes and Immunity 11th-13th February, sign up below for notifications
coursesandconferences.wellcomeconnectingscience.org/our-events/c...
It's immunulogy AND it's microbiology 🫁
AIR 2026: Genomic and Systems Approaches to Respiratory Infection, Microbiomes and Immunity 11th-13th February, sign up below for notifications
coursesandconferences.wellcomeconnectingscience.org/our-events/c...
It's immunulogy AND it's microbiology 🫁
Conferences
coursesandconferences.wellcomeconnectingscience.org
July 21, 2025 at 3:21 PM
Early notice of NEW Wellcome Conference -
AIR 2026: Genomic and Systems Approaches to Respiratory Infection, Microbiomes and Immunity 11th-13th February, sign up below for notifications
coursesandconferences.wellcomeconnectingscience.org/our-events/c...
It's immunulogy AND it's microbiology 🫁
AIR 2026: Genomic and Systems Approaches to Respiratory Infection, Microbiomes and Immunity 11th-13th February, sign up below for notifications
coursesandconferences.wellcomeconnectingscience.org/our-events/c...
It's immunulogy AND it's microbiology 🫁
⭐ Excellence fellowships accepting applications ⭐ for Black ECRs who have a degree from the UK. sanger.wd103.myworkdayjobs.com/en-US/Wellco...
I have an amazing spatial transcriptomics project available on the world's most important pathogen, TB: www.sanger.ac.uk/wp-content/u...
Please reach out!
I have an amazing spatial transcriptomics project available on the world's most important pathogen, TB: www.sanger.ac.uk/wp-content/u...
Please reach out!
www.sanger.ac.uk
July 16, 2025 at 8:40 AM
⭐ Excellence fellowships accepting applications ⭐ for Black ECRs who have a degree from the UK. sanger.wd103.myworkdayjobs.com/en-US/Wellco...
I have an amazing spatial transcriptomics project available on the world's most important pathogen, TB: www.sanger.ac.uk/wp-content/u...
Please reach out!
I have an amazing spatial transcriptomics project available on the world's most important pathogen, TB: www.sanger.ac.uk/wp-content/u...
Please reach out!
Reposted by Josie Bryant
BEAST X for Bayesian phylogenetic, phylogeographic and phylodynamic inference
www.nature.com/articles/s41...
www.nature.com/articles/s41...
BEAST X for Bayesian phylogenetic, phylogeographic and phylodynamic inference - Nature Methods
BEAST X advances Bayesian phylogenetic, phylogeographic and phylodynamic analysis by incorporating a broad range of complex models and leveraging advanced algorithms and techniques to boost statistica...
www.nature.com
July 7, 2025 at 6:25 PM
BEAST X for Bayesian phylogenetic, phylogeographic and phylodynamic inference
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Josie Bryant
Great faculty opportunities within the Cellular Genomics Programme @sangerinstitute.bsky.social
Please share with your networks and do contact me if you would like to find out more
sanger.wd103.myworkdayjobs.com/en-US/Wellco...
Please share with your networks and do contact me if you would like to find out more
sanger.wd103.myworkdayjobs.com/en-US/Wellco...
Group Leaders- Cellular Genomics
Do you want to help us improve human health and understand life on Earth? Make your mark by shaping the future to enable or deliver life-changing science to solve some of humanity’s greatest challenge...
sanger.wd103.myworkdayjobs.com
July 7, 2025 at 9:14 AM
Great faculty opportunities within the Cellular Genomics Programme @sangerinstitute.bsky.social
Please share with your networks and do contact me if you would like to find out more
sanger.wd103.myworkdayjobs.com/en-US/Wellco...
Please share with your networks and do contact me if you would like to find out more
sanger.wd103.myworkdayjobs.com/en-US/Wellco...
Reposted by Josie Bryant
New paper that looked at 15 million biomedical abstracts and found specific words that abruptly increased in frequency in 2024, likely due to the authors using LLMs.
Take home message: don't use the word "Delve"
www.science.org/doi/10.1126/...
Take home message: don't use the word "Delve"
www.science.org/doi/10.1126/...
July 3, 2025 at 6:52 PM
New paper that looked at 15 million biomedical abstracts and found specific words that abruptly increased in frequency in 2024, likely due to the authors using LLMs.
Take home message: don't use the word "Delve"
www.science.org/doi/10.1126/...
Take home message: don't use the word "Delve"
www.science.org/doi/10.1126/...
Reposted by Josie Bryant
One of my favourite serendipitous results from the lab came about because we were long-read sequencing bacterial:
Vibrio cholerae, which is "supposed to" have TWO circular chromosomes (3 + 1 million base pairs) often has just ONE fused chromosome (4 Mbp).
www.nature.com/articles/s41...
(1/n)
Vibrio cholerae, which is "supposed to" have TWO circular chromosomes (3 + 1 million base pairs) often has just ONE fused chromosome (4 Mbp).
www.nature.com/articles/s41...
(1/n)
Prevalent chromosome fusion in Vibrio cholerae O1 - Nature Communications
The pathogenic bacterium Vibrio cholerae typically has two circular chromosomes. Here, Cuénod et al. analyse 467 clinical isolates and identify several independent chromosome fusion events that are li...
www.nature.com
July 1, 2025 at 2:16 PM
One of my favourite serendipitous results from the lab came about because we were long-read sequencing bacterial:
Vibrio cholerae, which is "supposed to" have TWO circular chromosomes (3 + 1 million base pairs) often has just ONE fused chromosome (4 Mbp).
www.nature.com/articles/s41...
(1/n)
Vibrio cholerae, which is "supposed to" have TWO circular chromosomes (3 + 1 million base pairs) often has just ONE fused chromosome (4 Mbp).
www.nature.com/articles/s41...
(1/n)
Reposted by Josie Bryant
Sexually transmissible shigellosis has gone from an obscure cause of sporadic outbreaks to a sustained endemic AMR priority in only two decades! 🧫💊 Check out our latest preprint to understand how this happened 1/11
www.medrxiv.org/content/10.1...
www.medrxiv.org/content/10.1...
The natural history of the emergence of sexually transmissible shigellosis
Shigellosis is a gastrointestinal illness caused by bacteria belonging to one of four species of Shigella . Sexually transmissible shigellosis was first reported in 1974, but recently there has been a...
www.medrxiv.org
May 23, 2025 at 12:44 PM
Sexually transmissible shigellosis has gone from an obscure cause of sporadic outbreaks to a sustained endemic AMR priority in only two decades! 🧫💊 Check out our latest preprint to understand how this happened 1/11
www.medrxiv.org/content/10.1...
www.medrxiv.org/content/10.1...
Reposted by Josie Bryant
I am excited to begin my new journey as the Head of Cellular Genomics @sangerinstitute.bsky.social
We will decode and recode tissue ecosystems using AI + big data…
Our amazing faculty include Roser Vento-Tormo, @bayraktarlab.bsky.social, Mo Lotfollahi, Sam Behjati and Song Chen..
We will decode and recode tissue ecosystems using AI + big data…
Our amazing faculty include Roser Vento-Tormo, @bayraktarlab.bsky.social, Mo Lotfollahi, Sam Behjati and Song Chen..
Our newly appointed Head of the Cellular Genomics programme, @mhaniffa.bsky.social, shares her career journey and vision for the future of the programme. Read more below. ⤵️
sangerinstitute.blog/2025/05/20/i...
sangerinstitute.blog/2025/05/20/i...
May 23, 2025 at 10:26 PM
I am excited to begin my new journey as the Head of Cellular Genomics @sangerinstitute.bsky.social
We will decode and recode tissue ecosystems using AI + big data…
Our amazing faculty include Roser Vento-Tormo, @bayraktarlab.bsky.social, Mo Lotfollahi, Sam Behjati and Song Chen..
We will decode and recode tissue ecosystems using AI + big data…
Our amazing faculty include Roser Vento-Tormo, @bayraktarlab.bsky.social, Mo Lotfollahi, Sam Behjati and Song Chen..