Zamin Iqbal
@zaminiqbal.bsky.social
Professor of Algorithmic and Microbial Genomics at the University of Bath (UK). Pangenomes, drug resistance (esp TB), data structures for DNA search, plasmid evolution, global microbial surveillance. Open Data, reproducibility
Pinned
Congratulations to @zaminiqbal.bsky.social from @milnerevolution.bsky.social on being awarded the 2026 Mary Lyon Medal!
Honoured and quite blown-over to receive this award. I have been, and continue to be, very lucky - first with great mentors, and then really prodigious students, postdocs and collaborators. Working with them has been a joy.
Reposted by Zamin Iqbal
Yohan Hernandez–Courbevoie presenting REINDEER2 at Seqbim!
For those who missed it, the introduction thread of REINDEER2
bsky.app/profile/npma...
For those who missed it, the introduction thread of REINDEER2
bsky.app/profile/npma...
November 24, 2025 at 12:41 PM
Yohan Hernandez–Courbevoie presenting REINDEER2 at Seqbim!
For those who missed it, the introduction thread of REINDEER2
bsky.app/profile/npma...
For those who missed it, the introduction thread of REINDEER2
bsky.app/profile/npma...
Very excited to be in Adelaide to attend #ABACBS2025 . Australia is a powerhouse of microbial genomics, and indeed of bioinformatics, so am very much looking forward to meeting everyone, old friends and new, and speaking tomorrow!
November 24, 2025 at 12:11 AM
Very excited to be in Adelaide to attend #ABACBS2025 . Australia is a powerhouse of microbial genomics, and indeed of bioinformatics, so am very much looking forward to meeting everyone, old friends and new, and speaking tomorrow!
Reposted by Zamin Iqbal
November 23, 2025 at 9:42 AM
Friday jazz from Zam; current obsession
youtu.be/lFeKRmsBFeg?...
youtu.be/lFeKRmsBFeg?...
Triosence - Little Lost Wonder (Offcial Video)
YouTube video by triosenceVEVO
youtu.be
November 20, 2025 at 11:56 PM
Friday jazz from Zam; current obsession
youtu.be/lFeKRmsBFeg?...
youtu.be/lFeKRmsBFeg?...
Reposted by Zamin Iqbal
Baym continues to make freakin' art. Must see thread/paper
Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Intracellular competition shapes plasmid population dynamics
From populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g...
www.science.org
November 20, 2025 at 11:29 PM
Baym continues to make freakin' art. Must see thread/paper
Reposted by Zamin Iqbal
Brand new preprint from my lab, showing that TnpB, the ancestor of Cas12, acts as a gene drive in plasmids! And it turns out in conjugative plasmids that it acts as a primitive anti-self defense system, providing a potential link between its transposon effect and becoming CRISPR!
What is the best strategy to win any contest?
Eliminate your opponents of course.
Recently, my friend @fernpizza.bsky.social showed how plasmids compete intracellularly (check out his paper published in Science today!). With @baym.lol, we now know they can fight.
www.biorxiv.org/content/10.1...
Eliminate your opponents of course.
Recently, my friend @fernpizza.bsky.social showed how plasmids compete intracellularly (check out his paper published in Science today!). With @baym.lol, we now know they can fight.
www.biorxiv.org/content/10.1...
November 20, 2025 at 10:17 PM
Brand new preprint from my lab, showing that TnpB, the ancestor of Cas12, acts as a gene drive in plasmids! And it turns out in conjugative plasmids that it acts as a primitive anti-self defense system, providing a potential link between its transposon effect and becoming CRISPR!
Reposted by Zamin Iqbal
This work touches on many things. It shows within-cell evolution constrains which genes will spread on high-copy plasmids. It also gives a strong hint of the origins of highly-abundant “cryptic” plasmids, showing that multicopy plasmids have strong incentives to lose genes. 13/
November 20, 2025 at 9:42 PM
This work touches on many things. It shows within-cell evolution constrains which genes will spread on high-copy plasmids. It also gives a strong hint of the origins of highly-abundant “cryptic” plasmids, showing that multicopy plasmids have strong incentives to lose genes. 13/
Reposted by Zamin Iqbal
Now that we understood neutral dynamics, we turned to competition. What could cause one plasmid to replicate better than another? Our first thought was transcription might interfere with replication, and it turns out there was a much larger tradeoff than we expected! 7/
November 20, 2025 at 9:42 PM
Now that we understood neutral dynamics, we turned to competition. What could cause one plasmid to replicate better than another? Our first thought was transcription might interfere with replication, and it turns out there was a much larger tradeoff than we expected! 7/
Reposted by Zamin Iqbal
With this working, as a first test we took two plasmids, identical save for 8 point mutations changing the color, and competed them against one another. Here’s a video of what it looked like when we activated the recombinase. You can see the two compete in real time: 4/
November 20, 2025 at 9:42 PM
With this working, as a first test we took two plasmids, identical save for 8 point mutations changing the color, and competed them against one another. Here’s a video of what it looked like when we activated the recombinase. You can see the two compete in real time: 4/
Reposted by Zamin Iqbal
How the genes plasmids carry affect their hosts has been well studied, but this smaller scale of evolution has proven much tougher despite decades of theory. Plasmids are small and replication is fast and hard to measure. 2/
November 20, 2025 at 9:42 PM
How the genes plasmids carry affect their hosts has been well studied, but this smaller scale of evolution has proven much tougher despite decades of theory. Plasmids are small and replication is fast and hard to measure. 2/
Most exciting study have seen for ages, and Fernando the most excited speaker. Much anticipated. Highly recommended, a lot of food for thought (and quite a dense paper - lots to think about)
Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Intracellular competition shapes plasmid population dynamics
From populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g...
www.science.org
November 20, 2025 at 10:22 PM
Most exciting study have seen for ages, and Fernando the most excited speaker. Much anticipated. Highly recommended, a lot of food for thought (and quite a dense paper - lots to think about)
Reposted by Zamin Iqbal
🚀New preprint from our lab!
I am very excited to finally share what has been the main focus of my PhD for the past almost 3 years! It is about viral dark matter and a powerful tool we built to shed light on it. 🧬💡
Continue reading (🧵)
I am very excited to finally share what has been the main focus of my PhD for the past almost 3 years! It is about viral dark matter and a powerful tool we built to shed light on it. 🧬💡
Continue reading (🧵)
November 20, 2025 at 6:52 PM
🚀New preprint from our lab!
I am very excited to finally share what has been the main focus of my PhD for the past almost 3 years! It is about viral dark matter and a powerful tool we built to shed light on it. 🧬💡
Continue reading (🧵)
I am very excited to finally share what has been the main focus of my PhD for the past almost 3 years! It is about viral dark matter and a powerful tool we built to shed light on it. 🧬💡
Continue reading (🧵)
Just got an email from "reference-free SNP" which is pretty on-the-nose for spam
November 20, 2025 at 7:07 PM
Just got an email from "reference-free SNP" which is pretty on-the-nose for spam
Reposted by Zamin Iqbal
#AMR #Klebsiella cause >100,000 neonatal deaths globally each year.
Our new preprint shows more than half of #Klebsiella pneumoniae neonatal sepsis cases in African and South Asian are nosocomial, acquired through transmission in neonatal units. #WAAW
doi.org/10.1101/2025...
Our new preprint shows more than half of #Klebsiella pneumoniae neonatal sepsis cases in African and South Asian are nosocomial, acquired through transmission in neonatal units. #WAAW
doi.org/10.1101/2025...
![figure showing estimated proportion of cases in clusters, for each site. range from 0.04 to 0.93, mean estimate in random effects model is 0.57 [0.46,0.68]](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:q5nky4heg5sfix4get4zh2pw/bafkreibshmuvkuafxwd2uk3r42ss6ma2dhmaidbysgvufnbkbv5cn4guai@jpeg)
November 19, 2025 at 3:43 PM
#AMR #Klebsiella cause >100,000 neonatal deaths globally each year.
Our new preprint shows more than half of #Klebsiella pneumoniae neonatal sepsis cases in African and South Asian are nosocomial, acquired through transmission in neonatal units. #WAAW
doi.org/10.1101/2025...
Our new preprint shows more than half of #Klebsiella pneumoniae neonatal sepsis cases in African and South Asian are nosocomial, acquired through transmission in neonatal units. #WAAW
doi.org/10.1101/2025...
Reposted by Zamin Iqbal
The data was collected by the CABBAGE project, which has just been preprinted too: www.biorxiv.org/content/10.1...
www.biorxiv.org
November 19, 2025 at 12:27 PM
The data was collected by the CABBAGE project, which has just been preprinted too: www.biorxiv.org/content/10.1...
Reposted by Zamin Iqbal
Happy to share our new AMR resource which has phenotypic AMR (usually MIC data) collected from publications and databases. This is paired with assemblies and annotations
We're excited for users who might train new models, find phenotype/genotype mismatches, or any other use
We're excited for users who might train new models, find phenotype/genotype mismatches, or any other use
Antimicrobial resistance (AMR) is a growing health threat, making infections harder to treat and complicating routine medical care.
EMBL-EBI’s new AMR portal brings together laboratory resistance data and bacterial genomes in one open platform.
#WAAW2025 #ActOnAMR
www.ebi.ac.uk/about/news/t...
🧬💻
EMBL-EBI’s new AMR portal brings together laboratory resistance data and bacterial genomes in one open platform.
#WAAW2025 #ActOnAMR
www.ebi.ac.uk/about/news/t...
🧬💻
A new gateway to global antimicrobial resistance data
New online portal connects bacterial genomes with experimental resistance data to support antimicrobial resistance research.
www.ebi.ac.uk
November 19, 2025 at 12:27 PM
Happy to share our new AMR resource which has phenotypic AMR (usually MIC data) collected from publications and databases. This is paired with assemblies and annotations
We're excited for users who might train new models, find phenotype/genotype mismatches, or any other use
We're excited for users who might train new models, find phenotype/genotype mismatches, or any other use
Reposted by Zamin Iqbal
Alf Dubs is a 92 year old man who spent his life fighting for refugees, and in particular for refugee children. He fought the Tories tooth and nail during their last three terms, only to see Labour adopt far-right policies on immigration.
“But to use children as a weapon ... I’m lost for words.”
“But to use children as a weapon ... I’m lost for words.”
Labour Peer Who Fled The Nazis Condemns His Party's Immigration Crackdown
Lord Dubs said he was "lost for words".
www.huffingtonpost.co.uk
November 19, 2025 at 8:20 AM
Alf Dubs is a 92 year old man who spent his life fighting for refugees, and in particular for refugee children. He fought the Tories tooth and nail during their last three terms, only to see Labour adopt far-right policies on immigration.
“But to use children as a weapon ... I’m lost for words.”
“But to use children as a weapon ... I’m lost for words.”
Reposted by Zamin Iqbal
Hmmm
This work has so many implications on literature 😳😬
Fluorescein-based dyes are not valid reporters of oxidative stress in bacteria, and conclusions based on their use must be reconsidered | PNAS www.pnas.org/doi/10.1073/...
This work has so many implications on literature 😳😬
Fluorescein-based dyes are not valid reporters of oxidative stress in bacteria, and conclusions based on their use must be reconsidered | PNAS www.pnas.org/doi/10.1073/...
Fluorescein-based dyes are not valid reporters of oxidative stress in bacteria, and conclusions based on their use must be reconsidered | PNAS
Dihydrodichlorofluorescein derivatives have been employed as reporters of intracellular
reactive oxygen species (ROS) in innumerable studies. Their...
www.pnas.org
November 19, 2025 at 5:03 AM
Hmmm
This work has so many implications on literature 😳😬
Fluorescein-based dyes are not valid reporters of oxidative stress in bacteria, and conclusions based on their use must be reconsidered | PNAS www.pnas.org/doi/10.1073/...
This work has so many implications on literature 😳😬
Fluorescein-based dyes are not valid reporters of oxidative stress in bacteria, and conclusions based on their use must be reconsidered | PNAS www.pnas.org/doi/10.1073/...
Reposted by Zamin Iqbal
The @klebnet.bsky.social team are pleased to share slides from our “Klebsiella pneumoniae Genomic Epidemiology & Antimicrobial Resistance” lecture series!
Topics include Kleb diversity, lineages, AMR, hypervirulence, how to use Kaptive & Kleborate for typing, and more!
klebnet.org/2025/11/18/k...
Topics include Kleb diversity, lineages, AMR, hypervirulence, how to use Kaptive & Kleborate for typing, and more!
klebnet.org/2025/11/18/k...
Klebsiella pneumoniae genomics tutorials – KlebNET-GSP
klebnet.org
November 18, 2025 at 8:25 AM
The @klebnet.bsky.social team are pleased to share slides from our “Klebsiella pneumoniae Genomic Epidemiology & Antimicrobial Resistance” lecture series!
Topics include Kleb diversity, lineages, AMR, hypervirulence, how to use Kaptive & Kleborate for typing, and more!
klebnet.org/2025/11/18/k...
Topics include Kleb diversity, lineages, AMR, hypervirulence, how to use Kaptive & Kleborate for typing, and more!
klebnet.org/2025/11/18/k...
Reposted by Zamin Iqbal
Our new paper is out in @narjournal.bsky.social We show that natural transformation enables bacteria to shuffle integron cassettes, boosting their phenotypic diversity.
academic.oup.com/nar/article/... 1/5
academic.oup.com/nar/article/... 1/5
Bacterial natural transformation drives cassette shuffling and simplifies recombination in chromosomal integrons
Abstract. Integrons act as biobanks of gene cassettes conferring functions crucial for bacterial defense, including protection against phages and antibioti
academic.oup.com
November 17, 2025 at 3:44 PM
Our new paper is out in @narjournal.bsky.social We show that natural transformation enables bacteria to shuffle integron cassettes, boosting their phenotypic diversity.
academic.oup.com/nar/article/... 1/5
academic.oup.com/nar/article/... 1/5
Reposted by Zamin Iqbal
📣 New preprint from us at phagefoundry.org 📣
A solid machine learning framework & to predict strain-level phage-host interactions across diverse bacterial genera from genome sequences alone. Avery Noonan from the Arkin Lab led this massive effort
www.biorxiv.org/content/10.1...
A solid machine learning framework & to predict strain-level phage-host interactions across diverse bacterial genera from genome sequences alone. Avery Noonan from the Arkin Lab led this massive effort
www.biorxiv.org/content/10.1...
Phage Foundry
phagefoundry.org
November 16, 2025 at 5:58 PM
📣 New preprint from us at phagefoundry.org 📣
A solid machine learning framework & to predict strain-level phage-host interactions across diverse bacterial genera from genome sequences alone. Avery Noonan from the Arkin Lab led this massive effort
www.biorxiv.org/content/10.1...
A solid machine learning framework & to predict strain-level phage-host interactions across diverse bacterial genera from genome sequences alone. Avery Noonan from the Arkin Lab led this massive effort
www.biorxiv.org/content/10.1...
Writing down your ideas, and things you learn from papers, in one searchable place is a gift that keeps on giving. Even if it's impossible to organise the information to your satisfaction, it's repeatedly useful.
November 16, 2025 at 4:58 PM
Writing down your ideas, and things you learn from papers, in one searchable place is a gift that keeps on giving. Even if it's impossible to organise the information to your satisfaction, it's repeatedly useful.
Reposted by Zamin Iqbal
🚨 PhD Opportunity 🚨
Interested in microbiology, phages & water security?
Join me and Prof Cindy Smith to test phages as a sustainable alternative to chlorine in drinking-water biofilters.
Metagenomics, phage discovery & ecology — all in one exciting project!
Apply: www.gla.ac.uk/colleges/mvl...
Interested in microbiology, phages & water security?
Join me and Prof Cindy Smith to test phages as a sustainable alternative to chlorine in drinking-water biofilters.
Metagenomics, phage discovery & ecology — all in one exciting project!
Apply: www.gla.ac.uk/colleges/mvl...
November 15, 2025 at 3:30 PM
🚨 PhD Opportunity 🚨
Interested in microbiology, phages & water security?
Join me and Prof Cindy Smith to test phages as a sustainable alternative to chlorine in drinking-water biofilters.
Metagenomics, phage discovery & ecology — all in one exciting project!
Apply: www.gla.ac.uk/colleges/mvl...
Interested in microbiology, phages & water security?
Join me and Prof Cindy Smith to test phages as a sustainable alternative to chlorine in drinking-water biofilters.
Metagenomics, phage discovery & ecology — all in one exciting project!
Apply: www.gla.ac.uk/colleges/mvl...
Reposted by Zamin Iqbal
Amazing how the numbers vary between years and how the variability seems country specific. Almost as if there's something in their home country that they are trying to get away from, rather than something in the UK pulling them here. The latter would produce similar effects across countries.
Where do refugees to the UK come from? (House of Commons library)
November 16, 2025 at 2:49 PM
Amazing how the numbers vary between years and how the variability seems country specific. Almost as if there's something in their home country that they are trying to get away from, rather than something in the UK pulling them here. The latter would produce similar effects across countries.
Reposted by Zamin Iqbal
I am so excited to share our project with you! We find prokaryotic proteases activate toxic enzymes and pores as a modular strategy in phage defense. We studied four fascinating protease-toxin pairs that are abundant across bacterial genomes:
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Proteolytic activation of diverse antiviral defense modules in prokaryotes
Linked protease–effector modules are widespread in prokaryotic antiviral defense, yet the mechanisms of most remain poorly understood. Here we show that four of the most prevalent modules—metallo-β-la...
www.biorxiv.org
November 15, 2025 at 11:49 PM
I am so excited to share our project with you! We find prokaryotic proteases activate toxic enzymes and pores as a modular strategy in phage defense. We studied four fascinating protease-toxin pairs that are abundant across bacterial genomes:
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...