Amelia Barber
@ameliabarberphd.bsky.social
Junior group leader at the University of Jena (@uni-jena.de)
CIFAR Azrieli Global Scholar
Fungal pathoecology, antimicrobial resistance, and genome stuff.
Always up for an adventure or bike ride.
https://barber-lab.com
CIFAR Azrieli Global Scholar
Fungal pathoecology, antimicrobial resistance, and genome stuff.
Always up for an adventure or bike ride.
https://barber-lab.com
Pinned
Congrats to the group's first PhD student, the newly minted Dr. Brassington!!
Phillip relocated back to Oceania in the period between submitting his dissertation and his oral defense, so we had to make do with a virtual defense, but I am still incredibly proud of him.
Phillip relocated back to Oceania in the period between submitting his dissertation and his oral defense, so we had to make do with a virtual defense, but I am still incredibly proud of him.
Reposted by Amelia Barber
We're looking for a PhD student! If you're interested in #fungal #genomics & #TEs, meiotic drive, or pathogens, please consider applying. The project is about toxin/antidote genes in the human fungal pathogen A. fumigatus. uu.varbi.com/en/what:job/...
November 19, 2025 at 9:20 AM
We're looking for a PhD student! If you're interested in #fungal #genomics & #TEs, meiotic drive, or pathogens, please consider applying. The project is about toxin/antidote genes in the human fungal pathogen A. fumigatus. uu.varbi.com/en/what:job/...
Reposted by Amelia Barber
TEs aren’t just genomic parasites, they’re also engines of genomic novelty.
Our new study with ~2,000 Z. tritici genomes shows repeated TE mobilization waves during global expansion.
With @danielcroll.bsky.social & @guidopuccetti.bsky.social
🧬 www.nature.com/articles/s41...
#TEworldwide
Our new study with ~2,000 Z. tritici genomes shows repeated TE mobilization waves during global expansion.
With @danielcroll.bsky.social & @guidopuccetti.bsky.social
🧬 www.nature.com/articles/s41...
#TEworldwide
Historic transposon mobilisation waves create distinct pools of adaptive variants in a major crop pathogen - Nature Communications
In this study, the authors analysed a large genomic dataset to trace how jumping genes shaped the global spread of a major wheat pathogen and reveal bursts of activity over decades that drove adaptati...
www.nature.com
November 12, 2025 at 1:17 PM
TEs aren’t just genomic parasites, they’re also engines of genomic novelty.
Our new study with ~2,000 Z. tritici genomes shows repeated TE mobilization waves during global expansion.
With @danielcroll.bsky.social & @guidopuccetti.bsky.social
🧬 www.nature.com/articles/s41...
#TEworldwide
Our new study with ~2,000 Z. tritici genomes shows repeated TE mobilization waves during global expansion.
With @danielcroll.bsky.social & @guidopuccetti.bsky.social
🧬 www.nature.com/articles/s41...
#TEworldwide
Reposted by Amelia Barber
@tobybarilbio.bsky.social and I are very excited to release MycoMobilome! A very extensive effort to discover, QC and annotate TEs across the fungal kingdom.
👉 Ready-to-use for your own genome with a simple tutorial!
👉 Metadata about TEs discovered in your genome!
👉 Contribute and get recognition!
👉 Ready-to-use for your own genome with a simple tutorial!
👉 Metadata about TEs discovered in your genome!
👉 Contribute and get recognition!
1/ Ever needed to annotate TEs in a fungal genome, but didn't know where to start?
We have released #MycoMobilome, a community-focused non-redundant database of transposable element consensus sequences for the fungal kingdom, constructed from >4,000 fungal genomes!
www.biorxiv.org/content/10.1...
We have released #MycoMobilome, a community-focused non-redundant database of transposable element consensus sequences for the fungal kingdom, constructed from >4,000 fungal genomes!
www.biorxiv.org/content/10.1...
October 29, 2025 at 4:32 PM
@tobybarilbio.bsky.social and I are very excited to release MycoMobilome! A very extensive effort to discover, QC and annotate TEs across the fungal kingdom.
👉 Ready-to-use for your own genome with a simple tutorial!
👉 Metadata about TEs discovered in your genome!
👉 Contribute and get recognition!
👉 Ready-to-use for your own genome with a simple tutorial!
👉 Metadata about TEs discovered in your genome!
👉 Contribute and get recognition!
Reposted by Amelia Barber
1/ Ever needed to annotate TEs in a fungal genome, but didn't know where to start?
We have released #MycoMobilome, a community-focused non-redundant database of transposable element consensus sequences for the fungal kingdom, constructed from >4,000 fungal genomes!
www.biorxiv.org/content/10.1...
We have released #MycoMobilome, a community-focused non-redundant database of transposable element consensus sequences for the fungal kingdom, constructed from >4,000 fungal genomes!
www.biorxiv.org/content/10.1...
October 29, 2025 at 9:02 AM
1/ Ever needed to annotate TEs in a fungal genome, but didn't know where to start?
We have released #MycoMobilome, a community-focused non-redundant database of transposable element consensus sequences for the fungal kingdom, constructed from >4,000 fungal genomes!
www.biorxiv.org/content/10.1...
We have released #MycoMobilome, a community-focused non-redundant database of transposable element consensus sequences for the fungal kingdom, constructed from >4,000 fungal genomes!
www.biorxiv.org/content/10.1...
Reposted by Amelia Barber
A great turnout for our latest Microverse Seminar! 🍕🔬
@ameliabarberphd.bsky.social, Junior Group Leader #FungalInformatics, shared fascinating insights in her talk “From Ecology to Genomes: Unraveling Fungal Pathogenicity Across Scales.”
Lively discussions and great connections followed!
@ameliabarberphd.bsky.social, Junior Group Leader #FungalInformatics, shared fascinating insights in her talk “From Ecology to Genomes: Unraveling Fungal Pathogenicity Across Scales.”
Lively discussions and great connections followed!
October 29, 2025 at 8:02 AM
A great turnout for our latest Microverse Seminar! 🍕🔬
@ameliabarberphd.bsky.social, Junior Group Leader #FungalInformatics, shared fascinating insights in her talk “From Ecology to Genomes: Unraveling Fungal Pathogenicity Across Scales.”
Lively discussions and great connections followed!
@ameliabarberphd.bsky.social, Junior Group Leader #FungalInformatics, shared fascinating insights in her talk “From Ecology to Genomes: Unraveling Fungal Pathogenicity Across Scales.”
Lively discussions and great connections followed!
Congrats to the group's first PhD student, the newly minted Dr. Brassington!!
Phillip relocated back to Oceania in the period between submitting his dissertation and his oral defense, so we had to make do with a virtual defense, but I am still incredibly proud of him.
Phillip relocated back to Oceania in the period between submitting his dissertation and his oral defense, so we had to make do with a virtual defense, but I am still incredibly proud of him.
October 17, 2025 at 2:35 PM
Congrats to the group's first PhD student, the newly minted Dr. Brassington!!
Phillip relocated back to Oceania in the period between submitting his dissertation and his oral defense, so we had to make do with a virtual defense, but I am still incredibly proud of him.
Phillip relocated back to Oceania in the period between submitting his dissertation and his oral defense, so we had to make do with a virtual defense, but I am still incredibly proud of him.
Reposted by Amelia Barber
Registration open for #Fungal26 genetics-gsa.org/fungal-2026/ at Asilomar.
Homepage - 33rd Fungal Genetics Conference
Visit our website to learn more.
genetics-gsa.org
October 16, 2025 at 5:59 PM
Registration open for #Fungal26 genetics-gsa.org/fungal-2026/ at Asilomar.
Reposted by Amelia Barber
Population structure in a fungal human pathogen is associated with clinical prevalence
#Aspergillus flavus
@annemakerofhats.bsky.social @ameliabarberphd.bsky.social @rokaslab.bsky.social
#fungi #infection #PopulationGenomics #mycology
#Aspergillus flavus
@annemakerofhats.bsky.social @ameliabarberphd.bsky.social @rokaslab.bsky.social
#fungi #infection #PopulationGenomics #mycology
Population structure in a fungal human pathogen is potentially linked to pathogenicity - Nature Communications
Genetic diversity between clinical and environmental fungal isolates of Aspergillus flavus is poorly studied. Here, the authors analysed genomic data from a global set of clinical and environmental A. flavus isolates and report that clinical prevalence is associated with population structure.
bit.ly
October 16, 2025 at 2:47 PM
Population structure in a fungal human pathogen is associated with clinical prevalence
#Aspergillus flavus
@annemakerofhats.bsky.social @ameliabarberphd.bsky.social @rokaslab.bsky.social
#fungi #infection #PopulationGenomics #mycology
#Aspergillus flavus
@annemakerofhats.bsky.social @ameliabarberphd.bsky.social @rokaslab.bsky.social
#fungi #infection #PopulationGenomics #mycology
Reposted by Amelia Barber
Very excited to see the final version of our kingdom-scale fungal genome defense manuscript out in @plosbiology.org !
This work has been a major project of @tbadet.bsky.social during his time in our lab.
We hope to stimulate much more exciting work on fungal TEs.
journals.plos.org/plosbiology/...
This work has been a major project of @tbadet.bsky.social during his time in our lab.
We hope to stimulate much more exciting work on fungal TEs.
journals.plos.org/plosbiology/...
October 16, 2025 at 8:46 AM
Very excited to see the final version of our kingdom-scale fungal genome defense manuscript out in @plosbiology.org !
This work has been a major project of @tbadet.bsky.social during his time in our lab.
We hope to stimulate much more exciting work on fungal TEs.
journals.plos.org/plosbiology/...
This work has been a major project of @tbadet.bsky.social during his time in our lab.
We hope to stimulate much more exciting work on fungal TEs.
journals.plos.org/plosbiology/...
Reposted by Amelia Barber
Want to understand how entire fungal chromosomes can be horizontally transferred?
Join us to unravel the mechanism/consequences of horizontal chromosome transfer in a fungal pathogen as part of an ERC-funded project. Postdoc/PhD positions available.
fungal-evolutionary-genetics.de/open-positio...
Join us to unravel the mechanism/consequences of horizontal chromosome transfer in a fungal pathogen as part of an ERC-funded project. Postdoc/PhD positions available.
fungal-evolutionary-genetics.de/open-positio...
Open Positions
ERC-funded project on the mechanism of horizontal transfer of entire fungal chromosomes PhD PostDoc
fungal-evolutionary-genetics.de
October 13, 2025 at 9:39 AM
Want to understand how entire fungal chromosomes can be horizontally transferred?
Join us to unravel the mechanism/consequences of horizontal chromosome transfer in a fungal pathogen as part of an ERC-funded project. Postdoc/PhD positions available.
fungal-evolutionary-genetics.de/open-positio...
Join us to unravel the mechanism/consequences of horizontal chromosome transfer in a fungal pathogen as part of an ERC-funded project. Postdoc/PhD positions available.
fungal-evolutionary-genetics.de/open-positio...
Reposted by Amelia Barber
If you saw my talk on the population structure of #Aspergillus flavus at Fungal Genetics in 2024, you might have heard someone ask "how does Aspergillus oryzae fit into the picture?"
If so, you heard my answer was "wait and see--we're working on this exact topic"
Well, the wait is over! Preprint ⬇️
If so, you heard my answer was "wait and see--we're working on this exact topic"
Well, the wait is over! Preprint ⬇️
Population-Specific Transcriptomic Shifts Underlie Secondary Metabolic Diversification in Aspergillus flavus and the Domestication of Aspergillus oryzae https://www.biorxiv.org/content/10.1101/2025.10.02.680074v1
October 7, 2025 at 7:50 PM
If you saw my talk on the population structure of #Aspergillus flavus at Fungal Genetics in 2024, you might have heard someone ask "how does Aspergillus oryzae fit into the picture?"
If so, you heard my answer was "wait and see--we're working on this exact topic"
Well, the wait is over! Preprint ⬇️
If so, you heard my answer was "wait and see--we're working on this exact topic"
Well, the wait is over! Preprint ⬇️
Reposted by Amelia Barber
Open postdoc position in in my lab in Berlin @mpiib-berlin.mpg.de.
Join us to push the frontier in ancient microbial genomics. Please apply until Oct 17th. Reach out in case you have any questions.
www.mpiib-berlin.mpg.de/2193291/job_...
Join us to push the frontier in ancient microbial genomics. Please apply until Oct 17th. Reach out in case you have any questions.
www.mpiib-berlin.mpg.de/2193291/job_...
September 15, 2025 at 8:03 AM
Open postdoc position in in my lab in Berlin @mpiib-berlin.mpg.de.
Join us to push the frontier in ancient microbial genomics. Please apply until Oct 17th. Reach out in case you have any questions.
www.mpiib-berlin.mpg.de/2193291/job_...
Join us to push the frontier in ancient microbial genomics. Please apply until Oct 17th. Reach out in case you have any questions.
www.mpiib-berlin.mpg.de/2193291/job_...
Fabio doing some excellent scicomm about his postdoc project in the group!
🌱🔥🫁 From compost heaps to human lungs: Understanding how Aspergillus fumigatus has acquired the ability to infect humans
Opportunistic fungal pathogens like Aspergillus fumigatus primarily live in the environment, thriving in very diverse ecosystems such as soils and compost heaps.
Opportunistic fungal pathogens like Aspergillus fumigatus primarily live in the environment, thriving in very diverse ecosystems such as soils and compost heaps.
September 11, 2025 at 8:28 PM
Fabio doing some excellent scicomm about his postdoc project in the group!
Reposted by Amelia Barber
Excited to share our new publication, out today in Nature! www.nature.com/articles/s41.... @kanchanj.bsky.social led this fascinating fungal-bacterial interaction project. We are grateful for our wonderful collaborators Brian Peters and David Underhill.
Commensal yeast promotes Salmonella Typhimurium virulence - Nature
Commensal Candida albicans enhances the virulence and dissemination of Salmonella enterica subsp. enterica serovar Typhimurium.
www.nature.com
September 3, 2025 at 4:32 PM
Excited to share our new publication, out today in Nature! www.nature.com/articles/s41.... @kanchanj.bsky.social led this fascinating fungal-bacterial interaction project. We are grateful for our wonderful collaborators Brian Peters and David Underhill.
Just a few more days to apply! ⏰
My group at is hiring a PhD student to explore how fungal pathogens that live in the environment will adapt their genomes, acquire new phenotypes, and perhaps even increased infectivity as a result of climate change. Please share!
More info and applications at @ jobs.uni-jena.de/vrbup
More info and applications at @ jobs.uni-jena.de/vrbup
August 27, 2025 at 3:51 PM
Just a few more days to apply! ⏰
I thought the Aspergillus fumigatus pan-genome was pretty wild when we started this project.
Aspergillus flavus said, "hold my beer..." Not only does it have a strong population structure with differences between environmental and clinical strains, only 58%of genes are conserved across the species!
Aspergillus flavus said, "hold my beer..." Not only does it have a strong population structure with differences between environmental and clinical strains, only 58%of genes are conserved across the species!
Thrilled to share that the final chapter of my PhD with @rokaslab.bsky.social is now out in @natcomms.nature.com 🎉
Read it to find out how population structure impacts pathogenicity in Aspergillus flavus, a fungus that infects humans 🧪
rdcu.be/eAToj
Read it to find out how population structure impacts pathogenicity in Aspergillus flavus, a fungus that infects humans 🧪
rdcu.be/eAToj
Population structure in a fungal human pathogen is potentially linked to pathogenicity
Nature Communications - Genetic diversity between clinical and environmental fungal isolates of Aspergillus flavus is poorly studied. Here, the authors analysed genomic data from a global set of...
rdcu.be
August 22, 2025 at 6:38 AM
I thought the Aspergillus fumigatus pan-genome was pretty wild when we started this project.
Aspergillus flavus said, "hold my beer..." Not only does it have a strong population structure with differences between environmental and clinical strains, only 58%of genes are conserved across the species!
Aspergillus flavus said, "hold my beer..." Not only does it have a strong population structure with differences between environmental and clinical strains, only 58%of genes are conserved across the species!
Reposted by Amelia Barber
Really interesting work. Bottom line: re-annotate everything using the same pipeline for pangenome studies!
Determining presence-absence variation (PAV) across reference genomes is a major goal of pangenome analysis. It turns out that A LOT of gene PAV is due to methodological artifacts.
We explore the causes of this in soybean and cotton datasets in our recent preprint: www.biorxiv.org/content/10.1...
We explore the causes of this in soybean and cotton datasets in our recent preprint: www.biorxiv.org/content/10.1...
August 18, 2025 at 5:11 PM
Really interesting work. Bottom line: re-annotate everything using the same pipeline for pangenome studies!
A nice walkthrough on the limitations of generic slide titles and how assertive titles really help keep you on track and your audience following your desired narrative.
My group can attest that I agree 💯% that slides should have a concrete summary statement as the title, with very few exceptions.
My group can attest that I agree 💯% that slides should have a concrete summary statement as the title, with very few exceptions.
A simple design framework that will massively improve your slides and your public speaking
clauswilke.substack.com/p/slides-tha...
clauswilke.substack.com/p/slides-tha...
Slide designs that present themselves: The assertion–evidence template
Your slides are not your talk.
clauswilke.substack.com
August 15, 2025 at 3:39 PM
A nice walkthrough on the limitations of generic slide titles and how assertive titles really help keep you on track and your audience following your desired narrative.
My group can attest that I agree 💯% that slides should have a concrete summary statement as the title, with very few exceptions.
My group can attest that I agree 💯% that slides should have a concrete summary statement as the title, with very few exceptions.
Aspergillus fumigatus reference strain Af293 carries a mycovirus that boosts heat+oxidative stress resistance and infection fitness. 😲💥
I encourage you to check out Neta's thread and I'm delighted my group could play a small role in this exciting study!!
I encourage you to check out Neta's thread and I'm delighted my group could play a small role in this exciting study!!
🚨 Fungi + viruses + mammalian lungs? Buckle up! Our new paper in
@natmicrobiol.nature.com
uncovers the story of a deadly fungus and its gnarly viral hitchhiker — and how this duo may change how we diagnose & treat fungal disease 🍄🫁🚨 doi.org/10.1038/s415... ⬇️
@natmicrobiol.nature.com
uncovers the story of a deadly fungus and its gnarly viral hitchhiker — and how this duo may change how we diagnose & treat fungal disease 🍄🫁🚨 doi.org/10.1038/s415... ⬇️
Aspergillus fumigatus dsRNA virus promotes fungal fitness and pathogenicity in the mammalian host - Nature Microbiology
A mycovirus infecting the pathogenic fungus Aspergillus fumigatus enhances its stress tolerance and virulence in mice.
doi.org
August 14, 2025 at 1:40 PM
Aspergillus fumigatus reference strain Af293 carries a mycovirus that boosts heat+oxidative stress resistance and infection fitness. 😲💥
I encourage you to check out Neta's thread and I'm delighted my group could play a small role in this exciting study!!
I encourage you to check out Neta's thread and I'm delighted my group could play a small role in this exciting study!!
Reposted by Amelia Barber
New #preprint from talented graduate student for a workflow we have been using for a while into a formal usage www.biorxiv.org/content/10.1...
Phyling: phylogenetic inference from annotated genomes
Phyling is a fast, scalable, and user-friendly tool supporting phylogenomic reconstruction of species phylogenies directly from protein-encoded genomic data. It identifies orthologous genes by searchi...
www.biorxiv.org
August 6, 2025 at 6:43 PM
New #preprint from talented graduate student for a workflow we have been using for a while into a formal usage www.biorxiv.org/content/10.1...
Reposted by Amelia Barber
New PhD position @uni-jena.de and at our #ClusterOfExcellence! Join @ameliabarberphd.bsky.social's group to study #ClimateChange & #FungalPathogens. Interdisciplinary training, vibrant research network & great working conditions. Apply by Aug 31: jobs.uni-jena.de/jobposting/a... @uni-jena.de
Doctoral Researcher in the areas of Microbial Pathogens and Climate Change
jobs.uni-jena.de
July 30, 2025 at 7:14 AM
New PhD position @uni-jena.de and at our #ClusterOfExcellence! Join @ameliabarberphd.bsky.social's group to study #ClimateChange & #FungalPathogens. Interdisciplinary training, vibrant research network & great working conditions. Apply by Aug 31: jobs.uni-jena.de/jobposting/a... @uni-jena.de
Reposted by Amelia Barber
My group at is hiring a PhD student to explore how fungal pathogens that live in the environment will adapt their genomes, acquire new phenotypes, and perhaps even increased infectivity as a result of climate change. Please share!
More info and applications at @ jobs.uni-jena.de/vrbup
More info and applications at @ jobs.uni-jena.de/vrbup
July 29, 2025 at 3:41 PM
My group at is hiring a PhD student to explore how fungal pathogens that live in the environment will adapt their genomes, acquire new phenotypes, and perhaps even increased infectivity as a result of climate change. Please share!
More info and applications at @ jobs.uni-jena.de/vrbup
More info and applications at @ jobs.uni-jena.de/vrbup
My group at is hiring a PhD student to explore how fungal pathogens that live in the environment will adapt their genomes, acquire new phenotypes, and perhaps even increased infectivity as a result of climate change. Please share!
More info and applications at @ jobs.uni-jena.de/vrbup
More info and applications at @ jobs.uni-jena.de/vrbup
July 29, 2025 at 3:41 PM
My group at is hiring a PhD student to explore how fungal pathogens that live in the environment will adapt their genomes, acquire new phenotypes, and perhaps even increased infectivity as a result of climate change. Please share!
More info and applications at @ jobs.uni-jena.de/vrbup
More info and applications at @ jobs.uni-jena.de/vrbup
Last week we enjoyed a lovely day of socialising and networking with the groups of @mgblango.bsky.social and @slavi-jan.bsky.social. We broke into teams for a scavenger hunt and visited a palace outside Weimar. We were even joined by special guest @mulveylab.bsky.social while he was visiting!
July 29, 2025 at 2:36 PM
Last week we enjoyed a lovely day of socialising and networking with the groups of @mgblango.bsky.social and @slavi-jan.bsky.social. We broke into teams for a scavenger hunt and visited a palace outside Weimar. We were even joined by special guest @mulveylab.bsky.social while he was visiting!