Ben Auxier
@benauxier.bsky.social
Fungal geneticist interested in how fungi recognize themselves, and each other. Asst. Professor at WUR
Reposted by Ben Auxier
Congratulations to Joe Felsenstein on being awarded the 2026 Mendel Medal!
November 14, 2025 at 12:41 PM
Congratulations to Joe Felsenstein on being awarded the 2026 Mendel Medal!
Reposted by Ben Auxier
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 Ben Auxier
An empirical approach to evaluating the prevalence of long-lived balancing selection in humans--and important limitations. Work by @hannahmm.bsky.social
November 11, 2025 at 7:14 PM
An empirical approach to evaluating the prevalence of long-lived balancing selection in humans--and important limitations. Work by @hannahmm.bsky.social
Reposted by Ben Auxier
For anyone else whose Mac Outlook 365 has started making regular, massive faux pas through Autocorrect recently: Start typing new email > Edit > Spelling and Grammar > uncheck 'Correct Spelling Automatically'. Literally just called a new collaborator Baby because of this ... 🙄
November 10, 2025 at 12:29 PM
For anyone else whose Mac Outlook 365 has started making regular, massive faux pas through Autocorrect recently: Start typing new email > Edit > Spelling and Grammar > uncheck 'Correct Spelling Automatically'. Literally just called a new collaborator Baby because of this ... 🙄
So, maybe some of you have seen this new work on Neurospora nuclei. I have some words about it, as a comment on the preprint. Short version: The long history of Neurospora shows mutation and transformation experiments are not consistent with this result.
disq.us/t/4xk0nij
disq.us/t/4xk0nij
disq.us
November 10, 2025 at 8:50 PM
So, maybe some of you have seen this new work on Neurospora nuclei. I have some words about it, as a comment on the preprint. Short version: The long history of Neurospora shows mutation and transformation experiments are not consistent with this result.
disq.us/t/4xk0nij
disq.us/t/4xk0nij
Fungal Friends - Some of you may have seen the recent preprint on chromosomes in Neurospora nuclei. I have something to say about that, but waiting while bioRxiv moderates the comment
November 10, 2025 at 4:52 PM
Fungal Friends - Some of you may have seen the recent preprint on chromosomes in Neurospora nuclei. I have something to say about that, but waiting while bioRxiv moderates the comment
Reposted by Ben Auxier
"i asked grok" "i asked chatgpt" yeah well i asked carl sagan and he said the greatest enemy of knowledge is not ignorance but the illusion of knowledge 🧪
July 18, 2025 at 4:12 AM
"i asked grok" "i asked chatgpt" yeah well i asked carl sagan and he said the greatest enemy of knowledge is not ignorance but the illusion of knowledge 🧪
Reposted by Ben Auxier
My reviewing style has changed over time. Rather than litigate every little thing, and pushing my own ideas, I focus only on 2 things:
(1) Are the claims interesting/important?
(2) Does the evidence support the claims?
Most of my reviews these days are short and focused.
(1) Are the claims interesting/important?
(2) Does the evidence support the claims?
Most of my reviews these days are short and focused.
November 8, 2025 at 11:22 AM
My reviewing style has changed over time. Rather than litigate every little thing, and pushing my own ideas, I focus only on 2 things:
(1) Are the claims interesting/important?
(2) Does the evidence support the claims?
Most of my reviews these days are short and focused.
(1) Are the claims interesting/important?
(2) Does the evidence support the claims?
Most of my reviews these days are short and focused.
Reposted by Ben Auxier
Interesting story in this preprint.
A male infant was diagnosed with Fanconi anemia due to an X-linked frameshift mutation.
Three years later, his hematopoiesis became normal (without intervention). How?
www.medrxiv.org/content/10.1...
A male infant was diagnosed with Fanconi anemia due to an X-linked frameshift mutation.
Three years later, his hematopoiesis became normal (without intervention). How?
www.medrxiv.org/content/10.1...
Multi-lineage natural gene therapy mediated by embryonic triploid mosaicism in the context of Fanconi anaemia
Fanconi anemia is a rare inherited bone marrow failure syndrome caused by inactivation of genes in the Fanconi anemia/BRCA DNA repair pathway. We report a patient with X-linked Fanconi anemia, and aty...
www.medrxiv.org
November 5, 2025 at 8:04 AM
Interesting story in this preprint.
A male infant was diagnosed with Fanconi anemia due to an X-linked frameshift mutation.
Three years later, his hematopoiesis became normal (without intervention). How?
www.medrxiv.org/content/10.1...
A male infant was diagnosed with Fanconi anemia due to an X-linked frameshift mutation.
Three years later, his hematopoiesis became normal (without intervention). How?
www.medrxiv.org/content/10.1...
Reposted by Ben Auxier
New research in #GENETICS suggests accessory chromosomes in #fungi #fusarium might be maintained because of Spok genes and not because of their beneficial effects on virulence.
Learn more about this work from @fungage-lab.bsky.social and colleagues: buff.ly/R2CRa3O
Learn more about this work from @fungage-lab.bsky.social and colleagues: buff.ly/R2CRa3O
November 4, 2025 at 9:02 PM
New research in #GENETICS suggests accessory chromosomes in #fungi #fusarium might be maintained because of Spok genes and not because of their beneficial effects on virulence.
Learn more about this work from @fungage-lab.bsky.social and colleagues: buff.ly/R2CRa3O
Learn more about this work from @fungage-lab.bsky.social and colleagues: buff.ly/R2CRa3O
Reposted by Ben Auxier
While there may be "pay to publish" and "predatory" journals, the fact that an editor does not agree with the position of any given peer reviewer is not evidence of this. Peer review is merely advisory, it is not decision making. Confusion over this leads to some very bad reviewer practices.
As far as I see it, it is pay to publish. They have ignored my review comments before just went forward publishing a paper that was simply trash quality. The quality of some of the papers are very bad, which makes me question the editorial and review process. There are of course many good papers.
October 27, 2025 at 4:32 PM
While there may be "pay to publish" and "predatory" journals, the fact that an editor does not agree with the position of any given peer reviewer is not evidence of this. Peer review is merely advisory, it is not decision making. Confusion over this leads to some very bad reviewer practices.
Reposted by Ben Auxier
Our paper was included in the Collection "Microbial Genomics of Eukaryotes" from the @microbiologysociety.org 🧬 😁
#genomics #longreadsequencing
www.microbiologyresearch.org/content/micr...
#genomics #longreadsequencing
www.microbiologyresearch.org/content/micr...
October 24, 2025 at 6:55 PM
Our paper was included in the Collection "Microbial Genomics of Eukaryotes" from the @microbiologysociety.org 🧬 😁
#genomics #longreadsequencing
www.microbiologyresearch.org/content/micr...
#genomics #longreadsequencing
www.microbiologyresearch.org/content/micr...
Reposted by Ben Auxier
Proud of the latest edition of my free intro biostats book.
gitrepo: github.com/ybrandvain/b...
book: ybrandvain.github.io/biostats/
Not complete but at a good point to take a break, and I think its quite usable
dm me with comments , ideas etc
gitrepo: github.com/ybrandvain/b...
book: ybrandvain.github.io/biostats/
Not complete but at a good point to take a break, and I think its quite usable
dm me with comments , ideas etc
Applied Biostatistics
ybrandvain.github.io
October 24, 2025 at 2:33 PM
Proud of the latest edition of my free intro biostats book.
gitrepo: github.com/ybrandvain/b...
book: ybrandvain.github.io/biostats/
Not complete but at a good point to take a break, and I think its quite usable
dm me with comments , ideas etc
gitrepo: github.com/ybrandvain/b...
book: ybrandvain.github.io/biostats/
Not complete but at a good point to take a break, and I think its quite usable
dm me with comments , ideas etc
Reposted by Ben Auxier
📣 I’m excited to share two open positions in my lab @leibniz-hki.de. For this interdisciplinary project with @luziagyr.bsky.social, I’m seeking (1) an enthusiastic PhD student interested in fungal natural product research and genetic engineering, as well as (2) a technical assistant 👇🏻
October 21, 2025 at 2:48 PM
📣 I’m excited to share two open positions in my lab @leibniz-hki.de. For this interdisciplinary project with @luziagyr.bsky.social, I’m seeking (1) an enthusiastic PhD student interested in fungal natural product research and genetic engineering, as well as (2) a technical assistant 👇🏻
Reposted by Ben Auxier
Probably unpopular opinion:
I don’t think we need conservation efforts focused on microbes. Focus on the environments.
(The microbes and their pathways will always be fine…loss of microbes is a consequence of environmental degradation/loss and not a driver of it)
I don’t think we need conservation efforts focused on microbes. Focus on the environments.
(The microbes and their pathways will always be fine…loss of microbes is a consequence of environmental degradation/loss and not a driver of it)
October 20, 2025 at 3:43 PM
Probably unpopular opinion:
I don’t think we need conservation efforts focused on microbes. Focus on the environments.
(The microbes and their pathways will always be fine…loss of microbes is a consequence of environmental degradation/loss and not a driver of it)
I don’t think we need conservation efforts focused on microbes. Focus on the environments.
(The microbes and their pathways will always be fine…loss of microbes is a consequence of environmental degradation/loss and not a driver of it)
Reposted by Ben Auxier
it's real support from actual racists
September 8, 2025 at 3:16 PM
it's real support from actual racists
Reposted by Ben Auxier
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 Ben Auxier
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 Ben Auxier
You gently massage the data, cheekily omitting that one participant lingering teasingly beneath the exclusion cutoff. Then a final flourish, as you add the covariate you're almost ashamed to justify. You feel — you 𝘬𝘯𝘰𝘸 — it's wrong, and it's exhilarating.
...p = .049.
...p = .049.
You gently run your hand through the rack. You can feel it—pure cotton, rich wool, Irish linen. The plump buttonholes are handsewn; the buttons attached with a firm shank. You flip the price tag over. It's affordable
You buy the jacket and go home, which is only 15 mins away. Your apt is $600/month
You buy the jacket and go home, which is only 15 mins away. Your apt is $600/month
October 16, 2025 at 6:09 AM
You gently massage the data, cheekily omitting that one participant lingering teasingly beneath the exclusion cutoff. Then a final flourish, as you add the covariate you're almost ashamed to justify. You feel — you 𝘬𝘯𝘰𝘸 — it's wrong, and it's exhilarating.
...p = .049.
...p = .049.
Reposted by Ben Auxier
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 Ben Auxier
Editorial Manager account created
In honour of spooky month, share a 4 word horror story that only someone in your profession would understand.
rm -rf ~/
rm -rf ~/
"The chancellor approved it"
October 12, 2025 at 10:27 PM
Editorial Manager account created
"More of a comment"
In honor of spooky month, share a 4 word horror story that only someone in your profession would understand:
Archives banned making copies.
Archives banned making copies.
October 12, 2025 at 7:25 PM
Reposted by Ben Auxier
We roughly set up the tree today to get an idea on how it will look. Will get some tiny wire lights instead of these big bulky ones. Attached some red belted conks to give a mushroom/nature vibe lol. It will serve as our Christmas tree too. It's going to be a long winter I believe. My poor hubby 😂
October 11, 2025 at 5:39 PM
We roughly set up the tree today to get an idea on how it will look. Will get some tiny wire lights instead of these big bulky ones. Attached some red belted conks to give a mushroom/nature vibe lol. It will serve as our Christmas tree too. It's going to be a long winter I believe. My poor hubby 😂
Ooh, this looks interesting!
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 8, 2025 at 6:14 AM
Ooh, this looks interesting!