Daniel Croll
@danielcroll.bsky.social
We want to understand how pathogens adapt and cause diseases. Also passionate about TEs, pangenomes & population genomics, bioinformatics and conservation genomics.
Professor of Evolutionary Genetics @ University of Neuchatel 🇨🇭
Hobbies: 👧🏻👧🏼🏔️🏕️
Professor of Evolutionary Genetics @ University of Neuchatel 🇨🇭
Hobbies: 👧🏻👧🏼🏔️🏕️
Pinned
Big congratulations @tobybarilbio.bsky.social!
Please check out and share our final version of the transposon mobilization work in a fungal pathogen - out now in Nature Communications
www.nature.com/articles/s41...
Please check out and share our final version of the transposon mobilization work in a fungal pathogen - out now in Nature Communications
www.nature.com/articles/s41...
Reposted by Daniel Croll
Our new collaborative work led by @taliamycota.bsky.social
Jiajun Cui & Emma Caullireau between my lab @ucllifesciences.bsky.social @cloeucl.bsky.social & the Karasov Lab (tkarasovlab.org) @uofubiology.bsky.social
and collaborators: @plantricia.bsky.social et al.
tinyurl.com/5yx2wmz5
(1/n)
Jiajun Cui & Emma Caullireau between my lab @ucllifesciences.bsky.social @cloeucl.bsky.social & the Karasov Lab (tkarasovlab.org) @uofubiology.bsky.social
and collaborators: @plantricia.bsky.social et al.
tinyurl.com/5yx2wmz5
(1/n)
November 18, 2025 at 8:41 AM
Our new collaborative work led by @taliamycota.bsky.social
Jiajun Cui & Emma Caullireau between my lab @ucllifesciences.bsky.social @cloeucl.bsky.social & the Karasov Lab (tkarasovlab.org) @uofubiology.bsky.social
and collaborators: @plantricia.bsky.social et al.
tinyurl.com/5yx2wmz5
(1/n)
Jiajun Cui & Emma Caullireau between my lab @ucllifesciences.bsky.social @cloeucl.bsky.social & the Karasov Lab (tkarasovlab.org) @uofubiology.bsky.social
and collaborators: @plantricia.bsky.social et al.
tinyurl.com/5yx2wmz5
(1/n)
Reposted by Daniel Croll
The number of Project funding applications and the requested amounts have risen to record levels, consequently decreasing researchers' chances of receiving a grant.📈⚠️
Evaluation is under way, and funding decisions will follow in spring 2026.
➡️ buff.ly/gEdD3OY
#research #science
Evaluation is under way, and funding decisions will follow in spring 2026.
➡️ buff.ly/gEdD3OY
#research #science
New record in Project funding
SNSF Project funding reaches an all-time high with 1,451 applications and CHF 1.3 billion requested – while federal funding is stagnating.
buff.ly
November 24, 2025 at 8:30 AM
The number of Project funding applications and the requested amounts have risen to record levels, consequently decreasing researchers' chances of receiving a grant.📈⚠️
Evaluation is under way, and funding decisions will follow in spring 2026.
➡️ buff.ly/gEdD3OY
#research #science
Evaluation is under way, and funding decisions will follow in spring 2026.
➡️ buff.ly/gEdD3OY
#research #science
Reposted by Daniel Croll
Responses to Temperature Shocks in Zymoseptoria tritici Reveal Specific Transcriptional Reprogramming and Novel Candidate Genes for Thermal Adaptation | Phytopathology® apsjournals.apsnet.org/doi/full/10....
Responses to Temperature Shocks in Zymoseptoria tritici Reveal Specific Transcriptional Reprogramming and Novel Candidate Genes for Thermal Adaptation | Phytopathology®
Pathogens’ responses to sudden temperature fluctuations, spanning various temporal scales, are critical determinants of their survival, growth, reproduction, and homeostasis. Here, we combined phenoty...
apsjournals.apsnet.org
November 21, 2025 at 1:00 PM
Responses to Temperature Shocks in Zymoseptoria tritici Reveal Specific Transcriptional Reprogramming and Novel Candidate Genes for Thermal Adaptation | Phytopathology® apsjournals.apsnet.org/doi/full/10....
Reposted by Daniel Croll
Our latest pre-print on TE-mediated tandem duplication of the ToxB effector is now online...still a puzzle for us but we think it is in a Helitron! Together with amazing collaborators, Reem Aboukhaddour and Ryan Gourlie #TE #fungi
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
The virulence gene ToxB is both amplified and disrupted by transposons in the wheat pathogen Pyrenophora tritici-repentis
### Competing Interest Statement
The authors have declared no competing interest.
Agriculture and Agri-Food Canada, https://ror.org/051dzs374
Alberta Grain
Saskatchewan Wheat Development Commissio...
www.biorxiv.org
November 18, 2025 at 4:22 PM
Our latest pre-print on TE-mediated tandem duplication of the ToxB effector is now online...still a puzzle for us but we think it is in a Helitron! Together with amazing collaborators, Reem Aboukhaddour and Ryan Gourlie #TE #fungi
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
On my way to visit the very impressive CAS Institute of Microbiology in Beijing. Then, on to the AMC in Guangzhou.
Very excited about my first trip to China.
Very excited about my first trip to China.
November 18, 2025 at 3:48 PM
On my way to visit the very impressive CAS Institute of Microbiology in Beijing. Then, on to the AMC in Guangzhou.
Very excited about my first trip to China.
Very excited about my first trip to China.
Big congratulations @tobybarilbio.bsky.social!
Please check out and share our final version of the transposon mobilization work in a fungal pathogen - out now in Nature Communications
www.nature.com/articles/s41...
Please check out and share our final version of the transposon mobilization work in a fungal pathogen - out now in Nature Communications
www.nature.com/articles/s41...
November 12, 2025 at 3:38 PM
Big congratulations @tobybarilbio.bsky.social!
Please check out and share our final version of the transposon mobilization work in a fungal pathogen - out now in Nature Communications
www.nature.com/articles/s41...
Please check out and share our final version of the transposon mobilization work in a fungal pathogen - out now in Nature Communications
www.nature.com/articles/s41...
Reposted by Daniel Croll
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 Daniel Croll
My new Emmy Noether Group is recruiting!
🔬 Two PhD positions in plant pathogen evolution
🧬 Start: April 2026 (flexible)
📍 Dept. of Phytopathology & Plant Protection @rstam.bsky.social @uni-kiel.de
⏰ Apply by 15 Dec 2025
🔗 More info: www.uni-kiel.de/personal/de/...
Do get in touch or share 😊
🔬 Two PhD positions in plant pathogen evolution
🧬 Start: April 2026 (flexible)
📍 Dept. of Phytopathology & Plant Protection @rstam.bsky.social @uni-kiel.de
⏰ Apply by 15 Dec 2025
🔗 More info: www.uni-kiel.de/personal/de/...
Do get in touch or share 😊
Aktuelle Ausschreibungen
Aktuelle Ausschreibungen
www.uni-kiel.de
November 3, 2025 at 9:03 AM
My new Emmy Noether Group is recruiting!
🔬 Two PhD positions in plant pathogen evolution
🧬 Start: April 2026 (flexible)
📍 Dept. of Phytopathology & Plant Protection @rstam.bsky.social @uni-kiel.de
⏰ Apply by 15 Dec 2025
🔗 More info: www.uni-kiel.de/personal/de/...
Do get in touch or share 😊
🔬 Two PhD positions in plant pathogen evolution
🧬 Start: April 2026 (flexible)
📍 Dept. of Phytopathology & Plant Protection @rstam.bsky.social @uni-kiel.de
⏰ Apply by 15 Dec 2025
🔗 More info: www.uni-kiel.de/personal/de/...
Do get in touch or share 😊
Reposted by Daniel Croll
Still using 16S/ITS profiling? You might want to reconsider👀
Our new paper presents pangenome-informed amplicons that provide up to 10× higher phylogenetic resolution than full-length ribosomal markers- while remaining cost effective and scalable!
microbiomejournal.biomedcentral.com/articles/10....
Our new paper presents pangenome-informed amplicons that provide up to 10× higher phylogenetic resolution than full-length ribosomal markers- while remaining cost effective and scalable!
microbiomejournal.biomedcentral.com/articles/10....
High-resolution profiling of bacterial and fungal communities using pangenome-informed taxon-specific long-read amplicons - Microbiome
Background High-throughput sequencing technologies have greatly advanced our understanding of microbiomes, but resolving microbial communities at species and strain levels remains challenging. Results...
microbiomejournal.biomedcentral.com
October 30, 2025 at 1:32 PM
Still using 16S/ITS profiling? You might want to reconsider👀
Our new paper presents pangenome-informed amplicons that provide up to 10× higher phylogenetic resolution than full-length ribosomal markers- while remaining cost effective and scalable!
microbiomejournal.biomedcentral.com/articles/10....
Our new paper presents pangenome-informed amplicons that provide up to 10× higher phylogenetic resolution than full-length ribosomal markers- while remaining cost effective and scalable!
microbiomejournal.biomedcentral.com/articles/10....
Very proud to see part of @luzia-stalder.bsky.social inspiring PhD work now published in Microbiome!
We tackled the lack of resolution that affects many plant microbiome studies by designing new barcoding loci from scratch. Our multi-kb amplicons resolve Pseudomonas and fungal strain diversity.
We tackled the lack of resolution that affects many plant microbiome studies by designing new barcoding loci from scratch. Our multi-kb amplicons resolve Pseudomonas and fungal strain diversity.
Still using 16S/ITS profiling? You might want to reconsider👀
Our new paper presents pangenome-informed amplicons that provide up to 10× higher phylogenetic resolution than full-length ribosomal markers- while remaining cost effective and scalable!
microbiomejournal.biomedcentral.com/articles/10....
Our new paper presents pangenome-informed amplicons that provide up to 10× higher phylogenetic resolution than full-length ribosomal markers- while remaining cost effective and scalable!
microbiomejournal.biomedcentral.com/articles/10....
High-resolution profiling of bacterial and fungal communities using pangenome-informed taxon-specific long-read amplicons - Microbiome
Background High-throughput sequencing technologies have greatly advanced our understanding of microbiomes, but resolving microbial communities at species and strain levels remains challenging. Results...
microbiomejournal.biomedcentral.com
October 31, 2025 at 2:18 PM
Very proud to see part of @luzia-stalder.bsky.social inspiring PhD work now published in Microbiome!
We tackled the lack of resolution that affects many plant microbiome studies by designing new barcoding loci from scratch. Our multi-kb amplicons resolve Pseudomonas and fungal strain diversity.
We tackled the lack of resolution that affects many plant microbiome studies by designing new barcoding loci from scratch. Our multi-kb amplicons resolve Pseudomonas and fungal strain diversity.
@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 Daniel Croll
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 Daniel Croll
I’m excited to announce the launch of my lab at EPFL in Jan 2026 🎉. We’ll combine evolution & synthetic biology to study and (re)engineer bacterial communication.
I’m recruiting PhD students to start in the first semester of 2026.
Apply via EPFL PhD programs by Nov 1
drive.google.com/file/d/1cm-t...
I’m recruiting PhD students to start in the first semester of 2026.
Apply via EPFL PhD programs by Nov 1
drive.google.com/file/d/1cm-t...
October 20, 2025 at 6:14 PM
I’m excited to announce the launch of my lab at EPFL in Jan 2026 🎉. We’ll combine evolution & synthetic biology to study and (re)engineer bacterial communication.
I’m recruiting PhD students to start in the first semester of 2026.
Apply via EPFL PhD programs by Nov 1
drive.google.com/file/d/1cm-t...
I’m recruiting PhD students to start in the first semester of 2026.
Apply via EPFL PhD programs by Nov 1
drive.google.com/file/d/1cm-t...
Reposted by Daniel Croll
Fungal #GenomeSize variation is largely driven by TEs & lineage-specific genome defenses. @tbadet.bsky.social & @danielcroll.bsky.social show that presence/absence of RIP mutation systems influences #genome architecture, identifying a likely novel defense mechanism @plosbiology.org 🧪 plos.io/4hcC5tx
October 16, 2025 at 7:58 AM
Fungal #GenomeSize variation is largely driven by TEs & lineage-specific genome defenses. @tbadet.bsky.social & @danielcroll.bsky.social show that presence/absence of RIP mutation systems influences #genome architecture, identifying a likely novel defense mechanism @plosbiology.org 🧪 plos.io/4hcC5tx
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 Daniel Croll
Young lives cut short on an unimaginable scale: the 18,457 children on Gaza’s list of war dead
"Far from comprehensive, the list does not include the thousands still buried under the rubble of destroyed buildings, as well as the war’s many indirect victims"
www.theguardian.com/world/ng-int...
"Far from comprehensive, the list does not include the thousands still buried under the rubble of destroyed buildings, as well as the war’s many indirect victims"
www.theguardian.com/world/ng-int...
Young lives cut short on an unimaginable scale: the 18,457 children on Gaza’s list of war dead
Every name on a list compiled by health authorities in Gaza of the child victims of Israel’s offensive
www.theguardian.com
October 8, 2025 at 5:24 PM
Young lives cut short on an unimaginable scale: the 18,457 children on Gaza’s list of war dead
"Far from comprehensive, the list does not include the thousands still buried under the rubble of destroyed buildings, as well as the war’s many indirect victims"
www.theguardian.com/world/ng-int...
"Far from comprehensive, the list does not include the thousands still buried under the rubble of destroyed buildings, as well as the war’s many indirect victims"
www.theguardian.com/world/ng-int...
Reposted by Daniel Croll
Now with official press release. I'm very much looking forward to welcome @cbarragan.bsky.social in January
www.uni-kiel.de/en/details/n...
www.uni-kiel.de/en/details/n...
October 8, 2025 at 4:22 PM
Now with official press release. I'm very much looking forward to welcome @cbarragan.bsky.social in January
www.uni-kiel.de/en/details/n...
www.uni-kiel.de/en/details/n...
Reposted by Daniel Croll
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 ⬇️
Neuchâtel morning glory - I love this time of the year!
October 7, 2025 at 2:36 PM
Neuchâtel morning glory - I love this time of the year!
The🇨🇭Classics in full glory 🚴
October 2, 2025 at 4:11 PM
The🇨🇭Classics in full glory 🚴
This is so exciting news, Megan!! Switzerland🇨🇭 is lucky to have you (again) and I am so looking forward to have you soon as a colleague close-by.
We'll make sure to have you visit my beloved University of Neuchatel soon!
We'll make sure to have you visit my beloved University of Neuchatel soon!
There are no words to describe how excited and honored I am to take on the role. Already had such amazing support from the plant pathology community in Switz and cannot wait to grow the team further and see how far we can get in tackling our fungal foes. Look out for jobs starting in May 2026!
We warmly welcome Dr. Megan McDonald as Associate Professor of Plant Disease Dynamics. Her research on fungal diseases in crops will strengthen our expertise and collaborations across plant sciences. 🌱
September 18, 2025 at 6:38 PM
This is so exciting news, Megan!! Switzerland🇨🇭 is lucky to have you (again) and I am so looking forward to have you soon as a colleague close-by.
We'll make sure to have you visit my beloved University of Neuchatel soon!
We'll make sure to have you visit my beloved University of Neuchatel soon!
Reposted by Daniel Croll
Call for a tenure-track position at our Department of Plant Molecular Biology in Lausanne! We are searching for promising early-career researchers in the broad field of plant-organismal interactions. Deadline: November 30, 2025 - Please re-post!
career5.successfactors.eu/career?caree...
career5.successfactors.eu/career?caree...
Career Opportunities: DBMV: Tenure Track Assistant Professor towards Associate Professor in the field of Plant-organism (22484)
career5.successfactors.eu
September 17, 2025 at 3:01 PM
Call for a tenure-track position at our Department of Plant Molecular Biology in Lausanne! We are searching for promising early-career researchers in the broad field of plant-organismal interactions. Deadline: November 30, 2025 - Please re-post!
career5.successfactors.eu/career?caree...
career5.successfactors.eu/career?caree...
Cycling home time gets the autumn glow-up! 🚴♂️🍁
September 15, 2025 at 5:05 PM
Cycling home time gets the autumn glow-up! 🚴♂️🍁
What an amazing story of gut bacteria-fungi interactions! New paper out in Nature by @judith-behnsen.bsky.social's lab
www.nature.com/articles/s41...
www.nature.com/articles/s41...
www.nature.com
September 10, 2025 at 8:25 PM
What an amazing story of gut bacteria-fungi interactions! New paper out in Nature by @judith-behnsen.bsky.social's lab
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Daniel Croll
University of Calgary is hiring a tier I CRC professorship in crop genomics. Come work in one of the most beautiful corners of the world!
careers.ucalgary.ca/jobs/1668764...
careers.ucalgary.ca/jobs/1668764...
Canada Research Chair (Tier I) in Translational Crop Genomics in Sustainable Agriculture in
Calgary,
...
Canada Research Chair (Tier I) in Translational Crop Genomics in Sustainable Agriculture in
Calgary,
...
careers.ucalgary.ca
September 9, 2025 at 9:32 PM
University of Calgary is hiring a tier I CRC professorship in crop genomics. Come work in one of the most beautiful corners of the world!
careers.ucalgary.ca/jobs/1668764...
careers.ucalgary.ca/jobs/1668764...