Home – genomepanel_nf Nextflow pipeline for reference genome mapping, SNP calling and quality checks on large genome panels

Resequencing hundreds or thousands of individuals from the same species has become routine... but processing all those genomes efficiently? Still a headache!

Here's my solution that used to be lab-internal but that I am happy to share:

crolllab.github.io/genomepanel_...

Modifying meiotic recombination by targeting chromatin regulators to crossover hotspots in Arabidopsis Targeting chromatin modifiers to DNA hotspots reveals causal link between histone marks, transcription, and meiotic recombination.

📣Our paper is out! 🤩 We found that local modification of H3K9me3 using CRISPR/dCas9 at hotspots changes crossover activity, bringing us closer to targeted recombination in plants.🌱

Huge thanks to @szymanskalejman.bsky.social, Wojtek, Ania, and Karolina!

www.science.org/doi/10.1126/...

Congrats Claudia! :)

I am happy to announce the launch of a new Arabidopsis genomics resource! Check out arabidopsislyrata.org Now you can easily look at the natural genetic variation across the entire species range of A. lyrata and A. arenosa.

PhD position to study epigenomic diversity and altitude adaptation in Arabis alpina

✨Call open for a fully-funded PhD position✨
Looking for an enthusiastic student to join my upcoming Ambizione research group (🌱 Epigenome Diversity Lab 🌱, www.epidiversitylab.org) at ETH Zürich, starting August 2026! Apply here ↘️
jobs.ethz.ch/job/view/JOP...
Application deadline: January 31st, 2026

It was a pleasure collaborating with @hajkdrost.bsky.social again, building on ideas that originated from our previous review on stress-induced epigenetic variation : www.frontiersin.org/journals/pla...

We identified an initial set of 30+ toolkit genes from literature, but encourage the community to test & expand our model! Further questions incl. (1) how similar/diverse toolkits function across environments (2) how toolkit proteins affect (epi)genomic features in various cells/tissues/individuals

Studying the epigenetic toolkit (and allelic variation in toolkit genes) as an evolvable trait could help predict how different plant species and populations maintain homeostasis – both under short-term stress/nutrient fluctuations and long-term environmental shifts.

A conceptual model summarizing how the balance between environmental fluctuations and the epigenetic toolkit can affect plant homeostasis.

A draft network of 33 epigenetic toolkit proteins, whose encoding genes repeatedly occur as candidates under selection in different contexts in various plant studies.

How can plants maintain their genomic identity while also responding to the environment? @hajkdrost.bsky.social and I propose an "epigenetic toolkit" – a suite of epigenetic regulators that mediate the physiology-epigenome-genome crosstalk for adaptation. Read more here:
www.cell.com/trends/plant...

Thank you, Detlef!

Can we tune a plant’s epigenetic toolkit to disrupt plant homeostasis in ways that enable phenotypic innovation?

🌱Check out our new Opinion Paper with @thanvisrikant.bsky.social discussing this topic in @cp-trendsplantsci.bsky.social!

www.sciencedirect.com/science/arti...

Thank you, Wangsheng! :)

Thanks a lot Jacobo!!

Thanks, Marco! :)

Thank you so much, Adrian! :)

Thank you, Detlef! :)

Thank you, Satyaki! Hope you’re doing well :)

Thanks, Sunil!

Thank you!

Thanks Nacho!

Thank you, Vangeli! :)

Grateful to Kirsten Bomblies and Detlef Weigel @plantevolution.bsky.social for being wonderful mentors during my academic journey so far, and to Alex Widmer for hosting me in his group!

Excited to share that I’ve been awarded an @snsf.ch Ambizione grant to begin my independent research, starting summer 2026 at the Institute of Integrative Biology, ETH Zürich! I will use (epi)genomics to study altitude adaptation in Arabis alpina - stay tuned for more updates & PhD opportunities!

The genetic architecture of cell type–specific cis regulation in maize Gene expression and complex phenotypes are determined by the activity of cis-regulatory elements. However, an understanding of how extant genetic variants affect cis regulation remains limited. Here, ...

Grateful to share that our study on "The genetic architecture of cell type–specific cis regulation in maize" is now published in @science.org! Huge thank you to all co-authors and the 4 tough, but fair, reviewers who all helped to improve the study 🌽🧬 www.science.org/doi/10.1126/...

Partial redundancy buffers deleterious effects of mutating DNA methyltransferase 1-1 (MET1-1) in polyploid wheat Varying gene dosage through mutating DNA methyltransferase 1-1 (MET1-1 ) in polyploid wheat generates quantitative changes to CG methylation without the le

I’m very happy to share the published version of our paper on the role of MET1 in wheat 🌾 🧬

It’s been really exciting to discover more about DNA methylation in wheat and it’s huge polyploid genome

doi.org/10.1093/jxb/...