Axel Visel
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axelvisel.bsky.social
Axel Visel
@axelvisel.bsky.social
3.5K followers 600 following 260 posts
Genome Scientist. Studies how DNA makes humans, mice, plants, microbes. At Lawrence Berkeley National Lab and Joint Genome Institute. Views are my own.
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axelvisel.bsky.social
To find the right email address, go to PubMed and expand the "Affiliations". It's usually the last author (for biology articles).
September 23, 2025 at 1:23 PM
axelvisel.bsky.social
Looks like I made the puzzle too difficult. It's been a month and still no reports of anyone having found all 10.

Which confirms: Enhancer discovery is hard!
September 12, 2025 at 3:37 AM
axelvisel.bsky.social
Here is our speaker lineup:
jgi.doe.gov/work-with-us...

Featuring @nekton4plankton.bsky.social @annedekas.bsky.social @microyunha.bsky.social @masarunobu.bsky.social and more
Headshots of eight featured speakers at the 2025 NeLLi Symposium. Top row, left to right: John M. Archibald (Dalhousie University, keynote), Harriet Alexander (Woods Hole Oceanographic Institution), Matthew Brown (Mississippi State University), Anne Dekas (Stanford University). Bottom row, left to right: Yunha Hwang (Harvard University), Masaru Nobu (JAMSTEC), Vivek Natarajan (Google), Olga Zhaxybayeva (Dartmouth College).
August 25, 2025 at 9:47 PM
axelvisel.bsky.social
If you are interested in using DAPseq for your plant, algal, fungal or microbial genomes, consider applying to one of @jgi.doe.gov's user programs:

jgi.doe.gov/work-with-us...
User Programs | Joint Genome Institute
Learn more about our Community Science Program, as well as other collaborative opportunities available through the FICUS call and other special initiatives.
jgi.doe.gov
August 20, 2025 at 12:53 AM
axelvisel.bsky.social
And this news story by @jgi.doe.gov

jgi.doe.gov/user-science...
DAP-seq Drives Robust Mapping of Gene Regulation | Joint Genome Institute
Multi-species assays yield an unprecedented view of plant evolution and adaptation.
jgi.doe.gov
August 20, 2025 at 12:49 AM
axelvisel.bsky.social
Also see this related News and Views by Mary Galli and Andrea Gallavotti

www.nature.com/articles/s41...
A binding agreement - Nature Plants
Transcription factors are proteins that recognize and bind short, specific DNA sequences and regulate when, where and how genes are expressed in a cell. A recent large-scale study of transcription fac...
www.nature.com
August 20, 2025 at 12:48 AM
axelvisel.bsky.social
Yes, absolutely! They are clearly not all artifacts. But some of them are and the problem is more pronounced in plants than in animals. Fortunately, the preprint also highlights how a unified re-annotation strategy can reduce these artifacts, making whatever PAV remains even more interesting!
Screenshot of text from the preprint: "Unsurprisingly, within both flowering plants and amniotes, gene PAV becomes increasingly common with increasing divergence time—more diverged genomes share fewer orthologs, likely due to sequence deletions, pseudogenization and other forms of large-scale mutation followed by selection or drift. However, the absolute amount of gene PAV and the degree that PAV is affected by divergence time was remarkably different between plants and animals." https://www.biorxiv.org/content/10.1101/2025.08.14.670405v1.full
August 18, 2025 at 7:31 PM