Axel Visel
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axelvisel.bsky.social
Axel Visel
@axelvisel.bsky.social
Genome Scientist. Studies how DNA makes humans, mice, plants, microbes. At Lawrence Berkeley National Lab and Joint Genome Institute. Views are my own.
Starting in 15 minutes!
Very much looking forward to @axelvisel.bsky.social's talk "From Nucleotide to Megabase Scale: Enhancer Function in Development and Disease" in our @enhancedgenomics.bsky.social seminar series "The 3D Regulatory Genome"

📅 02 October 2025 (today!)
⏰ 4 pm GMT

Join:
us02web.zoom.us/webinar/regi...
October 2, 2025 at 2:47 PM
Reposted by Axel Visel
TOMORROW!
Register👉https://us02web.zoom.us/webinar/register/WN_do2hl_GoS8-_PkyHgANPPA
🧬Next speaker: @axelvisel.bsky.social (@berkeleylab.lbl.gov/@jgi.doe.gov) presents 'From Nucleotide
to Megabase Scale: Enhancer Function in Development and Disease'

👨‍🔬Moderated by @stefanschoenfelder.bsky.social
📅 Thu Oct 2, 4pm UK time
👉Register: us02web.zoom.us/webinar/regi...

#VirtualSeminar
October 1, 2025 at 10:41 AM
Looking forward to my @enhancedgenomics.bsky.social seminar next week

Register now to join us!
🧬Next speaker: @axelvisel.bsky.social (@berkeleylab.lbl.gov/@jgi.doe.gov) presents 'From Nucleotide
to Megabase Scale: Enhancer Function in Development and Disease'

👨‍🔬Moderated by @stefanschoenfelder.bsky.social
📅 Thu Oct 2, 4pm UK time
👉Register: us02web.zoom.us/webinar/regi...

#VirtualSeminar
September 24, 2025 at 12:52 PM
I often share links to paywalled research articles.

Quick reminder: NEVER pay those outrageous journal access fees. If you don’t have access, just email the corresponding author. They’re usually glad to share a PDF for free, whether or not you’re a “professional scientist.”
September 23, 2025 at 1:18 PM
Sequencing methods 🧬 have come a long way from census counts 🔢 to assembling genomes and understanding the functions 🧪 of bacteria and viruses.

New review by @jgi.doe.gov's Gitta Szabó, @emileyeloe-fadrosh.bsky.social, Tanja Woyke with @jeffinerca.bsky.social

www.nature.com/articles/s41...
A genomic view of Earth’s biomes - Nature Reviews Genetics
Genome-wide approaches have uncovered the vast microbial and viral diversity across ecosystems. This Review explores advances in metagenomics, single-cell sequencing and functional profiling to elucid...
www.nature.com
September 22, 2025 at 1:31 PM
From AI agents for giant virus discovery to biosynthetic gene clusters - the 2025 cohort of @jgi.doe.gov - @ucmerced.bsky.social summer interns once again took on some amazing projects 🌱🧬🤖

Check out their stories here:
jgi.doe.gov/user-science...

@berkeleylab.lbl.gov @biosci.lbl.gov
Expanding Horizons with the 2025 JGI-UC Merced Internship Cohort | Joint Genome Institute
Interns contributed to a number of projects, from refining lab protocols at the bench to applying artificial intelligence to aspects of research questions
jgi.doe.gov
September 17, 2025 at 12:13 AM
Congratulations to Allegra Aron, Jana Pilatova, @ryanziels.bsky.social, Andrew Vander Yacht, Itamar Shabtai, and Victoria Orphan!

@jgi.doe.gov @biosci.lbl.gov @berkeleylab.lbl.gov
September 16, 2025 at 6:23 PM
Reposted by Axel Visel
Don't miss the JGI's own Heejung Cho at this year's @berkeleylab.lbl.gov Research SLAM. The event will take place Sept. 18 at 3 p.m. PT. You can stream the event here: streaming.lbl.gov

Or attend in person at the Building 50 Auditorium!

@biosci.lbl.gov @axelvisel.bsky.social
September 10, 2025 at 7:01 PM
Reposted by Axel Visel
🚨NOTICE TO OUR USERS🚨

The Genome Portal will be replaced with the Data Portal application sometime next month.

Portal users can book a session with our team for technical help, feedback or a guided walk-through of the new Data Portal. 🖥️🧬

More information: jgi.doe.gov/analyze-data...
JGI Portals | Joint Genome Institute
Our data platforms are a key resource for the broader scientific community and require constant developments to meet the ever-changing demands of our users.NOTICEThe JGI Genome Portal is reaching its ...
jgi.doe.gov
September 8, 2025 at 6:24 PM
Reposted by Axel Visel
Abstracts are due Oct. 19 for the 2025 New Lineages of Life Symposium — 80 slots available!

See speakers below.

More info: jgi.doe.gov/work-with-us...

Full Agenda: jgi.doe.gov/work-with-us...

@axelvisel.bsky.social 🖥️🧬
September 2, 2025 at 4:56 PM
The JGI starter pack: Members, users, collaborators, and friends of the Joint Genome Institute @jgi.doe.gov

Still many open slots, if you are working with the JGI and want to be added, DM me.

go.bsky.app/7jENfK9
August 29, 2025 at 2:54 AM
Ready to explore New Lineages of Life with @jgi.doe.gov ? 🧬🦠

Registration for our 2025 NeLLi Symposium is now open. For the first time in collaboration with @unlv.edu

Mark the date: November 6-7 in Las Vegas, NV
You can now register for the November NeLLi Symposium!

Join us in November for talks focused on the most recent expansions of the Tree of Life, and the latest discoveries toward the evolution of cellular complexity and microbial symbiosis. 

Learn more: jointgeno.me/NeLLi

@nigelmouncey.bsky.social
2025 NeLLi Symposium | Joint Genome Institute
Las Vegas, NV Immediately followed by 1.5-day jamboree on November 6-7
jointgeno.me
August 25, 2025 at 9:39 PM
Postdoc opportunity with @tomasbruna.bsky.social here at @jgi.doe.gov @berkeleylab.lbl.gov:

Develop, benchmark, and apply Plant Genomic Language Models (gLMs) 🌿🧬💻

jobs.lbl.gov/jobs/computa...

#AI #PlantGenomics #gLMs #Postdoc
August 21, 2025 at 12:05 AM
On the cover of @natplants.nature.com this month:

@leobaumgart.bsky.social @greensi.bsky.social @abmora.bsky.social @omalley-regulome.bsky.social et al. map binding sites for 360 TFs across 10 🌿plant🌿 species using a new multiDAP approach

Here is Sharon's explainer 🧵:
bsky.app/profile/gree...
August 20, 2025 at 12:45 AM
In 2026, @jgi.doe.gov and EMSL will (for the first time!) hold a joint user meeting in Seattle from March 3-5

Program details to be announced, but our registration site just launched - so you can already secure your spot:

jgi.doe.gov/work-with-us...
August 19, 2025 at 5:30 PM
Congratulations to @jgi.doe.gov's 2025 Functional Genomics awardees:

@ostratodd.bsky.social @philmuslab.bsky.social @aaronrashotte.bsky.social @taylorlabgroup.bsky.social Hao Chen, Matthew Cope-Arguello, Olufemi Isimikalu, Paul Scesa, K. Scott, S. Wakao, B. Woolston

jgi.doe.gov/user-science...
JGI announces 2025 Functional Genomics awardees | Joint Genome Institute
This year's project goals range from engineering drought-tolerant woody bioenergy crops through transcriptional network mapping, developing microbial systems to convert renewable feedstocks into advan...
jgi.doe.gov
August 19, 2025 at 5:08 PM
🌿Plant pangenomes🌿 have a LOT of genomic presence-absence-variation.

Or do they???

A new @jgi.doe.gov preprint by @tomasbruna.bsky.social @jotlovell.bsky.social @avril-m-harder.bsky.social Avinash Sreedasyam takes a closer look

www.biorxiv.org/content/10.1...
August 18, 2025 at 6:28 PM
Reposted by Axel Visel
Improvements to DAP-seq technology enable it to handle larger genomes and could expand opportunities for bioenergy and bioengineering applications—via multiplexed assays and data integration with single-cell gene expression maps.

Full story: jgi.doe.gov/user-science...

@axelvisel.bsky.social 🖥️🧬 🌱
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 14, 2025 at 5:28 PM
Congratulations to Uma Grover on an outstanding poster presentation! 🎉

Uma joined @b-coli.bsky.social's and my group at @jgi.doe.gov @biosci.lbl.gov this summer as a @berkeleylab.lbl.gov SULI intern and carried out exciting work on single-cell profiling of plant-fungal interactions.
August 9, 2025 at 1:25 PM
Enhancers are "just DNA" - finding all of them in the genome is hard.

www.nature.com/articles/s41...
August 8, 2025 at 6:25 PM
Hiding in plain sight - how close are we to mapping ALL 🧬enhancers🧬 in the genome?

Our new paper by Mannion et al. takes a systematic look at "hidden enhancers" and why they remain so hard to find. With @mosterwalder.bsky.social, @jlopezrios.bsky.social & many more

www.nature.com/articles/s41...
August 8, 2025 at 6:10 PM
A new, MUCH improved #Eucalyptus genome:

- haplotype-resolved
- 99.4% complete
- 700x better contiguity
- 35k annotated genes

Kudos to Anneri Lötter, @tomasbruna.bsky.social and @jotlovell.bsky.social at @jgi.doe.gov‬, @jillwegrzyn.bsky.social‬, Alexander Myburg et al.

doi.org/10.1093/g3jo...
Researchers report a new reference genome for eucalyptus. Haplotype-resolved, it has 700-fold greater contiguity—
meaning the genome is reconstructed in larger, more complete segments. 🖥️🧬 🌱

More on our Plant Program: jgi.doe.gov/science-prog...

@axelvisel.bsky.social @biosci.lbl.gov
New and Improved: Eucalyptus Reference is Now Accessible | Joint Genome Institute
An improved genome assembly to support targeted tree breeding for the bioeconomy.
jgi.doe.gov
July 30, 2025 at 5:22 PM
🧬 @jgi.doe.gov is hiring! We're seeking an Advanced Analysis Manager to lead data infrastructure and software engineering supporting the generation, analysis, and dissemination of genomics data

Hybrid | SF Bay Area | Apply by Aug 7

jobs.lbl.gov/jobs/advance...

@biosci.lbl.gov @berkeleylab.lbl.gov
July 29, 2025 at 11:49 PM
Reposted by Axel Visel
Our new story in Nature Genetics: endogenous retroviruses can produce viral-like particles in the embryo resulting in apoptosis and congenital malformation. If this would happen in human, it wouldn't leave a trace. No WGS or other analysis would identify this. www.nature.com/articles/s41...
Enhancer adoption by an LTR retrotransposon generates viral-like particles, causing developmental limb phenotypes - Nature Genetics
Activation of an LTR retrotransposon inserted upstream of the Fgf8 gene produces viral-like particles in the mouse developing limb, triggering apoptosis and causing limb malformation. This phenotype c...
www.nature.com
July 24, 2025 at 8:56 AM
Reposted by Axel Visel
Pretty surreal to see my artwork on the cover of Nature Genetics! Big congrats to @julianeg.bsky.social, @stemundi.bsky.social and the others, and thank you Juliane for letting me help bring your research to life visually.

www.nature.com/ng/volumes/5...
July 23, 2025 at 8:06 AM