Axel Visel

Starting in 15 minutes!

TOMORROW!
Register👉https://us02web.zoom.us/webinar/register/WN_do2hl_GoS8-_PkyHgANPPA

Looking forward to my @enhancedgenomics.bsky.social seminar next week

Register now to join us!

To find the right email address, go to PubMed and expand the "Affiliations". It's usually the last author (for biology articles).

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.”

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...

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...

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

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

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

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!

Promotional graphic for Berkeley Lab Research SLAM featuring Heejung Cho from the Joint Genome Institute, with a logo incorporating a magnifying glass, and a decorative green pawn shape.

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

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 ...

🚨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...

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 🖥️🧬

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

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).

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

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

Graphic announcing a Computational Postdoctoral Fellow position. Text: Computational Postdoctoral Fellow – Plant Genomic Language Models (gLMs). JGI is seeking a Computational Postdoctoral Fellow to join a funded project at Berkeley Lab’s Joint Genome Institute applying genomic language models (gLMs) to unlock new biological insights in plants. Join one of the world’s leading genomics facilities to pioneer AI applications in plant biology, with access to cutting-edge computational resources and diverse genomic datasets. This project will focus on developing and exploring applications of gLMs to plant genomes, from identifying novel regulatory elements to revealing evolutionary patterns across species, with particular interest in cross-species and data-limited scenarios. In this role, you will design tasks and datasets to test and extend gLM capabilities, apply models to generate new biological hypotheses, and share findings through high-impact publications and presentations.

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

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.

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...

DAP-seq Drives Robust Mapping of Gene Regulation | Joint Genome Institute Multi-species assays yield an unprecedented view of plant evolution and adaptation.

And this news story by @jgi.doe.gov

jgi.doe.gov/user-science...

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...

Also see this related News and Views by Mary Galli and Andrea Gallavotti

www.nature.com/articles/s41...

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...

Promotional banner for the 2026 EMSL-JGI User Meeting. Theme: “Empowering Automated Laboratories – Integrating Experimentation with Data.” Event dates: March 3-5, 2026. Location: Seattle Marriott Waterfront, 2100 Alaskan Way, Seattle. The banner features a skyline of Seattle with Mount Rainier in the background, surrounded by colorful hexagonal graphics showing scientific imagery such as DNA, lab automation, microbial structures, and plants. EMSL and JGI logos are shown at the top.

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...

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...

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...

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

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!

For details, see @jotlovell.bsky.social's excellent explainer thread 🧵

bsky.app/profile/jotl...

A two-panel Scooby-Doo meme. In the top panel, Fred pulls the mask off a villain labeled “Presence-absence-variation in plant genomes.” In the bottom panel, the unmasked villain is revealed to be “Annotation artifacts.”

🌿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...

Screenshot of a ChatGPT 5 conversation. Prompt: "Make a schematic drawing of the abdominal cavity of a chipmunk, frontal view, and label all organs." The result shows a cartoon chipmunk with a cartoon of human inner organs superimposed. The organs are overall misplaced, with the liver approximately where the lung should be. Most organs are mislabeled. The liver is labeled as both liver and kidney, the large intestine as small intestine and spleen and urinary bladder. Only the stomach is labeled correctly.

Of a chipmunk

DAP-seq Drives Robust Mapping of Gene Regulation | Joint Genome Institute Multi-species assays yield an unprecedented view of plant evolution and adaptation.

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 🖥️🧬 🌱

If you are an undergraduate student in #STEM and interested in becoming an intern at @jgi.doe.gov (or elsewhere at @berkeleylab.lbl.gov) through @energygov.bsky.social's Science Undergraduate Laboratory Internship (SULI):

🔗 education.lbl.gov/internships/...
🔗 science.osti.gov/wdts/suli

Axel Visel, Uma Grover, and Benjamin Cole stand in front of Uma's poster at Berkeley Lab's 2025 Workforce Development & Education (WD&E) Summer Intern Poster Session. Her poster is entitled "Single-cel profiling of sorghum / AMF interaction"

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.

Enhancers are "just DNA" - finding all of them in the genome is hard.

www.nature.com/articles/s41...