Axel Visel

Last reminder: Sign up for the webinar now!

2025 Progress Report | Joint Genome Institute Learn more about the JGI's 2025 accomplishments, including research and data output.

Our FY25 Progress Report is now live! We broke our own record by sequencing more than 1Pb of data in a year—on top of serving 2,627 users w/active proposals, plus 17K researchers making use of our data.
🖥️ 🧬 🌱 🍄 🦠 🧪

Full report: https://jgi.doe.gov/user-science/science-stories/2025-progress-report

📣 We're joining up with @jgi.doe.gov in a joint Critical Minerals & Materials Call 👀: https://bit.ly/3MvzWy6

This is an opportunity to use the capabilities and expertise of both facilities. The call opens March 1. You can register for our Feb. 27 webinar now: https://bit.ly/3Oox1I0

Banner titled “Mining New Frontiers” for a Joint JGI-TMF User Proposal Call on Critical Minerals and Materials. It announces an informational webinar at 9am PT on Feb. 27, 2026. The design features a green, textured background suggesting plant leaves, with three circular images on the right: mineral ore samples, a close-up of microbial cells, and a seedling with visible roots in soil. A tagline reads “Bridging genomics and nanoscale science.” Logos for the Molecular Foundry, JGI, and Berkeley Lab appear along the bottom.

Critical Minerals and Materials

Genomics🧬 meets Nanoscience🔬 to enable recovery, reuse, and transformation of CMMs

New joint user opportunity from @jgi.doe.gov and @molecularfoundry.lbl.gov at @berkeleylab.lbl.gov

Join our informational webinar on Feb 27, 9am PT:
jgi.doe.gov/work-with-us...

Here is the thread with more background by @jotlovell.bsky.social :

bsky.app/profile/jotl...

Black-and-white composite image. In the background, a large American chestnut tree lies fallen and dead, its bare, splintered branches reaching outward in a devastated forest landscape. In the foreground are two historic New York Times newspaper clippings from the early 1900s. One headline reads “ALL CHESTNUT TREES HERE ARE DOOMED,” with subheadings describing blight spreading across New York and the last two trees in the Bronx dying. The other reads “CHESTNUT TREES FACE DESTRUCTION,” describing millions of trees dying from a canker with no remedy. Images from https://archive.nytimes.com/cityroom.blogs.nytimes.com/2011/03/23/planting-chestnuts-in-city-where-the-trees-blight-began/

“All chestnut trees here are doomed.” — NY Times, 1911

A century ago, pathogens wiped out over 4 billion American chestnuts.

New genomic resources are helping reverse their functional extinction. 🌳🧬

Jared Westbrook, @jgi.doe.gov's @jotlovell.bsky.social et al.:

www.science.org/doi/full/10....

Neil H. Shubin has been elected as the next NAS President! A leading evolutionary biologist and science communicator, Shubin will succeed Marcia McNutt on July 1. The Academy also named Cherry Murray as International Secretary and elected new councilors. Read more: www.nasonline.org/news/2026_pr...

Last reminder!

Here is @jotlovell.bsky.social's 🧵with more background

bsky.app/profile/jotl...

Four-panel “expanding brain” meme. Panel 1 shows a small glowing brain with the text “PAV reflects evolution.” Panel 2 shows a brighter brain with the text “PAV reflects genome quality.” Panel 3 shows an even brighter brain with the text “PAV reflects annotation method.” Panel 4 shows a fully illuminated brain with rays of light and the text “Re-annotate everything before interpreting biology.”

Myth of Fact?

🌿Plant pangenomes show massive presence-absence variation affecting protein-coding gene content 🧬

@jgi.doe.gov's @tomasbruna.bsky.social @jotlovell.bsky.social @avril-m-harder.bsky.social and Avinash Sreedasyam searched for answers

academic.oup.com/nargab/artic...

⏱️Deadline reminder: February 3rd, 2026

Register and submit your abstract for the upcoming @jgi.doe.gov -EMSL meeting in Seattle

Do it now, or do it like Kermit. Up to you.

jgi.doe.gov/work-with-us...

It's obviously a "fist hand shoe"

The German word for a glove makes a lot of sense. And of course, the extended version for a mitten, too.

There are also Beuteltiere, Kriechtiere, Nagetiere. But note that the Germans didn't make these up, they are just literal translations of the Latin names.

You may want to look up the German words for sloth, skunk, armadillo, marmot, mammal, platypus

Victorian-style AI slop. A small girl in a blue dress whose name is not Alice for copyright reasons stands in a forest and stares up at an absurdly giant mushroom, surrounded by many other biologically inaccurate fungi. The scene attempts to hint at fungal diversity, scale, and deep evolutionary relationships. Roughly what happens when you reanalyze ~2,000 fungal genomes and realize how much biology is still hiding in the woods.

What can we learn from comparing ~2,000 fungal genomes?

Find out about:

🍄evolutionary transitions
🍄lifestyles
🍄genome dynamics
🍄sampling gaps
🍄efforts to uncover the remaining fungal dark matter

New review by @jgi.doe.gov's Stephen Mondo and Igor Grigoriev

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

Line chart titled “Results per 100,000 citations in PubMed (2015–2025).” Three trends are shown. The term “new” (yellow) is consistently the most frequent, rising slightly from about 16,000 in 2015 to a peak around 18,200 in 2023, then declining to about 17,000 by 2025. “Novel” (red) increases gradually from roughly 7,400 in 2015 to just over 10,000 in 2025. “Innovative” (blue) shows the steepest growth, rising steadily from about 2,300 in 2015 to over 9,000 by 2025, with a notable acceleration after 2022.

It's because of all the innovations

In remembrance of Peer Bork  | EMBL EMBL and its community are deeply saddened by the death of Peer Bork, the organisation’s Interim Director General.

This is very sad news

'It is with great sadness that EMBL announces that Interim Director General Professor Peer Bork passed away from natural causes on 16 January 2026.'

www.embl.org/news/embl-an...

TF-MINDI is out! A new method to learn cis-regulatory codes through rich embeddings of TF binding sites. TF-MINDI decomposes motif neighbourhoods, and works downstream of any sequence-to-function deep learning model. We deeply study the enhancer code in human neural development, check out the thread

Agree this can happen. But that’s a failure of editorial practice and/or bad reviewing. Just like not citing relevant preexisting peer-reviewed work. Your preprint is still first in the public record.

A preprint is a public, timestamped disclosure that establishes priority.

If someone submits the same or a very similar idea, analysis, or data after your preprint, they must cite it, and reviewers must assess novelty relative to the preprint, regardless of journal publication status.

The 'Hell-Plant' of Death Valley offers hope to a hotter world We humans are a delicate bunch. We don’t have bark, boney exo-plates, or lush fur to protect us from hostile environments, so we have to steal what other creatures produce just to survive in regions a...

"Tidestromia oblongifolia took only two days to increase its photosynthetic capacity to produce energy and thrive in extreme heat, and by day 14 reached its ideal photosynthetic temperature of 45 °C (113 °F)"

#PlantScience #PlantStress #ClimateChange

Original paper: www.cell.com/current-biol...

Our work on #RegulatoryTrajectories is out today in Nat. Comms: www.nature.com/articles/s41...
Led by @raquelrouco.bsky.social, this study establishes a new framework to study how enhancer landscapes act sequentially at developmental loci and are silenced to shape gene expression patterns. (1/n)

Here is the meme-torial

bsky.app/profile/moor...

a man wearing a plaid shirt and a purple hat is saying here we go . ALT: a man wearing a plaid shirt and a purple hat is saying here we go .

Our paper on the Expanded Registry of candidate cis-Regulatory Elements (cCREs) is out 🎉
www.nature.com/articles/s41...

To celebrate, here’s a "meme-torial" walkthrough of the science.

Let’s get started 🧵 1/11

Now out: The new ENCODE registry of candidate cis-regulatory elements (🐭/👶)

Major consortium effort, led by @moorejille.bsky.social - stay tuned for her "meme-torial"

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

@berkeleylab.lbl.gov @biosci.lbl.gov

JGI Announces FY26 Large Scale Portfolio for Our Community Science Program | Joint Genome Institute

Congrats to the 14 researchers with proposals accepted for our 2026 Large Scale call! These projects accelerate bioenergy innovation through genomic discovery across diverse organisms and ecosystems. 🖥️🧬🦠🌱🧪🍄

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

@berkeleylab.lbl.gov @axelvisel.bsky.social

In honor of the IMG/M data portal's 20th anniversary, we want to hear how you use it in your work and what type of science it has enabled you to do.

You can share how IMG has helped your science using this form: https://jointgeno.me/IMGStoriesForm

@berkeleylab.lbl.gov @axelvisel.bsky.social 🖥️🧬 🦠

Predictive design of tissue-specific mammalian enhancers that function in vivo in the mouse embryo Enhancers control tissue-specific gene expression across metazoans. Although deep learning has enabled enhancer prediction and design in mammalian cell lines and invertebrate systems, it remains uncle...

Our preprint "Predictive design of tissue-specific mammalian enhancers that function in vivo in the mouse embryo" is on bioRxiv: www.biorxiv.org/content/10.6... . Amazing collaboration by @shenzhichen1999.bsky.social, Vincent Loubiere (@impvienna.bsky.social,@viennabiocenter.bsky.social),... (1/2)

Integrating Experimentation with Data | Joint Genome Institute Join the Joint Genome Institute and the Environmental Molecular Sciences Laboratory for “Empowering Automated Laboratories: Integrating Experimentation with Data.”

Deadline Jan. 9: Submit your abstract to give a short talk at our 2026 "Empowering Automated Laboratories" joint meeting with the Environmental Molecular Sciences Laboratory. 🖥️🧬🧪🌱🦠🍄

More info: usermeeting.jgi.doe.gov
Reg: bit.ly/EMSL-JGIusermeeting2026

@axelvisel.bsky.social @biosci.lbl.gov