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.
Reposted by Axel Visel
📣 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
February 13, 2026 at 9:46 PM
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...
February 13, 2026 at 6:21 PM
“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....
February 12, 2026 at 8:46 PM
Reposted by Axel Visel
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...
February 4, 2026 at 5:35 PM
Last reminder!
⏱️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...
February 3, 2026 at 9:13 PM
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...
February 2, 2026 at 8:57 PM
⏱️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...
January 27, 2026 at 7:32 PM
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...
January 20, 2026 at 8:34 PM
Reposted by Axel Visel
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...
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.
www.embl.org
January 16, 2026 at 6:06 PM
Reposted by Axel Visel
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
January 15, 2026 at 12:32 PM
Reposted by Axel Visel
"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...
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...
newatlas.com
January 12, 2026 at 12:43 PM
Reposted by Axel Visel
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)
Client Challenge
www.nature.com
January 12, 2026 at 11:48 AM
Reposted by Axel Visel
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
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 .
media.tenor.com
January 8, 2026 at 2:04 AM
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
January 7, 2026 at 9:45 PM
Reposted by Axel Visel
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
JGI Announces FY26 Large Scale Portfolio for Our Community Science Program | Joint Genome Institute
jgi.doe.gov
January 6, 2026 at 8:53 PM
Reposted by Axel Visel
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 🖥️🧬 🦠
December 26, 2025 at 7:46 PM
Reposted by Axel Visel
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)
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...
www.biorxiv.org
December 24, 2025 at 3:06 PM
Reposted by Axel Visel
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
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.”
usermeeting.jgi.doe.gov
December 22, 2025 at 4:17 PM
Excellent guide on how to be a constructive peer reviewer 🎓by @carldeboer.bsky.social

Required reading for new reviewers and a good refresher for the rest of us
I wrote a guide on constructive peer review. This is a polished version of an internal guide I had for my group. Of course, constructive feedback is welcome, peers!
deboer.bme.ubc.ca/2025/12/09/g...
December 9, 2025 at 7:49 PM
Reposted by Axel Visel
🧬🦠🚨 Another new paper alert, this time led by @maureenbug.bsky.social ! In collaboration with the Emerson lab and
@titus.idyll.org lab (@taylorreiter.bsky.social), both at UC Davis. Asking the question: what are we missing in short-read metagenome assembly, and why ?

doi.org/10.1093/narg...
Comparison of short-read and long-read metagenome assemblies in a natural soil community highlights systematic bias in recovery of high-diversity populations
Abstract. Comparisons of long-read and short-read (meta)genome assemblies typically show that short-read sequence assemblies are less error-prone, but stru
doi.org
December 9, 2025 at 3:25 AM
🔥Hot🔥 new preprint: Amoeba happily replicating at 63°C

Led by @hbrappap.bsky.social and @oliverio.bsky.social, with @jgi.doe.gov’s Tomáš Tyml and @fmschu.bsky.social

www.biorxiv.org/content/10.1...
November 26, 2025 at 3:25 PM
Soils contain an amazing diversity of functions encoded in plasmids.

The Global Soil Plasmidome Resource: 98,728 soil plasmids from 6,860 samples.

Led by @mattlabguy.bsky.social and @apcamargo.bsky.social at @jgi.doe.gov @biosci.lbl.gov @berkeleylab.lbl.gov

www.nature.com/articles/s41...
November 18, 2025 at 7:18 PM
Reposted by Axel Visel
🧬 AI is helping decode the genome's "switchboard." A Berkeley Lab and Stanford study in Nature shows how combining experiments with machine learning reveals where AI succeeds and falls short in predicting how DNA enhancers control gene activity.
Cracking the Genome’s Switchboard: How AI Helps Decode Gene Regulation
A single letter in the DNA code could change the course of human development
newscenter.lbl.gov
November 13, 2025 at 5:15 PM
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