Axel Visel
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 ViselNeil 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!
- ⏱️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...
- 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...
- 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...
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- Reposted by Axel ViselTF-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
- 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...
- Reposted by Axel ViselOur 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)
- 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
- Here is the meme-torial bsky.app/profile/moor...
- 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
- Reposted by Axel ViselOur 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
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- Reposted by Axel ViselOur 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)
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- 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
- 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...
- 🔥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...
- So happy to announce our new preprint, “A geothermal amoeba sets a new upper temperature limit for eukaryotes.” We cultured a novel amoeba from Lassen Volcanic NP (CA, USA) that divides at 63°C (145°F) 🔥 - a new record for euk growth! #protistsonsky 🧵
- 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...
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- Starting in 15 minutes!
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- Looking forward to my @enhancedgenomics.bsky.social seminar next week Register now to join us!
- 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.”
- 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...
- 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
- 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...
- 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!
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- 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/7jENfK9at://did:plc:mz53ebz6qz55in4pbih2kanh/app.bsky.graph.starterpack/3lanbn6hy6b2l
- 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
- 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
- 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...
- 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...
- 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...
- 🌿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...
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- 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...
- 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...
- 🧬 @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
- Reposted by Axel ViselOur 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...
- Reposted by Axel ViselPretty 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...
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- 🧬Viromics🧬 = using (meta-)genomics to study uncultivated viruses has yielded unprecedented insights into the diversity and global distribution of viruses @jgi.doe.gov's @simrouxvirus.bsky.social and Clement Coclet review the state of the field, available tools, and remaining challenges
- From 🟡 to 💎: Osteoblast-inspired "osteoyeast" turns human waste into high-value biomaterial for bone and dental applications Collaboration by @jgi.doe.gov, @molecularfoundry.lbl.gov & CABBI doi.org/10.1038/s414...
- 🧍♂human: XX = female, XY = male 🐓birds: ZZ = male, ZW = female Confused how this is possible? This new paper by @kaessmannlab.bsky.social et al. explores the underlying mechanisms
- Our study on a male-essential microRNA and the evolution of other dosage compensation mechanisms in birds is now out in Nature! www.nature.com/articles/s41...
