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Axel Visel

@axelvisel.bsky.social
3.6K followers 638 following 291 posts

Genome Scientist. Studies how DNA makes humans, mice, plants, microbes. At Lawrence Berkeley National Lab and Joint Genome Institute. Views are my own.

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Reposted by Axel Visel
National Microbiome Data Collaborative (NMDC) @microbiomedata.org · 28/09/2026
The NMDC will be merging its core, high-performing functionalities directly into DOE-BRIDGE. We extend our deepest gratitude to our core team, advisors, ambassadors and champions, DOE BER, and the community 🦠 🌎 Thank you for seven incredible years of collaboration! microbiomedata.org/faqs
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Joint Genome Institute @jgi.doe.gov · 15/09/2026
In a recent episode of Genome Insider, @jotlovell.bsky.social discussed why a single reference genome for Sorghum proved insufficient, and the value of a pangenome to represent the crop's full genetic diversity: jgi.doe.gov/user-science/podcasts/s… 🖥️ 🧬 🌱
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Joint Genome Institute @jgi.doe.gov · 09/09/2026
Perspective: Pangenomes are Only as Powerful as their Annotation Method Are researchers wasting resources following false trails — due to variations in interpretative methods? 🖥️🧬 🌱 @tomasbruna.bsky.social Full story below⬇️
jgi.doe.gov
Perspective: Pangenomes are Only as Powerful as their Annotation Method | Joint Genome Institute
Researchers may be wasting resources following false trails due to variations in interpretative methods.
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Joint Genome Institute @jgi.doe.gov · 07/08/2026
📣 Early Bird registration for our VEGA Symposium closes Sept. 19! Join us Nov. 18–19 to discuss characterizing uncultivated viral diversity and its role in biotech and industrial applications. 🖥️🧬🦠 More info: jointgeno.me/VEGA
Logo for the VEGA Symposium featuring a geometric globe and text reading "VEGA Viral EcoGenomics & Applications" alongside "Symposium hosted by the DOE Joint Genome Institute."
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Axel Visel @axelvisel.bsky.social · 03/09/2026
"The Mobilome in the Mire" DNA sleuths 🕵️‍♀️ @scbagby.bsky.social and 🕵️‍♂️ @simrouxvirus.bsky.social tracked a whole zoo of mobile genetic elements in thawing permafrost ❄️💧 for 8 years. Another Genome Insider podcast from @jgi.doe.gov 🎙️: jgi.doe.gov/user-science...
jgi.doe.gov
The Mobilome in the Mire | Joint Genome Institute
Join Sarah Bagby (Case Western Reserve University) and Simon Roux (JGI) as they talk about their recent work on a time series from Sweden’s Stordalen Mire. By looking at Mobile Genetic Elements, or MG...
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Axel Visel @axelvisel.bsky.social · 02/09/2026
🍄 @jgi.doe.gov's Fun-Guys and Fun-Gals have been busy this summer! ☀️ New fungal genomes in MycoCosm: ✔️ Hanseniaspora uvarum NRRL Y-1614 ✔️ Semicentenialea rex gs25 v1.0 ✔️ Amoeboaphelidium occidentale KS120 v1.0 ✔️ Neocallimastix sp FC1 v1.0 ✔️ Boletus sp. 2018DF043 v1.0 mycocosm.jgi.doe.gov 🍄🧬🔬
Four specimens of Boletus sp. 2018DF043, a bolete mushroom associated with oak forests in North Carolina, showing reddish-brown caps, yellow stems, and yellow-green pore surfaces. Photo credit: Rytas Vilgalys
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Axel Visel @axelvisel.bsky.social · 01/09/2026
Giant virus evolution unfolding in real time 🦠🔬👀 Analyzing 20 years of metagenomic data from Lake Mendota Cool work by @jgi.doe.gov postdoc Yumary Vasquez. Also involved: @miferg.bsky.social @robinrohwer.bsky.social @quendi.bsky.social @fmschu.bsky.social & others jgi.doe.gov/user-science...
jgi.doe.gov
A Broader Sense of Evolution Over Time | Joint Genome Institute
Analyzing how giant viruses—and interns—respond to environmental change.
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Axel Visel @axelvisel.bsky.social · 31/08/2026
A Global Catalog of Microbial Symbionts 🌍🦠🧬🫨 New resource from @jgi.doe.gov, led by @astrogenomics.bsky.social and @fmschu.bsky.social with contributions by @emileyeloe-fadrosh.bsky.social @miferg.bsky.social and many more 🔓 www.nature.com/articles/s41... @biosci.lbl.gov @berkeleylab.lbl.gov
nature.com
A genomic catalog of Earth’s bacterial and archaeal symbionts - Nature Biotechnology
Symbiotic relationships of microorganisms are predicted and cataloged with a machine learning tool.
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Shenzhi Chen @shenzhichen1999.bsky.social · 25/08/2026
Excited to share our paper in @natgenet.nature.com on the de novo design of tissue-specific mammalian enhancers that function in vivo in mouse embryos. 🧬🐭 www.nature.com/articles/s41...
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Biosciences Area at Berkeley Lab @biosci.lbl.gov · 19/08/2026
Jack Here! I met with #BioEGSB researcher Laura Cook to learn about her team's work to uncover the underlying mechanisms behind how faces 🐔 🐭 are structured. Laura's team is focused on studying enhancers—regions of genetic information that control when, where, and how much of a gene is expressed.🧬
Two people in lab coats look towards a computer monitor, the person on the left is pointing at the screen.Two researchers face the camera with a computer monitor in the background.A researcher wearing a protective gown and hair net looks into a microscope.A collage of many bird and rodent faces, the birds are in the top grids and the rodents in the bottom.
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Joint Genome Institute @jgi.doe.gov · 18/08/2026
Recently published in @natcomms.nature.com with support from @geochurch.bsky.social's JGI Functional Genomics proposal: Genome-building with SynOMICS reveals hidden rules of the genetic code & opens doors to industrially useful bacteria.@akosnyerges.bsky.social @berkeleylab.lbl.gov @biosci.lbl.gov
jgi.doe.gov
New Method Offers Safer, More Powerful Synthetic Organisms | Joint Genome Institute
Genome-building with SynOMICS reveals hidden rules of the genetic code and opens doors to virus-proof, industrially useful bacteria.
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Biosciences Area at Berkeley Lab @biosci.lbl.gov · 07/08/2026
Faces are one of the most diverse anatomical features, but how can the facial structure of birds and mammals vary so drastically when we share the majority of our DNA? Work from #BioEGSB researchers Laura Cook and @axelvisel.bsky.social uncovers what may be the driving force of facial morphology.
A collage highlighting the differences in faces between birds and mammals, the top column contains 5 birds, the bottom column contains 5 rodents.
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Joint Genome Institute @jgi.doe.gov · 03/08/2026
Interested in working with the JGI and never led a proposal with us? Now is your chance! We are accepting submissions to our New Investigator call for first-time PIs. Deadline to submit is Sept. 9. jointgeno.me/CSPnewPI @berkeleylab.lbl.gov @biosci.lbl.gov
jointgeno.me
CSP New Investigator Call | Joint Genome Institute
The CSP New Investigator Call is for investigators and research initiatives new to the JGI. Projects must be independent of ongoing JGI proposals, and lead PIs cannot have been lead PI on any previous...
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Evgeny Kvon @evgenykvon.bsky.social · 05/08/2026
A really cool preprint from Joanna Wysocka's lab showing that housekeeping genes use distal enhancers as dosage buffers against TF fluctuations, but only during critical cell fate transitions. Makes so much sense! www.biorxiv.org/content/10.6...
biorxiv.org
Enhancer buffering protects dosage-sensitive housekeeping genes during vulnerable developmental transitions
Housekeeping genes maintain robust expression across cell types despite dynamic transcription factor fluctuations, yet their haploinsufficiency is associated with many tissue-specific developmental di...
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Biosciences Area at Berkeley Lab @biosci.lbl.gov · 29/06/2026
Hi everyone, my name is Jack. I'm a SULI summer intern at Berkeley Lab. Over the next several weeks I’ll be creating posts sharing my experiences learning about cool research projects across the Biosciences Area. I hope you enjoy this series as I much as I enjoy making it!
Person with dark shoulder-length hair wearing a dark long-sleeve t-shirt and jeans stands near some large rocks in front of the facade of a building with a large number 92.
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Simon Roux @simrouxvirus.bsky.social · 12/06/2026
🚨 Registration for VEGA26 is 👏 officially open 👏 🚨 The 5th edition of our Viral EcoGenomics and Applications symposium will be held November 18-19, 2026, on the UC Berkeley campus 🧬 🦠 🔬 🧫 Event website ➡️ jgi.doe.gov/work-with-us... Registration link ➡️ cvent.me/e0RnA0
This image shows the VEGA logo (an Earth-shaped capsid colored with green continents and blue oceans), and the taglines: "VEGA Viral EcoGenomics & Applications", "Symposium hosted by the DOE Joint Genome Institute", "Novermber 18-19, 2026"
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Axel Visel @axelvisel.bsky.social · 08/05/2026
If it walks like a duck and develops like a duck ... the enhancers might still align to humans 🥚🦆 (chicken, actually, but you get the picture) Fun collaboration led by Stella Kyomen and @marketa-kau.bsky.social at @mpi-evolbio.bsky.social
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Joint Genome Institute @jgi.doe.gov · 05/05/2026
Genome Watch👀 "In search of phage tail-like particiles: nature's versatile nanomachines" highlights the importance of predictive models. 🖥️🧬 Full Story: rdcu.be/fgU2m @berkeleylab.lbl.gov @axelvisel.bsky.social @natureportfolio.nature.com
nature.com
In search of phage tail-like particles: nature’s versatile nanomachines - Nature Reviews Microbiology
This Genome Watch article highlights the importance of predictive models for identifying and characterizing the roles of phage tail-like particles as a tool for bioengineering and biocontrol.
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Axel Visel @axelvisel.bsky.social · 30/04/2026
JGI @jgi.doe.gov is looking for bold partners with expertise in lab automation 🤖, plant transformation 🌱, AI-supported imaging 🔬, and scalable bioengineering 🧬 Goal: build an automated system to identify, select, and process 10k+ transformed plant calluses/day Details: sam.gov/workspace/co...
AI-generated image of pale green plant callus tissue arranged in a Petri dish to form the letters “JGI” and a stylized DNA helix.
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Reposted by Axel Visel
Joint Genome Institute @jgi.doe.gov · 31/03/2026
📢 Letters of Intent for our Large Scale call, part of our Community Science Program, are due April 9. Projects should leverage systems-based approaches to address biofuel and bioproducts production. 🖥️ 🧬 More info: jgi.doe.gov/work-with-us/proposals/…
jgi.doe.gov
CSP Large Scale Call | Joint Genome Institute
The Community Science Program Large Scale Call is focused on genomic science projects that address sustainable biofuel and bioproducts production.
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tomoyahonda.bsky.social @tomoyahonda.bsky.social · 30/03/2026
Excited to share my latest work on synthetic biology and host–microbe interactions, now published in Nature Communications! www.nature.com/articles/s41...
nature.com
CRAGE-RB-PI-seq reveals transcriptional dynamics of plant-associated bacteria during root colonization - Nature Communications
This study reveals how plant-associated bacteria dynamically reprogram gene expression during root colonization, using a new high-throughput approach that overcomes low bacterial biomass and interfere...
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Molecular Foundry @molecularfoundry.lbl.gov · 24/03/2026
The Molecular Foundry turns 20 today. 🔬✨ Two decades of open-access nanoscience at @berkeleylab.lbl.gov— thousands of users, discoveries, and stories. Explore 20 years of impact: foundry.lbl.gov/impact/
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Joint Genome Institute @jgi.doe.gov · 19/03/2026
New research points to the oil-producing alga Auxenochlorella as a powerful platform for producing specialty oils, chemical feedstocks and industrial precursors—as well as to better enable the mining of critical minerals and materials. 🖥️🧬 @berkeleylab.lbl.gov @axelvisel.bsky.social @biosci.lbl.gov
jgi.doe.gov
Complete Genome of Oil-Rich Alga Reveals Ideal Platform for Bioengineering | Joint Genome Institute
Streamlined genome with precise gene targeting transforms oil-producing alga into a powerful platform for developing ​​bio-based industrial products.
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Reposted by Axel Visel
Darío Lupiáñez @dariloops.bsky.social · 06/03/2026
🚨 Job Alert - Please share! 🙏 Interested in 3D gene regulation in development & evolution? 🤓🧬 💥 Our lab at @cabd-upo-csic.bsky.social is expanding! We’re recruiting: ✅ PhD students ✅ Postdocs 💻🧪 Experimental or computational backgrounds welcome 👇 Details below
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Joint Genome Institute @jgi.doe.gov · 05/03/2026
📣Deadline 4/9: The JGI is currently accepting LOIs for our Community Science Program's Large Scale call — for mission-relevant genomic science projects that leverage systems-based approaches. Learn more: jointgeno.me/LargeScaleCSP @berkeleylab.lbl.gov @biosci.lbl.gov @axelvisel.bsky.social
jointgeno.me
CSP Large Scale Call | Joint Genome Institute
The Community Science Program Large Scale Call is focused on genomic science projects that address sustainable biofuel and bioproducts production.
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Axel Visel @axelvisel.bsky.social · 26/02/2026
Last reminder: Sign up for the webinar now!
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Reposted by Axel Visel
Joint Genome Institute @jgi.doe.gov · 24/02/2026
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: jgi.doe.gov/user-science/science-st…
jgi.doe.gov
2025 Progress Report | Joint Genome Institute
Learn more about the JGI's 2025 accomplishments, including research and data output.
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Reposted by Axel Visel
Molecular Foundry @molecularfoundry.lbl.gov · 13/02/2026
📣 We're joining up with @jgi.doe.gov in a joint Critical Minerals & Materials Call 👀: 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: bit.ly/3Oox1I0
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Axel Visel @axelvisel.bsky.social · 13/02/2026
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...
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.
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Axel Visel @axelvisel.bsky.social · 12/02/2026
“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....
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/
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National Academy of Sciences @nasonline.org · 04/02/2026
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...
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Axel Visel @axelvisel.bsky.social · 03/02/2026
Last reminder!
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Axel Visel @axelvisel.bsky.social · 02/02/2026
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...
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.”
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Axel Visel @axelvisel.bsky.social · 27/01/2026
⏱️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...
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Axel Visel @axelvisel.bsky.social · 20/01/2026
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...
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.
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Willem van Schaik @wvschaik.bsky.social · 16/01/2026
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...
embl.org
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.
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Stein Aerts @steinaerts.bsky.social · 15/01/2026
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
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Marc Somssich @somssich.bsky.social · 12/01/2026
"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...
newatlas.com
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...
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Guillaume Andrey @guandrey.bsky.social · 12/01/2026
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)
nature.com
Client Challenge
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Jill Moore @moorejille.bsky.social · 08/01/2026
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
media.tenor.com
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 .
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Axel Visel @axelvisel.bsky.social · 07/01/2026
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
AI slop depiction of regulatory landscapes, in a style that would give Caspar David Friedrich a cluster headache. Colorful cones erupt from the fog and launch rockets (presumably transcription factors) toward a suspiciously three-stranded DNA helix of unclear left- or right-handedness. Lone, brooding figures stare into the chromatin mist waiting for meaning to emerge, while Romantic ruins and cosmic arcs hint vaguely at long-range regulation, peak calling, and other things that ChatGPT definitely did not understand right.
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Joint Genome Institute @jgi.doe.gov · 06/01/2026
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.doe.gov
JGI Announces FY26 Large Scale Portfolio for Our Community Science Program | Joint Genome Institute
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Joint Genome Institute @jgi.doe.gov · 26/12/2025
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: jointgeno.me/IMGStoriesForm @berkeleylab.lbl.gov @axelvisel.bsky.social 🖥️🧬 🦠
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Alex Stark @alex-stark.bsky.social · 24/12/2025
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)
biorxiv.org
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...
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Joint Genome Institute @jgi.doe.gov · 22/12/2025
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
usermeeting.jgi.doe.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.”
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Axel Visel @axelvisel.bsky.social · 09/12/2025
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
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Simon Roux @simrouxvirus.bsky.social · 09/12/2025
🧬🦠🚨 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...
doi.org
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
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Axel Visel @axelvisel.bsky.social · 26/11/2025
🔥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...
A modified version of the “This is fine” meme, which usually shows a cartoon dog sitting calmly in a room that is on fire. The flames are labeled 63°C. In place of the dog’s face, there is a grayscale microscopic image of a heat-tolerant amoeba from the new preprint. A speech bubble above the character still reads “This is fine,” implying that the amoeba is unbothered by extreme heat. Preprint: https://www.biorxiv.org/content/10.1101/2025.11.24.690213v1
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Axel Visel @axelvisel.bsky.social · 18/11/2025
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...
A stylized infographic showing the workflow for building a global soil plasmidome resource on the left and a textured world map on the right. The workflow depicts three input data streams from metagenomic datasets and isolate plasmids, which pass through steps like quality control, clustering, functional annotation, CRISPR analysis, host assignment, and detection of gene categories such as biosynthetic clusters, antimicrobial resistance, antimicrobial peptides, and CAZymes. All outputs feed into a central SQL database. The world map shows sample locations across the globe as teal circles of varying size, highlighting regions from many plasmids were recovered. Adapted from Fig 1A and 1B in Fiamenghi et al., doi:10.1038/s41467-025-65102-6
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Berkeley Lab @berkeleylab.lbl.gov · 13/11/2025
🧬 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.
newscenter.lbl.gov
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
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