📣 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

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...

“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!

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...

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

"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)

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

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 🖥️🧬 🦠

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)

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

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

🧬🦠🚨 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...

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...

🧬 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.

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!

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

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

🚨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

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...

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 🖥️🧬 🌱

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...

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...

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

Our 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...

Pretty 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...

Save the Date for the 2026 annual User Meeting, held jointly this year with the Environmental Molecular Sciences Laboratory March 3–5. Topics include biodesign, synbio and AI-enabled lab automation, data integration and modeling. Sign up at jointgeno.me/newsletter to stay in the loop! 🖥️🧬🦠🌱🧪🍄

🧬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