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

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

No new genes needed to fly - just rewire what you have! 🦇🧬 Great new paper from the labs of @fany-real.bsky.social @stemundi.bsky.social @dariloops.bsky.social doi.org/10.1038/s415... #EvoDevo #SingleCell #BatWings

Finally out! 🥳 Our paper showing how a transposable element (TE) insertion can cause developmental phenotypes is now published @natgenet.nature.com 🧬🦠🐁 Below is a brief description of the major findings. Check the full version of the paper for more details: www.nature.com/articles/s41588-025-02248-5

Intriguing plot twist 🧐 Tissue-specific changes in 3D genome folding cause enhancer hijacking in Liebenberg syndrome But it’s NOT the overall expression level that drives the phenotype - it’s the proportion of cells hijacked into misexpressing Pitx1 that matters

Happy Birthday, UCSC Genome Browser 🥳 An essential resource for all of us, provided by @ucscgenomics.bsky.social

New research on range extenders, or REX genetic enhancer elements, from @ucirvine.bsky.social, #BioEGSB scientists @berkeleylab.lbl.gov & international collaborators! These bits of DNA that regulate gene expression allow enhancers to work far away from their target. www.bio.uci.edu/new-discover...

Getting the message across from a distance: 🧬REX🧬 is a “Range EXtender” element that can turn short-range into looooooooooooong-range enhancers Great collaboration led by @gracebower.bsky.social and @evgenykvon.bsky.social www.nature.com/articles/s41... @biosci.lbl.gov @berkeleylab.lbl.gov

🍄 FUNGUS ALERT 🍄 Where did all those fungi come from? A genomic perspective of fungal diversity and evolution by @jgi.doe.gov's Stephen Mondo and Igor Grigoriev @biosci.lbl.gov @berkeleylab.lbl.gov #fungi #genomes

Congratulations, @simrouxvirus.bsky.social 🥳

How do non-coding variants in enhancers lead to disease? Happy to share our recent work, led by @ewholling.bsky.social, in which we discovered that poised chromatin sensitizes enhancers to aberrant activation by non-coding mutations, contributing to disease. www.biorxiv.org/content/10.1... 1/

NEWS: 🧬 A single DNA letter could rewrite the story of human development. New research from our Lab and @stanforduniversity.bsky.social reveals how tiny mutations in enhancers – non-coding regions that regulate gene activity – can cause big biological changes. 🧪

Textbooks: “Enhancers are just a bunch of TFBSs” But how do they REALLY work? New paper with many contributors here @berkeleylab.lbl.gov, @anshulkundaje.bsky.social, @anusri.bsky.social A 🧵 (1/n) Free access link: rdcu.be/erD22

Our latest paper is out in its final form in @theplantcell.bsky.social We show that in plants the same DNA sequence can act as an insulator or silencer depending on the surrounding regulatory context. Read the full paper at: doi.org/10.1093/plce...

🧬 From decoding microbiomes to boosting bioenergy crops, the @jgi.doe.gov supports breakthroughs in genomic research and develops world-class technologies for the scientific community. 🧪

New pre-print out \o/ All about CRISPR, metagenomes, and what you learn when you collect (a lot of) spacers from natural communities, with @apcamargo.bsky.social @urineri.bsky.social @lhug.bsky.social but also Uri Gophna, Nikhil George (not on Bsky I think) & others at JGI doi.org/10.1101/2025...

The #OpenGreenGenomes Project, supported through our #CommunityScience Program, represents 35 major evolutionary plant lineages — including M. polymorpha, or liverwort. For decades it has been used as a model for evolutionary studies. 🖥️🧬🌱 @jleebensmack.bsky.social @maximebonhomme.bsky.social

Delighted & excited to share our latest preprint on non-canonical enhancers in human pluripotent stem cells, the result of a fantastic and fun collaboration with @guenesdoganlab.bsky.social‬: www.biorxiv.org/content/10.1... 🧵 below

✨ Berkeley Lab's @nersc.bsky.social, @delltechnologies.bsky.social, and NVIDIA announce new public-private partnership for game-changing US Dept. of Energy Doudna supercomputer, (NERSC-10, strengthening U.S. capabilities, accelerating discovery, and powering future science. 🧪

Happy to share🆕 #OpenAccess review, #Genomics🧬-assisted #breeding for designing #salinity-smart future #crops🌾" is out in PBJ @sebiology.bsky.social @aabiologists.bsky.social 😍👏🎉 onlinelibrary.wiley.com/doi/10.1111/... #GAB @plantteaching.bsky.social @coeplantsuccess.bsky.social @ipes-food.org

How to find Evolutionary Conserved Enhancers in 2025? 🐣-🐭 Check out our paper - fresh off the press!!! We find widespread functional conservation of enhancers in absence of sequence homology Including: a bioinformatic tool to map sequence-diverged enhancers! rdcu.be/enVDN github.com/tobiaszehnde...

I’m very excited to share our work on the early evolution of animal regulatory genome architecture - the main project of my postdoc, carried out across two wonderful and inspirational labs of @arnausebe.bsky.social and @mamartirenom.bsky.social. www.nature.com/articles/s41...

We released our preprint on the CREsted package. CREsted allows for complete modeling of cell type-specific enhancer codes from scATAC-seq data. We demonstrate CREsted’s robust functionality in various species and tissues, and in vivo validate our findings: www.biorxiv.org/content/10.1...