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!

🚨 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

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

Genome Watch👀 "In search of phage tail-like particiles: nature's versatile nanomachines" highlights the importance of predictive models. 🖥️🧬 Full Story: https://rdcu.be/fgU2m @berkeleylab.lbl.gov @axelvisel.bsky.social @natureportfolio.nature.com

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...

📢 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: https://jgi.doe.gov/work-with-us/proposals/community-science-program/large-scale

Excited to share my latest work on synthetic biology and host–microbe interactions, now published in Nature Communications! www.nature.com/articles/s41...

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/

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

🚨 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

📣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

Last reminder: Sign up for the webinar now!

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: https://jgi.doe.gov/user-science/science-stories/2025-progress-report

📣 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...