Lightnews — Scholar-powered news

Axel Visel @axelvisel.bsky.social · 6d

Starting in 15 minutes!

Stefan Schoenfelder @stefanschoenfelder.bsky.social · 6d

Very much looking forward to @axelvisel.bsky.social's talk "From Nucleotide to Megabase Scale: Enhancer Function in Development and Disease" in our @enhancedgenomics.bsky.social seminar series "The 3D Regulatory Genome"

📅 02 October 2025 (today!)
⏰ 4 pm GMT

Join:
us02web.zoom.us/webinar/regi...

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Reposted by Axel Visel

Enhanced Genomics @enhancedgenomics.bsky.social · 7d

TOMORROW!
Register👉https://us02web.zoom.us/webinar/register/WN_do2hl_GoS8-_PkyHgANPPA

Enhanced Genomics @enhancedgenomics.bsky.social · 14d

🧬Next speaker: @axelvisel.bsky.social (@berkeleylab.lbl.gov/@jgi.doe.gov) presents 'From Nucleotide
to Megabase Scale: Enhancer Function in Development and Disease'

👨‍🔬Moderated by @stefanschoenfelder.bsky.social
📅 Thu Oct 2, 4pm UK time
👉Register: us02web.zoom.us/webinar/regi...

#VirtualSeminar

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Axel Visel @axelvisel.bsky.social · 14d

Looking forward to my @enhancedgenomics.bsky.social seminar next week

Register now to join us!

Enhanced Genomics @enhancedgenomics.bsky.social · 14d

🧬Next speaker: @axelvisel.bsky.social (@berkeleylab.lbl.gov/@jgi.doe.gov) presents 'From Nucleotide
to Megabase Scale: Enhancer Function in Development and Disease'

👨‍🔬Moderated by @stefanschoenfelder.bsky.social
📅 Thu Oct 2, 4pm UK time
👉Register: us02web.zoom.us/webinar/regi...

#VirtualSeminar

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Axel Visel @axelvisel.bsky.social · 15d

To find the right email address, go to PubMed and expand the "Affiliations". It's usually the last author (for biology articles).

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Axel Visel @axelvisel.bsky.social · 15d

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.”

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Axel Visel @axelvisel.bsky.social · 16d

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...

A genomic view of Earth’s biomes - Nature Reviews Genetics

Genome-wide approaches have uncovered the vast microbial and viral diversity across ecosystems. This Review explores advances in metagenomics, single-cell sequencing and functional profiling to elucid...

www.nature.com

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Axel Visel @axelvisel.bsky.social · 21d

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

Expanding Horizons with the 2025 JGI-UC Merced Internship Cohort | Joint Genome Institute

Interns contributed to a number of projects, from refining lab protocols at the bench to applying artificial intelligence to aspects of research questions

jgi.doe.gov

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Axel Visel @axelvisel.bsky.social · 21d

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

Joint Genome Institute @jgi.doe.gov · 22d

Welcome the six researchers accepted to the FICUS program for FY26! Focus areas for projects include biofuels, biomaterials & bioproducts; hydrobiogeochemistry; & novel applications of molecular techniques.

🖥️🧬 @axelvisel.bsky.social @danudwary.secondarymetabolism.com @simrouxvirus.bsky.social

Six join FICUS program in 2026 | Joint Genome Institute

Pictured from left to right are: [above] Allegra Aron, Jana Pilatova and Ryan Ziels; [below] Andrew Vander Yacht, Itamar Shabtai and Victoria Orphan The JGI is excited to welcom

jgi.doe.gov

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Axel Visel @axelvisel.bsky.social · 26d

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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Reposted by Axel Visel

Joint Genome Institute @jgi.doe.gov · 27d

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

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Reposted by Axel Visel

Joint Genome Institute @jgi.doe.gov · 29d

🚨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...

JGI Portals | Joint Genome Institute

Our data platforms are a key resource for the broader scientific community and require constant developments to meet the ever-changing demands of our users.NOTICEThe JGI Genome Portal is reaching its ...

jgi.doe.gov

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Reposted by Axel Visel

Joint Genome Institute @jgi.doe.gov · Sep 2

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 🖥️🧬

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Axel Visel @axelvisel.bsky.social · Aug 29

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

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Axel Visel @axelvisel.bsky.social · Aug 25

Here is our speaker lineup:
jgi.doe.gov/work-with-us...

Featuring @nekton4plankton.bsky.social @annedekas.bsky.social @microyunha.bsky.social @masarunobu.bsky.social and more

Headshots of eight featured speakers at the 2025 NeLLi Symposium. Top row, left to right: John M. Archibald (Dalhousie University, keynote), Harriet Alexander (Woods Hole Oceanographic Institution), Matthew Brown (Mississippi State University), Anne Dekas (Stanford University). Bottom row, left to right: Yunha Hwang (Harvard University), Masaru Nobu (JAMSTEC), Vivek Natarajan (Google), Olga Zhaxybayeva (Dartmouth College).

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Axel Visel @axelvisel.bsky.social · Aug 25

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

Joint Genome Institute @jgi.doe.gov · Aug 25

You can now register for the November NeLLi Symposium!

Join us in November for talks focused on the most recent expansions of the Tree of Life, and the latest discoveries toward the evolution of cellular complexity and microbial symbiosis.

Learn more: jointgeno.me/NeLLi

@nigelmouncey.bsky.social

2025 NeLLi Symposium | Joint Genome Institute

Las Vegas, NV Immediately followed by 1.5-day jamboree on November 6-7

jointgeno.me

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Axel Visel @axelvisel.bsky.social · Aug 21

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

Graphic announcing a Computational Postdoctoral Fellow position. Text: Computational Postdoctoral Fellow – Plant Genomic Language Models (gLMs). JGI is seeking a Computational Postdoctoral Fellow to join a funded project at Berkeley Lab’s Joint Genome Institute applying genomic language models (gLMs) to unlock new biological insights in plants. Join one of the world’s leading genomics facilities to pioneer AI applications in plant biology, with access to cutting-edge computational resources and diverse genomic datasets. This project will focus on developing and exploring applications of gLMs to plant genomes, from identifying novel regulatory elements to revealing evolutionary patterns across species, with particular interest in cross-species and data-limited scenarios. In this role, you will design tasks and datasets to test and extend gLM capabilities, apply models to generate new biological hypotheses, and share findings through high-impact publications and presentations.

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Axel Visel @axelvisel.bsky.social · Aug 20

If you are interested in using DAPseq for your plant, algal, fungal or microbial genomes, consider applying to one of @jgi.doe.gov's user programs:

jgi.doe.gov/work-with-us...

User Programs | Joint Genome Institute

Learn more about our Community Science Program, as well as other collaborative opportunities available through the FICUS call and other special initiatives.

jgi.doe.gov

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Axel Visel @axelvisel.bsky.social · Aug 20

And this news story by @jgi.doe.gov

jgi.doe.gov/user-science...

DAP-seq Drives Robust Mapping of Gene Regulation | Joint Genome Institute

Multi-species assays yield an unprecedented view of plant evolution and adaptation.

jgi.doe.gov

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Axel Visel @axelvisel.bsky.social · Aug 20

Also see this related News and Views by Mary Galli and Andrea Gallavotti

www.nature.com/articles/s41...

A binding agreement - Nature Plants

Transcription factors are proteins that recognize and bind short, specific DNA sequences and regulate when, where and how genes are expressed in a cell. A recent large-scale study of transcription fac...

www.nature.com

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Axel Visel @axelvisel.bsky.social · Aug 20

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...

Nature Plants August 2025 cover. Abstract artwork of overlapping colorful waveforms in red, orange, yellow, and purple on a black background, resembling mountain ridges or transcription factor binding profiles. The caption reads “Cistromes uncovered.”

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Axel Visel @axelvisel.bsky.social · Aug 19

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...

Promotional banner for the 2026 EMSL-JGI User Meeting. Theme: “Empowering Automated Laboratories – Integrating Experimentation with Data.” Event dates: March 3-5, 2026. Location: Seattle Marriott Waterfront, 2100 Alaskan Way, Seattle. The banner features a skyline of Seattle with Mount Rainier in the background, surrounded by colorful hexagonal graphics showing scientific imagery such as DNA, lab automation, microbial structures, and plants. EMSL and JGI logos are shown at the top.

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Axel Visel @axelvisel.bsky.social · Aug 19

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...

JGI announces 2025 Functional Genomics awardees | Joint Genome Institute

This year's project goals range from engineering drought-tolerant woody bioenergy crops through transcriptional network mapping, developing microbial systems to convert renewable feedstocks into advan...

jgi.doe.gov

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Axel Visel @axelvisel.bsky.social · Aug 18

Yes, absolutely! They are clearly not all artifacts. But some of them are and the problem is more pronounced in plants than in animals. Fortunately, the preprint also highlights how a unified re-annotation strategy can reduce these artifacts, making whatever PAV remains even more interesting!

Screenshot of text from the preprint: "Unsurprisingly, within both flowering plants and amniotes, gene PAV becomes increasingly common with increasing divergence time—more diverged genomes share fewer orthologs, likely due to sequence deletions, pseudogenization and other forms of large-scale mutation followed by selection or drift. However, the absolute amount of gene PAV and the degree that PAV is affected by divergence time was remarkably different between plants and animals." https://www.biorxiv.org/content/10.1101/2025.08.14.670405v1.full

Axel Visel @axelvisel.bsky.social · Aug 18

For details, see @jotlovell.bsky.social's excellent explainer thread 🧵

bsky.app/profile/jotl...

John Lovell @jotlovell.bsky.social · Aug 18

Determining presence-absence variation (PAV) across reference genomes is a major goal of pangenome analysis. It turns out that A LOT of gene PAV is due to methodological artifacts.

We explore the causes of this in soybean and cotton datasets in our recent preprint: www.biorxiv.org/content/10.1...

pangenome 'expansion' curves for cotton and soybean

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Axel Visel @axelvisel.bsky.social · Aug 18

🌿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...

A two-panel Scooby-Doo meme. In the top panel, Fred pulls the mask off a villain labeled “Presence-absence-variation in plant genomes.” In the bottom panel, the unmasked villain is revealed to be “Annotation artifacts.”

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