axelvisel.bsky.social - Profile | ThreadSky | a Reddit-style client for Bluesky

✨ 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. 🧪

submitted 3 days ago • 1 comment

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

submitted 4 days ago • 2 comments

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...

submitted 5 days ago • 6 comments

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...

submitted 25 days ago • 12 comments

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...

submitted 59 days ago • 1 comment

The Primary Template-Directed Amplification method offers high recovery of single-cell genomes — often yielding above 80% completion! Read more on the work, first published in ISME Comms: jgi.doe.gov/user-science... @berkeleylab.lbl.gov @danudwary.secondarymetabolism.com @axelvisel.bsky.social

submitted 41 days ago • 0 comments

Today is the LAST DAY to submit a Letter of Intent for our Large Scale call, through our #CommunityScience Program. We’re looking for projects that leverage systems-based approaches to unravel functional capabilities. More details in the links below! 🖥️🧬 @berkeleylab.lbl.gov @axelvisel.bsky.social

submitted 52 days ago • 0 comments

Congratulations to the 30 new users whose proposals have been accepted for our New Investigator call, part of our #CommunityScience Program. Learn more about their projects below. jointgeno.me/CSPNI_FY25 🖥️🧬🧪🦠🌱🍄 @nigelmouncey.bsky.social @axelvisel.bsky.social @berkeleylab.lbl.gov

submitted 53 days ago • 1 comment

Tomato/potato/eggplant 🍅🥔🍆 pan-genome

submitted 58 days ago • 0 comments

We are hosting a workshop titled “Genomes Online Database (GOLD) – A curated metadata resource for powering discoveries” at the Biocuration 2025 conference on April 6th, 10:30 AM to 12:30PM US CST. Register to Join over the Zoom at t.co/WojICcd73s

submitted 59 days ago • 0 comments

DEADLINE Monday 4/7 for the IMG/M workshop! Join us to learn about data and workflows for our web-based platform, which enables users to analyze data with existing bioinformatic methods — bridging the gap from sequence to biology. More info: mgm.jgi.doe.gov 🖥️🧬🧪🦠

submitted 60 days ago • 0 comments

exciting news for our scientific community! www.nygenome.org/news-events/...

submitted 66 days ago • 4 comments

Highlights from our 2024 Progress Report: ⭐2,475 researchers had active proposals ⭐15,000 made use of our data ⭐39,870 projects completed as of FY24 ⭐871 Tb of sequence generated ⭐9.7 Mb of DNA synthesized ⭐13,700 metabolomics samples processed 🖥️🧬 🧪🦠🌱🍄 @berkeleylab.lbl.gov @nigelmouncey.bsky.social

submitted 75 days ago • 2 comments

🌟 Congrats+good luck to Yumary Vasquez of the JGI's Single Cell Research Group. She’ll compete at the National Lab SLAM in D.C. 3/5—streaming here: sites.google.com/lbl.gov/nlresearchslam/home. Going Viral…Literally: jointgeno.me/SLAM_Yumary 🖥️🧬🧪🦠 @axelvisel.bsky.social @simrouxvirus.bsky.social

submitted 89 days ago • 0 comments

Just very happy to have our paper out today! A big thanks to all our co-authors, and to Nikolai and @steinaerts.bsky.social for the teamwork over the past years. If you are interested in using our models for cross-species enhancer studies, check out crested.readthedocs.io/en/stable/mo... 🙂

submitted 107 days ago • 3 comments

Reminder of an exciting conference 'Hidden Cell, Dark Genome', Edinburgh 3-4th April 2025! Sessions: • Regulatory functions of the dark genome • Uncharted proteins and RNA complexity • Cellular diversity • Atomic structures at the cellular scale Early bird and registration deadline: 28th February!

submitted 112 days ago • 1 comment

If you're an early career researcher based in the U.S. and working on 🦠Microbiome Data🧬💻: The @microbiomedata.org Ambassador Program is a great opportunity to learn, network, and contribute

submitted 114 days ago • 0 comments

Fellowship opportunity for grad students: DOE Office of Science Graduate Student Research #SCGSR program now open for applications JGI @jgi.doe.gov is part of @berkeleylab.lbl.gov and can host students. To discuss possible projects, please reach out to our scientists! science.osti.gov/wdts/scgsr

submitted 114 days ago • 0 comments

2025 EMBO workshop on "Enhancer Mechanics and Enhanceropathies" now open for registration I was at the 2023 workshop in Marseille and it was a great event - recommend!

submitted 115 days ago • 0 comments

The rumors are true! Quick links below ⬇️ Looking to work w/theJGI? Start here: jgi.doe.gov/work-with-us For data-downloading users: jgi.doe.gov/analyze-data Read about cool user research here: jgi.doe.gov/user-science And here's who makes it all happen! jgi.doe.gov/who-we-are jgi.doe.gov 🖥️🧬🧪🦠🌱🍄

submitted 123 days ago • 0 comments

Wild: Viable mice from 2 sperms. Very involved - among other things, it requires making a "20KO" first - 20 different loci deleted/edited to avoid imprinting effects. And low survival rate, but proof of concept nonetheless. www.cell.com/cell-stem-ce...

submitted 123 days ago • 1 comment

The JGI @jgi.doe.gov just released its new, completely revamped website Cool user science, information about our user programs, access to data portals and analysis tools and much more! Check it out at jgi.doe.gov

submitted 124 days ago • 0 comments

Touring BioEPIC, the new Biological and Environmental Program Integration Center on the @berkeleylab.lbl.gov campus. Great views of the San Francisco East Bay and the Golden Gate Bridge in the distance. #BestViewFromALab

submitted 129 days ago • 0 comments

New 🧬resource💻 for craniofacial researchers from @justincotney.bsky.social's lab: A single-cell RNA-seq atlas of human craniofacial development www.biorxiv.org/content/10.1...

submitted 131 days ago • 0 comments

Microbes to humans:

submitted 135 days ago • 0 comments

Genomes assembled from #metagenomes (a.k.a. MAGs) are awesome and have revolutionized our ability to study uncultivated microbes ...BUT: they still don't capture a lot of the 🦠 species that are out there New @jgi.doe.gov paper led by Dongying Wu and Natalia Ivanova: www.science.org/doi/10.1126/...

submitted 135 days ago • 1 comment

The research community has flocked to the social-media platform Bluesky. Tell us about your experience https://go.nature.com/42fihQG

submitted 138 days ago • 11 comments

Microbial Genomics & Metagenomics Workshop Want to learn how to use IMG, GOLD, and other @jgi.doe.gov -hosted platforms and tools for microbial and metagenomics? Register now for the 33rd MGM Workshop in Berkeley Early bird rates available until Jan 31! mgm.jgi.doe.gov

submitted 138 days ago • 0 comments

How does haploinsufficiency of developmental transcription factors cause phenotypes? Intriguing new work from @benoitbruneau.bsky.social' lab suggests it's not just by affecting individual regulatory sequences, but through bigger impacts on lineage-specific 3D chromatin organization.

submitted 139 days ago • 1 comment

Evo-devo aficionados, don't miss this really cool paper by @mathithiru.bsky.social, @crumplab.bsky.social et al. Development of the mammalian outer ear and fish gills share regulatory programs (with cross-compatible enhancers!), suggesting a common evolutionary origin of these structures.

submitted 141 days ago • 2 comments

For researchers in 🦷dental, 👅oral, and 🙄craniofacial research, there is a now a new data science resource from NIDCR The "DDS Data-Driven Science Hub" (built by @vv2024.bsky.social) features: - Human phenotypes - Multiomes - Animals and microbiomes - Imaging Check it out at: www.ddshub.nih.gov

submitted 143 days ago • 0 comments

Very excited to announce that the single cell/nuc. RNA/ATAC/multi-ome resource from ENCODE4 is now officially public. This includes raw data, processed data, annotations and pseudobulk products. Covers many human & mouse tissues. 1/ www.encodeproject.org/single-cell/...

submitted 145 days ago • 6 comments

Now available as preprint: The ENCODE 4 expanded registry of regulatory elements - 2.35M 🧍 human cCREs - 927k 🐭 mouse cCREs www.biorxiv.org/content/10.1... Led by @moorejille.bsky.social, this preprint summarizes data and analyses generated by hundreds of contributors across ENCODE 4

submitted 144 days ago • 2 comments

🚨Postdoc position(s) alert🚨 If you like to develop new bioinformatic tools for human microbiome analysis, are interested by virus/phages, we (JGI Viral Genomics and Microbiome Data groups) may have a great position for you ! No official job posting yet, but email or DM if you are interested !

submitted 145 days ago • 0 comments

Exciting new work from @evgenykvon.bsky.social's lab: dual-enSERT for directly comparing the in vivo activities of the 🔴reference sequence and a 🟢variant of a developmental enhancer - within the same transgenic mouse embryo!

submitted 145 days ago • 1 comment

Our ChromBPNet preprint out! www.biorxiv.org/content/10.1... Huge congrats to Anusri! This was quite a slog (for both of us) but we r very proud of this one! It is a long read but worth it IMHO. Methods r in the supp. materials. Bluetorial coming soon below 1/

submitted 158 days ago • 8 comments