Reposted by Axel ViselNational Microbiome Data Collaborative (NMDC) @microbiomedata.org · 28/09/2026The NMDC will be merging its core, high-performing functionalities directly into DOE-BRIDGE. We extend our deepest gratitude to our core team, advisors, ambassadors and champions, DOE BER, and the community 🦠 🌎 Thank you for seven incredible years of collaboration! microbiomedata.org/faqs 014
Reposted by Axel ViselJoint Genome Institute @jgi.doe.gov · 15/09/2026In a recent episode of Genome Insider, @jotlovell.bsky.social discussed why a single reference genome for Sorghum proved insufficient, and the value of a pangenome to represent the crop's full genetic diversity: jgi.doe.gov/user-science/podcasts/s… 🖥️ 🧬 🌱 041
Reposted by Axel ViselJoint Genome Institute @jgi.doe.gov · 09/09/2026Perspective: Pangenomes are Only as Powerful as their Annotation Method Are researchers wasting resources following false trails — due to variations in interpretative methods? 🖥️🧬 🌱 @tomasbruna.bsky.social Full story below⬇️ jgi.doe.govPerspective: Pangenomes are Only as Powerful as their Annotation Method | Joint Genome InstituteResearchers may be wasting resources following false trails due to variations in interpretative methods. 01610
Reposted by Axel ViselJoint Genome Institute @jgi.doe.gov · 07/08/2026📣 Early Bird registration for our VEGA Symposium closes Sept. 19! Join us Nov. 18–19 to discuss characterizing uncultivated viral diversity and its role in biotech and industrial applications. 🖥️🧬🦠 More info: jointgeno.me/VEGA 051
Axel Visel @axelvisel.bsky.social · 03/09/2026"The Mobilome in the Mire" DNA sleuths 🕵️♀️ @scbagby.bsky.social and 🕵️♂️ @simrouxvirus.bsky.social tracked a whole zoo of mobile genetic elements in thawing permafrost ❄️💧 for 8 years. Another Genome Insider podcast from @jgi.doe.gov 🎙️: jgi.doe.gov/user-science...jgi.doe.govThe Mobilome in the Mire | Joint Genome InstituteJoin Sarah Bagby (Case Western Reserve University) and Simon Roux (JGI) as they talk about their recent work on a time series from Sweden’s Stordalen Mire. By looking at Mobile Genetic Elements, or MG... 172
Axel Visel @axelvisel.bsky.social · 02/09/2026🍄 @jgi.doe.gov's Fun-Guys and Fun-Gals have been busy this summer! ☀️ New fungal genomes in MycoCosm: ✔️ Hanseniaspora uvarum NRRL Y-1614 ✔️ Semicentenialea rex gs25 v1.0 ✔️ Amoeboaphelidium occidentale KS120 v1.0 ✔️ Neocallimastix sp FC1 v1.0 ✔️ Boletus sp. 2018DF043 v1.0 mycocosm.jgi.doe.gov 🍄🧬🔬 2142
Axel Visel @axelvisel.bsky.social · 01/09/2026Giant virus evolution unfolding in real time 🦠🔬👀 Analyzing 20 years of metagenomic data from Lake Mendota Cool work by @jgi.doe.gov postdoc Yumary Vasquez. Also involved: @miferg.bsky.social @robinrohwer.bsky.social @quendi.bsky.social @fmschu.bsky.social & others jgi.doe.gov/user-science...jgi.doe.govA Broader Sense of Evolution Over Time | Joint Genome InstituteAnalyzing how giant viruses—and interns—respond to environmental change. 172
Axel Visel @axelvisel.bsky.social · 31/08/2026A Global Catalog of Microbial Symbionts 🌍🦠🧬🫨 New resource from @jgi.doe.gov, led by @astrogenomics.bsky.social and @fmschu.bsky.social with contributions by @emileyeloe-fadrosh.bsky.social @miferg.bsky.social and many more 🔓 www.nature.com/articles/s41... @biosci.lbl.gov @berkeleylab.lbl.govnature.comA genomic catalog of Earth’s bacterial and archaeal symbionts - Nature BiotechnologySymbiotic relationships of microorganisms are predicted and cataloged with a machine learning tool. 03217
Reposted by Axel ViselShenzhi Chen @shenzhichen1999.bsky.social · 25/08/2026Excited to share our paper in @natgenet.nature.com on the de novo design of tissue-specific mammalian enhancers that function in vivo in mouse embryos. 🧬🐭 www.nature.com/articles/s41... 35826
Reposted by Axel ViselBiosciences Area at Berkeley Lab @biosci.lbl.gov · 19/08/2026Jack Here! I met with #BioEGSB researcher Laura Cook to learn about her team's work to uncover the underlying mechanisms behind how faces 🐔 🐭 are structured. Laura's team is focused on studying enhancers—regions of genetic information that control when, where, and how much of a gene is expressed.🧬 031
Reposted by Axel ViselJoint Genome Institute @jgi.doe.gov · 18/08/2026Recently published in @natcomms.nature.com with support from @geochurch.bsky.social's JGI Functional Genomics proposal: Genome-building with SynOMICS reveals hidden rules of the genetic code & opens doors to industrially useful bacteria.@akosnyerges.bsky.social @berkeleylab.lbl.gov @biosci.lbl.govjgi.doe.govNew Method Offers Safer, More Powerful Synthetic Organisms | Joint Genome InstituteGenome-building with SynOMICS reveals hidden rules of the genetic code and opens doors to virus-proof, industrially useful bacteria. 072
Reposted by Axel ViselBiosciences Area at Berkeley Lab @biosci.lbl.gov · 07/08/2026Faces are one of the most diverse anatomical features, but how can the facial structure of birds and mammals vary so drastically when we share the majority of our DNA? Work from #BioEGSB researchers Laura Cook and @axelvisel.bsky.social uncovers what may be the driving force of facial morphology. 111
Reposted by Axel ViselJoint Genome Institute @jgi.doe.gov · 03/08/2026Interested in working with the JGI and never led a proposal with us? Now is your chance! We are accepting submissions to our New Investigator call for first-time PIs. Deadline to submit is Sept. 9. jointgeno.me/CSPnewPI @berkeleylab.lbl.gov @biosci.lbl.govjointgeno.meCSP New Investigator Call | Joint Genome InstituteThe CSP New Investigator Call is for investigators and research initiatives new to the JGI. Projects must be independent of ongoing JGI proposals, and lead PIs cannot have been lead PI on any previous... 0812
Reposted by Axel ViselEvgeny Kvon @evgenykvon.bsky.social · 05/08/2026A really cool preprint from Joanna Wysocka's lab showing that housekeeping genes use distal enhancers as dosage buffers against TF fluctuations, but only during critical cell fate transitions. Makes so much sense! www.biorxiv.org/content/10.6...biorxiv.orgEnhancer buffering protects dosage-sensitive housekeeping genes during vulnerable developmental transitionsHousekeeping genes maintain robust expression across cell types despite dynamic transcription factor fluctuations, yet their haploinsufficiency is associated with many tissue-specific developmental di... 15721
Reposted by Axel ViselBiosciences Area at Berkeley Lab @biosci.lbl.gov · 29/06/2026Hi 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! 042
Reposted by Axel ViselSimon Roux @simrouxvirus.bsky.social · 12/06/2026🚨 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 12717
Axel Visel @axelvisel.bsky.social · 08/05/2026If 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 1175
Reposted by Axel ViselJoint Genome Institute @jgi.doe.gov · 05/05/2026Genome Watch👀 "In search of phage tail-like particiles: nature's versatile nanomachines" highlights the importance of predictive models. 🖥️🧬 Full Story: rdcu.be/fgU2m @berkeleylab.lbl.gov @axelvisel.bsky.social @natureportfolio.nature.com nature.comIn search of phage tail-like particles: nature’s versatile nanomachines - Nature Reviews MicrobiologyThis Genome Watch article highlights the importance of predictive models for identifying and characterizing the roles of phage tail-like particles as a tool for bioengineering and biocontrol. 021
Axel Visel @axelvisel.bsky.social · 30/04/2026JGI @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... 062
Reposted by Axel ViselJoint Genome Institute @jgi.doe.gov · 31/03/2026📢 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: jgi.doe.gov/work-with-us/proposals/…jgi.doe.govCSP Large Scale Call | Joint Genome InstituteThe Community Science Program Large Scale Call is focused on genomic science projects that address sustainable biofuel and bioproducts production. 002
Reposted by Axel Viseltomoyahonda.bsky.social @tomoyahonda.bsky.social · 30/03/2026Excited to share my latest work on synthetic biology and host–microbe interactions, now published in Nature Communications! www.nature.com/articles/s41...nature.comCRAGE-RB-PI-seq reveals transcriptional dynamics of plant-associated bacteria during root colonization - Nature CommunicationsThis study reveals how plant-associated bacteria dynamically reprogram gene expression during root colonization, using a new high-throughput approach that overcomes low bacterial biomass and interfere... 142
Reposted by Axel ViselMolecular Foundry @molecularfoundry.lbl.gov · 24/03/2026The 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/ 092
Reposted by Axel ViselJoint Genome Institute @jgi.doe.gov · 19/03/2026New 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.govjgi.doe.govComplete Genome of Oil-Rich Alga Reveals Ideal Platform for Bioengineering | Joint Genome InstituteStreamlined genome with precise gene targeting transforms oil-producing alga into a powerful platform for developing bio-based industrial products. 043
Reposted by Axel ViselDarío Lupiáñez @dariloops.bsky.social · 06/03/2026🚨 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 14238
Reposted by Axel ViselJoint Genome Institute @jgi.doe.gov · 05/03/2026📣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.socialjointgeno.meCSP Large Scale Call | Joint Genome InstituteThe Community Science Program Large Scale Call is focused on genomic science projects that address sustainable biofuel and bioproducts production. 022
Reposted by Axel ViselJoint Genome Institute @jgi.doe.gov · 24/02/2026Our 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: jgi.doe.gov/user-science/science-st…jgi.doe.gov2025 Progress Report | Joint Genome InstituteLearn more about the JGI's 2025 accomplishments, including research and data output. 054
Reposted by Axel ViselMolecular Foundry @molecularfoundry.lbl.gov · 13/02/2026📣 We're joining up with @jgi.doe.gov in a joint Critical Minerals & Materials Call 👀: 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: bit.ly/3Oox1I0 052
Axel Visel @axelvisel.bsky.social · 13/02/2026Critical 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... 021
Axel Visel @axelvisel.bsky.social · 12/02/2026“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.... 270
Reposted by Axel ViselNational Academy of Sciences @nasonline.org · 04/02/2026Neil 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... 516032
Axel Visel @axelvisel.bsky.social · 02/02/2026Myth 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... 141
Axel Visel @axelvisel.bsky.social · 27/01/2026⏱️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... 053
Axel Visel @axelvisel.bsky.social · 20/01/2026What 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... 0107
Reposted by Axel ViselWillem van Schaik @wvschaik.bsky.social · 16/01/2026This 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...embl.orgIn remembrance of Peer Bork | EMBLEMBL and its community are deeply saddened by the death of Peer Bork, the organisation’s Interim Director General. 33010
Reposted by Axel ViselStein Aerts @steinaerts.bsky.social · 15/01/2026TF-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 16038
Reposted by Axel ViselMarc Somssich @somssich.bsky.social · 12/01/2026"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...newatlas.comThe 'Hell-Plant' of Death Valley offers hope to a hotter worldWe humans are a delicate bunch. We don’t have bark, boney exo-plates, or lush fur to protect us from hostile environments, so we have to steal what other creatures produce just to survive in regions a... 12511
Reposted by Axel ViselGuillaume Andrey @guandrey.bsky.social · 12/01/2026Our 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)nature.comClient Challenge 23718
Reposted by Axel ViselJill Moore @moorejille.bsky.social · 08/01/2026Our 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 🧵 1/11media.tenor.coma man wearing a plaid shirt and a purple hat is saying here we go .ALT: a man wearing a plaid shirt and a purple hat is saying here we go . 1269
Axel Visel @axelvisel.bsky.social · 07/01/2026Now 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 12710
Reposted by Axel ViselJoint Genome Institute @jgi.doe.gov · 06/01/2026Congrats 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.socialjgi.doe.govJGI Announces FY26 Large Scale Portfolio for Our Community Science Program | Joint Genome Institute 1123
Reposted by Axel ViselJoint Genome Institute @jgi.doe.gov · 26/12/2025In 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: jointgeno.me/IMGStoriesForm @berkeleylab.lbl.gov @axelvisel.bsky.social 🖥️🧬 🦠 012
Reposted by Axel ViselAlex Stark @alex-stark.bsky.social · 24/12/2025Our 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)biorxiv.orgPredictive design of tissue-specific mammalian enhancers that function in vivo in the mouse embryoEnhancers control tissue-specific gene expression across metazoans. Although deep learning has enabled enhancer prediction and design in mammalian cell lines and invertebrate systems, it remains uncle... 210448
Reposted by Axel ViselJoint Genome Institute @jgi.doe.gov · 22/12/2025Deadline 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.govusermeeting.jgi.doe.govIntegrating Experimentation with Data | Joint Genome InstituteJoin the Joint Genome Institute and the Environmental Molecular Sciences Laboratory for “Empowering Automated Laboratories: Integrating Experimentation with Data.” 021
Axel Visel @axelvisel.bsky.social · 09/12/2025Excellent 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 060
Reposted by Axel ViselSimon Roux @simrouxvirus.bsky.social · 09/12/2025🧬🦠🚨 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...doi.orgComparison of short-read and long-read metagenome assemblies in a natural soil community highlights systematic bias in recovery of high-diversity populationsAbstract. Comparisons of long-read and short-read (meta)genome assemblies typically show that short-read sequence assemblies are less error-prone, but stru 15626
Axel Visel @axelvisel.bsky.social · 26/11/2025🔥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... 1225
Axel Visel @axelvisel.bsky.social · 18/11/2025Soils 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... 0127
Reposted by Axel ViselBerkeley Lab @berkeleylab.lbl.gov · 13/11/2025🧬 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.newscenter.lbl.govCracking the Genome’s Switchboard: How AI Helps Decode Gene RegulationA single letter in the DNA code could change the course of human development 032