iiinova — where your digital self keeps evolving

Reposted by sharon greenblum

Ronan @omalley-regulome.bsky.social · 10/02/2026

New preprint! The same TFs can drive distinct regulatory programs depending on where they bind.  TSS → rapid stress responses  Intronic & upstream → cell-type programs  Enhancer-like CRMs → embryo/meristem programs  Coding-sequence binding → repression www.biorxiv.org/content/10.6...

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sharon greenblum @greensi.bsky.social · 07/02/2026

our new preprint is out! if a transcription factor binds near a gene, does it matter exactly where? keep an eye out for a 🧵soon!

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Reposted by sharon greenblum

Axel Visel @axelvisel.bsky.social · 22/09/2025

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...

nature.com

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...

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Reposted by sharon greenblum

Marianna Karageorgi @mkarag.bsky.social · 15/09/2025

How do populations maintain an evolutionary memory? I am happy to share that our work with Dmitri Petrov @petrovadmitri.bsky.social, Paul Schmidt, and colleagues on dominance reversal and stabilization of insecticide resistance in changing environments over time is now published at Nature EE.

nature.com

Beneficial reversal of dominance maintains a large-effect resistance polymorphism under fluctuating insecticide selection - Nature Ecology & Evolution

Measuring selection and dominance in fitness of the insecticide-resistant Ace alleles in Drosophila melanogaster, the authors show evidence for beneficial reversal of dominance, a mechanism that can s...

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Reposted by sharon greenblum

Joint Genome Institute @jgi.doe.gov · 26/08/2025

Do YOU use data from across multiple sources? (See list in link below) We want to know: ✅HOW you gather comprehensive data for the same sample; ✅WHERE you look; and ✅WHAT OBSTACLES you face Sign up by 8/31 to share: jointgeno.me/UserResearch2025 @berkeleylab.lbl.gov @nigelmouncey.bsky.social

jointgeno.me

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Reposted by sharon greenblum

Axel Visel @axelvisel.bsky.social · 21/08/2025

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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sharon greenblum @greensi.bsky.social · 20/08/2025

these are all real DAP-seq peaks! specifically, peaks in the promoter of SWEET11 (a sugar transport gene) and its orthologs across 10 plant species the darker colored peaks are binding sites for transcription factors that have maintained regulation of SWEET11 across 100+M years of plant evolution

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Reposted by sharon greenblum

Axel Visel @axelvisel.bsky.social · 20/08/2025

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...

jgi.doe.gov

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.

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Reposted by sharon greenblum

Peter Sudmant @psudmant.bsky.social · 13/08/2025

The Sudmant lab at UC Berkeley is seeking a postdoc to work on a fully funded NIH project to understand differences in DNA repair and somatic mutation across the primate tree of life. Please spread widely to those who may be interested aprecruit.berkeley.edu/JPF05052

aprecruit.berkeley.edu

Postdoctoral Scholar – Genomics, Aging, Somatic Mutation, Structural Variation, Evolution , Cancer – Integrative Biology

University of California, Berkeley is hiring. Apply now!

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sharon greenblum @greensi.bsky.social · 20/08/2025

August’s Nature Plants cover story shows how we integrated large-scale multiDAP and snRNA data to reveal drivers of cell type identity and evolution in flowering plants. www.nature.com/nplants/volu... We packed a lot into this paper! Here’s a single-cell spin on what we found:

nature.com

Nature Plants - Cistromes uncovered

Transcription factors (TFs) have specific patterns of binding to gene promoter regions, which have similarities and differences within TF families and...

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Reposted by sharon greenblum

Ben Good @benjaminhgood.bsky.social · 16/08/2025

Excited to share a new preprint w/ the Sonnenberg lab, led by Matt Carter, @zzzhiru.bsky.social & @mattolm.bsky.social. We analyzed the microbiomes of two non-industrialized populations from opposite sides of the globe to try to reconstruct the recent evolutionary history of our gut microbiota.

biorxiv.org

Prehistoric Global Migration of Vanishing Gut Microbes With Humans

The gut microbiome is crucial for health and greatly affected by lifestyle. Many microbes common in non-industrialized populations are disappearing or extinct in industrialized populations. Understand...

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Reposted by sharon greenblum

Nandita Garud @nanditagarud.bsky.social · 22/07/2025

I am seeking a postdoc for my group at UCLA. We work at the intersection of population genetics x microbiome (garud.eeb.ucla.edu). If interested, please message me!

garud.eeb.ucla.edu

Garud Lab

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Reposted by sharon greenblum

Marianna Karageorgi @mkarag.bsky.social · 22/01/2025

How is functional variation at large-effect loci maintained in natural populations? Thrilled to share our work showing how beneficial dominance reversal helps fruit flies maintain a resistance polymorphism as selection varies in their environment! A thread 🧵 1/n www.biorxiv.org/content/10.1...

biorxiv.org

Dominance reversal maintains large-effect resistance polymorphism in temporally varying environments

A central challenge in evolutionary biology is to uncover mechanisms maintaining functional genetic variation1. Theory suggests that dominance reversal, whereby alleles subject to fluctuating selectio...

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Reposted by sharon greenblum

Berkeley Lab @berkeleylab.lbl.gov · 02/12/2024

The Dark Energy Spectroscopic Instrument (DESI) scientists mapped how nearly 6 million galaxies cluster across 11 billion years of cosmic history. Their observations line up with what Einstein's theory of general relativity predicts. 🧪 newscenter.lbl.gov/2024/11/19/n...

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Reposted by sharon greenblum

Katherine Xue @ksxue.bsky.social · 19/11/2024

Hi friends new and old! I study how microbes interact and evolve in complex communities like the human gut microbiome.🦠🧬💩 I'm thrilled to share that I'm starting a lab at UC Irvine in April 2025 and am recruiting at all levels - please spread the word! kxuelab.com More about my work below...🧵1/n

kxuelab.com

Xue lab at UC Irvine

Ecology and evolution in the human gut microbiome

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