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...

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!

bioRxiv Genomics@biorxiv-genomic.bsky.social · 6mo ago

Positional grammar of transcription factor binding partitions developmental and stress-response regulation in plants https://www.biorxiv.org/content/10.64898/2026.02.05.703842v1

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...

nature.com

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.

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...

nature.com

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

Joint Genome Institute@jgi.doe.gov · 12mo ago

Calling for user research participants! To inform bioenergy research data integration, we are seeking feedback to improve ways of finding data across Dept. of Energy sources. Fill out this short survey by Aug. 31 to volunteer for a 45-minute interview: jointgeno.me/UserResearch2025 🖥️🧬 🧪🍄🌱🦠

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

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

Nature Plants@natplants.nature.com · 12mo ago

The August issue is now fully online, with a beautiful cover that might be a nostalgia trigger for some of us (young people can find an explanation in the Editorial): www.nature.com/nplants/volu...

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

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

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

University of California, Berkeley is hiring. Apply now!

aprecruit.berkeley.edu

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:

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.

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...

biorxiv.org

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!

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...

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...

biorxiv.org

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...

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

Xue lab at UC Irvine

Ecology and evolution in the human gut microbiome

kxuelab.com