Delighted to see our latest paper out in @natgenet.nature.com ! The brilliant @jhamley98.bsky.social developed MCCv, allowing chromatin architecture to be visualised at base-pair resolution for each allele—a powerful way to identify functional genetic variants. www.nature.com/articles/s41... 🧵

1/ New preprint! with @solersanchisx.bsky.social @cwjpugh.bsky.social @federicobilleci.bsky.social @jonnyfrazer.bsky.social and Mafalda Dias, we introduce a scalable framework to improve stability prediction and separate folding from functional constraints. www.biorxiv.org/content/10.6...

Blending physics-based and inverse folding models to disentangle variant effects on stability and function

Protein sequences are constrained not only by the need to fold into stable structures, but also by specific functional requirements imposed by natural selection. Yet predictions of how amino-acid chan...

biorxiv.org

In a study of 78,664 participants, over 24,000 protein QTLs linked to 1,116 proteins were identified, revealing genetic effects on disease pathways and cell types. PMID:42097137, Cell 2026, @Cell https://www.cell.com/cell/fulltext/S0092-8674(26)00385-5 #Medsky #Pharmsky #RNA #ASHG #ESHG 🧪

AD brains show >1,000x enrichment of somatic SNVs in cancer driver genes, linked to clonal hematopoiesis, driving inflammation in microglia-like macrophages. PMID:42019491, Cell 2026, @Cell https://www.cell.com/cell/fulltext/S0092-8674(26)00341-7 #Medsky #Pharmsky #RNA #ASHG #ESHG 🧪

New lab preprint - Deep learning models are most often difficult to interpret black box models. What if we engineer them with interpretation in mind? Dennis Gankin carefully studied so-called biologically inspired neural networks and found an interesting phenomenon www.biorxiv.org/content/10.6...

Leveraging multiplicity in biologically informed neural networks to uncover disease heterogeneity

Biologically inspired neural networks (BINNs) embed pathway, ontology, or protein-interaction structure directly into neural networks, promising interpretable disease prediction where hidden nodes map...

biorxiv.org

I'm happy to share our latest on #coral single-cell biology: a transcriptomic timecourse of heat stress in Stylophora pistillata, from bleaching to recovery 🪸🌊 This project was spearheaded by Shani Levy and carried through in @arnausebe.bsky.social's lab at @crg.eu. www.biorxiv.org/content/10.6...

The anatomy of an AI-supported academic article is becoming more apparent. I desk reviewed ~70 manuscripts this week for our journal. Reckon 20ish had significant AI assistance. On top of hundreds of others recently I'm starting to see patterns. Are other editors are seeing the same or similar? 1/

After four years, several updates and a handful of CRAN releases, 𝗹𝘁𝗰 𝗰𝗼𝗹𝗼𝗿 𝗽𝗮𝗹𝗲𝘁𝘁𝗲 𝗥-𝗽𝗮𝗰𝗸𝗮𝗴𝗲, reached a version I feel genuinely good about sharing with the community. github.com/loukesio/ltc...

Our preprint is now out in @natgenet.nature.com ! doi.org/10.1038/s415... We measured Sox2 promoter bursting dynamics with the SCR enhancer positioned at different distances within a genomic locus devoid of confounding effects in mESC: Main findings in the 🧵 below:

Enhancer control of promoter activity and variability via frequency modulation of clustered transcriptional bursts - Nature Genetics

Tünnermann et al. use live-cell imaging to study promoter activity under the control of an enhancer inserted at different genomic distances. RNA production from the promoter occurs in clusters of tran...

doi.org

Luca Giorgetti lab @FMI@lucagiorgetti.bsky.social · 2y ago

Celebrating 10 years of our lab with a new preprint: www.biorxiv.org/content/10.1... How does enhancer location within a TAD control transcriptional bursts from a cognate promoter? Experiments by Jana Tünnermann and modelling by Gregory Roth

I'm excited to share that Corgi is out in @natcomms.nature.com! We refine context-aware sequence-to-function models by using FiLM to condition the model on trans-regulator expression levels. This way Corgi can generalize to unseen cell types. www.nature.com/articles/s41... 🧵Thread 1/n

Context-aware sequence-to-function model of human gene regulation - Nature Communications

This study introduces Corgi and Corgi+ , biology-inspired deep neural network models of regulatory DNA sequences that can generalize to unseen cell types. They accurately impute epigenomic d...

nature.com

First taste at #SMBE2026: joining the intriguing GHIST2026 challenge as a participant. We have 6 months to see who will be the best at detecting selective sweeps, demographic changes and infer relatedness patterns. Let the Hunger Games begin.

Really incredible work from the Tcheandjieu Lab that finally helps us to decipher what is going on at the 9p21 locus and its association with coronary disease on different ancestral backgrounds. www.cell.com/ajhg/fulltex...

Linkage disequilibrium and allelic heterogeneity explain variation in coronary artery disease risk at 9p21 across populations and reduced effect in Africans

Using cross-ancestry fine-mapping across global and local ancestry groups, this study dissects the 9p21.3 coronary artery disease locus and shows how ancestry-specific haplotype structure shapes assoc...

cell.com

We are very excited to share our latest. We thought that soft sweeps would be the only type of sweep spreading across human gut microbiomes. Turns out many are hard! Reach @peterlaurin.bsky.social 's thread on why! And tomorrow at #SMBE2026 I will share this work and more!

Peter Laurin@peterlaurin.bsky.social · 3mo ago

Super excited to share new work with my advisor @nanditagarud.bsky.social! We re-examine the rapidity of adaptation in the human gut microbiome and begin to characterize the adaptive architecture of selective sweeps spreading across human guts. www.biorxiv.org/content/10... 1/n:

Just in time for #SMBE2026! Here's DEEP for detecting ghost/superarchaic introgression: scalable, robust, and no ARG! We find ~0.5% genome with superarchaic ancestry in East Asians and Oceanians, plus a notable signal at HLA Come find our poster tonight (#241)! www.biorxiv.org/content/10.6...

Scalable ARG-free Detection of Denisovan-mediated Superarchaic Introgression Reveals Heterogeneous Patterns across Populations

Ghost introgression from unsampled hominin lineages has emerged as an increasingly important component of human evolutionary history. Recent studies suggest that deeply divergent hominin lineages may ...

biorxiv.org

Terrific resource, now on @biorxivpreprint.bsky.social: The Vertebrate Genomes Project Phase I: A global reference genome resource 🧪🧬 www.biorxiv.org/content/10.6...

The Vertebrate Genomes Project Phase I: A global reference genome resource

The Vertebrate Genomes Project (VGP) aims to produce complete and near-error-free reference genomes for all ∼70,000 extant vertebrate species. Organized in four phases, it progressively targets all ve...

biorxiv.org

Ancient human DNA from the cave walls! 🤯 Wonderful new paper led by Alba Bossoms Mesa and a great team of people that made this work possible.

ellie_ancient@elenaessel.bsky.social · 4mo ago

So happy and proud to see this paper out in @natcomms.nature.com today! We show that traces of human DNA can persist on cave walls for thousands of years. Absolutely fantastic work by the wonderful Alba Bossoms Mesa at @mpi-eva-leipzig.bsky.social and a great team! www.nature.com/articles/s41...

(1/n) Very excited to share tri-lab collab (Mirny & Zechner) led by Harvey, Henrik & Jack: Q: How do enhancers & promoters interact in space (contact vs. action-at-a-distance) and time (stable vs. transient)? A: Transient E-P contact (~25-42 nm lasting ~10-20 sec): www.biorxiv.org/content/10.6...

Gift link

Opinion | The Science That Turned Lizard Venom Into GLP-1s Is Under Attack

nytimes.com

Cool Sankey diagram of the ranked choice voting results of Maine’s Democratic gubernatorial primary. Think how transformative this could be if more states adopted it.

New review out in Current Biology with colleagues in the Plant Cell Atlas (@plantcellatlas.bsky.social)! We discuss how single-cell genomics is reshaping our understanding of plant cell-type identity and evolution across the Green Lineage. bit.ly/4eAip2Q

The secret's out – thrilled to share I’ve been selected as a member of the inaugural class of @sciam.bsky.social's Young American Scientists! It's been so fun to learn about the work of the other 27 awardees from around the country. www.scientificamerican.com/issue/sa/202...

Awesome work led by Serena Tucci showing how ong-­ term isolation and archaic introgression shape functional genetic variation in Near Oceania @science.org 🧪🧬💀 www.science.org/doi/10.1126/...

Long-term isolation and archaic introgression shape functional genetic variation in Near Oceania

Near Oceanic populations harbor substantial cultural, phenotypic, and genetic diversity yet are drastically underrepresented in human genomics. We generated 177 high-coverage Near Oceanian whole genom...

science.org

I'm excited to share that our work studying gene dosage response curves (GDRCs) is now out in Cell Genomics (@cellpress.bsky.social). www.cell.com/cell-genomic... [1/n]

Buffering of gene dosage response curves for human complex traits

Milind et al. explore why loss-of-function variants and duplications tend to have average effects in the same direction on 94 complex traits. Using gene dosage response curves (GDRCs), they gather evi...

cell.com

"(...) plasmids are chromatinized in an organized, sequence-dependent manner and adopt a heterogeneous and incomplete chromatin architecture relative to nuclear-encoded chromatin fibers" www.cell.com/molecular-ce...

Chromatin architectures underlying plasmid-based assays for regulatory variant effects

Mallory et al. develop plasmid Fiber-seq to map chromatin architecture along individual transfected plasmids at near-nucleotide resolution, which reveals that plasmids adopt heterogeneous chromatin pa...

cell.com

This is awful to hear, describing how Sean Eddy (HMMER, infernal, pfam, rfam) has been defunded. The letter said his work "had been determined to be of absolutely no value to the US taxpayer, and therefore it was being specifically terminated," www.npr.org/2026/05/21/n...

Researchers say the Trump administration is finding new ways to punish science

Even with federal grants largely restored, scientists say the Trump administration is still preventing those funds from reaching them. The consequences, they say, are already becoming clear.

npr.org

@johanduchene.bsky.social @sholtodavid.bsky.social Spent the last hour looking, found ten more apparently manipulated Western blots in Thermo Fisher's antibody verification data (across eight different catalogued products). Thread below. www.thermofisher.com/antibody/pro...

Beautiful new study from @elphegenoralab.bsky.social and Leonid Mirny's lab: Cohesin-bridged encounters mediate enhancer-promoter communication, predicting how enhancer effect scales with genomic distance and - for the first time - how CTCF sites modulate enhancer-promoter communciation! 🧵 below

Elphege Nora Lab at UCSF@elphegenoralab.bsky.social · 5mo ago

Why can't we explain enhancer action despite 2 decades of chromosome conformation technologies? 😬 Our new study spearheaded by Leonid Mirny's group points to a flaw in our assumptions, and to a solution from physical principles By @timothyfoldes.bsky.social 💻& @karissalhansen.bsky.social 🧪 🧵👇

Why can't we explain enhancer action despite 2 decades of chromosome conformation technologies? 😬 Our new study spearheaded by Leonid Mirny's group points to a flaw in our assumptions, and to a solution from physical principles By @timothyfoldes.bsky.social 💻& @karissalhansen.bsky.social 🧪 🧵👇

Single-cell proteomics illuminated new mechanisms of mammalian development. We found that spatially polarized protein distributions and intracellular protein gradients emerge during the earliest stages of mammalian embryogenesis and bias subsequent cell fate decisions. www.cell.com/cell/fulltex...

New pre-print 📣 “Undruggable” cancer mutations remain very hard to target with current modalities. What if we could instead sense mutant transcripts and convert that recognition into selective cell killing? Check out this work led by postdoc Jingkun Zeng: www.biorxiv.org/content/10.6...