Update: scE2G is now online at Nature Genetics! Since the preprint, we added a new benchmark on a fully held-out CRISPR dataset. scE2G continues to show state-of-the-art performance, reinforcing that it generalizes well nature.com/articles/s41588-026-02695-8 1/

Jesse Engreitz@jengreitz.bsky.social · 2y ago

Introducing scE2G: a new model to link enhancers to target genes using single-cell data. Excited that scE2G will enable building enhancer maps in hundreds of cell types in the human body! Wonderful collaboration with @randersson.bsky.social @613weilin.bsky.social @mayayayas.bsky.social Thread👇

Riboseek is a fast RNA/DNA search. More sensitive than nhmmer at 250x speed. Structure-aware realignment produces MSAs approaching rMSA quality. Plus 1.7M precomputed RNA MSAs, and an API to search your own 📄 www.biorxiv.org/content/10.6... 💾 github.com/steineggerla... 🌐 search.foldseek.com/riboseek

It's cautionary tale for LLM use though. Data aren't democratic; some are better. Reminds me of something a biologist recently said to me of an AI colleague: "His models are fantastic. It's just a shame he doesn't realize the output's garbage because half the papers fed into it are wrong.." 5/n

Everyone reduces dimensions. We reduced cells. Read our latest work on bioRxiv: Quantitative Description of C. elegans mRNA Landscapes From High Coverage Single-Cell Transcriptomes www.biorxiv.org/content/10.6...

Thrilled to post thread re: new single-cell lineage of mouse embryo reconstructed w/ DNA Typewriter. One animal, zygote to late organogenesis (E13.5). Tree has 1,340,794 transcriptionally profiled, annotated tips (cells), 1,142,588 dated internal nodes, rooted at zygote 1/n

Obviously a strong supporter of this type of tool, but troubled by the literature review. No reference to @chribue.bsky.social work on combinatorial enhancers, and our EXTRA-seq -> kilobase-scale E-P landscapes in a native locus (no minP). Same principle, just ONT.

Jay Shendure@jshendure.bsky.social · 6d ago

New preprint from Shendure Lab on Locus-Scale aka Long-@$$ MPRAs led by the amazing Abby McGee & @carinabiar.bsky.social Most MPRAs test ~300 bp fragments next to a promoter. But real enhancers are bigger, act combinatorially and from a distance. 1/n www.biorxiv.org/content/10.6...

New preprint from Shendure Lab on Locus-Scale aka Long-@$$ MPRAs led by the amazing Abby McGee & @carinabiar.bsky.social Most MPRAs test ~300 bp fragments next to a promoter. But real enhancers are bigger, act combinatorially and from a distance. 1/n www.biorxiv.org/content/10.6...

I am very excited to share the work of my PhD with @eddaschulz.bsky.social, now on BioRxiv! 🎉 🧵⬇️ (1/9) How does the transcription↔️chromatin crosstalk ensure monoallelic expression?

bioRxivpreprint@biorxivpreprint.bsky.social · last wk.

Transcription-dependent heterochromatin at the Xist promoter shapes the random choice of the inactive X chromosome https://www.biorxiv.org/content/10.64898/2026.07.22.737064v1

Next summer's Epigenetics GRC (I'm co-chairing with Deborah Bouch'is) is shaping up nicely with an all-star lineup of speakers working on a broad range of organisms and systems and everything from molecular mechanisms to new phenomena. Apply and put it on your calendar! www.grc.org/epigenetics-...

Academic tweeps! How do your institutes implement support for scientists in the rapidly changing AI-era - i.e, who is training the students to use Claude Code, and making sure they don't wreckt the cluster? Does it work well? Tell here/DM + pls RT (heading a sub-committee...)

1/ New paper alert! 🎉🧬 Our study on #9p21 gene regulation is out in #CellGenomics: "Chromatin topology and distal elements underlie divergent cell-type-specific regulation of 9p21 locus cell cycle genes" (Torlai Triglia, Miller, et al. www.cell.com/cell-genomic... 🧵

How did octopuses evolve novel traits? Rishav Mitra, Richard Han, Trey Scott, et al serendipitously discover a unique ribosome adaptation that increases the accuracy of protein synthesis and evolved alongside their elaborate nervous systems vs deep sea relatives. www.biorxiv.org/content/10.6...

Yale’s trustees face a decision with profound consequences

The US Government aims to defund basic science, dismantle academia & intellectual freedom ➡️ in service of political ideology & corporate interest In its own words 🚨 Was chapters in Project2025 static.heritage.org/project2025/... 🚨 Now official blueprint published www.whitehouse.gov/wp-content/u...

If you don't like a paper, it is obviously totally fine to point out the issues. But please do NOT make egregious and unpleasant comments about the first author's qualifications. A first author who is usually a trainee. Beyond inappropriate and unprofessional.

Nelly found that transcription-dependent H3K9me3 restricts lncRNA Xist expression to one allele

@nellykanata.bsky.social · last wk.

I am very excited to share the work of my PhD with @eddaschulz.bsky.social, now on BioRxiv! 🎉 🧵⬇️ (1/9) How does the transcription↔️chromatin crosstalk ensure monoallelic expression?

Transcription-dependent heterochromatin at the Xist promoter shapes the random choice of the inactive X chromosome https://www.biorxiv.org/content/10.64898/2026.07.22.737064v1

“It would be sort of confirmation for me that I am useful,” Gonzales said. Alternatively, his absence might successfully promote the group discussion and collaboration he wanted to happen, which he said would also be a “fantastic outcome.”

Why One PI Stopped Attending His Own Lab Meetings | The Scientist

By skipping lab meetings, Daniel Gonzales aims to boost engagement and foster group-led discussions among his team.

the-scientist.com

The STRAIGHT-IN (Dual) kit is now available via @addgene.bsky.social! 🧬 A complete 24-plasmid toolkit for installing up to two orthogonal CLYBL landing pads, DASIT-based enrichment without FACS, and efficient large DNA integration in human cells. Link: www.addgene.org/kits/gallowa... 🧵

We developed an in situ RNA amplification method, RT&T-AMP, that uses reverse transcription followed by transcription to generate amplicons at original transcript sites with uniform transcript body coverage, enabling to imaging of short RNA sequences anywhere along transcripts.

You dont need advanced ML models to see base-resolution transcription factor occupancy and element-wise cis-regulatory logic. Just turn to a 40yo technology and basic stats. Still waiting for a structural biologist to help with 3d-modeling of composite regulatory DNA elements from DNase I profiles.

An encyclopedia of enhancer-gene regulatory interactions — online today! nature.com/articles/s4158… Now with an improved model, expanded maps across 1400+ biosamples, larger validation CRISPR datasets, and guidance on applying the model 1/

Andreas Gschwind@argschwind.bsky.social · 3w ago

Thrilled to share that our ENCODE enhancer–gene mapping paper is now out in Nature! An encyclopedia of human enhancer–gene regulatory interactions: www.nature.com/articles/s41... Thread 👇 1/

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 · last yr.

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

We are looking for someone to lead the new Facility for Protein Biochemistry & Biophysics at the MPI of Immunobiology and Epigenetics in Freiburg — please spread the word and apply if you are interested!

Max Planck Institute of Immunobiology and Epigenetics@mpi-ie.bsky.social · last mo.

🚀 Job alert: We’re starting a new Facility – and you can lead it! The MPI-IE & @mariekeoudelaar.bsky.social are hiring a Head of Protein Biochemistry & Biophysics to launch and lead a brand-new Core Facility in Freiburg 🇩🇪. Once-in-lifetime-chance. Details ⬇️ jobs.ie-freiburg.mpg.de/jobposting/b...

1/ Very excited to share the first publication from my lab! In this work, we developed an efficient strategy to precisely mutate mammalian histone genes in their native genomic context using CRISPR prime editing: www.nature.com/articles/s41...

Identifying critical lysines in mammalian histone H3 with high-throughput CRISPR prime editing - Nature Genetics

This study uses a precise and efficient clustered regularly interspaced short palindromic repeats (CRISPR) prime editing system to substitute lysine residues in histone H3, individually or in combinat...

nature.com

Myoglobin Fold (1987) by Irving Geis Used with permission from the Howard Hughes Medical Institute. All rights reserved. Learn more about Irving Geis and his his iconic images of DNA, hemoglobin, and other important macromolecules at PDB-101 pdb101.rcsb.org/sci-...

June 19 is World Sickle Cell Day. Sickle cell anemia is caused by change of a single glutamate to a valine in hemoglobin, which makes the protein prone to aggregation into long filaments. Image of Hemoglobin S by Irving Geis.

My department @eth-dbiol.bsky.social at ETH Zurich is hiring for a tenured professor in mol cell bio and biochemistry (associate/full). The position is within the Institute of Biochemistry (www.bc.biol.ethz.ch) and it is fairly open within their scope of research. www.nature.com/naturecareer...

Professor of Molecular Cell Biology and Biochemistry - Zurich, Switzerland job with ETH Zurich | 12861386

The Department of Biology at ETH Zurich invites applications for the above-mentioned tenured professorship at the Institute of Biochemistry

nature.com

Congratulations to #mdcBerlin researcher Altuna Akalin on his appointment as Professor of Bioinformatics and Health Data Science at Charité! The new W2 professorship recognizes his contributions to computational biology. More details: 👉 www.mdc-berlin.de/news/news/al... 👈 with @al2na.bsky.social