"Here we describe a systematic effort (‘Codebook’) to determine the sequence specificity of 332 putative and poorly characterized human TFs." www.nature.com/articles/s41...

An expanded codebook of human transcription factor DNA-binding specificity - Nature

Results from a panel of assays that analyse different aspects of DNA sequence specificity reveal more than 100 new motifs to aid the characterization of putative human transcription factors.

nature.com

Congratulations to CRG's @benlehner.bsky.social on receiving the 2026 Premio Rei Jaume I for Biomedical Research. The award recognises his pioneering discoveries on genetic variation, evolution and disease, helping transform our understanding of biology and human health. #genomics #genetics #CRG

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...

One of the major pains of academia is having to click through labyrinths of webpages to submit papers. Now, thanks to Joe Rich (and AI), problem solved! His tool is called PaperPush and is available at github.com/pachterlab/p... It's super easy to use! 1/🧵

GitHub - pachterlab/paperpush

Contribute to pachterlab/paperpush development by creating an account on GitHub.

github.com

The Chen Lab @ EMBL Rome (current population: 1) is hiring! Looking for an experimental Lab Manager w/ a PhD and experience in molecular bio and mouse-based neuro research. Apply if you like: mouse behaviors, high-throughput sequencing, good coffee & ancient history tinyurl.com/48h66vfh

Lab Manager

The European Molecular Biology Laboratory (EMBL) is one of the world’s leading life science research organizations. With sites across Europe, EMBL fosters an international, collaborative, and inclusiv...

tinyurl.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... 🧵

scWeave: A deep learning model that bidirectionally translates between gene expression and chromatin structure at single cell resolution https://www.biorxiv.org/content/10.64898/2026.07.13.738265v1

We just started our summer break, but we're also planning our September-December seminar schedule! If you have an exciting chromatin/transcription story that will be ready for the spotlight by then, use the survey below to nominate yourself to give a #FNucleosome talk 🧬🧬 forms.gle/1EKYN2Nt79ar...

Application to speak in the Fragile Nucleosome series

Thank you for your interest in our seminar series! We use a variety of different session formats but, in general, trainees can plan for a ~15 min talk + 5min Q/A and PIs can plan for a ~25min talk +...

forms.gle

“move from preprint to peer-reviewed publication leaves the central claims of most abstracts intact, indicating preprints are a reliable source…papers that were never posted as preprints were retracted at roughly twice the rate of those that were…” www.biorxiv.org/content/10.6...

Tracking claim changes from preprint to publication across 72,644 biomedical studies using large language models

Preprints now disseminate a large share of biomedical research before peer review. Because they have not yet passed peer review, some scientists regard preprint claims as unverified or potentially unr...

biorxiv.org

This year, mostly same content, I gave students mini Chocolate bars to complete the survey in class. No conditions for how they rated the class and honor system that they completed survey at all. Way better ratings than previous years.

Daniel Munro@dkmunro.bsky.social · 2mo ago

Once had a chance to do an interesting A/B test in two sections of the same class. In both, all the same content, engagement, standards, etc. But I saved my best irrelevant-to-the-course jokes for one section. Guess which was rated higher?

Large-scale, spatially resolved panoramic CRISPR screening in native tissue environments using Perturb-DBiT -@rongfan8.bsky.social @yaleschoolofmed.bsky.social www.nature.com/articles/s41...

Large-scale, spatially resolved panoramic CRISPR screening in native tissue environments using Perturb-DBiT - Nature Biotechnology

In vivo CRISPR genetic perturbations are spatially mapped at scale.

nature.com

Great preprint by @vram142.bsky.social & Co www.biorxiv.org/content/10.6... "fiber homotypy," where chromatin fibers with similar nucleosome spacing interact more frequently in 3D --> Related to our previous "nucleosome homology recognition" in chromatin royalsocietypublishing.org/rsif/article...

Brutal IP burn: "You have ordinary skill in the art."

We had similar findings (not emphasized in the publication) in our study of variant characterization at TNFAIP3. Different "monocyte" cell lines looked very distinct. "B cell" lines looked very distinct. Cell lines are often bad proxies for primary cells in terms of gene regulation.

bioRxiv Genomics@biorxiv-genomic.bsky.social · 2mo ago

Deciphering the limitations of immortalized hepatocyte cell lines for the study of liver cis-regulatory elements https://www.biorxiv.org/content/10.64898/2026.06.05.730479v1

Gigabase-scale deletion scanning of the human genome https://www.biorxiv.org/content/10.64898/2026.05.29.728882v1

Understanding where genomics models work and fail will be critical to their successful deployment. Meta models can tell us this, and give some insight into failure modes. 3/3 for @muntakimrafi.bsky.social this week. CSHL AIxBIO to boot (sorry to miss!) What a week!

Abdul Muntakim Rafi@muntakimrafi.bsky.social · 2mo ago

1/11 Seq2exp models can predict how any DNA variant changes gene exp.However, in reality,sometimes they nail it,sometime sthey get the direction flat wrong (true for every model).Right now you have no way to tell which is which for any single prediction. So we built one (gRely)

Which active learning methods are best for genomics models? See Rafi's thread on our recent preprint, below. www.biorxiv.org/content/10.6... Rafi is having a good week - he's got one more preprint to post!

Abdul Muntakim Rafi@muntakimrafi.bsky.social · 2mo ago

1/14 Sequence-to-expression (S2E) models keep getting better at reading cis-regulatory logic. But they haven't solved it. On tasks like variant effect prediction they're still far from accurate. Remember, solving cis-regulation is the goal and we're not going to settle for less!

There is widespread homology across our genomes. How does this impact genomics models? Major update to our preprint! 🎉 We tested more models and more tasks; the overall findings were robust, but one conclusion on how future models should be trained differs⚠️ www.biorxiv.org/content/10.1...

gRely: Relyability for genome trained sequence-to-expression models https://www.biorxiv.org/content/10.64898/2026.05.23.727431v1

Our Decima paper is now published in Nature Methods! Full text: rdcu.be/fkASS. Decima can predict gene expression in specific cell types and cell states from DNA sequence. I would say more but @drkbio.bsky.social and Johannes Linder wrote this great news & views: www.nature.com/articles/s41...

Decoding sequence determinants of gene expression in diverse cellular and disease states

Nature Methods - Decima learns to predict cell-type-specific gene expression based on DNA sequences, contributing to the analysis of gene regulation and design of context-specific regulatory elements.

rdcu.be

CIHR has launched a trial ballon that suggests shifting to one competition a year. This is the worst idea I have heard in a long time. The only benefit is making top-line success rates look better than they are. Keep it as is, do in-person reviews, and keep the pain in the open.

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 🧪 🧵👇

I think the LLMs finally found me. Got like 5 review requests this weekend.

🚨 New preprint! How does noncoding variation drive complex traits? We built a massive atlas of cattle regulatory variants (>150k emVars!) and directly tested them in both bovine AND human cells. 🐄🧬🚶‍♂️ Read it here: www.biorxiv.org/content/10.6...

I think both journals and authors vastly underestimate the reputational harm that comes from sending bad papers out for review. Demonstrates disrespect for our time, and poor judgement. I remember it next time I am asked to review, and will rethink submitting to that journal.

Lee Zamparo@lzamparo.bsky.social · 3mo ago

Struggling desperately to get to the end of this dreadful paper I've been assigned to review. So, so boring.

It's been a long time coming to finally see this in print! While not the first paper from my lab, it is one of the very first projects we started working on from day 1 links.springernature.com/f/a/1IP7gCfA...

Pooled CRISPRi screening reveals fungal-specific drug target candidates - Nature Microbiology

This study presents a pooled CRISPRi screening approach in Candida albicans to investigate essential genes at scale, revealing environment- and strain-dependent gene sensitivities and conserved vulner...

links.springernature.com

"In this study, we present a genome-scale map of genetic interactions in the human haploid cell line HAP1, based on CRISPR-based perturbation of ∼4 million gene pairs. The resulting network comprises ∼89,000 high-confidence gene-gene interactions" doi.org/10.1016/j.ce...

Thrilled to have my first PhD paper with @mmdesai.bsky.social out! @science.org Link: www.science.org/doi/10.1126/... Thread below: #mevosky #evosky #evobio #popgen #evolsky #ecoevo #molevol

Sex decreases the pleiotropic costs of local adaptation by purging hitchhiking load

Understanding the evolutionary mechanisms that maintain sex despite its direct costs is a long-standing challenge. Previous work has shown that sexual recombination can accelerate adaptation, in part ...

science.org

Shreyas Pai@theshreyaspai.bsky.social · last yr.

Why is sex so common if it's so costly? Super excited to share our new preprint “Sex decreases the pleiotropic costs of local adaptation”, where we bring a new angle to this age-old evolutionary question. Co-led by Parris Humphrey, in Michael Desai's lab. Short thread here: (1/n)

New preprint @cxqiu.bsky.social @jshendure.bsky.social ! Can we learn regulatory grammars of human cell types — by training on mouse development and transferring across 241 mammalian genomes? Introducing STEAM & a whole-organism scATAC-seq atlas from E10 to birth. www.biorxiv.org/content/10.6...

Genetic background shapes AI-predicted variant effects [new] ...uncovering heterogeneous predictions where variants shift between pathogenic and benign outcomes across diverse genomic contexts, crucial for interpretation.