Excited to share Nona: a unifying multimodal masking framework for functional genomics. Models for DNA have evolved along separate paths: sequence-to-function (AlphaGenome), language models (Evo2), and generative models (DDSM). Can these be unified under a single paradigm? 1/15

This is such an interesting paper. Why? Because the binding of transcription factor (TF) proteins to DNA governs how our genes are turned on/off/up/down, & so is the primary issue for how our genes work in development and how our cells respond to just about anything.🧵 www.nature.com/articles/s41...

The low-affinity sites overlap in interwoven ways, making them a sort of selection committee that decides whether or not prospective TFs are granted access to the high-affinity site. Here's how the authors depict it. /6

Robust footprinting with sample-specific Tn5 bias correction for bulk and single cell ATAC-seq [new] Corrects Tn5 bias in ATAC-seq; improves footprinting, finds elements & reduces false positives.

Did transposable elements shape brain evolution — and if so, which ones, and in which cell states and lineages? Led by @tyamadat.bsky.social, we explored this question in cerebellum development using sequence-based deep learning models! www.biorxiv.org/content/10.1...

Gene regulatory innovations from transposable elements in mammalian cerebellum development [new] Cerebellum gene reg. driven by TEs, w/cell-type & sp.-specific expression, esp. primate HERVL in granule cells.

Very happy to see this work finally online 🥳 It was really interesting to write a short manuscript mixing method presentation & broader insights on data preprocessing. 📝 Thank you to my co-supervisors @cantinilab.bsky.social & @juliosaezrod.bsky.social for their feedback on this side work! 🫶 5/5

Experiment-guided AlphaFold3 resolves accurate protein ensembles [new] AlphaFold3, by integrating NMR, X-ray, or cryo-EM data, can generate accurate protein conformation ensembles reflecting experimental conditions.

15 years in the making, we confirmed that mitochondria - the powerhouse of the cell - have an unusual localization in patients who experience psychosis (including schizophrenia and bipolar disorders). You’ll never guess what kind of patient cells we used to make this discovery… 🧵

Which mutations rewire function of regulatory DNA? Excited to share SEAM: Systematic Explanation of Attribtuion-based Mechanisms. SEAM is an explainable AI method that dissects cis-regulatory mechanisms learned by seq2fun genomic deep learning models. Led by @EESetiz 1/N 🧵👇

Excited for a major milestone in our efforts to map enhancers and interpret variants in the human genome: The E2G Portal! e2g.stanford.edu This collates our predictions of enhancer-gene regulatory interactions across >1,600 cell types and tissues. Uses cases 👇 1/

Excited to see our review now on arXiv, written together with @fpesce.bsky.social and @lindorfflarsen.bsky.social doi.org/10.48550/arX...

Wow, more than 2.4M of assembled bacteria in the new release of ABT! We plan to index these using our efficient colored De Bruijn graph index, Fulgor. We recently conducted experiments with nearly 1M genomes…getting there :) www.biorxiv.org/content/10.1...

New preprint alert! Corgi imitates cellular gene regulation and integrates DNA sequence and trans-regulator information. This allows Corgi to make accurate predictions in unseen cell types. Also, it can simulate trans-regulator perturbations in silico.

Wow, maybe genomic imprinting as we know it is just the tip of then iceberg. Hopefully this helps usher in a wave of mechanistic studies www.nature.com/articles/s41...

This is not a HiC map! Ever wondered if multiple enhancers get activated simultaneously? We measured chromatin accessibility on thousands of molecules by nanopore to create genome-wide co-accessibility maps. Proud of @mathias-boulanger.bsky.social @kasitc.bsky.social Biology in the thread👇

Joint decomposition of Hi-C maps reveals salient features of genome architecture across tissues and development [new] Hi-C jointly decmp. samples: captures cell states, improves gene pred.

Excited to see this published with additional data following our preprint a while back. Cool combination (in our biased view) of controlled TF expression and machine learning to decode chromatin sensitivity. www.sciencedirect.com/science/arti....

www.sciencedirect.com/science/arti... Check this: A scar-free strategy enables seamless editing of multi MB regions without residual sequences

Excited to share work with Zhidian Zhang, @milot.bsky.social, @martinsteinegger.bsky.social, and @sokrypton.org biorxiv.org/content/10.1... TLDR: We introduce MSA Pairformer, a 111M parameter protein language model that challenges the scaling paradigm in self-supervised protein language modeling🧵

Our paper benchmarking foundation models for perturbation effect prediction is finally published 🎉🥳🎉 www.nature.com/articles/s41... We show that none of the available* models outperform simple linear baselines. Since the original preprint, we added more methods, metrics, and prettier figures! 🧵

To all post-docs: The Genome Biology dept ‪@embl.org has an Independent faculty position. Fantastic place to set up your lab –great package: core funding, fantastic Ph.D. students, cutting edge core facilities & great colleagues. Closing date Sept 19th embl.wd103.myworkdayjobs.com/en-US/EMBL/j...

In a new Perspective article, Josh Morgan discusses how progress in cell biology is hindered by significance testing and the need for a shift to effect size estimation. rupress.org/jcb/article/... #Technology #Reproducibility #CellCycle #CellDivision #Statistics

Thrilled to co-advertise this postdoc or PhD position with @erhardtlab.bsky.social! Join us, if RNP assembly on centromeres, RNA modifications, & bioinformatics are your thing. More info also on modiclab.org.

🧪 Open PhD or Postdoc position 🧪 The project is in collaboration with my new collegue Miha Modic. If you are interesed in RNA modification, centromeres and bioinformatics this is for you! Miha has more positions to fill, infos on his linkedin: linkedin.com/in/miha-modic-9aa8a752.

Everyone working in a STEM field should read this - ‘writing is thinking’ www.nature.com/articles/s44...

Wang et al, 2025. Genome-Wide Investigation of Transcription Factor Occupancy and Dynamics Using cFOOT-seq www.biorxiv.org/content/10.1...

Staff scientist position (computational): I am looking for a computational scientist to join my genomics lab at Stanford. They should have an outstanding skillset in ML/statistical methods for genomic applications, postdoc experience and a strong publication record. #sciencejobs

’We couldn’t live without it’: the UCSC Genome Browser turns 25. #UCSC #GenomeBrowseer #Bioinformatics #Genomics #TechnologyFeatures @nature.com 🧬 🖥️ www.nature.com/articles/d41...

Now I've looked more closely at these two recent papers in Nature, and they are both excellent examples of why we need new narratives for talking about molecular biology to non-specialists. 🧵 www.nature.com/articles/s41... www.nature.com/articles/s41...

How do non-coding variants in enhancers lead to disease? Happy to share our recent work, led by @ewholling.bsky.social, in which we discovered that poised chromatin sensitizes enhancers to aberrant activation by non-coding mutations, contributing to disease. www.biorxiv.org/content/10.1... 1/

We are delighted to share our new preprint “The evolution of gene regulatory programs controlling gonadal development in primates” www.biorxiv.org/content/10.1...

@saramostafavi.bsky.social (@Genentech) & I (@Stanford) r excited to announce co-advised postdoc positions for candidates with deep expertise in ML for bio (especially sequence to function models, causal perturbational models & single cell models). See details below. Pls RT 1/

Last week I released bpnet-lite v0.5.0. BPNet/ChromBPNet are powerful models for understanding regulatory genomics from @anshulkundaje.bsky.social's group, and now it's way easier to go from raw data to trained models and analysis + results in PyTorch Try it out with `pip install bpnet-lite`

Textbooks: “Enhancers are just a bunch of TFBSs” But how do they REALLY work? New paper with many contributors here @berkeleylab.lbl.gov, @anshulkundaje.bsky.social, @anusri.bsky.social A 🧵 (1/n) Free access link: rdcu.be/erD22

In vivo mapping of mutagenesis sensitivity of human enhancers www.nature.com/articles/s41...

Are you interested what proportion of differentially expressed genes in bacteria can be explained by cis non-coding variants? Then head over to our latest preprint, in which Bamu used her dry- and wet-lab skills to answer this and other related questions! www.biorxiv.org/content/10.1...

Excited to share my first PhD paper in the @sbmontgom.bsky.social lab with @tamigj.bsky.social (www.biorxiv.org/content/10.1...)! Standard QTL methods treat each gene independently. But what if a single variant regulates multiple nearby genes at once - what we call “allelic proxitropy”? 🧵 ⬇️

You can now view #VariantEffect25 presentations from @pollyfordyce.bsky.social @davidjadams.bsky.social @nickywhiffin.bsky.social along with many many others! on our YouTube channel www.youtube.com/@cmap_cegs84... (hat tip to @isabellease.bsky.social for the excellent illustrations)

Universities hold patents on 50% of FDA approved drugs, and research done at universities contributed to 90% of current medications. Think about what we stand to lose if federal funding is cut by 50% 🧪 www.statnews.com/2025/06/06/u...

Released a new version of my little data processing tool, `bam2bw`. As you might expect, it goes directly from BAM to un/stranded bigwig(s), but now also supports fragment.tsv files. No more intermediary sorting and bedGraph steps! Way faster + less disk than before. github.com/jmschrei/bam...

These are not just grants. This is thousands of people who devoted their lives and careers - taking pay cuts, working long hours, living with uncertainty - all for the chance to try to make people's lives a bit better for you and your loved ones. This breaks my heart.

This is your health on MAGA.

I wrote a quick application note on Tomtom-lite, a Python implementation of the Tomtom algorithm for comparing PWMs against each other. This implementation can be 10-1000x faster and, as a Python function, can be integrated into your workflows easier. www.biorxiv.org/content/10.1...

1/ DNA sequence models like Borzoi predict gene expression and variant effects across tissues — but how can someone adapt the model to a custom experiment? @drkbio.bsky.social, Johannes Linder and I propose a solution via parameter-efficient fine-tuning (PEFT). www.biorxiv.org/content/10.1...

Delighted & excited to share our latest preprint on non-canonical enhancers in human pluripotent stem cells, the result of a fantastic and fun collaboration with @guenesdoganlab.bsky.social‬: www.biorxiv.org/content/10.1... 🧵 below

Please check out our new approach to modeling somatic mutation signatures. DAMUTA has independent Damage and Misrepair signatures whose activities are more interpretable and more predictive of DNA repair defects, than COSMIC SBS signatures 🧬🖥️🧪 www.biorxiv.org/content/10.1...

50 Years of Cell Biology: German Society for Cell Biology Meeting, October 26 – 29, 2025 | Heidelberg, Germany Early bird registration deadline: June 15, 2025

New method drop: HCR-Proxy, a modular proximity labelling approach to profile local proteome composition around RNA at nanoscale, subcompartmental resolution. Thereby we resolved nested nucleolar layers and uncovered the grammar of spatial protein partitioning. www.biorxiv.org/content/10.1...

Joint probabilistic modeling of pseudobulk and single-cell transcriptomics enables accurate estimation of cell type composition https://www.biorxiv.org/content/10.1101/2025.05.28.656123v1