Still time to apply until January, 19th!

🧬 @science.org A SWI/SNF-specific Ig-like domain, SWIFT, is a transcription factor binding platform | Science www.science.org/doi/10.1126/... @ckadoch.bsky.social @danafarber.bsky.social @harvardmed.bsky.social @broadinstitute.org @hhmi-science.bsky.social 🔬 #chromatin #transcription #cancer 🧫

Describe your neurons like the Allen Institute! 🧠📈 Join us at our Cell Types Workshop to learn how we define cell types  and how to use our research tools. Programming experience not required. 🗓️ Apr. 6-8 in Seattle ⏳Apply by Jan. 9 🔗 https://alleninstitute.org/events/2026-cell-types-workshop/

Looking to start your lab in generative biology / AI? Come join us at the @sangerinstitute.bsky.social Sanger is core-funded so you can generate data at scale to train the next generation of models and understanding. Design/Engineering/Chemistry/Proteins/Pathways! pls RT tinyurl.com/GenGenFaculty

Bento: Benchmarking Classical and AI Docking on Drug Design-Relevant Data [new] Classical & AI Docking Benchmarking: Evaluates docking tools on drug design data. Key aspects: curated data, generalization limits, pocket similarity.

Intrinsic DNA sequence determinants and tissue-specific regulation of human replication origins [new] DNA seq. grammar predicts replication start. Tissue specificity via chromatin access + genetic code mods.

A foundational model for joint sequence-function multi-species modeling at scale for long-range genomic prediction https://www.biorxiv.org/content/10.64898/2025.12.22.695963v1

A foundational model for joint sequence-function multi-species modeling at scale for long-range genomic prediction [new] U-Net: Representation learning, prediction, & controllable seq. gen. using genomic data.

Our new preprint is out: www.biorxiv.org/content/10.6... We show that GRN benchmarks commonly used can overestimate performance due to negative-sampling choices, sometimes allowing simple degree-based baselines to rival more complex GNNs. A reminder of why bias-aware evaluation matters!

Our preprint "Predictive design of tissue-specific mammalian enhancers that function in vivo in the mouse embryo" is on bioRxiv: www.biorxiv.org/content/10.6... . Amazing collaboration by @shenzhichen1999.bsky.social, Vincent Loubiere (@impvienna.bsky.social,@viennabiocenter.bsky.social),... (1/2)

Pooled single-cell CRISPRa/i screens for functional genomics in bacteria at scale [new] Pooled CRISPRa/i screens with scRNA-seq overcome bacterial data sparsity. It maps gene function, regulatory networks, & interactions at scale.

While stories of singular DNA changes that drove evolution of human brain/behaviour remain seductive, advances across multiple fields of biology cast doubt on such simplistic narratives of our origins. A new paper from my lab shows how biobanks may speak to this fundamental question.🧪 Explainer🧵👇1/n

We (@sobuelow.bsky.social & @kejohansson.bsky.social) tested AF-CALVADOS using the recently described PeptoneBench SAXS benchmark that contains SAXS data for >400 proteins with different amounts of order and disorder. The results look pretty good 😇 so we are sharing here while updating the preprint📝

🚀 New preprint! The Human Cytokine Dictionary - 9.7M cells, 12 donors, 90 cytokines - our largest human single-cell perturbation atlas yet. Users can map cytokine activity in their own data. Huge thanks to Lukas, Sören, Larsen, Parse Bio & Seelig lab! 🔗 www.biorxiv.org/content/10.6...

Fine-scale chromatin mapping uncovers principles of cis-regulatory element interactions. #NBThighlight www.cell.com/cell/fulltex...

Can one map the genome-wide binding (1) and its protein partners (2) simultaneously from the same sample? Yes, one can. with CUT&ID ✂️🪪 Spearheaded — singlehandedly — by @annanordin.bsky.social No need of transgenesis, cloning and overexpression. Check it out, it's fast and its works.

GWAS has been an incredible discovery tool for human genetics: it regularly identifies *causal* links from 1000s of SNPs to any given trait. But mechanistic interpretation is usually difficult. Our latest work on causal models for this is out yesterday: www.nature.com/articles/s41... A short🧵:

Had an amazing first year at Center SynGen @zmbh.uni-heidelberg.de! Building a computational group in an experimental institute sparked more collaboration than I imagined. If you love comp bio and working with amazing scientists, this role is a huge chance. Curious? Reach out! t.ly/udiwJ

A few py2Dmol updates 🧬 py2dmol.solab.org Integration with AlphaFoldDB (will auto fetch results). Drag and drop results from AF3-server or ColabFold for interactive experience! (1/4)

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.

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/