It's conference week in Cambridge. Yesterday I presented Corgi in the MIT/MGB AI Cures conference, and today I'm at the Broad Institute for the Variant to Function conference.

Delighted to finally announce a preprint describing the Q100 project! “A complete diploid human genome benchmark for personalized genomics” For which we finished HG002 to near-perfect accuracy: www.biorxiv.org/content/10.1... 🧵[1/14]

We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics. www.biorxiv.org/content/10.1... (1/n)

Just got my flu vaccine shot. Don't forget yours this season!

🥳 Thrilled to share that our lab has been awarded an ERC StGrant for our project SigReg: Signal to Regeneration! How can we unlock limb regeneration in adult mammals? It’s time to apply what we learned from 🐸 ➡️ 🐭 Thank you @erc.europa.eu for supporting ambitious science!!!

New ERC Starting Grant for Juliane Glaser to study role of epigenetic mechanisms, specifically the control of transposable elements, in mammalian embryonic development. Read all details here: www.ie-freiburg.mpg.de/6057908/2025... Congratulations @julianeg.bsky.social @erc.europa.eu #ERCStG

Wavefunction Collapse xkcd.com/3134/

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.

If you like transcription regulation and its mechanisms, this WIP list is for you. I'm sure I've forgotten lots of people, so don't hesitate to let me know so I can add you to the list. go.bsky.app/8vTgeXB

Climate warming is not a recent phenomenon; it has had detectable impacts on plants for at least 134 years! The onset of phenological plant response to climate warming @newphyt.bsky.social nph.onlinelibrary.wiley.com/doi/10.1111/... 🧪🌎🌿🌐🌳 🍁 #PlantBiology @cideinvestiga.bsky.social @csic.es

Looking forward to spending the next couple of months at MIT, collaborating with @bergerlab.bsky.social on deep learning methods in computational biology!

@jengreitz.bsky.social l & my lab want to co-hire a computational biologist/biostatistician with project management expertise to help map the regulatory code of the human genome and discover genetic mechanisms of disease. Details below careersearch.stanford.edu/jobs/computa... Plz RT

Honored to receive the @isrbio.bsky.social Rising Star Award for our work in regeneration biology! Grateful to the committee and our colleagues for the recognition. A huge motivation for the lab. Excited to give the award talk in Madison next week and connect with everyone! 😎🥳🍾 shorturl.at/LnkSt

I really dislike how science has started calling almost any fancy computational technique AI. 🧪 The framing of this entire article makes it sound like a benevolent AI independently made these drugs. That is *pure fantasy*. Instead: a team of scientists made a machine learning model for a study.

Hiding in plain sight - how close are we to mapping ALL 🧬enhancers🧬 in the genome? Our new paper by Mannion et al. takes a systematic look at "hidden enhancers" and why they remain so hard to find. With @mosterwalder.bsky.social, @jlopezrios.bsky.social & many more www.nature.com/articles/s41...

Our paper is now out in final form at Nature Genetics! For those who missed the preprint, we used large-scale Perturb-seq targeting transcription factors to push primary fibroblasts into diverse transcriptional states, including those observed in cell atlas studies.

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! 🧵

🧬 New study from the Kinkley Lab! 🧬 In collaboration with the Vingron and Hnisz labs at the MPIMG the team has gained new insights how the epigenetic reader PHF13 regulates it´s affinity to bind to chromatin. Read more: www.molgen.mpg.de/2025-07-28-o... Congrats to first author Francesca Rossi!

Director at Max Planck - a unique position! The Open Call for Expressions of Interest in Max Planck Directorships is open now and can be submitted by the 31st of October 2025. ➡️ mpg.de/directors - Please share the Open Call among potential candidates.

A resource of RNA-binding protein motifs across eukaryotes reveals evolutionary dynamics and gene-regulatory function go.nature.com/4mc1SmQ

Very excited that our most significant work, a collaboration w/ Dr. Can Cenik at UT Austin on translational gene regulation, was finally published in Nature Biotechnology in a dual set of studies: Paper 1 -- an AI model trained to predict translation rates from mRNA sequences: rdcu.be/exN1l

I'm excited to share work on a research direction my team has been advancing: connecting machine learning derived genetic variant embeddings to downstream tasks in human genetics. This work was led by the amazing Divyanshi Srivastava! www.biorxiv.org/content/10.1...

I will present my recent work Corgi, a context-aware sequence-to-activity model, at the IMSB/ECCB 2025 next week at the RegSys track. Send me a message if you want to meet! #ISMBECCB2025

How did the bat get its wings? New research from a collaboration between the labs of Stefan Mundlos (MPIMG), Dario G. Lupiáñez, and Francisca M. Real (@cabd-upo-csic.bsky.social) show how genetic programs were reused during the evolution of mammalian flight. --> www.molgen.mpg.de/news-2025-fl...

Finally out! 🥳 Our paper showing how a transposable element (TE) insertion can cause developmental phenotypes is now published @natgenet.nature.com 🧬🦠🐁 Below is a brief description of the major findings. Check the full version of the paper for more details: www.nature.com/articles/s41588-025-02248-5

Our paper describing the Range Extender element which is required and sufficient for long-range enhancer activation at the Shh locus is now available at @nature.com. Congrats to @gracebower.bsky.social who led the study. Below is a brief summary of the main findings www.nature.com/articles/s41... 1/

We wrote a review on Transposable Elements (TEs) and almost all aspects of TE silencing and their roles in biological processes & disease. www.nature.com/articles/s41...

Job alert: Join us for a postdoc in AI in genetics at @EMBL Heidelberg! Great collaboration with @Adrian Cortes @GSK, aiming to develop new tools to elucidate genetic effects using population-scale cohorts and single-cell readouts. Please share! embl.wd103.myworkdayjobs.com/de-DE/EMBL/d...

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.

⚠️ I am really excited to share the work of Anastasios Balaskas, an excellent PhD candidate in the lab, with the wider world. Tasos made a significant advance: generating a stem cell-based embryo model that contains both posterior and anterior neural tissues of the late-stage gastrulating embryo.

@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/

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

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...

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

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...

Looking forward to Kathie Pollard talk on human variant interpretation this Wed. at the Kipoi seminar!

We're thrilled to introduce PromoterAI — a tool for accurately identifying promoter variants that impact gene expression. 🧵 (1/)

Some exciting news! 🥳👍 finally dropped our open-source AI model to predict translation rates from mRNA sequences online for free academic use! Hope it's widely used among RNA scientists! Code: github.com/Sanofi-Publi...; Model: zenodo.org/records/1537...; Preprint: www.biorxiv.org/content/10.1...

How to find Evolutionary Conserved Enhancers in 2025? 🐣-🐭 Check out our paper - fresh off the press!!! We find widespread functional conservation of enhancers in absence of sequence homology Including: a bioinformatic tool to map sequence-diverged enhancers! rdcu.be/enVDN github.com/tobiaszehnde...

My sympathy and support for all the international students and postdocs at Harvard. I can only imagine how scary this must feel. Stay strong. And if there's anything I can do to help those in compbio, please reach out. All of us need to rally to help them out. 1/

Our review "Predicting gene expression from DNA sequence using deep learning models" is finally out! 🤗

❗Don’t miss: Dr. Anna Alessandra Monaco, postdoc in the lab of Stefan Mundlos, will give a talk at the Pint of Science Festival about her research project entitled “Junk that shapes us: the Dark Genome's role in Evolution.” 👉 pintofscience.de @annaamonaco.bsky.social @stemundi.bsky.social