New online! Decoding the regulatory genome with large-scale deep learning
Nature Reviews Genetics, Published online: 03 November 2025; doi:10.1038/s41576-025-00914-2In this Journal Club, Peter Koo reflects on the 2021 publication of Enformer and its impact on the use of deep learning for modelling the regulatory genome.
We find regulatory DNA is readily reprogrammable with a few key mutations! We observed similar phenomenon across all genomic DNNs we tested! 12/N
Check out the paper to find out more!
Code: github.com/evanseitz/se...
Paper: www.biorxiv.org/content/10.1...
Peter Koo
Peter Koo
Beware of LLM blindspots. #AI4Science
SEAM is a powerful tool that helps to: 1) explore the high evolvability landscape of regulatory sequences; 2) identifies mutations that drive mechanistic changes; and 3) dissect motif syntax and context dependencies. 11/N
Exciting symposium on AI and Biology at EMBO | EMBL in Heidelberg on 10-13 March 2026!
Excellent lineup of invited speakers across various scales of biology!
Deadline for abstract submission is coming up ā Dec 2.
š www.embl.org/about/info/c...
#EESAIBio @EMBLEvents
Save the date: The premier AI x Bio meeting of 2026 will be held at CSHL on May 26-31!
The program brings together 50+ invited leaders in genomics, transcriptomics, protein design, drug discovery, neuro-AI, pathology, agentic AI, and more!
Abstract due: March 26
meetings.cshl.edu/meetings.asp...
This was led by @EESeitz
, a former postdoc who was jointly advised by me and Justin Kinney at CSHL, and also in collaboration with David McCandlish @TheDMMcC
It's a beautiful followup to SQUID, our surrogate modeling approach to interpret genomic DNNs!
www.nature.com/articles/s42...
Hello Bluesky!
Virtual registration is open for the 90th CSHL Symposium: AI in Biology!
Amazing lineup of speakers!
Join live on Zoom w/ Q&A, and access recordings on demand for ~48 hrs after each talk, with archive access pending speaker approval.
meetings.cshl.edu/virtualregis...
#cshlsymp26
Cold Spring Harbor Laboratory Meetings & Courses -- a private, non-profit institution with research programs in cancer, neuroscience, plant biology, genomics, bioinformatics.
Cold Spring Harbor Laboratory Meetings & Courses -- a private, non-profit institution with research programs in cancer, neuroscience, plant biology, genomics, bioinformatics.
The regulatory genome encodes the logic that governs gene expression, enabling cells to respond to developmental, environmental, and evolutionary cues. This logic arises from complex cis-regulatory me...
