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AbMAP, our work on adapting PLMs for antibodies, is now out in PNASNews. A veritable zoo of PLMs now exists, so why should you care? Well, AbMAP reflects an opinionated design philosophy about antibody representation. If that design fits your need, it may be great for you! 1/

“If we could help to stop drug companies from going into clinical trials with the wrong thing, it would really save a lot of money," says Math Prof MIT CSAIL Bonnie Berger Lab Bonnie Berger ’86, PhD ’90 MIT Science MIT Alumni MIT Dept of BE news.mit.edu/2025/new-compu…

Decoding the Functional Interactome of Non-Model Organisms with PHILHARMONIC 1. PHILHARMONIC introduces a novel computational approach to infer protein-protein interaction (PPI) networks and functional modules in non-model organisms. It leverages deep learning-based network

MIT CSAIL’s new generative model can efficiently create molecular dynamics videos 🧵 Their "MDGen" system emulates molecular dynamics, connecting static structures. It's an early step toward designing molecules w/desired dynamics.

“Machine learning methods that learn from physical simulation represent a burgeoning new frontier in AI for science”- Bonnie Berger ’86, PhD ’90 buy, re: MDGen tool that aims to emulate the dynamics of molecules Bonnie Berger Lab MIT Science MIT Alumni news.mit.edu/2025/toward-vi…

GenAI models can now create realistic video imagery of a dog wagging its tail, but what about reproducing the complex physics of molecular dynamics? #JameelClinic researchers propose a new model capable of predicting a molecule's trajectory. MIT News: news.mit.edu/2025/toward-vi…

Excited to share PoET-2, our next breakthrough in protein language modeling. It represents a fundamental shift in how AI learns from evolutionary sequences. 🧵 1/13

How can we enable collaborative genome-wide association studies while preserving privacy in biobank-scale datasets?Nature Genetics Bonnie Berger Lab "Secure and federated genome-wide association studies for biobank-scale datasets" • Sharing genomic data across institutions could

"Secure and federated genome-wide association studies for biobank-scale datasets" is out in Nature Genetics! Joint work with Hoon Cho and Hubaux. Read more: doi.org/10.1038/s41588…

Rapid and accurate prediction of protein homo-oligomer symmetry using Seq2Symm Nature Communications 1/ This study presents Seq2Symm, a deep learning model fine-tuned from ESM2 for predicting the symmetry of homo-oligomeric protein assemblies, outperforming template-based and prior deep

Note: our lab has also made a Bluesky! Follow here: bsky.app/profile/berger…. For now, lab members will post on both X and bsky.

A new approach to decipher the links between genomic proximity, chromatin conformation, and gene function. We leverage scGPT to derive better quantitative estimates and hypothesize a synergy between TADs and condensates. Joint w Rohit Singh & Huan Liang

Congrats Youn! and team, Bonnie Berger Lab Hultgren Lab Broad Institute @mit Georg K Gerber Brigham and Women's Hospital Mass General Brigham Research Harvard Medical School Ashlee M Earl