AI@HHMI drives AI-in-the-Loop Discovery — a new mode of research in which scientists' expertise and AI’s analytical power operate in a continuous loop — and holds Janelia-led, HHMI Investigator-led, and jointly led projects within a single initiative, so that collaboration is built into its structure rather than layered on. Infrastructure and methods built for AI-in-the-Loop work become available across the Institute, and insights from the wider HHMI community come back the same way. 

By placing AI at the center of iterative research cycles, we accelerate the pace at which scientists move from hypothesis to insight, unlocking new biological understanding and paths toward advances in human health. The initiative’s AI scientists, computational scientists, engineers, and robotics experts drive one of the most significant platforms on which HHMI science is built, and self-assemble into small teams that work closely with biological and biomedical scientists to help design and execute a wide range of ambitious, AI-based research projects.

Join Janelia’s Next Chapter

HHMI’s pioneering research center outside of Washington, DC, is designed to foster bold scientific exploration. Outfitted with state-of-the-art laboratories and shared resources, the campus is home to a vibrant scientific community. 

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AI-in-the-Loop 

We’re harnessing AI to help design experiments, build automated pipelines, collect high-quality data, and create generalizable learning models capable of inferring the underlying principles within that data.

Our AI experts, engineers, and computational scientists — working in close collaboration with our biological scientists — play a crucial role in creating and curating new datasets and integrating AI into all phases of scientific discovery. 

Current Projects

AI@HHMI projects have broad, dramatic implications for the acceleration of scientific discovery. 

Luke Lavis, Senior Group Leader at Janelia, and David Baker, HHMI Investigator at the University of Washington, will use AI-driven de novo protein design to create specific protein binders for bright small-molecule fluorophores. These novel proteins will be further elaborated into fluorescent indicators and fluorophore ligases, yielding a suite of advanced tools to enable breakthrough imaging experiments.

Read more about the flurophore binder design project and the new class of imaging probes called NovoTags.
Erick Matsen and Jesse Bloom, HHMI Investigators at the Fred Hutchinson Cancer Center, will develop AI models that promise to transform our ability to forecast how protein sequences evolve over time, with broad implications for immunology, virology, and protein design.
Gerry Rubin, Senior Group Leader at Janelia, will lead a project to accelerate production of molecularly annotated connectomes in fruit fly and fish brains by physically expanding tissue samples to achieve nanoscale resolution with light microscopy and using AI to analyze these images.
Alison Tebo and Srini Turaga, Group Leaders at Janelia, will apply AI to the design of genetically encoded metabolic sensors. They will leverage both existing and newly generated mutational data from fluorescent biosensors to develop AI models that predict sequence-function relationships and guide the design of improved biosensors. This approach will deliver optimized sensors for key metabolic targets while establishing a generalizable framework that dramatically reduces biosensor development time.

Read more about the biosensors project and what they’ve developed so far.
Jakob Troidlexternal link, opens in a new tab, AI Scientist at Janelia, will lead a team of scientists and engineers in developing next-generation AI-driven microscopy image analysis tools. This includes the curation and assembly of foundational, multi-modal microscopy datasets, alongside the design of AI models capable of generalizing across a broad spectrum of image analysis tasks.

Eric Gouaux and Mike Rosen, HHMI Investigators at Oregon Health & Science University and UT Southwestern, respectively, plan to combine AI with novel experimental strategies to interpret cryo-electron tomography (cryo-ET) images of elusive protein complexes within synapses and cellular nuclei.

Read more about the molecular architecture of protein assemblies project.
Rhiju Das, HHMI Investigator at Stanford University, will lead a project that integrates AI with gigascale biochemical datasets and internet-scale crowdsourcing to advance RNA 3Dstructure prediction.
Michael Reiser, Senior Group Leader at Janelia, and Mark J. Schnitzer, HHMI Investigator at Stanford University, will develop autonomous robotic systems for dextrous handling and experimenting with individual Drosophila. When paired with AI-in-the-loop experiment control, the platform will remove the manual bottleneck in fly preparation and enable previously infeasible large-scale screening across genetics, behavior, and neural function

Misha Ahrens, Senior Group Leader at Janelia, will lead a team of researchers using AI to build biologically grounded models of larval zebrafish that link cellular activity in the brain and body with neural connectomes, behavior, and learning.
“For almost two decades, Janelia has pushed AI to crack hard biological questions. Where else can you watch an animal hunt in VR, record its whole brain, and then map its connectome? Mind-blowing neuroscience, tools, computation, and theory to make sense of it — all under one roof. AI@HHMI scales that up: industry’s nimble, project-focused teams plus academia’s intellectual freedom, both pointed at fully open science and deep understanding.”

— Stephan Saalfeld
Head of AI@HHMI

 

Join our ai@hhmi Team

We’re hiring a dedicated team of AI scientists, AI engineers, robotics engineers, and data scientists

Our AI scientists self-assemble into small teams and work closely with scientists from across the broader HHMI community — HHMI Investigators, Freeman Hrabowski Scholars, Janelia-based scientists, and more — to help design and execute a wide range of ambitious, AI-based biomedical research projects.

Projects are reviewed regularly by HHMI and Janelia leadership, and the most promising ideas are implemented using Janelia’s unique Project Team system, which enables the execution of projects larger than any single lab can perform on its own. This flexible, collaborative structure allows us to quickly and efficiently pursue the best ideas as they arise, and to direct resources to new projects when older ones are complete.

Learn more about working at Janelia. 

Current Openings

AI Scientist – Computational Chemistry

AI Scientist – Protein Structure and Function

AI Engineer - AI+CryoETexternal link, opens in a new tab
OTHER hhmi janelia INITIATIVES
Theory@HHMI

Guiding biological inquiry by distilling complex systems into concepts that are precise enough to test, and general enough to transfer. 

Biology

Building a mechanistic understanding of how vertebrate brains generate behavior — from molecular machinery and neural circuits to physiology, computation, and action.

Tools@HHMI

Opening new windows into biological insights through technologies built to observe living systems with unprecedented precision and scale.
 
HHMI Careers
Janelia Research Campus

HHMI’s pioneering research center outside Washington, DC, is designed to foster collaboration and bold scientific exploration. The campus — outfitted with state-of-the-art laboratories, shared resources, and more — inspires a vibrant scientific community. A wide range of housing options are available to Janelia employees and visiting scientists.

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