Research

Research Areas

Advancing computational biology through four interconnected research directions, each powering one of our foundation models.

Knowledge-Guided Discovery

Multi-modal knowledge extraction from scientific literature, databases, and experimental data. Our Research model leverages structured and unstructured biological knowledge to surface insights that would take human researchers months to compile.

Applications

Pathway DiscoveryLiterature MiningExperimental DesignKnowledge Graphs

Related Open-Source Tools

Physics-Informed Dynamics

Thermodynamically-constrained cellular behavior modeling that respects fundamental biological principles. Our Dynamics model learns from diverse cellular data while enforcing physical plausibility for reliable predictions.

Applications

Metabolic Flux PredictionBioprocess OptimizationScale-Up ModelingGrowth Forecasting

Related Open-Source Tools

Genetic Information Flow

Multi-scale modeling from DNA to RNA to protein, capturing the full central dogma of molecular biology. Our Central Dogma model predicts how genetic sequences translate into functional proteins with quantified confidence.

Applications

Codon OptimizationExpression PredictionProtein EngineeringRegulatory Element Design

Related Open-Source Tools

Design Space Optimization

Efficient navigation of combinatorial genetic design spaces using advanced optimization and generative methods. Our Perturbation model suggests minimal, high-impact edits to achieve desired phenotypes across multiple objectives.

Applications

Strain OptimizationMulti-Objective DesignMinimal Perturbation StrategiesTrade-Off Analysis

Related Open-Source Tools

Publications

Coming soon. Our team is preparing manuscripts for submission.

In the meantime, explore our open-source tools which demonstrate our research methods.

Explore Our Open-Source Ecosystem

Our research is grounded in open-source tools built on JAX/Flax NNX, freely available under the MIT license.

Interested in Collaborating?

We work with academic labs and industry partners to advance computational biology. Get in touch to explore collaboration opportunities.