Principal Computational Scientist

Singleton Bio is an early-stage therapeutics company using generative AI models of human tissue to discover therapeutic targets in immunological and inflammatory diseases. Our mission requires strategic thinking, nimbleness, and deep expertise in several areas including computational biology, immunobiology, in vitro and in vivo pharmacology. This new startup company is recruiting for talented, experienced, and passionate individuals who are looking to meaningfully contribute to the creation of new medicines.

Our Cell Interaction Foundation Model (CIFM) or “virtual tissue model” platform is a geometric graph neural network trained on spatial genomics data from millions of human cells. Built on more than a decade of virtual cell and tissue modeling research, the model learns the relationship between a cell’s expression state and its tissue microenvironment, and is used to simulate how tissue responds to perturbations at scale.

Singleton is a fast-paced, dynamic environment where teammates will have broad exposure to the intersection of artificial intelligence-driven tissue models and drug development. We are rapidly building the Company and are looking for scientists to join us on this mission. Singleton Bio, located in South San Francisco, CA, is seeking an exceptional individual to join our team as a Principal Computational Scientist
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Singleton Bio is an early-stage therapeutics company using generative AI models of human tissue to discover therapeutic targets in immunological and inflammatory diseases. Our mission requires strategic thinking, nimbleness, and deep expertise in several areas including computational biology, immunobiology, in vitro and in vivo pharmacology. This new startup company is recruiting for talented, experienced, and passionate individuals who are looking to meaningfully contribute to the creation of new medicines.

Our Cell Interaction Foundation Model (CIFM) or “virtual tissue model” platform is a geometric graph neural network trained on spatial genomics data from millions of human cells. Built on more than a decade of virtual cell and tissue modeling research, the model learns the relationship between a cell’s expression state and its tissue microenvironment, and is used to simulate how tissue responds to perturbations at scale.

We are seeking a Principal Computational Scientist to help lead the development of the virtual tissue model as Singleton’s core discovery platform. As the company’s first computational hire, you will take ownership of the model, training data, in silico perturbation screens, and analysis pipeline to support target identification, next-generation model architecture, and downstream drug development applications. You will work closely with all members of the Singleton team including the CTO, who leads model architecture;

our Head of Computational Biology; and the pharmacology team.

This role suits a scientist who has trained deep learning models on single-cell or spatial data and has also taken responsibility for how those models are evaluated and used.

• Own the CIFM codebase and trained models on Singleton infrastructure, including training, inference, checkpointing, and versioning
• Retrain and adapt the model on Singleton’s growing spatial transcriptomics corpus, and assess where additional data or model capacity improves performance
• Design and run the benchmarks used to evaluate model performance, including baseline comparisons, patient- and section-level held-out splits, and out-of-distribution tests across tissues and assay platforms
• Characterize model limitations and uncertainty, and communicate them clearly to internal teams and external partners
• Run in silico perturbation screens to…