Protein Principal Scientist

The opportunity

Substrate is building a network of fully autonomous wet labs, cloud-based data production facilities for AI biology, integrated with foundation models to become the critical infrastructure layer for AI-driven biological discovery. Our first node opens in King’s Cross, London, with several integrated workcells and two scientific verticals online by mid‑2027. Our customers range from foundation model labs to global pharma.

Protein science is the first scientific vertical we are bringing online. The vertical covers expression and purification, biophysical characterisation, cell-based functional assays, and develop ability assays. Manual development of the day‑1 assay menu is starting now, and full autonomous execution on workcells is targeted for mid‑2027. You and the Protein Scientist will be the bench scientists who develop, validate, and operate the assays through that transition: running protocols by hand, setting reproducibility and quality thresholds, working alongside automation engineers as the assays move onto instrumentation, and validating equivalence at every step.

The Head of Protein Science you will work under is being hired alongside you.

Substrate is spinning out of Automata, the UK lab automation company that has built the workcell platform our labs run on. Our four co‑founders are Mostafa ElSayed (CEO and founder of Automata), Oli Hoy (formerly VP Customer Experience at Automata), Alexey Morgunov (AI Scientist co‑founder, leading the intelligence software product), and a Founding Biology Lead joining shortly. We are aiming to have ramped up to 32 people by the end of Q1 2027.

We are funded in parallel by a combination of venture funding and government grants. We are not a cloud lab and we are not a CRO. We are an autonomous lab platform with closed‑loop integration available as one operating mode for foundation model partners.

You will be at the bench. The work is to develop, validate, and operate the assays that will eventually run autonomously on Substrate’s workcells. In the first phase, that means manual assay development: running protocols by hand, setting reproducibility and quality thresholds, and proving each assay out before it moves onto instrumentation. As the workcells arrive, the work shifts toward instrumented execution, equivalence validation, and the engineering judgement calls that decide which manual steps get automated and which stay in human hands.

You will own a slice of the assay menu end to end: scoping it with the Head, designing the manual protocol, validating it to acceptance thresholds, authoring the SOPs that translate to workcell design, and seeing it through to automated execution. Scientists will work alongside you at the bench, executing the experiments, contributing to validation work, and growing into protocol authorship over the first year.

You will work directly with our automation engineering and software teams on the boundary between scientific protocols and autonomous execution.

What is unusual about the work is that no assay in this vertical is being retrofitted onto automation. Every protocol is designed for AI‑in‑the‑loop execution from the first manual run. The data each assay produces – output structure, metadata, provenance, consistency across runs – is treated as a first‑class scientific constraint, because that data feeds directly into foundation model training pipelines for our customers.

Your decisions at the bench affect what the orchestrator has to do and what data flows back to model partners.

• Land in the lab. Set up your bench at our King’s Cross site and start manual assay development alongside the Head of Protein Science.
• Get hands on the first priority assays as the day‑1 menu locks. Run protocols by hand, capture the data structure and metadata decisions that will translate to workcell design.
• Contribute to the day‑1 menu decisions and begin authoring SOPs for your slice of the assay portfolio. Help interview the Scientists and Lab Technicians joining alongside.

• Develop and validate the first protein…