Head of Functional Genomics

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. We are hiring a Head of Functional Genomics to build and lead the functional genomics vertical from scratch.

The vertical covers the full pipeline: cell line engineering, perturbation library design, screen execution, and bulk and single-cell sequencing readouts, with the resulting data feeding customer pipelines that include foundation model training for virtual cell models. This is the second scientific vertical we are bringing online: manual development is starting now, and full autonomous execution on workcells is targeted for mid-to-late 2027.

You will own the screening menu, scope it against early customer demand, shape the workcells the screens will eventually run on, and build the team that operates the function at scale. You will be the senior functional genomics scientist in the company at hire.

About Substrate 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.

The role You will own functional genomics end-to-end. Day one priorities are the scientific pieces of standing up a vertical from scratch: scoping the priority screening menu against early customer demand, developing and validating those screens manually, setting quality thresholds, and hiring the Principal Scientists, Scientists, and Lab Technicians who will operate the function at scale.

The vertical will eventually span cell line engineering across catalogue lines and iPSC-derived models, perturbation library design and production, pooled screen execution, and bulk and single-cell sequencing readouts; the day-1 wedge is one end-to-end workflow through these stages, scoped narrowly to a focused starting subset within each, and you decide what that scope looks like.

Two parts of the role are not standard, and they are why this role is so crucial to Substrate’s success. The first is that the functional genomics vertical is being built AI-first from day one. Every screen is designed from scratch for full AI-in-the-loop automation, not retrofitted onto a manual workflow. You do the work by hand first, exactly as you would in a high-end pharma research lab, and then work with Automata’s automation scientists to shape the workcells the screens will eventually run on. You will define the quality thresholds for each transition stage, decide which manual judgement calls have to be re-engineered out, and own the validation that proves equivalence at each step.

The second is closed-loop work with foundation model partners. Substrate’s distinctive operating mode is producing structured, machine-readable experimental data fast enough to feed directly into foundation model training. That changes how functional genomics screens get designed: cell line provenance, library composition, perturbation metadata, sequencing QC, and consistency across runs become first-class scientific constraints. You will work directly with model partners on screen co-design, and with our software and intelligence teams on how the resulting data flows back into customer pipelines and into Substrate’s own data factory.

You will also be the executive partner to the co-founders on anything functional-genomics related: the screening roadmap, the proprietary functional genomics dataset programme on the reserved fraction of lab capacity, and the customer conversations where functional genomics depth is decisive.

What you will do in your first twelve months PHASE 0: NOW TO AUG 2026 Land in the lab. Set up workspace at our King’s Cross site and start manual screen development. Scope the day-1 wedge against early customer demand: which cell line, which perturbation library, which sequencing readout, validated as one end-to-end workflow before the menu starts to expand. Hire the first Principal Scientist and Lab Technician alongside you. Define the roles, run the processes, close the offers.

PHASE 1: SEP TO DEC 2026 Develop and validate the first screens manually. Set the reproducibility and quality thresholds that will serve as acceptance criteria for the moves to instrumented and to fully autonomous execution. Co-design protocols with the software and automation engineering teams so that the manual versions you validate are automation-ready by design. Decide which manual judgement calls have to be engineered out before they hit a workcell. Begin co-design conversations with the first commercial customers, including the foundation model partners coming online from mid-2027.

PHASE 2: JAN TO MAR 2027 Workcells arrive in the lab. Move the validated screens onto them, running with instrumentation and human intervention in the loop ahead of full autonomous operation later in 2027. Validate equivalence against the manual baselines. Grow the team. Bring on the second Principal Scientist and the first scientists at the bench to support throughput as the screening menu opens to customers. Ship the first revenue on the functional genomics vertical from manual and semi-automated services.

Who you are You are an experienced functional genomics scientist who has built or led a screening function at a biotech, pharma R&D, or CRO. You are comfortable in the detail at the bench and you are comfortable setting direction for a team. The shape of the problem is what attracts you: a screening portfolio that has to be designed for autonomous execution from day one, in a business where the data the lab produces is itself part of the product. You have hired and managed scientists, principal scientists, and technicians. You have set quality thresholds and held people to them. You have run screens that supported real customers, internal teams in pharma or biotech or external customers in a CRO setting, and you understand what enterprise-grade scientific operations look like. You are pragmatic about being hands‑on at the bench in the first six to nine months, and excited about the team you will build behind you. You enjoy interviewing, hiring, mentoring, and setting standards. You will be in the lab at our King’s Cross site at the cadence the science demands. That cadence will be heavy in the manual development phase and ease as the function grows and protocols move onto instrumentation. You are comfortable with that.

MUST HAVE Seven or more years of experience in functional genomics or related disciplines (target validation, perturbation screening), with at least three in a senior or team‑leading role at a biotech, pharma R&D, or CRO. End‑to‑end hands‑on experience in at least one screening modality (typically CRISPR knockout or CRISPRi knockdown), covering cell line preparation, library design, screen execution, and sequencing readout, with working familiarity across single‑cell readouts and validation workflows. Track record of leading a small scientific team end to end: hiring, setting quality standards, and managing performance against scientific outputs. Customer‑facing experience, either as a CRO scientific lead working with external customers, or as a pharma or biotech scientist embedded with internal customer teams.

NICE TO HAVE Hands‑on experience in cell line engineering, particularly iPSC differentiation or CRISPR‑edited stable cell line generation. Direct experience moving screens from manual workflows onto lab automation platforms. Familiarity with structured experimental data capture, LIMS, ELN, or analogous data infrastructure. Experience working with computational or AI/ML colleagues on closed‑loop perturbation programmes. Background at an AI‑native biotech or foundation model company.

Why this is unusual Most senior functional genomics roles in industry sit either inside a pharma R&D group (slow iteration, internal customers only), inside a CRO (external customers, faster iteration, but optimised for service throughput rather than scientific decisions about screen design), or inside an AI‑native biotech (fast iteration, but a single internal customer in the company’s own pipeline). This is none of the three. You will be designing a screening menu that has to be automation‑ready from the first manual experiment, working with foundation model labs on closed‑loop programmes that do not have a precedent in any of those settings, and owning the proprietary dataset programme that turns the lab itself into a commercial asset. It is also a functional genomics role with significant software and AI surface area. Your design decisions affect what the orchestrator has to do, what data flows back to model partners, and which manual judgements get re‑engineered out of the workflow. Some scientists find that energising; some find it outside their lane. Worth knowing in advance which one you are.

Compensation and equity We pay competitively against the London market for senior functional genomics scientists at venture‑backed companies, calibrated to seniority and to the specific scope of this role. We will discuss numbers with serious candidates after first conversations. Equity is meaningful, with vesting on the standard four‑year schedule and a one‑year cliff. We can talk through the philosophy and the maths in detail when we meet.

How we work Working pattern is hybrid with a strong in‑person bias dictated by the lab. In the manual development phase you will be at our King’s Cross site most days; this eases as the function grows, principal scientists are in seat, and protocols move onto instrumentation. Most of the founding team are in the office most days regardless. 30 days annual leave. A learning budget you can use for conferences, courses, books, and time. The founding team operates on a weekly cadence with a Monday planning meeting and a Friday close, and a quarterly offsite. We are direct with each other, we write things down, and we expect to be challenged.

The team you will join You will initially report to Alexey Morgunov, our science and AI focused co‑founder. We are recruiting a Founding Biology Lead, the co‑founder who will own scientific operations across the verticals; once they join, your reporting line will likely move to them. You will work most closely with the Head of Protein Science, who is being hired alongside you, and with the software and automation engineering teams on the boundary between scientific protocols and autonomous execution. You are the first protein‑science hire. Substrate is currently three co‑founders growing to roughly 32 people by the end of Q1 2027.

How to apply Apply via Ashby with whatever you think shows your work best: a CV, a published paper or technical report you are proud of, an example of an assay you have taken from idea to validated workflow. We read everything that comes in. Our process is three stages. An initial conversation with Alexey to understand what you want from the role and what we want from it. Followed by a technical session covering your scientific track record, the assay menu you would build, and how you would build and lead the protein science team. Finally, an in‑person founder‑team session at our King’s Cross site covering scope, terms, and any final questions. We aim to move fast on candidates we are excited about; expect roughly two to three weeks end to end. If you are not sure whether you are a fit, send a note anyway to alexey@substratebio.ai. The most useful conversations we have had so far have been with people who were not sure. Substrate is an equal opportunity employer. We make hiring decisions on merit, scope‑fit, and the strength of the working relationship we expect to build with each hire. Applications welcome from candidates of any background.