Member of Technical Staff, Intelligence - Functoional Genomics

Substrate Bio Ltd; Greater London; On-site; GBP 90,000 - 130,000; Full time

Benefits offered by this job

30 days annual leave

Pension 10% employer contribution

Bupa private health cover

Job summary

Substrate Bio Ltd in London is seeking a senior computational biologist to own the analysis of functional genomics data, collaborating with scientists designing and running CRISPR screens and multi-omics readouts.

You will build pipelines, QC, differential expression, and integrate proteomics, transcriptomics, and imaging readouts, ensuring reproducibility with the software team. The role is on-site at King’s Cross with regular lab time.

Qualifications

• A PhD, or a master’s with two to three years of relevant experience, in genomics, bioinformatics, computational biology, statistics or a related field.
• Strong Python or R, with good engineering habits such as Git, code review and reproducible workflows, and working with coding agents.
• Hands‑on single‑cell RNA‑seq analysis, for example with Scanpy or Seurat, including CRISPR screen QC such as guide assignment and knockdown efficiency.
• Statistical and machine learning methods on biological data, including linear and mixed models, multiple testing, and handling batch effects and confounders.
• Working closely with wet‑lab scientists, and explaining results clearly to people outside your field.

Responsibilities

• Own the analysis of functional genomics data and build pipelines that scale with throughput.
• Perform QC, guide assignment, differential expression analysis and modelling of perturbation effects.
• Develop an image‑based profiling pipeline and integrate multi‑omic readouts.
• Present results with uncertainty and QC to scientists and leadership, and collaborate with the software team to ensure reproducibility.

Skills

Python or R

Git

scRNA-seq

Statistics & ML

Interdisciplinary collaboration

Education

PhD or MSc with 2-3 years

Tools

Nextflow

Snakemake

Docker

AWS

Job description

LOCATION: King’s Cross, London · PATTERN: Hybrid, with regular time in the lab

The opportunityWe’re a stealth startup in AI and bio, building infrastructure for data generation. The team is small and elite, the problems are hard, and the foundations are being laid right now. You’d help write them from the first line, with real ownership and a direct line to the founders. This role owns the analysis of our functional genomics data. You would be the main computational partner to the scientists who run our perturbation screens, from how a screen is designed to which hits we call and how we show the evidence for them.

About usAI for biology has a data problem. The data that matters most doesn’t exist yet, so we’re building the infrastructure to produce it, with quality and traceability built in from day one. We’re in stealth and heads-down on execution. We’ll share more about what we’re building once you’ve spoken with the team.

The roleYou will join the intelligence team and own the analysis of our functional genomics data, working day to day with the scientists who design and run the screens. You will work with them from experimental design through to picking hits, and build the pipelines that let the analysis keep up as screening throughput grows. This is a hands‑on role with real influence over how we generate and use our data.

The data is multimodal. Single‑cell and pooled CRISPR screens are read out by sequencing, by Cell Painting and other high‑content imaging, and by proteomics, often on the same perturbations. Much of the job is making those readouts agree with each other, with statistics that hold up when a screen crosses several factors at once.

You will work with the software team, who own how data is captured and stored. You build the analysis on top of that, and you own its quality.

Your first 90 days

• FIRST 30 DAYS ◆ Learn how the scientists design and run the screens, and what each readout produces, from sequencing to imaging and proteomics.


• DAYS 30 TO 60 ◆ Own the analysis of the first single‑cell and pooled CRISPR screens you work on: QC, guide assignment, differential expression and modelling of perturbation effects. ◆ Build the first image‑based profiling pipeline for Cell Painting, from feature extraction and normalisation to phenotypic scoring.


• DAYS 30 TO 60 ◆ Advise on the design of upcoming screens, covering power, replication, library coverage, plate layout and batch effects.


• DAYS 60 TO 90 ◆ Integrate proteomic, transcriptomic and imaging readouts of the same perturbations, with statistics that hold up for multi‑factor designs.


• DAYS 60 TO 90 ◆ Make the pipelines reproducible and versioned, with the software team, so they scale as throughput grows.


• DAYS 60 TO 90 ◆ Present results with their uncertainty and QC to the scientists and to leadership.

Who you are

You have a background in genomics, and you have analysed real screening or single‑cell data and built things other people relied on. That might have been in a functional genomics or screening group in biotech or pharma, an academic lab, a core facility, or a computational group that worked closely with one. Nobody arrives with every part of this role. If you are strong in most of it and quick to learn the rest, we want to hear from you.

You like working next to the bench. Much of the value is in the conversations with the scientists before a screen runs, and you can explain a result to someone who was not in the room. You write code other people can run, and you care how a result reads to the person receiving it. We do not hire people into boxes. This role will stretch past its description, sometimes into the lab and sometimes into conversations about how our data is used. Early hires here are expected to pick up what is in front of them.

MUST HAVE

• A PhD, or a master’s with two to three years of relevant experience, in genomics, bioinformatics, computational biology, statistics or a related field.


• Strong Python or R, with good engineering habits such as Git, code review and reproducible workflows, and working with coding agents.


• Hands‑on single‑cell RNA‑seq analysis, for example with Scanpy or Seurat, including CRISPR screen QC such as guide assignment and knockdown efficiency.


• Statistical and machine learning methods on biological data, including linear and mixed models, multiple testing, and handling batch effects and confounders.


• Working closely with wet‑lab scientists, and explaining results clearly to people outside your field.

NICE TO HAVE

• Perturb‑seq or combinatorial‑barcoding single‑cell RNA‑seq, such as Parse Evercode.


• Image‑based profiling, such as CellProfiler or pycytominer, or deep‑learning image analysis.


• Multi‑omic integration methods.


• Workflow managers such as Nextflow or Snakemake, containers such as Docker, and cloud or HPC computing such as AWS.

Why this is unusualMost screening analysis happens after the fact, on files from a lab someone else runs, with little record of how each plate was handled. Here you sit with the scientists who run the screens, you can ask how a plate was handled and get an answer, and your analysis goes out with the data. It also crosses readouts that usually live in separate teams. Sequencing, imaging and proteomics from the same perturbations come through one small team, and the analysis has to hold up across all of them.

Some people find that energising; some find it outside their lane. It’s worth knowing in advance which one you are.

How we work

The role is based in London, at our lab and office in King’s Cross. Time in person with the scientists matters for this work. The wider founding team is distributed across London, New York and Europe and travels, so you will work with people who are not always in the building. We work in the open. Decisions are written down and work happens in Slack. The whole company meets once a week at the start of the week, and there is a regular offsite. Each person owns their area and makes the call inside it, and we will expect that of you early rather than late. UK benefits are 30 days of annual leave plus public holidays, a pension with a 10% employer contribution, and Bupa private health cover. More is added as the team grows.

The team you will join

You will report into the intelligence team. You will work most closely with the functional genomics scientists who design and run the screens, and with the software team. You will be the first person on the intelligence team whose focus is functional genomics data, joining a small team.

Our process

Our process has four stages. A short screening call about the role and the practicalities. A behavioural interview about how you work and what you value, run from the same template for every candidate. A technical stage built on a real analysis problem from our lab, not a puzzle. You spend a few hours writing up how you would approach it, using the tools you would use on the job, coding agents included, with a short note on the decisions you made. We care about judgement more than hours, so a focused answer beats an exhaustive one. We then go through it with you in person. Then references, aimed at whatever we still want to understand. If you are not sure whether you are a fit, apply anyway. We would rather read it and decide.

We are 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.