Omics Data Scientist

Omics Data Scientist About Us Spore.Bio is a deeptech startup founded in 2023 that is redefining microbiological quality control in pharmaceutical, food & beverage, and cosmetics manufacturing. Where Spore.Bio deploys biophotonic and deep-learning technology on factory floors, Spore.Labs takes Spore.Bio 's core technology into new territory: from AMR detection to microbiome research and beyond. Spore.labs is looking for a new talent ready to take real ownership, prototype solutions, build incrementally a robust ML pipeline, benchmark SOTA approaches and grow alongside the department they help build. About the Role Data-driven AMR prediction requires access to signals that reveal both the root causes of resistance and the downstream consequences that expose activated pathways. The Omics Data Scientist will be responsible for building omics processing pipelines that extract the cleanest possible signals from multiple modalities (whole genome sequencing, transcriptomics, and proteomics) ensuring experimental reproducibility, data standardisation, and correction of technical biases. Working closely with the Spore.Labs Omics Coordinator, you will extract relevant features and deliver AI-ready omics data. You will also establish mono-modal baselines to validate signal presence, reproduce state-of-the-art results from the literature, and contribute to the multimodal architecture that grounds spectral and imaging-based representations in the biology of microorganisms. Missions Design pipelines for whole genome sequence, transcriptomics and proteomics normalization, denoising, standardization and feature engineering. Benchmark omics based AMR prediction from the literature as well as omics baselines Develop and implement deep learning models (transformers, graph neural networks, autoencoders) for multi-OMICs integration supporting predictive modeling and mechanistic interpretation. Adapt and implement computational biology approaches for translational diagnostic applications. Collaborate closely with microbiologists, computer vision experts, and optical physicists to ensure biological interpretability of AI models. Contribute to scientific publications, conferences, and intellectual property (patents) highlighting novel insights from integrated OMICs and optical data. About You We value curiosity, initiative, and a willingness to learn. Not every box needs to be ticked to apply; we are recruiting for trajectory as much as for current skills. Strong motivation to work at the interface of biology, optics, and AI in a multidisciplinary deeptech environment is a genuine plus. Academic background: engineer degree, Master's degree, or PhD in computational biology or machine learning applied to Omics. Professional experience: A minimum of 2 years of proven hands-on omics processing and omics-based deep learning model training. Previous experience in microbial omics data is a strong plus. Programming: Proficient in python, comfortable leveraging omics processing software, documents systematically, uses continuous integration tools and best coding practices. Reliability and autonomy: Able to organise their working day independently once roadmaps are established, anticipate scheduling constraints (computation time, data availability), check for spurious correlation and deliver statistically meaningful conclusions. Team mindset: Comfortable contributing across tasks in a small laboratory environment. Clear written and verbal scientific communication in English. Why Join Us? Be part of a core interdisciplinary team driving the development of a disruptive diagnostic technology with real global health impact Work at the frontier of microbiology, advanced optics, and machine learning in a team where scientific rigour is the default Process real clinical and research samples that feed a concrete diagnostic platform from an early career stage Genuine room to grow: as the laboratory scales, responsibility and independence scale with it, in a permanent position (CDI) in Paris What we offer We believe that flexibility and trust are important parts of a company. Our work environment reflects this thanks to: Flexible remote: If you live in Paris, you can work from our office or from your place with no constraints. On top of that, we offer many perks such as: • A budget for remote work equipment • A Gymlib subscription for you to stay in shape wherever you are • Premium health insurance (Alan in France) • A Swile card for your meals, if you are based in France • Frequent team events and in-person gatherings every quarter! Recruitment Process 30-minute introductory call with a team member Home assignment technical test (2 days to handover the work) 45-minute technical interview (questions on ML/Omics and scientific practices) Lab visit Exchange with the Founders Department Spore.Labs Locations Paris Remote status Hybrid Employment type Full-time