Research engineer [F/M] for AI-driven molecular and spatial analysis of tumor cell plasticity

Inria; Villeurbanne; Hybrid; EUR 36,000 - 48,000; Full time

Benefits offered by this job

Public transport reimbursement

RTT leave and exceptional leave

Teleworking after 6 months

Professional equipment and events

Job summary

Inria Lyon, a leading research center in Villeurbanne, offers a two-year research engineer position in BioTiC within AIMPACT. You will transform a prototype network analysis tool into a robust Python package, add visualization features, and author notebooks.

The role emphasizes collaboration with cancer biology and AI partners and publication of results. The candidate will work at Inria’s Lyon site, with opportunities to visit Grenoble and Rennes, and will benefit from a strong

Qualifications

• MSc degree or equivalent in computer science, mathematics or a related field.
• Strong interest in bioinformatic data analysis and/or software development.
• Experience in one or more areas: software engineering, statistics and ML/AI, explainability, single-cell data analysis, network inference, data visualization.

Responsibilities

• Transform a prototype software for differential network analysis into a professional Python package.
• Develop novel visualization features and create extensive documentation.
• Prepare example notebooks and identify candidate regulatory processes for AIMPACT’s partners.
• Disseminate work through publications and international conferences.

Skills

Software engineering

Statistics

Machine learning / AI

Explainability

Single-cell data analysis

Network inference

Data visualization

Python/R programming

Education

MSc degree or equivalent in CS/Math or related

Tools

Python

R

Job description

Research engineer [F/M] for AI-driven molecular and spatial analysis of tumor cell plasticity

The Inria research centre in Lyon is the 9th Inria research centre, formally created in January 2022. It brings together approximately 410 people in 20 research teams and research support services.

Its staff are distributed in Villeurbanne, Lyon Gerland, and Saint-Etienne.

The Lyon centre is active in the fields of software, distributed and high-performance computing, embedded systems, quantum computing and privacy in the digital world, but also in digital health and computational biology.

A two-year research engineer position is available in team BioTiC at Inria Lyon. At BioTiC, we study cellular systems through computational models and bioinformatic data analysis, in order to better understand their organizational principles. In our team, we value working together, being innovative, and providing opportunities for professional and personal growth.

The position is within the framework of project AIMPACT, a collaboration between Magali Richard, Yuna Blum, Sophie Achard (CNRS), Anton Crombach (Inria), and Alex Petersen (Brigham Young University, Utah, USA). The overall goal of this project is to better understand tumor cell plasticity, that is to say the ability of cancer cells to dynamically reprogram their transcriptional programs in response to environmental cues. You will be advised by Anton Crombach , whilst working together with other members of the project. Y ou will be located at Inria’s La Doua site and you will have regular opportunities to visit partners in Grenoble and Rennes.

You will benefit from the expertise at BioTiC regarding bioinformatic data analysis and computational modelling of biological systems; and through AIMPACT’s partners you will profit from world‑class knowledge regarding statistics, machine learning and AI, and cancer biology. Overall, the project will foster your career in terms of building up cutting‑edge expertise on high‑dimensional data analysis, network inference, statistics, machine learning and AI, and data visualization techniques – areas that are strongly demanded in academia and industry.

AIMPACT focuses on the identification of molecular mechanisms associated with tumor cell plasticity. Tumor cell plasticity refers to the ability of cancer cells to alter their transcriptional programs in response to environmental cues, enabling them to adapt and evade therapies. Unlike normal cells that have stable cell types, tumor cells can dynamically switch between molecular states, acquiring more aggressive features. This non‑genetic adaptability is orchestrated by epigenetic modifications, transcription factor activity, and gene regulatory networks (GRNs). Tumor plasticity has been widely observed across multiple cancers and here we study it in pancreatic ductal adenocarcinoma (PDAC), one of the most lethal malignancies. Despite recent advances, our ability is limited to predict and control tumor plasticity. Addressing this gap requires innovative AI methods that can integrate multi‑modal data, incorporate uncertainty, provide interpretable insights, and capture the dynamic nature of cellular state transitions in their spatial context—capabilities that lie beyond conventional approaches.

Your primary goal within the project will be to transform a prototype software for differential network analysis into a professional Python package. This will includ e, but is not limited to, developing novel visualization features , creating extensive documentation, preparing example notebooks, and identifying candidate regulatory processes for further analysis by AIMPACT’s partners . You will also have time to pursue additional initiatives, for instance designing and implementing novel analysis tools that build on the existing prototype. Naturally, w e are open to discuss other initiatives on a case‑by‑case basis.

The goal of this two‑year research engineer position is to provide and use cutting‑edge tools to better understand how drug tolerance manifests itself in gene regulatory processes. This means your main activities are:

• transform a prototype software for differential network analysis into a Python package
• apply differential network analysis on networks generated by AIMPACT’s partners
• predict genes and genetic interactions linked to drug‑tolerance for further analysis by our partners

Finally, you are strongly encouraged to disseminate your work through publications in international journals and by presenting it at national and international conferences.

The project requires skills in computer science, mathematics, and (cancer) biology. A successful candidate has experience in one or more of the following areas:software engineering, statistics and machine learning / AI, explainability, single‑cell data analysis, network inference, data visualization, programming in Python/R. Affinity with cancer biology and the challenge of cellular state transition in pancreatic cancer is considered a real advantage. Good oral and written communication skills in English are essential.

Avantages

• Partial reimbursement of public transport costs
• Leave: 7 weeks of annual leave + 10 extra days off due to RTT (statutory reduction in working hours) + possibility of exceptional leave (sick children, moving home, etc.)
• Possibility of teleworking (after 6 months of employment) and flexible organization of working hours
• Professional equipment available (videoconferencing, loan of computer equipment, etc.)
• Social, cultural and sports events and activities

The applicant should have a strong basis in computer science/mathematics or similar field ( MSc degree or equivalent), ideally oriented toward bioinformatic data analysis and/or software development . An essential quality for this project is a keen interest to apply one’s computational skills to help answering biological questions. An interest in single‑cell technologies and network inference is considered a real asset, as is wanting to communicate and collaborate with ( computational ) biologists that study cancer.