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

Research engineer [F/M] for AI-driven molecular and spatial analysis of tumor cell plasticity Download job offer in PDF format Contract type : Fixed-term contract Level of qualifications required : Graduate degree or equivalent Other valued qualifications : Master's degree or equivalent Fonction : Temporary scientific engineer About the research centre or Inria department 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. Context 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. You 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. Assignment 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 include, 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, we are open to discuss other initiatives on a case-by-case basis. Main activities 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 - create documentation, prepare example notebooks, design new visualization features - 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. Skills 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. Benefits package • Subsidized meals • 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 • Access to vocational training • Social security coverage Remuneration from €2,692 gross per month Apply for this position Share • Facebook • Linkedin • Twitter • Email General Information • Theme/Domain : Computational Biology Biologie et santé, Sciences de la vie et de la terre (BAP A) • Town/city : Villeurbanne • Inria Center : Centre Inria de Lyon • Starting date : 2027-03-01 • Duration of contract : 2 years • Deadline to apply : 2026-11-10 Warning : you must enter your e-mail address in order to save your application to Inria. Applications must be submitted online on the Inria website. Processing of applications sent from other channels is not guaranteed. Instruction to apply Applications must be submitted online via the Inria website. Processing of applications submitted via other channels is not guaranteed. Defence Security : This position is likely to be situated in a restricted area (ZRR), as defined in Decree No. 2011-1425 relating to the protection of national scientific and technical potential (PPST).Authorisation to enter an area is granted by the director of the unit, following a favourable Ministerial decision, as defined in the decree of 3 July 2012 relating to the PPST. An unfavourable Ministerial decision in respect of a position situated in a ZRR would result in the cancellation of the appointment. Recruitment Policy : As part of its diversity policy, all Inria positions are accessible to people with disabilities. Contacts • Inria Team : BIOTIC • Recruiter : Crombach Antonius / anton.crombach@inria.fr The keys to success 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. About Inria Inria, the French national institute for research in digital science and technology, supports the French government in national research and innovation strategies in the digital field, acting as Digital Programs Agency. Inria leads over 300 research and innovation projects with its 3,500 scientists, engineers, and support staff, in partnership with universities and the digital ecosystem (businesses, entrepreneurs, and public stakeholders). Together, we explore strategic fields such as artificial intelligence, cybersecurity, quantum computing, cloud technologies, digital transformation in healthcare, digital twins, and digital technologies for defence. We develop practical solutions such as software, tech startups, partnerships with national companies, and cutting-edge training programmes. Our goal is to drive scientific, technological, and industrial excellence to ensure France’s digital sovereignty.