Postdoc in agentic AI for spatial biology of the human gut

Vacancies Postdoc in agentic AI for spatial biology of the human gutKTH Royal Institute of Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health Job descriptionHow do cells organize into complex human tissues, and can AI accelerate our understanding of tissue architecture in health and disease? The Koplev lab at KTH Royal Institute of Technology and SciLifeLab is recruiting an ambitious postdoctoral researcher to lead the development of AI-driven computational methods for modelling human tissue architecture using single-cell and spatial transcriptomics data.The position is part of a research project funded by Digital Futures, conducted in collaboration with Assistant Professor Wei Ouyang's AICell Lab. The project aims to develop autonomous AI scientist systems capable of performing end-to-end bioinformatics analysis, including writing and executing code, critically evaluating results, refining analytical approaches, and generating testable biological hypotheses. A central research challenge is establishing how such AI systems can be rigorously benchmarked, validated, and supervised to enable scientific discovery.The research will focus on human gastrointestinal diseases, including Crohn's disease, ulcerative colitis, and colorectal cancer. We will integrate large collections of spatial transcriptomics datasets to investigate how cellular interactions, extracellular signalling, and transcriptional regulation shape tissue organization. The project will develop and evaluate machine learning approaches for identifying cell types, characterizing spatial tissue niches, and integrating biological information across tissues and disease states.The successful candidate will lead computational research projects at the intersection of artificial intelligence, machine learning, and spatial biology. Responsibilities will include: • Developing and evaluating AI agents for automated analysis of single-cell and spatial transcriptomics data. • Developing computational methods for analysing tissue architecture, cellular interactions, and spatial niches. • Integrating large-scale transcriptomics datasets across technologies, tissues, and diseases. • Establishing benchmarking and validation frameworks for AI-generated bioinformatics analyses. • Investigating biological mechanisms of tissue organization, including immune cell migration and intercellular signalling. • Disseminating research findings through scientific publications, conferences, and open-source software.The successful candidate will join a growing and collaborative research group at the Department of Gene Technology and SciLifeLab, working closely with leading international researchers in computational biology, machine learning, and spatial genomics. The lab's broader research programme investigates tissue architecture across the gastrointestinal tract, heart, and cardiovascular system, providing opportunities to develop new scientific directions according to the candidate's interests and expertise.In addition to leading independent research, the postdoctoral researcher will contribute to the scientific development of the group, including mentoring students and supporting collaborative projects. The position offers opportunities to develop scientific leadership skills and establish an independent research profile in preparation for a future career as a group leader or senior research scientist.More information: https://www.scilifelab.se/researchers/simon-koplev/QualificationsRequirements • A doctoral degree or an equivalent foreign degree. This eligibility requirement must be met no later than the time the employment decision is made. • Substantial research expertise in computational biology methods for single-cell or spatial transcriptomics data. • Proven scientific excellence as evidenced by strong scientific publications and track record relative to career stage. • Strong programming skills (Python or R) and familiarity with high-performance computing. • Exceptional collaborative abilities. • Self-motivated individual with ability to work independently. • Teaching and mentorship abilities or interests in personal development. • Awareness of diversity and equal opportunity issues, with specific focus on gender equality.Preferred qualifications • A doctoral degree or an equivalent foreign degree, obtained within the last three years prior to the application deadline. • Highly creative researcher with broad scientific curiosity. • Mastery of data visualization and scientific communication. • Experience developing or applying advanced machine learning methods, including deep learning, foundation models, large language models, or autonomous AI agents.We welcome applicants from diverse backgrounds and with complementary strengths.Great emphasis will be placed on personal skills.Join us at KTHKTH shapes the future through education, research and innovation. As a leading international technical university, we play an active role in advancing the transition towards a sustainable society. At KTH, you have the opportunity to grow and develop in a creative and dynamic environment, with good working conditions and attractive benefits. Equality, diversity and equal opportunities are essential to quality and form an integral part of KTH’s core values as a university and public authority.Learn more about our benefits and what it's like to work and grow at KTH.Trade union representativesContact information to trade union representatives.To apply for the positionLog into KTH's recruitment system to apply for this position. You are responsible for ensuring that your application is complete according to the instructions in the ad.The application must include: • CV including relevant professional experience and knowledge. • Brief letter of motivation describing why you want to conduct research, your academic interests and how they relate to your previous studies and future goals. Max two pages. • Copy of diploma from your PhD. Translations into English or Swedish if the original documents have not been issued in any of these languages.Your complete application must be received at KTH no later than the last day of application, midnight CET/CEST (Central European Time/Central European Summer Time).About the employmentThe position offered is for, at the most, two years.A position as a postdoctoral fellow is a time-limited qualified appointment focusing mainly on research, intended as a first career step after a dissertation.Other informationFor information about processing of personal data in the recruitment process.It may be the case that a position at KTH is classified as a security-sensitive role in accordance with the Protective Security Act (2018:585). If this applies to the specific position, a security clearance will be conducted for the applicant in accordance with the same law with the applicant's consent. In such cases, a prerequisite for employment is that the applicant is approved following the security clearance.We firmly decline all contact with staffing and recruitment agencies and job ad salespersons. Disclaimer: In case of discrepancy between the Swedish original and the English translation of the job announcement, the Swedish version takes precedence.Apply hereType of employmentTemporary positionContract typeFull timeFull-time equivalent100 %First day of employmentAccording to agreementSalaryMonthly salaryNumber of positions1LocationStockholmCountyStockholms länCountrySwedenReference numberPA-2026-3723Published29.Oct.2026Last application date28.Nov.2026ContactSimon Koplevkoplev@kth.se