Doctoral Candidate 10 – Transformer-based design of disease-assoiated tumour microenvironments
Claassen, University of Tübingen, Tübingen, Germany
This project focuses on developing transformer-based deep learning models to analyse tumour microenvironment (TME) features linked to disease states. The doctoral candidate will use spatial proteomics data and set transformer architectures to learn patterns of cell–cell interactions. By leveraging attention mechanisms, the project aims to generate interpretable insights into disease-associated TME processes. Ultimately, the goal is to enable in silico design of therapeutic TME modifications and identify actionable molecular targets. Please use this PDF application form and send it to spaXio@plus.ac.at. Be sure to also use the reference letter template. Applications still welcome.
Doctoral Candidate 13 – Digital Twin Modeling
Morlot, Deeplife, Paris/Marseille, France
This position focuses on building digital twins of tumour-relevant cell types by integrating single-cell and spatial multi-omics data. The candidate will develop predictive computational models to simulate metastatic niche interactions and support experimental validation for breast and colon cancer research. The ideal candidate will posses strong programmin skills but also understanding of wet lab techniques. Please use this PDF application form and send it to spaXio@plus.ac.at. Be sure to also use the reference letter template. Applications still welcome.
See "Projects" for further details.
We are excited to introduce Alessia Gabardi as another doctoral candidate joining the spaXio journey!
Alessia Gabardi is a Biotechnology graduate with a strong passion for cancer research. Throughout her academic and research journey, she has developed a solid background in molecular and cellular biology, with a particular interest in extracellular vesicles and their role in biomarker discovery and cancer progression.
She completed her Bachelor of Science in Biomolecular Sciences and Technologies at the University of Trento, where she investigated the mechanistic regulation of the miR-34 family. She then earned her Master of Science in Cellular and Molecular Biotechnology at the same institution, with a thesis focused on the modulation of RNA secreted in extracellular vesicles.
From 2024 to 2025, she worked as a research fellow on the PNRR MUR PRIN 2022 project “Regulation of vesicular RNA secreted as a biomarker in triple-negative breast cancer,” in collaboration with the University of Trieste and Humanitas Research Hospital in Milan. The project aimed to identify novel plasma RNA biomarkers to improve patient stratification and treatment in triple-negative breast cancer.
In March 2026, Alessia joined the spaXio project, where she focuses on investigating the role of extracellular vesicles in cancer progression. Her research specifically explores how extracellular vesicles contribute to the priming of pre-metastatic niches, a crucial step in the metastatic cascade.
By studying extracellular vesicles as key mediators of intercellular communication, her work aims to shed light on how tumors can influence distant microenvironments even before metastatic cells arrive. This research will contribute to a deeper understanding of the early events driving metastasis.
As her contribution to the spaXio puzzle, Alessia chose to represent extracellular vesicles circulating in the bloodstream, highlighting their potential role in tumor dissemination and in preparing distant tissues for metastasis. Despite their emerging importance, many mechanistic aspects of how extracellular vesicles mediate pre-metastatic niche formation remain to be elucidated.
Next up Marie Landwehr, our PhD candidate from spaXio Project 6:
Marie earned her Bachelor’s degree in Molecular Life Sciences from the University of Hamburg. During her studies, she completed an Erasmus semester at the University of Strasbourg and conducted her bachelor’s thesis in immunology performing high-resolution live calcium imaging at the University Medical Center Hamburg-Eppendorf. She then pursued a Master’s degree in Molecular Life Sciences at the University of Hamburg. Through her academic training and research experience, Marie developed a strong interest in immuno-oncology and neurobiology. This led her to complete an Erasmus-funded lab rotation at the Champalimaud Foundation in Lisbon, where she investigated adult neurogenesis in Drosophila. For her master’s thesis, Marie worked on antibody-based immunotherapies targeting neuroblastoma at the Research Institute Children’s Cancer Center in Hamburg.
In April 2026, Marie began her PhD at Aix-Marseille University. Her project focuses on understanding the metastatic niche of breast cancer brain metastases. She will develop advanced in-vitro models using patient-derived tumouroids co-cultured with microglia and astrocytes. By modelling the metastatic niche in-vitro, she aims to uncover mechanisms underlying tumour cell survival, as well as the influence of brain-resident cells on tumour growth and therapy resistance. Her project incorporates techniques such as spatial proteomics and 3D imaging. In addition, she will perform drug screening targeting both tumour and brain-resident cells with the goal of developing new therapies for breast cancer patients with brain metastases.
Outside the laboratory, Marie likes to travel, learn languages and read. She is also passionate about arts and enjoys painting.
In her piece, Marie visualizes the dynamic crosstalk between metastatic tumour cells and tissue-resident cells within the microenvironment, showing how healthy tissue is remodelled into a tumour-supportive niche. With her contribution to the puzzle, she aims to highlight the need to better understand which interactions shape and sustain metastatic niches.
Today, we introduce Agapi Simaiaki, our PhD candidate from spaXio Project 9:
Agapi holds a Bachelor’s degree in Biology with a focus on Biomolecular Sciences and Biotechnology from the University of Crete (Greece). During her undergraduate studies, as well as her Erasmus+ internship at Lund University in Sweden, she gained hands-on experience in molecular diagnostics and cancer mechanobiology, developing a strong interest in molecular and cellular oncology.
Motivated by an increasing curiosity about data-driven approaches, Agapi pursued graduate studies in Bioinformatics, first at the University of Crete and later at Uppsala University (Sweden). Throughout her Master’s studies, she worked on cancer-related projects involving neural networks, rule-based machine learning, and statistical modeling. In her Master’s thesis, she combined machine learning, dynamic modeling, and genetic algorithms to analyze live-cell imaging–derived temporal drug response data from a large-scale glioblastoma screening. This work contributed to improved representations of cellular drug responses and the identification of effective drug combinations, further strengthening her passion for integrating advanced computational methods with experimental biology to address complex biomedical questions.
In April 2026, she began her PhD at the Autonomous University of Madrid (Spain) in collaboration with the Spanish National Research Council (CSIC), as part of the spaXio network. Her research focuses on advancing the understanding of the pre-metastatic niches and how they become permissive to tumor cell colonization, with a novel focus on the lymphatic system. She investigates how tumor, immune, and stromal cells dynamically interact within these environments, and how these interactions are reshaped by therapeutic interventions. By combining advanced 3D cell imaging approaches, morphodynamic analysis, computer vision-based methods, and data-driven modeling, Agapi aims to capture dynamic transitions in cellular states associated with metastatic potential. Her work seeks to uncover the mechanisms driving metastasis and contribute to the development of clinically relevant biomarkers and therapeutic strategies.
Outside of research, Agapi enjoys independent cinema, working out, and cooking for friends, as a way to bring people together over a nice homemade meal. She also loves spending time by the sea and traveling, with an excitement in exploring new cultures and perspectives.
When it comes to the spaXio puzzle contribution, she chose to depict the pre-metastatic niche in the lung, focusing on the vascular support in metastatic colonization. The piece highlights how blood and lymphatic vessels may contribute to the formation of a permissive microenvironment that enables tumor cell extravasation and early metastatic growth.
Today, we introduce Keisi Kadriu, our PhD candidate from spaXio Project 2:
Keisi is an Italian student who earned her Bachelor’s degree in Biotechnology from the University of Genova. During her internship, she developed a strong understanding of protein interactions and an interest in exploring less-studied biological processes, as well as their potential clinical applications.
Driven by her passion for research, she pursued a Master’s degree in Medical and Pharmaceutical Biotechnology at the University of Genova. Her Master’s thesis focused on pharmacological repositioning in glioblastoma, with particular attention to tumor resistance mechanisms mediated by extracellular vesicles derived from glioblastoma stem cells.
Motivated to deepen her knowledge of cancer biology, Keisi began her PhD in March 2026 at the Paris-Lodron University of Salzburg in Austria. Her research investigates how cellular interactions and metabolic processes within metastatic niches influence breast cancer progression. She aims to understand how immune and stromal cells support metastasis, identify shared mechanisms across different environments, and explore potential targets for clinical application.
Outside of her academic pursuits, Keisi is a curious and intellectually driven individual who enjoys listening to music and learning about a wide range of topics. She is also passionate about caring for plants and is interested in understanding the biological mechanisms underlying their growth.
Keisi has continued our spaXio puzzle initiative 🧩— She created this figure to illustrate how cancer cells interact with different cells in the metastatic niche and adapt to different organ environments, emphasizing the role of cellular interactions in metastatic progression.
The first doctoral candidates have been successfully recruited and have started their spaXio journey. Unfortunately, ongoing global challenges have required us to reopen applications for positions that have not yet been filled.
Doctoral Candidate 4 – Involvment of metabolites in cancer progression and metatasis formation
Strittmatter, Technical University Munich, Munich, Germany
This project focuses on investigating metabolic alterations that drive cancer progression and metastasis. The doctoral candidate will use advanced techniques such as mass spectrometry imaging, LC-MS/MS, and spatial metabolomics to analyse tumours, metastatic tissues, and tumour-derived extracellular vesicles in mouse models. By integrating metabolomic data with transcriptomic profiles, the project aims to uncover metabolic signatures associated with aggressive cancer behaviour and identify potential therapeutic targets. . Please use this PDF application form and send it to spaXio@plus.ac.at. Be sure to also use the reference letter template. Deadline for submission: 8th of May 2026 23:59 European summer time. The position has been filled.
Doctoral Candidate 10 – Transformer-based design of disease-assoiated tumour microenvironments
Claassen, University of Tübingen, Tübingen, Germany
This project focuses on developing transformer-based deep learning models to analyse tumour microenvironment (TME) features linked to disease states. The doctoral candidate will use spatial proteomics data and set transformer architectures to learn patterns of cell–cell interactions. By leveraging attention mechanisms, the project aims to generate interpretable insights into disease-associated TME processes. Ultimately, the goal is to enable in silico design of therapeutic TME modifications and identify actionable molecular targets. Please use this PDF application form and send it to spaXio@plus.ac.at. Be sure to also use the reference letter template. Applications still welcome.
See "Projects" for further details.
While our first doctoral candidates have already begun their spaXio journey, several positions are still open (details coming soon).
Today, we’re happy to introduce Patricia Goncalves, our PhD candidate from spaXio Project 3:
Patricia holds a Bachelor’s degree in Biomedical Laboratory Sciences from the School of Health of Porto (Portugal). Throughout multiple clinical internships, she gained insight into the challenges associated with cancer diagnosis and management, which led her to pursue a Master’s in Molecular Medicine and Oncology at the Faculty of Medicine of Porto (Portugal). Her master’s thesis focused on uncovering the molecular mechanisms underlying chemoresistance to gemcitabine in metastatic pancreatic cancer (PDAC), particularly phenotypic plasticity.
Driven by her curiosity and motivation to deepen her expertise in 3D models, Patricia completed a postgraduate Erasmus+ internship at the Danish Cancer Institute in Copenhagen (Denmark). During this six-month period, she conducted a high-throughput drug screening using patient-derived tumor organoids, aiming to identify promising biomarkers and drug combinations against high-grade serous ovarian cancer.
In March 2026, Patricia started her PhD at the Paris-Lodron University of Salzburg (Austria).
As part of spaXio, Patricia is studying the metastasis process of colorectal cancer and how the primary tumor reprograms both local and metastatic tumor niches. Thus, she is employing a range of cutting-edge methods, such as murine organoid genetic engineering, 3D co-culture systems and high-resolution spatial transcriptomics. This project will contribute to a better understanding of the formation of permissive pre-metastatic niches, overall tumoral spatial organization and intercellular communication.
As her contribution to the spaXio puzzle, she aimed to represent tumor dissemination via peripheral blood. Despite being a key event in tumor progression, several mechanistic details of this process remain unclear.
In her free time, Patricia enjoys exploring new places and cultures, as well as reading and watching movies.
Patricia has also launched our spaXio puzzle initiative 🧩—a creative way to visualize the complex process of metastasis and its treatment. Each doctoral researcher will design one puzzle piece, gradually revealing the full metastatic picture step by step. Together, these pieces will form not just a scientific visualization, but a powerful symbol of collaboration, shared goals, and our collective journey.
Stay tuned as the puzzle unfolds!
The first doctoral candidates have been successfully recruited and will soon begin their spaXio journey. Several other projects are currently in the selection and match-making phase. See the status of individual projects here.
Unfortunately, no perfect match has yet been found for Projects 12 and 13. We have therefore reopened the application process for these positions. We are specifically seeking two motivated bioinformaticians to help unravel metastatic processes in colon and breast cancer.
Doctoral Candidate 12 – Computational Data Science
Nahnsen, University of Tübingen, Tübingen, Germany
This position focuses on developing scalable and reproducible computational pipelines for integrating multi-omics and imaging data in cancer research. The candidate will work with nf-core and Nextflow workflows to prepare heterogeneous datasets for machine learning and collaborative analysis of spatial transcriptomics and proteomics data. Please use this PDF application form and send it to spaXio@plus.ac.at. Be sure to also use the reference letter template. Deadline for submission: 18th of February 2026 23:59.
Doctoral Candidate 13 – Digital Twin Modeling
Morlot, Deeplife, Paris, France
This position focuses on building digital twins of tumour-relevant cell types by integrating single-cell and spatial multi-omics data. The candidate will develop predictive computational models to simulate metastatic niche interactions and support experimental validation for breast and colon cancer research. The ideal candidate will posses strong programmin skills but also understanding of wet lab techniques. Please use this PDF application form and send it to spaXio@plus.ac.at. Be sure to also use the reference letter template. Deadline for submission: 18th of February 2026 23:59.
See "Projects" for further details.
We’re excited to share that all applications have been carefully reviewed for eligibility and suitability—thank you to everyone who applied! We’ve already identified several outstanding candidates, and first-round interviews are now underway, focusing on applicants’ primary project choices. For projects where we’re still seeking the best possible match, a second round of interviews based on secondary project selections will take place early next year. Stay tuned for more updates!
We are thrilled to share that we’ve received more than 200 applications for our program. The evaluation process will be conducted collaboratively by the respective project supervisors. We look forward to reviewing all the innovative and inspiring submissions and will keep you updated as the selection process progresses.
Less than a week left to apply for our future docotoral candidates!
Join the spaXio Doctoral Network, where we’re decoding the biology of metastasis through spatial omics, organoid models, and computational biology. Don’t miss your chance to be part of this cutting-edge research community.
Further details here.
spaXio, an EU-funded Marie Skłodowska-Curie Actions (MSCA) Doctoral Network within the CIVIS European University Alliance (civis.eu), is recruiting 14 PhD candidates to investigate how cancer metastasizes and interacts with the immune system using spatial multi-omics, 3D tumoroids, and AI-driven analysis. Candidates will receive interdisciplinary, cutting-edge training across academia and industry, preparing them to become future leaders in cancer, immuno-oncology, and spatial biology.
Application starts on the 14th of October! Further details here.
The third edition of the Summer School "Immuno-Oncology in the Spatial Omics Era" is currently underway, supported by spaXio members. Hosted by the Institute Cancer and Immunology, the programme brings together international Master’s and PhD students to explore how spatial omics technologies are transforming cancer research. Participants engage in hands-on workshops, theoretical sessions, and problem-based learning to understand tumor immunity at the molecular and tissue levels. Renowned experts are delivering advanced seminars on spatial transcriptomics, proteomics, and metabolic imaging. This immersive programme emphasizes the integration of cutting-edge research with practical laboratory experience.
The first successful run of the Xenium spatial transcriptomics platform has been completed in Salzburg! This cutting-edge technology—now installed at the Paris Lodron University Salzburg—was made possible thanks to funding from the FFG funded-CellComm initiative and the incredible support of the Centre for Tumour Biology and Immunology, as well as the Department of Biosciences and Medical Biology.
The Xenium will play a vital role in spatially resolved omics for spaXio’s mission to uncover the secrets of metastatic niches.
The international research project spaXio (spatial crosstalk in immuno-oncology), coordinated by the University of Salzburg, has been selected for funding through the Marie Skłodowska-Curie Actions Doctoral Networks program of the European Union.
spaXio brings together leading scientists from institutions in Salzburg, Tübingen, Marseille, Madrid, Lausanne, and Munich, in close collaboration with academic, clinical, and industry partners across Europe and the United States. The project aims to explore how cancer spreads to distant organs by investigating the spatial and temporal interactions between tumor cells, immune cells, the microbiome, and their surrounding tissue environments.
Using spatial omics technologies, 3D tumor models, and AI-driven digital twins, the consortium will develop new approaches to understand metastasis and identify targeted therapies.
At its core, spaXio will train 13 interdisciplinary doctoral researchers, equipping them with cutting-edge scientific and transferable skills to shape the future of personalized cancer treatment.