Supervisor:Estibaliz Gómez de Mariscal

Project Short Summary 

Cell migration drives tumour growth, invasion and metastasis. During migration, intracellular architecture dynamically reorganises to drive cellular responses and adaptation to the microenvironment. Yet deciphering how this reorganisation is orchestrated is hampered by difficulties in resolving, quantifying and linking these complex dynamics. This project will develop smart microscopy and AI-powered methods to map intracellular reorganisation across cell-state trajectories during migration. Integrated with molecular approaches (spatial omics), it aims to identify key transitions and therapeutic candidates.

There are two PhD Fellowships available for this project!

Visit the Gómez-de-Mariscal Lab page to learn more about the group.

Supervisor: Sophia Maschalidi 

Project Short Summary 

There are different ways for cells to die offering outstanding possibilities for effective anti-tumor immunity. This PhD will investigate aims to study cell clearance by comparing different modalities of cell death that can be employed in cancer therapy. Using multi‑omics, in vivo models, and human microphysiological tumor systems, the project will map dynamic transcriptomic responses. By examining tumor‐cell disposal from all angles, this project will uncover previously unrecognized players that govern effective anti‐tumour immunity. These insights have the potential to inform the design of more effective therapies. 

Visit the Maschalidi Lab page to learn more about the group.

Supervisor: Carolina Trenado-Yuste 

Project Short Summary 

Metastasis of cancer cells from their primary tumor to distant organs remains the leading cause of cancer-related deaths. Cancer cells preferentially colonize specific organs, a phenomenon known as organotropism. In breast cancer (BC), common metastatic sites include bone, liver, lung, and brain. This project aims to investigate how the biophysical properties of BC cells influence organ-specific dissemination, to determine whether early-stage biophysical parameters can serve as clinically relevant biomarkers to predict secondary colonization sites.

Visit the Trenado-Yuste Lab page to learn more about the group.

Supervisor: Leslie Rubio Rodríguez-Kirby 

Project Short Summary 

PICTURESquE seeks to elucidate the neuroimmune mechanisms underlying neuropsychiatric-based diseases by integrating cutting-edge spatial multi-omic technologies with functional experimental approaches. This program aims to map cellular states, interactions, and inflammatory signaling across spatial compartments with high resolution, uncover long-range cross-compartmental propagation pathways, thereby refining our mechanistic understanding and enabling the identification of targeted therapeutic strategies for improved intervention and disease modification.

Visit the Rubio Rodríguez-Kirby Lab page to learn more about the group.

Supervisor: Matt Franklin 

Project Short Summary  

Guided by the lab’s catalog of satellite-binding transcription factors, the student will investigate the functional connections between satellite repeats and ribosomal DNA. Our preliminary data suggest that the satellite-associated proteome impacts ribosomal DNA transcription. Using a combination of microscopy, targeted proteomics, and satellite DNA manipulation, the student will mechanistically examine the regulation of ribosome biogenesis via satellite repeats in the contexts of stem cell biology and oncogenesis. 

Visit the Franklin Lab page to learn more about the group.

Supervisor: Matt Franklin 

Project Short Summary  

This PhD project will develop Repeatome, a multi-omics database for repetitive DNA biology. The student will integrate satellite DNA annotations with proteomic, transcriptomic, epigenomic, long-read sequencing, and microscopy datasets to characterize how repetitive regions change across cellular states, development, and disease. The project combines computational genomics, database development, and multi-omics analysis to create an accessible community resource for exploring the regulation and biological functions of the repeat genome.

Supervisor: André Dias

Project Short Summary 

Understanding how the human embryo develops remains one of the greatest challenges in biology and a pressing medical need. The earliest stages of development are still poorly understood and are often described as a “black box”. Building on our FCT Advanced Computing project MERLINN (Mammalian Embryo Regulatory and Lineage Inference using Neural Networks), this PhD project will integrate multimodal embryonic transcriptomics, stem cell-based embryo model (SCBEM) datasets, and AI-driven modelling to uncover the regulatory mechanisms governing human body axis formation.

Visit the Dias Lab page to learn more about the group.

Supervisor: André Dias

Project Short Summary 

Understanding early human embryo development remains one of the greatest challenges in biology and a pressing medical need. This project will explore the emergence and differentiation of human tail axial progenitors using gastruloids, a 3D stem cell-based embryo model (SCBEM). Combining cutting-edge approaches, including multi-omics and 3D imaging, the project will dissect the molecular mechanisms regulating human tail formation and investigate how their disruption contributes to congenital malformations.

Visit the Dias Lab page to learn more about the group.