Understanding the development of the 
early human embryo remains not only one of the greatest challenges in biology but also a major unmet medical need.
Many congenital disorders and pregnancy complications in humans originate during the earliest stages of development, yet our understanding of these processes remains limited and relies heavily on animal models despite important species-specific differences. Guided by the modular organisation of embryonic development, our group engineers stem cell-based embryo models (SCBEMs) that recreate specific human developmental processes and body regions. By integrating experimental and computational approaches, including multi-omics and artificial intelligence (AI), we use these models to uncover the fundamental principles governing human gastrulation and early organogenesis. Moreover, these high-throughput human-specific platforms also enable the study of congenital disorders and teratogenicity, while helping reduce reliance on animal models in line with the 3Rs principles in research.
Our laboratory brings together researchers from diverse backgrounds and disciplines to foster curiosity-driven, interdisciplinary and creative research in an open and collaborative environment where the next generation of scientists can thrive.
PROJECTS
Project description
MERLINN is an advanced computing project that aims to elucidate early human embryonic development through large-scale integration and analysis of single-cell transcriptomic datasets using machine learning approaches. In particular, we will reconstruct key developmental trajectories and infer the gene regulatory networks (GRNs) governing human germ layer specification.
With support from the Fundação para a Ciência e a Tecnologia (FCT), we will also benchmark human stem cell-based embryo models (SCBEMs) against an in vivo embryonic reference and perform cross-species comparative analyses to identify conserved and species-specific developmental programs. Overall, MERLINN will provide new insights into the molecular mechanisms governing human developmental biology and advance the engineering of more faithful human SCBEMs.
Principal Investigator: André Dias
Start date: 01/09/2026
End date: 31/08/2027
Funded under: Fundação para a Ciência e a Tecnologia (FCT)
Grant agreement ID: 2026.07699.CPCA.A1
Project description
STEMBRYO BIOMED is an interdisciplinary project that aims to improve our understanding of human developmental biology through an integrated systems biology framework encompassing multi-omics, artificial intelligence (AI) and stem cell-based embryo models (SCBEMs) such as gastruloids.
With support from NIMSB, we will engineer human gastruloids modelling various body tissues and use them as platforms to investigate human development in health and disease. Overall, STEMBRYO BIOMED will provide new insights into the mechanisms regulating human body axis formation and the emergence of congenital disorders.
Principal Investigator: André Dias
Start date: 01/09/2026
End date: 31/12/2030
Funded under: NIMSB
TEAM
Group Leader
André Dias obtained his PhD in Integrative Biology and Biomedicine at the Instituto Gulbenkian de Ciência (Portugal). Supported by an FCT fellowship, he worked under the supervision of Dr. Moisés Mallo and undertook a secondment in the lab of Prof. Val Wilson (Centre for Regenerative Medicine – University of Edinburgh, UK), where he investigated the molecular mechanisms governing mammalian body plan formation. Among his conceptual and experimental contributions to the characterisation of axial progenitors, he uncovered an incomplete epithelial-to-mesenchymal transition (EMT) at the core of body axis elongation. Funded by an EMBO Postdoctoral fellowship and a MELIS-AGAUR grant, he then explored the role of signalling during mammalian gastrulation under the mentorship of Prof. Alfonso Martinez Arias (Universitat Pompeu Fabra, Spain). Using a stem cell-based embryo model, he discovered that NODAL and WNT signalling regulate two opposing developmental modules orchestrating anterior and posterior body formation. He later joined the lab of Dr. Anna Bigas (Hospital del Mar Research Institute, Spain) to determine the transcriptional roadmap underlying human hematopoietic stem cell development. André has also taught at the Universidade de Lisboa (Portugal) and Universitat de Barcelona (Spain), where he contributed to the training and mentoring of the next generation of scientists.
As Principal Investigator at NIMSB, Dr. Dias leads a systems biology research programme focused on understanding early human embryo development to address biomedical questions. He is dedicated to mentoring early-career scientists, fostering international and interdisciplinary collaborations, and cultivating an open and inclusive research environment. Committed to the responsible advancement of human stem cell research, he promotes informed dialogue between the scientific community and society, helping shape a field that balances scientific innovation with ethical reflection.
SELECTED PUBLICATIONS
Alfonso Martinez Arias, André Dias, Maneesha Inamdar. Stem cell-based embryo models as a tool for reproductive biology, Molecular Human Reproduction (2026). (doi:10.1093/molehr/gaag030)
André Dias*, Pau Pascual-Mas, Gaëlle Robertson, Gabriel Torregrosa-Cortés, Suzan Stelloo, Pablo Casaní-Galdón, Stephen Babin, Yuliia Romaniuk, Alexandre Mayran, Alexandra E. Wehmeyer, Jordi Garcia-Ojalvo, Harold M. McNamara, Michiel Vermeulen, Sebastian J. Arnold, & Alfonso Martinez Arias*. Opposing Nodal and Wnt signalling activities govern the emergence of the mammalian body plan. bioRxiv (2025). (doi: 10.1101/2025.01.11.632562) *co-corresponding authors
Tina Balayo#, Sharna Lunn, Pau Pascual-Mas, Ulla-Maj Fiuza, Amruta Vasudevan, Joshua D. Frenster, Joel B. Josende García, Hannah Y. Galloon, Raquel Flores Peirats, Alfonso Martínez Arias, André Dias#*, & David A. Turner*. N2B27 media formulations influence gastruloid development. Development (2025). (doi:10.1242/dev.204774) #co-first authors, *co-corresponding authors
Anahí Binagui-Casas #, André Dias #*, Charlène Guillot #, Vicki Metzis #, & Dillan Saunders #. Building consensus in neuromesodermal research: Current advances and future biomedical perspectives. Current Opinion in Cell Biology (2021). (doi:10.1016/j.ceb.2021.08.003) #co-first authors, *corresponding author
Luisa de Lemos #, André Dias #, Ana Nóvoa, & Moisés Mallo. Epha1 is a cell-surface marker for the neuromesodermal competent population. Development (2022). (doi:10.1242/dev.198812. #co-first authors
André Dias, Anastasiia Lozovska, Filip J Wymeersch, Ana Nóvoa, Anahi Binagui-Casas, Daniel Sobral, Gabriel G Martins, Valerie Wilson, & Moisés Mallo. A Tgfbr1/Snai1-dependent developmental module at the core of vertebrate axial elongation. eLife (2020). (doi:10.7554/eLife.56615)