Dissecting infant leukemia developmental origins with a hemogenic gastruloid model. Ragusa D., Suen C-W., Torregrosa Cortés G., Dijkhuis L., Byrne C., Ionescu G-A., Cerveira J., Kranc K., Bigas A., Garcia-Ojalvo J., Martinez Arias A., Pina C., biorXiv 2022

Droplet-based single-cell total RNA-seq reveals differential non-coding expression and splicing patterns during mouse development. Hollfelder, F., Salmen, F., De Jonghe, J., Kaminski, T., Alemany, A., Parada, G., Yanagida, A., Kohler, T., Battich, N., van den Brekel, F., Ellermann, A., Martinez Arias, A., Nichols, J., Hemberg, M., van Oudenaarden, A., Nature Biotechnology 2022

Cell-state transitions and collective cell movement generate an endoderm-like region in gastruloids. Hashmi, A., Tlili, S., Perrin, P., Lowndes, M., Peradziryi, H., Brickman, J., Martinez Arias, A., Lenne, P.-F. eLife 2022

Gastruloids: Pluripotent stem cell models of mammalian gastrulation and embryo engineering. Martinez Arias, A., Marikawa, Y., & Moris, N. Developmental Biology 2022


Bioengineered embryoids mimic post-implantation development in vitro. Girgin, M. U., Broguiere, M., Hoehnel, S., Brandenberg, N., Mercier, B., Martinez Arias, A. & Lutolf, M. Nature Communications 2021

In vitro teratogenicity testing using a 3D, embryo-like gastruloid system. Mantziou, V., Baillie-Benson, P., Jaklin, M., Kustermann, S., Martinez Arias, A., Moris, N. Reproductive Toxicology 2021

Gastruloid Development Competence Discriminates Different States of Pluripotency. Cermola, F., D’Aniello, C., Tatè, R., De Cesare, D., Martinez Arias, A., Minchiotti, G., Jorge Patriarca, E. Stem Cell Reports 2021

The primitive streak and cellular principles of building an amniote body through gastrulation. Sheng, G., Martinez Arias, A. & Sutherland, A. Science 2021

The cell in the age of the genomic revolution: Cell Regulatory Networks. Gorfinkiel, N. & Martinez Arias, A. Cells & Development 2021.

Human gastrulation: The embryo and its models. Ghimire, S., Mantziou, V., Moris, N., Martinez Arias, A. Developmental Biology 2021

Biomedical and societal impacts of in vitro embryo models of mammalian development. Moris, N., Alev, C., Pera, M., Martinez Arias, A. Stem Cell Reports 2021

Establishment of the vertebrate body plan: Rethinking gastrulation through stem cell models of early embryogenesis. Steventon, B., Busby, L. & Martinez Arias, A. Developmental Cell 2021

In vitro models of spinal motor circuit’s development in mammals: achievements and challenges. Nedelec, S. & Martinez Arias, A. Current Opinion in Neurobiology 2021


An in vitro model of early anteroposterior organization during human development. Moris, N., Anlas, K., van den Brink, S.C., Alemany, A., Schröder, J., Ghimire, S., Balayo, T., van Oudenaarden, A. & Martinez Arias, A. Nature 2020.

Single-cell and spatial transcriptomics reveal somitogenesis in gastruloids. van den Brink SC, Alemany A, van Batenburg V, Moris N, Blotenburg M, Vivié J, Baillie-Johnson P, Nichols J, Sonnen KF, Martinez Arias A, van Oudenaarden A. Nature 2020.

Axis Specification in Zebrafish Is Robust to Cell Mixing and Reveals a Regulation of Pattern Formation by Morphogenesis. Fulton, T., Trivedi, V., Attardi, A., Anlas, K., Dingare, C., Martinez Arias, A., Steventon, B. Current Biology 2020.

Pluripotent stem cell models of early mammalian development. Baillie-Benson, P., Moris, N. & Martinez Arias, A. Current Opinion in Cell Biology 2020.

Experimental embryology of gastrulation: pluripotent stem cells as a new model system. Moris, N., Martinez Arias, A. & Steventon, B. Current Opinion in Genetics & Development 2020.


Reverse-engineering growth and form in Heidelberg. Levin M, Martinez Arias A. Development 2019.

Neuro-mesodermal progenitors (NMPs): a comparative study between pluripotent stem cells and embryo-derived populations. Edri S, Hayward P, Jawaid W, Martinez Arias A. Development 2019.

An epiblast stem cell-derived multipotent progenitor population for axial extension. Edri S, Hayward P, Baillie-Johnson P, Steventon BJ, Martinez Arias A. Development 2019.


Multi-axial self-organization properties of mouse embryonic stem cells into gastruloids. Beccari L, Moris N, Girgin M, Turner DA, Baillie-Johnson P, Cossy AC, Lutolf MP, Duboule D, Martinez Arias A. Nature 2018

Debate ethics of embryo models from stem cells. Rivron N, Pera M, Rossant J, Martinez Arias A, Zernicka-Goetz M, Fu J, van den Brink S, Bredenoord A, Dondorp W, de Wert G, Hyun I, Munsie M, Isasi R. Nature 2018.

On the nature and function of organizers. Martinez Arias A, Steventon B. Development 2018.


Anteroposterior polarity and elongation in the absence of extra-embryonic tissues and of spatially localised signalling in gastruloids: mammalian embryonic organoids. Turner, D.A., Girgin, M., Alonso-Crisostomo, L., Trivedi, V., Baillie-Benson, P., Glodowski, C., Hayward, P., Collignon, J., Gustavsen, C., Serup, P., Steventon, B., Lutolf, M., Martinez Arias, A. Development 2017.

The hope and the hype of organoid research. Huch M, Knoblich JA, Lutolf MP, Martinez Arias A. Development 2017.

Evo-engineering and the cellular and molecular origins of the vertebrate spinal cord. Steventon B, Martinez Arias A. Developmental Biology 2017.

The Hidden Memory of Differentiating Cells. Moris, N. & Martinez Arias, A. Cell Systems 2017.

Evo-engineering and the cellular and molecular origins of the vertebrate spinal cord. Steventon, B. & Martinez Arias, A. Developmental Biology 2017.


Nac1 Coordinates a Sub-network of Pluripotency Factors to Regulate Embryonic Stem Cell Differentiation. Malleshaiah M, Padi M, Rué P, Quackenbush J, Martinez Arias A, Gunawardena J. Cell Reports 2016.

A draft map of the mouse pluripotent stem cell spatial proteome. Christoforou A, Mulvey CM, Breckels LM, Geladaki A, Hurrell T, Hayward PC, Naake T, Gatto L, Viner R, Martinez Arias A, Lilley KS. Nature Communications 2016.

Organoids and the genetically encoded self-assembly of embryonic stem cells. Turner DA, Baillie-Johnson P, Martinez Arias A. BioEssays 2016.


Generation of Aggregates of Mouse Embryonic Stem Cells that Show Symmetry Breaking, Polarization and Emergent Collective Behaviour In Vitro. Baillie-Johnson P, van den Brink SC, Balayo T, Turner DA, Martinez Arias A. J Vis Exp. 2015.

Emergent material properties of developing epithelial tissues. Machado PF, Duque J, Étienne J, Martinez Arias A, Blanchard GB, Gorfinkiel N. BMC Biology 2015.

FGF/MAPK signaling sets the switching threshold of a bistable circuit controlling cell fate decisions in embryonic stem cells. Schröter C, Rué P, Mackenzie JP, Martinez Arias A. Development 2015.

A loss-of-function and H2B-Venus transcriptional reporter allele for Gata6 in mice. Freyer L, Schröter C, Saiz N, Schrode N, Nowotschin S, Martinez Arias A, Hadjantonakis AK. BMC Dev Biol. 2015.

Inhibition of ?-catenin-TCF1 interaction delays differentiation of mouse embryonic stem cells. Chatterjee SS, Saj A, Gocha T, Murphy M, Gonsalves FC, Zhang X, Hayward P, Akgöl Oksuz B, Shen SS, Madar A, Martinez Arias A, DasGupta R. J Cell Biol. 2015.

Dynamic Proteomic Profiling of Extra-Embryonic Endoderm Differentiation in Mouse Embryonic Stem Cells. Mulvey CM, Schröter C, Gatto L, Dikicioglu D, Fidaner IB, Christoforou A, Deery MJ, Cho LT, Niakan KK, Martinez Arias A, Lilley KS. Stem Cells 2015.

Cell dynamics and gene expression control in tissue homeostasis and development. Rué P, Martinez Arias A. Mol Syst Biol. 2015


Wnt/B-catenin and FGF signalling direct the specification and maintenance of a neuromesodermal axial progenitor in ensembles of mouse embryonic stem cells. Turner DA, Hayward PC, Baillie-Johnson P, Rué P, Broome R, Faunes F, Martinez Arias A. Development 2014.

Symmetry breaking, germ layer specification and axial organisation in aggregates of mouse embryonic stem cells. van den Brink SC, Baillie-Johnson P, Balayo T, Hadjantonakis AK, Nowotschin S, Turner DA, Martinez Arias A. Development 2014.

Brachyury cooperates with Wnt/?-catenin signalling to elicit primitive-streak-like behaviour in differentiating mouse embryonic stem cells. Turner DA, Rué P, Mackenzie JP, Davies E, Martinez Arias A. BMC Biology 2014.

An interplay between extracellular signalling and the dynamics of the exit from pluripotency drives cell fate decisions in mouse ES cells. Turner DA, Trott J, Hayward P, Rué P, Martinez Arias A. Biol Open. 2014.


Single cell lineage analysis of mouse embryonic stem cells at the exit from pluripotency. Trott J, Martinez Arias A. Biol Open. 2013

A competitive protein interaction network buffers Oct4-mediated differentiation to promote pluripotency in embryonic stem cells. Muñoz Descalzo S, Rué P, Faunes F, Hayward P, Jakt LM, Balayo T, Garcia-Ojalvo J, Martinez Arias A. Mol Syst Biol. 2013.

A molecular basis for developmental plasticity in early mammalian embryos. Martinez Arias A, Nichols J, Schröter C. Development 2013.


Interactions between the amnioserosa and the epidermis revealed by the function of the u-shaped gene. Lada K, Gorfinkiel N, Martinez Arias A. Biol Open. 2012.

Towards a statistical mechanics of cell fate decisions. Garcia-Ojalvo J, Martinez Arias A. Curr Opin Genet Dev. 2012.

Chromatin decondensation and nuclear softening accompany Nanog downregulation in embryonic stem cells. Chalut KJ, Höpfler M, Lautenschläger F, Boyde L, Chan CJ, Ekpenyong A, Martinez-Arias A, Guck J. Biophys J. 2012.

Activation of Notch in lgd mutant cells requires the fusion of late endosomes with the lysosome. Schneider M, Troost T, Grawe F, Martinez-Arias A, Klein T. J Cell Sci. 2012.

Cell signalling regulates dynamics of Nanog distribution in embryonic stem cell populations. Luo Y, Lim CL, Nichols J, Martinez Arias A, Wernisch L. J R Soc Interface 2012.

Correlations between the levels of Oct4 and Nanog as a signature for naïve pluripotency in mouse embryonic stem cells. Muñoz Descalzo S, Rué P, Garcia-Ojalvo J, Martinez Arias A. Stem Cells 2012.

Drosophila midgut homeostasis involves neutral competition between symmetrically dividing intestinal stem cells. de Navascués J, Perdigoto CN, Bian Y, Schneider MH, Bardin AJ, Martínez-Arias A, Simons BD. EMBO J. 2012

Interplay between gene expression noise and regulatory network architecture. Chalancon G, Ravarani CN, Balaji S, Martinez Arias A, Aravind L, Jothi R, Babu MM. Trends Genet. 2012.

The structure of Wntch signalling and the resolution of transition states in development. Muñoz Descalzo S, Martinez Arias A. Semin Cell Dev Biol. 2012.

Dissecting ensemble networks in ES cell populations reveals micro-heterogeneity underlying pluripotency. Trott J, Hayashi K, Surani A, Babu MM, Martinez Arias A. Mol Biosyst. 2012


Patterned cell adhesion associated with tissue deformations during dorsal closure in Drosophila. Mateus AM, Martinez Arias A. PLoS One 2011.

Gene expression heterogeneities in embryonic stem cell populations: origin and function. Martinez Arias A, Brickman JM. Curr Opin Cell Biol. 2011.

Probing the druggability of protein-protein interactions: targeting the Notch1 receptor ankyrin domain using a fragment-based approach. Abdel-Rahman N, Martinez Arias A, Blundell TL. Biochem Soc Trans. 2011.

Endocytic and recycling endosomes modulate cell shape changes and tissue behaviour during morphogenesis in Drosophila. Mateus AM, Gorfinkiel N, Schamberg S, Martinez Arias A. PLoS One 2011.


Cytoskeletal dynamics and supracellular organisation of cell shape fluctuations during dorsal closure. Blanchard GB, Murugesu S, Adams RJ, Martinez Arias A, Gorfinkiel N. Development 2010.

Mechanisms of ligand-mediated inhibition in Notch signaling activity in Drosophila. Fiuza UM, Klein T, Martinez Arias A, Hayward P. Dev Dyn. 2010.

Publications prior to 2010 can be found here.