Prof. La Manno Lab – Laboratory of Brain Development and Biological Data Science

We are a computational and developmental biology lab with a focus on understanding the complexities and dynamics of brain development. Our approach combines single-cell genomics, spatial omics technologies, and machine learning tools. Our use of techniques like RNA velocity allow us to trace the future states of individual cells, predicting developmental trajectories and cellular fate decisions in the process of differentiating embryonic stem cells into mature neurons.

A significant aspect of our research is the exploration of lipid heterogeneity at the single-cell level. We believe this emerging field holds the key to understanding how different biochemical drivers, including lipids, influence the dynamic process of brain development.

Our long-term goal is to unravel the intricate gene regulatory programs that drive the formation of cell types in the nervous system. By doing so, we hope to contribute to the understanding of neurodevelopmental disorders and the improvement of cell replacement therapies.

Team

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The people in the lab

Selected Publications

Sphingolipids Control Dermal Fibroblast Heterogeneity

Cell-to-cell lipid heterogeneity affects the determination of cell states, adding a new regulatory component to the self-organization of multicellular systems.

Molecular architecture of the developing mouse brain

We report a comprehensive single-cell transcriptomic atlas of the embryonic mouse brain between gastrulation and birth. We identified almost eight hundred cellular states that describe a developmental program for the functional elements of the brain and its enclosing membranes.

Spatial tissue profiling by imaging-free molecular tomography

We describe an imaging-free framework to localize high-throughput readouts within a tissue by cutting the sample into thin strips in a way that allows subsequent image reconstruction. We applied the technique to the brain of the Australian bearded dragon, Pogona vitticeps. Our results reveal the molecular anatomy of the telencephalon of this lizard, providing evidence for a marked regionalization of the reptilian pallium and subpallium.

LATEST PUBLICATIONS

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Clinically compliant cryopreservation of differentiated retinal pigment epithelial cells

L. Baque-Vidal; H. Main; S. Petrus-Reurer; A. R. Lederer; N-E. Beri et al.

Cytotherapy. 2024-04-01. Vol. 26, num. 4, p. 340-350. DOI : 10.1016/j.jcyt.2024.01.014.

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Deciphering the nature of cell state transitions in single cells using quantitative modeling of temporal dynamics

A. R. Lederer / G. La Manno (Dir.)

Lausanne, EPFL, 2024.

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Meeting our Makers: Uncovering the cis-regulatory activity of transposable elements using statistical learning

C. D. S-T. Pulver / D. Trono (Dir.)

Lausanne, EPFL, 2024.

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AI futuristic technology in language and communication © iStock

A new AI language model that mimics the organization of the brain

Published:24.04.25 — EPFL researchers have developed the first AI model of language in the brain that captures both how neurons are arranged and how they function.

Pavan Ramdya - 2025 EPFL/Alain Herzog - CC-BY-SA 4.0

“Fruit flies are a major source of inspiration in robotics”

Published:04.04.25 — Researchers at EPFL’s Neuroengineering Laboratory, led by Pavan Ramdya, aim to replicate the workings of the brain of the common fruit fly, Drosophila melanogaster. We spoke with Ramdya about the exciting prospects for robotics.

Camille Goemans, professeure au Laboratoire d’interaction médicament-microbiote à l’EPFL - 2025 EPFL/Alain Herzog - CC-BY-SA 4.0

Gut microbiome serves as a “second brain” regulating our bodies

Published:26.03.25 — The microorganisms in our intestines play an important role in many bodily processes, from digestion to emotions, and are a key factor in our overall health. A number of modern diseases could be traced to disturbances in the gut microbiome.

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