Team

The people in the lab

Alexandre Bouillon

Master Student

Luca Fusar Bassini

Doctoral Student

Alessandro Valente

Doctoral Student

Daniil Bobrovskiy

Master’s Student

Albert Dominguez Mantes

Doctoral Student

Halima Hannah Schede

Doctoral Student

Leila Alieh

Postdoctoral researcher

Antonio Herrera Camacho

Postdoctoral Researcher

Irina Khven

Doctoral Student

Alex Lederer

Doctoral Student

Alumni

Previous members

Open Positions

Join us

Gioele La Manno

Assistant Professor

Outreach

Popular science, News and Media

Gioele is appointed Tenure Track Assistant Professor

The Board of the Swiss Federal Institutes of Technology has announced the appointment of professors at EPFL, including our group leader Gioele!

Gioele gives the TEDx talk: “Scientists at the mirror”

Who is science made by? And how do you become a researcher? Gioele La Manno describes the journey to become a scientist, sharing a point of view on many misconception of the figure of the scientist

Molecular atlas reveals how brain cells develop

Using a combination of sequencing techniques and mathematical methods, our lab has traced the genetic programs that direct the development of each cell in the brain. This molecular map help understanding how the brain develops and provide insights into a range of brain disorders. Nature paper here

Streamlining stem cells to treat macular degeneration

Our lab in collaboration with the Lanner lab has tested and confirmed a protocol for growing human embryonic stem cells into retina cells to treat eye diseases such as age-related macular degeneration. Stem Cell Reports paper here

From cell “fat” to cell fate

Using single-cell lipidomics our lab and the lab of Giovanni D’Angelo discovered the existence of lipotypes, cell states characterized by their lipid composition. We describe how lipid composition can play a key role in determining functional transitions. Science paper here

“Molecular Tomographer” algorithm maps gene expression in space

Our lab has developed an algorithm that can work out the spatial pattern of gene expression inside the body without the need for microscopes and complicated equipment used currently. Nature Biotech paper here

Two EPFL life scientists awarded SNSF grants

The lab is the recipient of one of the 79 grants awarded this year across all scientific disciplines. I am really honored by this recognition. This SNF grant will allow us to study, using cutting-edge technologies, the complex cellular dynamics of progenitor cells during brain development.

The lab has been awarded a SPARK SNF grant!

We are honored to have been warded a SNF SPARK grant to work on ‘A novel strategy for optics-free tomography-based spatial molecular profiling of tissues’ SPARK is a new funding scheme designed for projects that show unconventional thinking and introduce a unique approach.

The lab has been awarded a Human Cell Atlas CZI grant

The Chan Zuckerberg Initiative (CZI) has awarded a grant to the lab of Gioele La Manno, together with the Karolinska Institute and The University of Edinburgh. The collaborative research aims at new therapies for multiple sclerosis, and will be part of the Human Cell Atlas project.

Meet (me) the first ELISIR Fellow

I have been appointed the first Scholar of the EPFL Life Sciences Early Independence Research program (ELSIR), a revolutionary fellowship that gives talented PhD graduates the kind of research independence they could usually only get much later in their career.

New method reveals cell development

Researchers at Karolinska Institutet and Harvard Medical School report in the journal Nature that they have developed a technique for capturing dynamic processes in individual cells. Apart from studying disease processes, the method can be used to observe in detail how specialised cells are formed during embryonic development.

Midbrain study gives boost to Parkinson’s research

Two research teams at Karolinska Institutet have identified the dopamine-producing cells in the midbrain of mice and humans. They have also developed a method of assessing the quality of in-vitro cultured dopamine-producing cells, which can be of great benefit to research on Parkinson’s disease. The results are published in the academic journal Cell.

Special nerve cells cause goose bumps and nipple erection

The sympathetic nerve system has long been thought to respond the same regardless of the physical or emotional stimulus triggering it. However, in a new study from Karolinska Institutet published in the journal Nature Neuroscience, scientists show that the system comprises different neurons that regulate specific physiological functions, such as erectile muscle control.

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1 min read

Luca Fusar Bassini and Alessandro Valente join the lab for a PhD. Luca is a Biologist with a keen interest in developing computational methods to obtain unprecedented biological insight, Alessandro is Biotechnologist with experience in stem cell engineering in organoids. They are both going to work on the lipidome-transcriptome axis in neurulation. Welcome Luca and Alessandro!

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1 min read

We wrote a piece with Giovanni D’Angelo titled “The lipotype hypothesis” on Nature Reviews Molecular Cell Biology! Considering recent evidence on lipid-cell response to interaction cues, we proposed that cell variability in lipid composition assists the divergence of differentiation trajectories, leading to the establishment of several cell identities.

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1 min read

It is super exciting to release this resource we have been working so long for: an atlas of all the cell states appearing in mouse brain development, between gastrulation and birth!

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2 min read

A new project granted! We will work towards “A Probabilistic Framework for RNA Velocity Statistical Tests Using Pyro” together with Luca Pinello lab in Boston and Eli Bingham, the creator of Pyro. more info here

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1 min read

Using single-cell lipidomics our lab and the lab of Giovanni D’Angelo discovered the existence of lipotypes. Cell’s lipid composition can play a key role in determining what that cell will become. Science paper here

CONTINUE READING

Selected Publications

Cell-to-cell lipid heterogeneity affects the determination of cell states, adding a new regulatory component to the self-organization of multicellular systems.
Science, 2022
PDF PubMed

Human embryonic stem cell-derived retinal pigment epithelial cells (hESC-RPE) are studied as potential treatment for age-related macular degeneration (AMD). The study conducts single-cell transcriptomic profiling of an hESC-RPE differentiation protocol developed for clinical use, demonstrating its ability to produce a pure RPE pool.
Stem Cell Reports, 2022
PDF

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.
Nature, 2021
PDF Supplementary

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.
Nature Biotechnology, 2021
PDF Data Code

Here we show that RNA velocity - the time derivative of RNA abundance - can be estimated by distinguishing unspliced and spliced mRNAs in standard single-cell RNA sequencing protocols. RNA velocity is a vector that predicts the future state of individual cells on a timescale of hours.
Nature, 2018
PDF Supplementary

Publications

. Sphingolipids Control Dermal Fibroblast Heterogeneity. Science, 2022.

PDF PubMed

. Molecular profiling of stem cell-derived retinal pigment epithelial cell differentiation established for clinical translation. Stem Cell Reports, 2022.

PDF

. Molecular architecture of the developing mouse brain. Nature, 2021.

PDF Supplementary

. Spatial tissue profiling by imaging-free molecular tomography. Nature Biotechnology, 2021.

PDF Data Code

. RNA velocity in single cells. Nature, 2018.

PDF Supplementary

. Molecular architecture of the mouse nervous system. Cell, 2018.

PDF Dataset Supplementary

. Spatial organization of the somatosensory cortex revealed by cyclic smFISH. Nature Methods, 2018.

PDF DataPage

. STRT-seq-2i: dual-index 5ʹ single cell and nucleus RNA-seq on an addressable microwell array. Scientific Reports, 2017.

PDF Supplementary

. Molecular analysis of the midbrain dopaminergic niche during neurogenesis. biorxiv, 2017.

PDF

. Induction of functional dopamine neurons from human astrocytes in vitro and mouse astrocytes in a Parkinson's disease model. Nature Biotechnology, 2017.

PDF

. Molecular diversity of midbrain development in mouse, human, and stem cells. Cell, 2016.

PDF Supplementary Data visualizations

. Visceral motor neuron diversity delineates a cellular basis for nipple-and pilo-erection muscle control. Nature Neuroscience, 2016.

PDF Supplementary

. Single-cell transcriptomics reveals that differentiation and spatial signatures shape epidermal and hair follicle heterogeneity. Cell Systems, 2016.

PDF

. Oligodendrocyte heterogeneity in the mouse juvenile and adult central nervous system. Science, 2016.

PDF Supplementary

. Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq. Science, 2015.

PDF Supplementary

. Quantitative single-cell RNA-seq with unique molecular identifiers. Nature methods, 2014.

PDF Supplementary

Software

Below the scientific software I have been working on:

velocyto

A package for the analysis of expression dynamics in single cell RNA seq data. For more information go to the velocyto homepage

cytograph

A tool for building analysis pipeline for big single cell RNA sequencing projects

loompy

Core implementation the standard format to store and work with single cell expression data. For more information go to the loompy homepage

nbregression

Negative binomial generalized linear model for single cell expression data

cmdstan-py

An alternative, lightweight, python interface to the Bayesian Modeling language Stan.

BackSPIN

Reference implementation of the clustering algorithm described in Zeisel et al. 2015

ceftools

An older file format designed to store smaller single-cell RNA seq datasets