Publications de Gioele La Manno

Spotiflow: accurate and efficient spot detection for fluorescence microscopy with deep stereographic flow regression

Joachim Lingner, Suliana Manley, Gioele La Manno, Irina Khven, Martin Weigert, Eftychia Kyriacou, Can Aztekin, Albert Dominguez Mantes, Georgios Tsissios, Evangelia Skoufa

Identification of spot-like structures in large, noisy microscopy images is a crucial step for many life-science applications. Imaging-based spatial transcriptomics (iST), in particular, relies on the precise detection of millions of transcripts in low sig ...

2025

Clinically compliant cryopreservation of differentiated retinal pigment epithelial cells

Cheng Zhao, Gioele La Manno, Alex Russell Lederer

Background aims: Age-related macular degeneration (AMD) is the most common cause of blindness in elderly patients within developed countries, affecting more than 190 million worldwide. In AMD, the retinal pigment epithelial (RPE) cell layer progressively d ...

Elsevier Sci Ltd2024

Applying single-cell and single-nucleus genomics to studies of cellular heterogeneity and cell fate transitions in the nervous system

Gioele La Manno

Single-cell and single-nucleus genomic approaches can provide unbiased and multimodal insights. Here, we discuss what constitutes a molecular cell atlas and how to leverage single-cell omics data to generate hypotheses and gain insights into cell transitio ...

NATURE PORTFOLIO2024

Statistical inference with a manifold-constrained RNA velocity model uncovers cell cycle speed modulations

Felix Naef, Colas Noé Droin, Lorenzo Talamanca, Gioele La Manno, Alex Russell Lederer, Irina Khven, Antonio Herrera Camacho, Albert Dominguez Mantes

Across biological systems, cells undergo coordinated changes in gene expression, resulting in transcriptome dynamics that unfold within a low-dimensional manifold. While low-dimensional dynamics can be extracted using RNA velocity, these algorithms can be ...

2024

Profiling the chromatin landscape of adult human oligodendroglia using single-cell epigenomics

Gioele La Manno, Alex Russell Lederer, Zahra Moslehi

Wiley2023

The lipotype hypothesis

Giovanni D'Angelo, Gioele La Manno

Giovanni D'Angelo and Gioele La Manno present the concept of lipotypes, and suggest that lipid composition is an important regulator of cell fate. ...

NATURE PORTFOLIO2023

The Key Players of CNS function: Exploring the Effects of Region, Age, and Sex on Human Glia Diversity

Gioele La Manno, Zahra Moslehi

Wiley2023

Brain matters: unveiling the distinct contributions of region, age, and sex to glia diversity and CNS function

Nina-Lydia Kazakou, Gioele La Manno, Zahra Moslehi

The myelinated white matter tracts of the central nervous system (CNS) are essential for fast transmission of electrical impulses and are often differentially affected in human neurodegenerative diseases across CNS region, age and sex. We hypothesize that ...

BMC2023

Heterogeneity and developmental dynamics of mammalian neocortical progenitors

Gioele La Manno, Antonio Herrera Camacho, Leila Haj Abdullah Alieh

The central nervous system develops from a pool of neural progenitors which, depending on their location and time of division, generate cells committed to differentiate into specific kinds of neurons or glia. In the last decades, the developmental neurobio ...

Elsevier2023

Sphingolipids control dermal fibroblast heterogeneity

Olivier Burri, Sylvia Ho, Romain Guiet, Galina Glousker, Giovanni D'Angelo, Laura Capolupo, Gioele La Manno, Alex Russell Lederer, Irina Khven

Human cells produce thousands of lipids that change during cell differentiation and can vary across individual cells of the same type. However, we are only starting to characterize the function of these cell-to-cell differences in lipid composition. Here, ...

American Association for the Advancement of Science2022

Self-organizing in vitro mouse neural tube organoids mimic embryonic development

Matthias Lütolf, Jisoo Park, Gioele La Manno, Irina Khven, Hao-An Hsiung

The embryonic neural tube is the origin of the entire adult nervous system, and disturbances in its development cause life-threatening birth defects. However, the study of mammalian neural tube development is limited by the lack of physiologically realisti ...

COMPANY BIOLOGISTS LTD2022

Molecular profiling of stem cell-derived retinal pigment epithelial cell differentiation established for clinical translation

Gioele La Manno, Alex Russell Lederer, Irina Khven

Human embryonic stem cell-derived retinal pigment epithelial cells (hESC-RPE) are a promising cell source to treat age-related macular degeneration (AMD). Despite several ongoing clinical studies, a detailed mapping of transient cellular states during in v ...

CELL PRESS2022

Clonal relations in the mouse brain revealed by single-cell and spatial transcriptomics

Gioele La Manno

Ratz et al. present an easy-to-use method to barcode progenitor cells, enabling profiling of cell phenotypes and clonal relations using single-cell and spatial transcriptomics, providing an integrated approach for understanding brain architecture. ...

NATURE PORTFOLIO2022

Cell type prioritization in single-cell data

Grégoire Courtine, Quentin Barraud, Mark Andrew Anderson, Claudia Kathe, Marco Milano, Jordan Squair, Matthieu Pierre Gautier, Gioele La Manno, Thomas Haynes Hutson, Michael Alexander Skinnider

The cell types affected by biological perturbations in complex tissues are uncovered by single-cell analysis. ...

NATURE PUBLISHING GROUP2021

Molecular architecture of the developing mouse brain

Gioele La Manno, Alex Russell Lederer, Irina Khven

The mammalian brain develops through a complex interplay of spatial cues generated by diffusible morphogens, cell-cell interactions and intrinsic genetic programs that result in probably more than a thousand distinct cell types. A complete understanding of ...

NATURE PORTFOLIO2021

Confronting false discoveries in single-cell differential expression

Grégoire Courtine, Quentin Barraud, Mark Andrew Anderson, Claudia Kathe, Nicholas David James, Jordan Squair, Matthieu Pierre Gautier, Gioele La Manno, Thomas Haynes Hutson, Rémi Bernard René Hudelle, Michael Alexander Skinnider

Differential expression analysis of single-cell transcriptomics allows scientists to dissect cell-type-specific responses to biological perturbations. Here, the authors show that many commonly used methods are biased and can produce false discoveries. ...

Nature Portfolio2021

Oligodendroglia heterogeneity in the post-mortem human CNS with region, age and sex

Gioele La Manno

WILEY2021

Spatial tissue profiling by imaging-free molecular tomography

Fabrice David, Gioele La Manno

Several techniques are currently being developed for spatially resolved omics profiling, but each new method requires the setup of specific detection strategies or specialized instrumentation. Here we describe an imaging-free framework to localize high-thr ...

2021

The emergence and promise of single-cell temporal-omics approaches

Gioele La Manno, Alex Russell Lederer

Single-cell transcriptomics enables the measurement of gene expression in complex biological systems at the resolution of individual cells. Multivariate analysis of single-cell data helps describe the variation in expression accompanying cellular processes ...

CURRENT BIOLOGY LTD2020

A cell fitness selection model for neuronal survival during development

Gioele La Manno

Developmental cell death plays an important role in the construction of functional neural circuits. In vertebrates, the canonical view proposes a selection of the surviving neurons through stochastic competition for target-derived neurotrophic signals, imp ...

Nature Research2019