Publications by Michael Alexander Skinnider

Single-cell and spatial atlases of spinal cord injury in the Tabulae Paralytica

Grégoire Courtine, Bernard Schneider, Jocelyne Bloch, Quentin Barraud, Nicholas David James, Matthieu Pierre Gautier, Claudia Kathe, Thomas Haynes Hutson, Michael Alexander Skinnider, Michael V. Sofroniew

Here, we introduce the Tabulae Paralytica—a compilation of four atlases of spinal cord injury (SCI) comprising a single-nucleus transcriptome atlas of half a million cells, a multiome atlas pairing transcriptomic and epigenomic measurements within the same ...

Springer Science and Business Media LLC2024

Best practices for differential accessibility analysis in single-cell epigenomics

Grégoire Courtine, Jordan Squair, Michael Alexander Skinnider

Differential accessibility (DA) analysis of single-cell epigenomics data enables the discovery of regulatory programs that establish cell type identity and steer responses to physiological and pathophysiological perturbations. While many statistical method ...

Nature Research2024

Artificial intelligence for natural product drug discovery

Philippe Schwaller, Florian Huber, Albert Hofstetter, Michael Alexander Skinnider

Developments in computational omics technologies have provided new means to access the hidden diversity of natural products, unearthing new potential for drug discovery. In parallel, artificial intelligence approaches such as machine learning have led to e ...

Nature Portfolio2023

Recovery of walking after paralysis by regenerating characterized neurons to their natural target region

Grégoire Courtine, Bernard Schneider, Jocelyne Bloch, Quentin Barraud, Jordan Squair, Mark Andrew Anderson, Katia Galan, Nicholas David James, Matthieu Pierre Gautier, Laetitia Danielle Philippine Baud

Axon regeneration can be induced across anatomically complete spinal cord injury (SCI), but robust functional restoration has been elusive. Whether restoring neurological functions requires directed regeneration of axons from specific neuronal subpopulatio ...

American Association for the Advancement of Science2023

Prioritization of cell types responsive to biological perturbations in single-cell data with Augur

Grégoire Courtine, Jordan Squair, Matthieu Pierre Gautier, Michael Alexander Skinnider

Advances in single-cell genomics now enable large-scale comparisons of cell states across two or more experimental conditions. Numerous statistical tools are available to identify individual genes, proteins or chromatin regions that differ between conditio ...

NATURE RESEARCH2021

Enabling reproducible re-analysis of single-cell data

Grégoire Courtine, Jordan Squair, Michael Alexander Skinnider

2021

Confronting false discoveries in single-cell differential expression

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

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

Cell type prioritization in single-cell data

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

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

NATURE PUBLISHING GROUP2021

Transcriptional Dynamics Of Neurorehabilitation In Spinal Cord Injury At Single-Nucleus Resolution

Grégoire Courtine, Jordan Squair, Laetitia Danielle Philippine Baud, Claudia Kathe, Michael Alexander Skinnider

MARY ANN LIEBERT, INC2019