Leander Dony
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View article: Nicheformer: a foundation model for single-cell and spatial omics
Nicheformer: a foundation model for single-cell and spatial omics Open
Tissue makeup depends on the local cellular microenvironment. Spatial single-cell genomics enables scalable and unbiased interrogation of these interactions. Here we introduce Nicheformer, a transformer-based foundation model trained on bo…
View article: CellFlow enables generative single-cell phenotype modeling with flow matching
CellFlow enables generative single-cell phenotype modeling with flow matching Open
High-content phenotypic screens provide a powerful strategy for studying biological systems, but the scale of possible perturbations and cell states makes exhaustive experiments unfeasible. Computational models that are trained on existing…
View article: Chronic exposure to glucocorticoids amplifies inhibitory neuron cell fate during human neurodevelopment in organoids
Chronic exposure to glucocorticoids amplifies inhibitory neuron cell fate during human neurodevelopment in organoids Open
Disruptions in the tightly regulated process of human brain development have been linked to increased risk for brain and mental illnesses. While the genetic contribution to these diseases is well established, important environmental factor…
View article: Nicheformer: a foundation model for single-cell and spatial omics
Nicheformer: a foundation model for single-cell and spatial omics Open
Tissue makeup relies fundamentally on the cellular microenvironment. Spatial single-cell genomics allows probing the underlying cellular interactions in an unbiased, scalable fashion. To learn a unified cell representation that accounts fo…
View article: Chronic exposure to glucocorticoids amplifies inhibitory neuron cell fate during human neurodevelopment in organoids
Chronic exposure to glucocorticoids amplifies inhibitory neuron cell fate during human neurodevelopment in organoids Open
Disruptions in the tightly regulated process of human brain development have been linked to increased risk for brain and mental illnesses. While the genetic contribution to these diseases is well established, important environmental factor…
View article: Chronic exposure to glucocorticoids amplifies inhibitory neuron cell fate during human neurodevelopment in organoids
Chronic exposure to glucocorticoids amplifies inhibitory neuron cell fate during human neurodevelopment in organoids Open
Disruptions in the tightly regulated process of human brain development have been linked to increased risk for brain and mental illnesses. While the genetic contribution to these diseases is well established, important environmental factor…
View article: Chronic exposure to glucocorticoids amplifies inhibitory neuron cell fate during human neurodevelopment in organoids
Chronic exposure to glucocorticoids amplifies inhibitory neuron cell fate during human neurodevelopment in organoids Open
Disruptions in the tightly regulated process of human brain development have been linked to increased risk for brain and mental illnesses. While the genetic contribution to these diseases is well established, important environmental factor…
View article: Chronic exposure to glucocorticoids amplifies inhibitory neuron cell fate during human neurodevelopment in organoids
Chronic exposure to glucocorticoids amplifies inhibitory neuron cell fate during human neurodevelopment in organoids Open
Disruptions in the tightly regulated process of human brain development have been linked to increased risk for brain and mental illnesses. While the genetic contribution to these diseases is well established, important environmental factor…
View article: An integrated transcriptomic cell atlas of human neural organoids
An integrated transcriptomic cell atlas of human neural organoids Open
Neural tissues generated from human pluripotent stem cells in vitro (known as neural organoids) are becoming useful tools to study human brain development, evolution and disease. The characterization of neural organoids using single-cell g…
View article: Human neurogenesis is altered via glucocorticoid-mediated regulation of<i>ZBTB16</i>expression
Human neurogenesis is altered via glucocorticoid-mediated regulation of<i>ZBTB16</i>expression Open
Summary Glucocorticoids are important for proper organ maturation and their levels are tightly regulated during development. Here we use human cerebral organoids and mice to study cell-type specific effects of glucocorticoids on neurogenes…
View article: An integrated cell atlas of the human lung in health and disease
An integrated cell atlas of the human lung in health and disease Open
Organ- and body-scale cell atlases have the potential to transform our understanding of human biology. To capture the variability present in the population, these atlases must include diverse demographics such as age and ethnicity from bot…
View article: An integrated cell atlas of the human lung in health and disease
An integrated cell atlas of the human lung in health and disease Open
Organ- and body-scale cell atlases have the potential to transform our understanding of human biology. To capture the variability present in the population, these atlases must include diverse demographics such as age and ethnicity from bot…
View article: Data-driven dynamical modelling of a pathogen-infected plant gene regulatory network: a comparative analysis
Data-driven dynamical modelling of a pathogen-infected plant gene regulatory network: a comparative analysis Open
Recent advances in synthetic biology have enabled the design of genetic feedback control circuits that could be implemented to build resilient plants against pathogen attacks. To facilitate the proper design of these genetic feedback contr…
View article: Cell-Type-Specific Impact of Glucocorticoid Receptor Activation on the Developing Brain: A Cerebral Organoid Study
Cell-Type-Specific Impact of Glucocorticoid Receptor Activation on the Developing Brain: A Cerebral Organoid Study Open
These findings suggest that excessive glucocorticoid exposure could interfere with neuronal maturation in utero, leading to increased disease susceptibility through neurodevelopmental processes at the interface of genetic susceptibility an…
View article: Out-of-distribution prediction with disentangled representations for single-cell RNA sequencing data
Out-of-distribution prediction with disentangled representations for single-cell RNA sequencing data Open
Learning robust representations can help uncover underlying biological variation in scRNA-seq data. Disentangled representation learning is one approach to obtain such informative as well as interpretable representations. Here, we learn di…
View article: Theislab sfaira Model Repository
Theislab sfaira Model Repository Open
This is the official model weights repository provided with the sfaira python package. sfaira is a data and model zoo for single-cell RNA-seq data developed in the group of Prof. Fabian Theis at Helmholtz Munich. * = These authors contribu…
View article: Theislab sfaira Model Repository
Theislab sfaira Model Repository Open
This is the official model weights repository provided with the sfaira python package. sfaira is a data and model zoo for single-cell RNA-seq data developed in the group of Prof. Fabian Theis at Helmholtz Munich. * = These authors contribu…
View article: Sfaira accelerates data and model reuse in single cell genomics
Sfaira accelerates data and model reuse in single cell genomics Open
Exploratory analysis of single-cell RNA-seq data sets is currently based on statistical and machine learning models that are adapted to each new data set from scratch. A typical analysis workflow includes a choice of dimensionality reducti…
View article: [DEPRECATED] Theislab sfaira Model Repository
[DEPRECATED] Theislab sfaira Model Repository Open
THIS WEIGHTS REPOSITORY IS NO LONGER COMPATIBLE WITH THE CURRENT VERSION OF SFAIRA. PLEASE FIND THE LATEST VERSION HERE: https://doi.org/10.5281/zenodo.4836516 This is the official model weights repository provided with the sfaira python p…
View article: [DEPRECATED] Theislab sfaira Model Repository
[DEPRECATED] Theislab sfaira Model Repository Open
THIS WEIGHTS REPOSITORY IS NO LONGER COMPATIBLE WITH THE CURRENT VERSION OF SFAIRA. PLEASE FIND THE LATEST VERSION HERE: https://doi.org/10.5281/zenodo.4836516 This is the official model weights repository provided with the sfaira python p…
View article: Cell-type specific impact of glucocorticoid receptor activation on the developing brain
Cell-type specific impact of glucocorticoid receptor activation on the developing brain Open
A fine-tuned balance of glucocorticoid receptor (GR) activation is essential for organ formation, with disturbances influencing health outcomes. Excess GR-activation in utero has been linked to brain-related negative outcomes, with unclear…
View article: Comprehensive single cell mRNA profiling reveals a detailed roadmap for pancreatic endocrinogenesis
Comprehensive single cell mRNA profiling reveals a detailed roadmap for pancreatic endocrinogenesis Open
Deciphering mechanisms of endocrine cell induction, specification and lineage allocation in vivo will provide valuable insights into how the islets of Langerhans are generated. Currently, it is ill defined how endocrine progenitors segrega…