Tanja Vogel

Epigenetic perturbation unravels diverse origins, state conversions and de-differentiation of cortical astrocytes

This study investigates the role of DOT1L in astrogenesis, identifying its role in maintaining astrocyte states and revealing multiple origins and state conversions of cortical astrocytes.

Regulation of protein abundance in neurons by selective translation of 3'UTR isoforms

The paper shows that long 3'UTR isoforms in neurons are less efficiently translated than short ones, mediated by ELAV and Pumilio, and that disrupting this mechanism reduces viability and stress resilience.

Mapping spatial cell-cell communication programs by tailoring chains of cells for transformer neural networks

The paper introduces scCChain, a transformer-based framework for mapping spatial cell-cell communication programs in spatial transcriptomics data, identifying hotspots at single-cell and spot resolution.

Sparse dimensionality reduction for analyzing single-cell-resolved interactions

The paper introduces a sparse dimensionality reduction workflow for analyzing single-cell cell-cell interactions using the Boosting Autoencoder approach, with a Jupyter notebook for implementation.

Adding layers of information to scRNA-seq data using pre-trained language models

The paper fine-tunes biomedical language models to integrate text-based knowledge with scRNA-seq data, enhancing cell identity preservation and adding functional and disease-related context.

DNMT1-Mediated Regulation of Somatostatin-positive Interneuron Migration Impacts Cortical Architecture and Function

This study shows that DNMT1 regulates the migration of somatostatin-expressing interneurons, affecting cortical layer structure and function in mice.

Infusing structural assumptions into dimensionality reduction for single-cell RNA sequencing data to identify small gene sets

The paper introduces a boosting autoencoder method to incorporate structural assumptions into dimensionality reduction for single-cell RNA sequencing data, identifying small gene sets that explain latent dimensions.

miRNA-mediated expression of RBFOX2 governs the splicing transition from progenitors to neurons in the developing brain

This study identifies miR-92a-3p as a regulator of RBFOX2 expression, which controls the splicing transition from neural progenitors to neurons in the developing mouse cortex.

The lincRNA Pantr1 is a FOXG1 target gene conferring site-specific chromatin binding of FOXG1

The paper identifies Pantr1 as a lncRNA regulated by FOXG1 that facilitates FOXG1's site-specific chromatin binding and impacts neuronal development.

DOT1L deletion impairs the development of cortical Parvalbumin-expressing interneurons

This study shows that DOT1L deletion reduces and alters the distribution of GABAergic interneurons, particularly Parvalbumin-expressing cells, in the cortical plate.

Integrative multi-omics analyses reveal multi-modal FOXG1 functions acting on epigenetic processes and in concert with NEUROD1 to regulate synaptogenesis in the mouse hippocampus

The paper uses multi-omics data to show FOXG1 regulates transcription and epigenetic processes in mouse hippocampal neurons, working with NEUROD1 to control synaptogenesis.

DOT1L activity affects cell lineage progression in the developing brain by controlling metabolic programs

This study shows that DOT1L activity regulates AP lineage progression in the developing mouse neocortex by controlling metabolic programs and gene expression.

Single-cell transcriptomic resolution of stem cells and their developmental trajectories in the hippocampus reveals epigenetic control of cell state perseverance

The paper uses single-cell RNA sequencing to study hippocampal development in DOT1L-mutant mice, identifying distinct neural stem cell populations and their developmental trajectories, revealing DOT1L's role in cell state preservation and hippocampal maturation.

Making many out of few: deep generative models for single-cell RNA-sequencing data

This study evaluates deep generative models for scRNA-seq data, finding that they can support experimental design but have limitations in capturing cell type proportions and bimodal gene distributions.

DOT1L Methyltransferase Activity Preserves SOX2-Enhancer Accessibility And Prevents Activation of Repressed Genes In Murine Stem Cells

This study investigates how DOT1L methyltransferase activity affects chromatin states and gene expression during neuronal differentiation of mouse embryonic stem cells.