Stephan Fischer

Identification of pleiotropic genes and biological mechanisms underlying the shared genetic component between asthma, neuropsychiatric disorders, and substance use behaviors

The paper identifies pleiotropic genes and mechanisms linking asthma, neuropsychiatric disorders, and substance use behaviors through multi-trait GWAS and single-cell transcriptomics.

Ontogeny drives stage-specific effects of a Gata1 mutation

The paper shows that a Gata1 mutation affects megakaryocyte development differently in fetal and adult stages due to distinct progenitor origins.

Improving replicability in single-cell RNA-Seq cell type discovery with Dune

Dune improves replicability of cell type discovery in scRNA-Seq by optimizing the trade-off between cluster resolution and cross-dataset consistency.

The transcriptional legacy of developmental stochasticity

Longitudinal gene expression in identical armadillo quadruplets reveals a major role for developmental stochasticity.

Learning single-cell chromatin accessibility profiles using meta-analytic marker genes

The paper benchmarks neuronal cell-type annotation in scATAC-seq data using marker genes and introduces a deep learning model to predict chromatin accessibility from DNA sequence.

Whole-cortex in situ sequencing reveals peripheral input-dependent cell type-defined area identity

The paper uses BARseq to analyze transcriptomic signatures in mouse cortex, showing that cell type composition defines area identity and is shaped by peripheral inputs.

Defining the extent of gene function using ROC curvature

This paper introduces Functional Equivalence Classes (FECs) to assess gene function generalizability by analyzing ROC curve shapes, revealing shared and tissue-specific markers.

How many markers are needed to robustly determine a cell's type?

The paper investigates how many markers are needed to robustly determine cell types using data from the BICCN, finding that 10 to 200 meta-analytic markers provide optimal performance.

Evolution of cellular diversity in primary motor cortex of human, marmoset monkey, and mouse

The paper compares cellular diversity in the primary motor cortex across human, marmoset, and mouse using single-nucleus transcriptomics and epigenomics, finding conserved cell types and species-specific adaptations.

An integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types

The paper creates a comprehensive atlas of mouse primary motor cortex cell types using integrated transcriptomic and epigenomic data from over 600,000 samples.

Cellular Anatomy of the Mouse Primary Motor Cortex

The paper provides a detailed cellular-resolution map of the mouse primary motor cortex, defining cell types and their connectivity.

Replicability of spatial gene expression atlas data from the adult mouse brain

The paper assesses the replicability of spatial gene expression data from the adult mouse brain between two datasets, finding that classification performance is higher within datasets than across platforms.

Multiscale Co-expression in the Brain

The paper analyzes scRNA-seq data from the primary motor cortex to show that gene-gene co-expression relationships are consistent across different scales, revealing a multiscale regulatory landscape.

Integrating barcoded neuroanatomy with spatial transcriptional profiling reveals cadherin correlates of projections shared across the cortex

The paper introduces BARseq2 to map neuronal projections and gene expression in mice, finding shared cadherin signatures across cortical areas.

High-throughput mapping of long-range neuronal projection using in situ sequencing

The paper introduces BARseq, a method for high-throughput mapping of neuronal projections in the mouse auditory cortex, revealing novel projection types in specific cell subtypes.