Frank J. Steemers

High-content single-cell combinatorial indexing

This paper introduces a novel adaptor-switching strategy, s3, that significantly improves usable reads per cell in single-cell genomics assays while maintaining high-throughput capabilities.

Spatially-mapped single-cell chromatin accessibility

The paper introduces sciMAP-ATAC, a method for spatially resolved single-cell chromatin accessibility profiling, and applies it to study cortical lamination, spatial trajectories, and ischemic infarct progression in mouse and human tissues.

Characterizing the temporal dynamics of gene expression in single cells with sci-fate

The paper introduces sci-fate, a method to profile both newly synthesized and total transcriptomes in single cells, and applies it to study cortisol response dynamics in over 6,000 cells.

Transcriptomic evidence that von Economo neurons are regionally specialized extratelencephalic-projecting excitatory neurons

The paper identifies von Economo neurons as a regionally specialized subtype of extratelencephalic-projecting excitatory neurons using single nucleus RNA-sequencing and cross-species comparisons.

High-throughput mapping of meiotic crossover and chromosome mis-segregation events in interspecific hybrid mice

The paper develops sci-LIANTI, a single-cell DNA sequencing method, to map meiotic crossovers and chromosome mis-segregation in hybrid mice, finding frequent mitotic segregation during meiosis.

Improved single-cell ATAC-seq reveals chromatin dynamics of in vitro corticogenesis

The paper introduces an improved single-cell ATAC-seq method, scip-ATAC-seq, which enhances chromatin dynamics analysis in human corticogenesis organoids.

Droplet-based combinatorial indexing for massive scale single-cell epigenomics

The paper introduces a droplet-based combinatorial indexing method for high-throughput scATAC-seq, enabling large-scale single-cell chromatin accessibility profiling in mouse and human cells.

The accessible chromatin landscape of the hippocampus at single-cell resolution

The paper presents a single-cell chromatin accessibility map of the mouse hippocampus using sci-ATAC-seq, identifies cell-type-specific regulatory networks, and provides a resource for future studies.

Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type

The paper identifies a novel human cortical GABAergic interneuron subtype with unique transcriptomic, morphological, and physiological features not observed in rodents.

Scalable and efficient single-cell DNA methylation sequencing by combinatorial indexing.

The paper introduces sci-MET, a scalable single-cell DNA methylation sequencing method, achieving 69% read alignment rates and successfully deconvolving a mixture of three human cell lines.

The cis-regulatory dynamics of embryonic development at single cell resolution

The paper profiles chromatin accessibility in Drosophila embryos to uncover cis-regulatory programs and cell fate determinants during development.

Comprehensive single cell transcriptional profiling of a multicellular organism by combinatorial indexing

This paper introduces sci-RNA-seq, a combinatorial indexing method for single-cell RNA sequencing, and applies it to profile 42,035 C. elegans cells, identifying 27 cell types and their specific genes.

Chromatin accessibility dynamics of myogenesis at single cell resolution

The paper introduces Cicero, a statistical method to link regulatory elements to target genes using single-cell chromatin accessibility data, and applies it to study myogenesis.

Construction of thousands of single cell genome sequencing libraries using combinatorial indexing

The paper introduces SCI-seq, a method to generate thousands of low-cost single-cell libraries for somatic copy number variant detection across various tissues.