Silvia Domcke

High-throughput identification of chromatin-opening transcription factors

The paper identifies chromatin-opening transcription factors in mouse embryonic stem cells using CRISPRa screens, revealing autonomous, opportunistic, and hierarchical mechanisms.

Addressing technical variations in ATAC-seq data and improving motif accessibility analyses

The paper introduces three R/bioconductor packages to address technical variations in ATAC-seq data and improve motif accessibility analysis.

Evolutionary transfer learning enables organism-wide inference of mammalian enhancer landscapes

The paper develops STEAM, an evolution-augmented deep learning model, to predict mammalian enhancer landscapes across species using comparative genomics and single-cell data.

Lineage recording in monoclonal gastruloids reveals heritable modes of early development

The paper develops monoclonal gastruloids from single mouse embryonic stem cells and uses DNA Typewriter to reveal heritable lineage biases in early development.

Barcoded monoclonal embryoids are a potential solution to confounding bottlenecks in mosaic organoid screens

The paper develops monoclonal embryoids with genetic barcoding to overcome clonal complexity bottlenecks in mosaic organoid screens, enabling more accurate quantification of genetic perturbation effects.

Multiplex, single-cell CRISPRa screening for cell type specific regulatory elements

The paper describes a CRISPRa screening method combining multiplex perturbations with sc-RNA-seq to identify cell-type-specific regulatory elements and their target genes.

Multiplex single-cell chemical genomics reveals the kinase dependence of the response to targeted therapy

The paper uses a combined single-cell genetic and chemical screening platform to analyze kinase dependencies in glioblastoma response to targeted therapy, identifying adaptive signaling and potential combination therapies.

Non-coding variants are a rare cause of recessive developmental disorders in trans with coding variants

The paper identifies non-coding variants in trans with coding variants in patients with developmental disorders, finding them to be a rare cause of recessive disorders.

Multiplex profiling of developmental enhancers with quantitative, single-cell expression reporters

This paper develops scQers, single-cell quantitative expression reporters, to measure enhancer activity across multicellular systems with high precision and range.

A temporally resolved, multiplex molecular recorder based on sequential genome editing

This paper introduces DNA Ticker Tape, a system for in vivo molecular recording that sequentially records events using CRISPR-Cas9 and prime editing, demonstrating its ability to record complex event histories and cell lineage.