Cole Trapnell

A prime-editing recorder in one mouse embryo yields a dated, zygote-rooted lineage tree of 1.28M cells at E13.5, enabling clonal dominance, sibling-fate and cell-type coupling analyses.

This study identifies GM-CSF as a regulator of pulmonary lymphocyte homeostasis by controlling alveolar macrophage function and preventing lymphocytosis.

This study identifies distinct transcriptional programs in zebrafish cranial motor neurons during development, showing that identity precedes axon targeting and is conserved across species.

The paper shows that in annual killifish, neutrophils develop before gastrulation, challenging the conserved BMP-driven myeloid lineage model.

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

The paper develops a high-throughput Visual Cell Sorting workflow to link nuclear compartment morphology to single-nucleus transcriptomes, identifying a conserved transcriptional signature of nucleolar size linked to proteostasis.

This study profiles 5.3 million cells from 55 rhesus macaques across their lifespan to map age-related changes in brain cell types and identify molecular signatures linked to aging and Alzheimer's disease.

The paper maps single-cell dynamics of endothelial-to-hematopoietic transition from iPSCs and identifies FGF signaling modulation to improve hematopoietic output.

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.

This study uses Fiber-seq to analyze TE regulatory potential in maize, revealing epigenetic patterns and gene interaction mechanisms.

The paper uses single-cell RNA-seq to study signaling pathway dependencies in zebrafish pectoral fin development, identifying new cell types and signaling relationships.

This paper introduces two tools to infer genetic requirements from single-cell sequencing data of perturbed embryos, revealing new roles for transcription factors in zebrafish development.

The paper identifies a BMP-dependent attractor state in melanoma precursor cells that precedes neural crest fate and is associated with ID1 expression in human melanoma.

The paper uses single-nucleus ATAC-Seq and RNA-Seq to analyze age and sex differences in human heart cells, identifying gene expression and chromatin changes linked to these factors.

The paper introduces SCOPE, an optics-free method to reconstruct 2D and 3D shapes using DNA barcode proximity graphs from sequencing data.

This study shows that dystrophin deficiency disrupts cell junction formation during embryonic myogenesis in human pluripotent stem cells.

This study uses sci-Plex to analyze how Activin and BMP4 gradients affect mesoderm patterning and hemogenic endothelial cell production in mouse embryonic stem cells.

12.4 million single-nucleus transcriptomes from 83 staged mouse embryos (E8 to P0) yield 190 cell types, a zygote-to-pup cell-type tree, and rapid postnatal transcriptional shifts.

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.

The paper introduces sciPlex-ATAC-seq for high-capacity multiplexing of single-cell chromatin accessibility, demonstrating its use in chemical epigenomics and immune stimulation studies.

The paper uses single-cell RNA-seq to study temperature sensitivity in zebrafish embryos, finding that notochord sheath cells are particularly vulnerable due to protein misfolding.

The paper uses sci-Plex to analyze retinal organoids and identifies that early Wnt signaling increases retinal cell classes.

The paper identifies rare fetal liver HSCs with unique features like differentiation latency and dormancy signatures using single cell RNA-sequencing and a niche-mimicking culture platform.

The paper uses single-cell transcriptomics to study zebrafish skin development, identifying new cell types and signaling mechanisms involved in pigment pattern and scale formation.

The paper uses single-cell RNA sequencing to analyze zebrafish inner ear cells, identifying distinct hair cell and supporting cell subtypes and their spatial organization.

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

The paper presents single cell transcriptomic data from zebrafish embryos with genetic perturbations to analyze developmental variation and cell type composition.

The paper uses single-cell RNA sequencing to systematically phenotype mouse genetic models, identifying molecular and cellular changes across multiple mutants and wildtypes.

The paper integrates single-cell RNA-seq, ATAC-seq, and Hi-C data to study nuclear configuration and gene expression changes during stem cell differentiation and X inactivation, revealing discrete structural changes and delayed chromatin compaction.