Cole Trapnell

A DNA Typewriter records the cell lineage history of a mouse, from zygote to late organogenesis

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.

GM-CSF Programs Alveolar Macrophages to Maintain Pulmonary Lymphocyte Homeostasis

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

Distinct transcriptional programs define cranial motor neuron subtypes during vertebrate development

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

Early immune cell development precedes gastrulation in annual killifish

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

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.

Embryo-scale Visual Cell Sorting reveals a conserved transcriptomic signature of nucleolar size linked to proteostasis

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.

Single-cell, multi-region profiling of the macaque brain across the lifespan

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.

Developmental regulation of endothelial-to-hematopoietic transition from induced pluripotent stem cells

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

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.

The regulatory potential of transposable elements in maize

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

Embryo-scale single-cell chemical transcriptomics reveals dependencies between cell types and signaling pathways

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

A statistical framework for inferring genetic requirements from embryo-scale single-cell sequencing experiments

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.

A multiplexed, single-cell sequencing screen identifies compounds that increase neurogenic reprogramming of murine Muller glia.

BMP-dependent oligoclonal cancer attractor state precedes neural crest fate in melanoma initiation

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.

Single-cell analysis of chromatin and expression reveals age- and sex-associated alterations in the human heart

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.

Optics-free reconstruction of shapes, images and volumes with DNA barcode proximity graphs

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

Multiplexed single cell transcriptomics optimizes mesodermal patterning and hemogenic endothelial output from murine embryonic 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.

A single-cell transcriptional timelapse of mouse embryonic development, from gastrula to pup

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.

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.

High-Capacity Sample Multiplexing for Single Cell Chromatin Accessibility Profiling

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.

Proteostasis governs differential temperature sensitivity across embryonic cell types

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.

Single-cell sequencing of individual retinal organoids reveals determinants of cell fate heterogeneity

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

Differentiation latency, cell division symmetry, and dormancy signatures define fetal liver HSCs at single cell resolution

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.

Transcriptomic profiling of tissue environments critical for post-embryonic patterning and morphogenesis of zebrafish skin

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.

Single-Cell Transcriptomic Profiling of the Zebrafish Inner Ear Reveals Molecularly Distinct Hair Cell and Supporting Cell Subtypes

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.

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.

Deep molecular, cellular and temporal phenotyping of developmental perturbations at whole organism scale

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

Single cell, whole embryo phenotyping of pleiotropic disorders of mammalian development

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

Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivation

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.

Multipotent progenitors and hematopoietic stem cells arise independently during the endothelial to hematopoietic transition in the early mouse embryo

The paper shows that multipotent progenitors and HSC arise from distinct HE populations during mouse embryogenesis, identified through clonal assays and single-cell transcriptomics.