Cole Trapnell

Career Trajectory

Research Cluster Map

Direct collaborators. Node size = influence, colour = community, dashed = past collaboration.

• Early immune cell development precedes gastrulation in annual killifish

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-06-26

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

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-05-26

• Author response: Optics-free reconstruction of shapes, images and volumes with DNA barcode proximity graphs

  2026-04-28

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

  eLife · 2026-04-28 · 1 citations

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

  eLife · 2026-04-28 · 1 citations

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

  2026-04-06 · 1 citations

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

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-11-01

• Primordial germ cell specification and early developmental cell states in Pacific oyster

  BMC Genomics · 2025-10-23 · 1 citations

• Differentiation latency and dormancy signatures define fetal liver hematopoietic stem cells at single-cell resolution

  Cell Reports · 2025-09-23 · 1 citations

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

  Stem Cell Reports · 2025-09-23 · 3 citations

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

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-05-24 · 4 citations

• The regulatory potential of transposable elements in maize

  Nature Plants · 2025-05-13 · 17 citations

• Longitudinal Single-Cell Analysis of Asbestos-Induced Pulmonary Fibrosis

  American Journal of Respiratory and Critical Care Medicine · 2025-05-01

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

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-04-04 · 4 citations

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

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-04-03 · 3 citations

• An Improved, High-Yield Method for Isolating Nuclei from Individual Zebrafish Embryos for Single-Nucleus RNA Sequencing

  Zebrafish · 2025-03-05

• Transcriptional activation of regenerative hematopoiesis via microenvironmental sensing

  Nature Immunology · 2025-02-25 · 6 citations

• Combinatorial mapping of E3 ubiquitin ligases to their target substrates

  Molecular Cell · 2025-02-01 · 20 citations

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

  eLife · 2024-12-12 · 1 citations

• Author response: A multiplexed, single-cell sequencing screen identifies compounds that increase neurogenic reprogramming of murine Muller glia

  2024-12-12