Trapnell, Cole

On the design of CRISPR-based single-cell molecular screens

Hill, A. J., McFaline-Figueroa, J. L., Starita, L. M., Gasperini, M. J., Matreyek, K. A., Packer, J., Jackson, D., Shendure, J., & Trapnell, C. (2018) · Nature Methods

CRISPR and Genetic EngineeringSingle-cell and spatial transcriptomics

Cited by 262

Single-cell transcriptome sequencing: recent advances and remaining challenges

Liu, S., & Trapnell, C. (2016) · F1000Research

Single-cell and spatial transcriptomicsGenomics and Phylogenetic Studies

Cited by 230

Inferring Causal Gene Regulatory Networks from Coupled Single-Cell Expression Dynamics Using Scribe

Qiu, X., Rahimzamani, A., Wang, L., Ren, B., Mao, Q., Durham, T., McFaline-Figueroa, J. L., Saunders, L., Trapnell, C., & Kannan, S. (2020) · Cell Systems

Gene Regulatory Network AnalysisSingle-cell and spatial transcriptomics

Cited by 185

Thyroid hormone regulates distinct paths to maturation in pigment cell lineages

Saunders, L. M., Mishra, A. K., Aman, A. J., Lewis, V. M., Toomey, M. B., Packer, J. S., Qiu, X., McFaline-Figueroa, J. L., Corbo, J. C., Trapnell, C., et al. (2019) · eLife

Developmental Biology and Gene Regulationmelanin and skin pigmentation

Cited by 170

What Is Your Conceptual Definition of “Cell Type” in the Context of a Mature Organism?

Clevers, H., Rafelski, S., Elowitz, M. B., Klein, A., Shendure, J., Trapnell, C., Lein, E., Lundberg, E. K., Uhlén, M., Martinez-Arias, A., et al. (2017) · Cell Systems

Single-cell and spatial transcriptomicsDevelopmental Biology and Gene Regulation

Cited by 108

Single-cell analyses reveal early thymic progenitors and pre-B cells in zebrafish

Rubin, S. A., Baron, C. S., Pessoa Rodrigues, C., Duran, M., Corbin, A. F., Yang, S. P., Trapnell, C., & Zon, L. I. (2022) · Journal of Experimental Medicine

Zebrafish Biomedical Research ApplicationsT-cell and B-cell Immunology

Cited by 56

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

Aman, A. J., Saunders, L. M., Carr, A. A., Srivatasan, S., Eberhard, C., Carrington, B., Watkins-Chow, D., Pavan, W. J., Trapnell, C., & Parichy, D. M. (2023) · eLife

Developmental Biology and Gene RegulationZebrafish Biomedical Research Applications

Cited by 30

Chromatin accessibility dynamics of myogenesis at single cell resolution

Pliner, H. A., Packer, J., McFaline-Figueroa, J. L., Cusanovich, D. A., Daza, R., Srivatsan, S., Qiu, X., Jackson, D., Minkina, A., Adey, A., et al. (2017) · bioRxiv (Cold Spring Harbor Laboratory)

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 16