Welch, Joshua D.

Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution

Rodriques, S. G., Stickels, R. R., Goeva, A., Martin, C. A., Murray, E., Vanderburg, C. R., Welch, J., Chen, L. M., Chen, F., & Macosko, E. Z. (2019) · Science

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 2,424

Single-Cell Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity

Welch, J. D., Kozareva, V., Ferreira, A., Vanderburg, C., Martin, C., & Macosko, E. Z. (2019) · Cell

Single-cell and spatial transcriptomicsGene Regulatory Network Analysis

Cited by 1,193

A multimodal cell census and atlas of the mammalian primary motor cortex

BRAIN Initiative Cell Census Network (BICCN), BRAIN Initiative Cell Census Network (BICCN) Corresponding authors, Callaway, E. M., Dong, H.-W., Ecker, J. R., Hawrylycz, M. J., Huang, Z. J., Lein, E. S., Ngai, J., Osten, P., et al. (2021) · Nature

Single-cell and spatial transcriptomicsGenomics and Chromatin Dynamics

Cited by 522

A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex

Yao, Z., Liu, H., Xie, F., Fischer, S., Adkins, R. S., Aldridge, A. I., Ament, S. A., Bartlett, A., Behrens, M. M., Van den Berge, K., et al. (2021) · Nature

Single-cell and spatial transcriptomicsGenomics and Chromatin Dynamics

Cited by 398

An integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types

Yao, Z., Liu, H., Xie, F., Fischer, S., Booeshaghi, A. S., Adkins, R. S., Aldridge, A. I., Ament, S. A., Pinto-Duarte, A., Bartlett, A., et al. (2020) · Nature

Single-cell and spatial transcriptomicsGenomics and Chromatin Dynamics

Cited by 397

MATCHER: manifold alignment reveals correspondence between single cell transcriptome and epigenome dynamics

Welch, J. D., Hartemink, A. J., & Prins, J. F. (2017) · Genome Biology

Single-cell and spatial transcriptomicsEpigenetics and DNA Methylation

Cited by 140

Multi-omic single-cell velocity models epigenome–transcriptome interactions and improves cell fate prediction

Li, C., Virgilio, M. C., Collins, K. L., & Welch, J. D. (2023) · Nature Biotechnology

Single-cell and spatial transcriptomicsGene Regulatory Network Analysis

Cited by 130

PerturbNet predicts single-cell responses to unseen chemical and genetic perturbations

Yu, H., & Welch, J. D. (2022) · Molecular Systems Biology

Single-cell and spatial transcriptomicsGene Regulatory Network Analysis

Cited by 57

PerturbNet predicts single-cell responses to unseen chemical and genetic perturbations

Yu, H., Qian, W., Song, Y., & Welch, J. D. (2025) · Molecular Systems Biology

Single-cell and spatial transcriptomicsGene Regulatory Network Analysis

Cited by 57

MichiGAN: sampling from disentangled representations of single-cell data using generative adversarial networks

Yu, H., & Welch, J. D. (2021) · Genome Biology

Single-cell and spatial transcriptomicsGene Regulatory Network Analysis

Cited by 38

HIV-1 Vpr combats the PU.1-driven antiviral response in primary human macrophages

Virgilio, M. C., Ramnani, B., Chen, T., Disbennett, W. M., Lubow, J., Welch, J. D., & Collins, K. L. (2024) · Nature Communications

HIV Research and Treatmentinterferon and immune responses

Cited by 14