Greenleaf, William J.

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

Buenrostro, J. D., Giresi, P. G., Zaba, L. C., Chang, H. Y., & Greenleaf, W. J. (2013) · Nature Methods

Genomics and Chromatin DynamicsEpigenetics and DNA Methylation

Cited by 6,422

ATAC-seq: a method for assaying chromatin accessibility genome-wide

Buenrostro, J. D., Wu, B., Chang, H. Y., & Greenleaf, W. J. (2015) · Current Protocols in Molecular Biology

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 3,289

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

Corces, M. R., Trevino, A. E., Hamilton, E. G., Greenside, P. G., Sinnott-Armstrong, N. A., Vesuna, S., Satpathy, A. T., Rubin, A. J., Montine, K. S., Wu, B., et al. (2017) · Nature Methods

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 2,496

Single-cell chromatin accessibility reveals principles of regulatory variation

Buenrostro, J. D., Wu, B., Litzenburger, U. M., Ruff, D., Gonzales, M. L., Snyder, M. P., Chang, H. Y., & Greenleaf, W. J. (2015) · Nature

Genomics and Chromatin DynamicsSingle-cell and spatial transcriptomics

Cited by 2,308

Chromatin accessibility and the regulatory epigenome

Klemm, S. L., Shipony, Z., & Greenleaf, W. J. (2019) · Nature Reviews Genetics

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 1,793

chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data

Schep, A. N., Wu, B., Buenrostro, J. D., & Greenleaf, W. J. (2017) · Nature Methods

Genomics and Chromatin DynamicsSingle-cell and spatial transcriptomics

Cited by 1,680

ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis

Granja, J. M., Corces, M. R., Pierce, S. E., Bagdatli, S. T., Choudhry, H., Chang, H. Y., & Greenleaf, W. J. (2021) · Nature Genetics

Single-cell and spatial transcriptomicsGenomics and Chromatin Dynamics

Cited by 1,392

The chromatin accessibility landscape of primary human cancers

Corces, M. R., Granja, J. M., Shams, S., Louie, B. H., Seoane, J. A., Zhou, W., Silva, T. C., Groeneveld, C., Wong, C. K., Cho, S. W., et al. (2018) · Science

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 1,230

Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution

Corces, M. R., Buenrostro, J. D., Wu, B., Greenside, P. G., Chan, S. M., Koenig, J. L., Snyder, M. P., Pritchard, J. K., Kundaje, A., Greenleaf, W. J., et al. (2016) · Nature Genetics

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 1,151

HiChIP: efficient and sensitive analysis of protein-directed genome architecture

Mumbach, M. R., Rubin, A. J., Flynn, R. A., Dai, C., Khavari, P. A., Greenleaf, W. J., & Chang, H. Y. (2016) · Nature Methods

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 1,139

Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion

Satpathy, A. T., Granja, J. M., Yost, K. E., Qi, Y., Meschi, F., McDermott, G. P., Olsen, B. N., Mumbach, M. R., Pierce, S. E., Corces, M. R., et al. (2019) · Nature Biotechnology

Single-cell and spatial transcriptomicsGenomics and Chromatin Dynamics

Cited by 980

Integrated Single-Cell Analysis Maps the Continuous Regulatory Landscape of Human Hematopoietic Differentiation

Buenrostro, J. D., Corces, M. R., Lareau, C. A., Wu, B., Schep, A. N., Aryee, M. J., Majeti, R., Chang, H. Y., & Greenleaf, W. J. (2018) · Cell

Genomics and Chromatin DynamicsSingle-cell and spatial transcriptomics

Cited by 670

The human body at cellular resolution: the NIH Human Biomolecular Atlas Program

HuBMAP Consortium, Writing Group, Snyder, M. P., Lin, S., Posgai, A., Atkinson, M., Regev, A., Rood, J., Rozenblatt-Rosen, O., Gaffney, L., et al. (2019) · Nature

Single-cell and spatial transcriptomicsGenomics and Chromatin Dynamics

Cited by 595

Origin and differentiation of human memory CD8 T cells after vaccination

Akondy, R. S., Fitch, M., Edupuganti, S., Yang, S., Kissick, H. T., Li, K. W., Youngblood, B. A., Abdelsamed, H. A., McGuire, D. J., Cohen, K. W., et al. (2017) · Nature

T-cell and B-cell ImmunologyImmune responses and vaccinations

Cited by 517

Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia

Granja, J. M., Klemm, S., McGinnis, L. M., Kathiria, A. S., Mezger, A., Corces, M. R., Parks, B., Gars, E., Liedtke, M., Zheng, G. X. Y., et al. (2019) · Nature Biotechnology

Single-cell and spatial transcriptomicsGenomics and Chromatin Dynamics

Cited by 498

Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements

Mumbach, M. R., Satpathy, A. T., Boyle, E. A., Dai, C., Gowen, B. G., Cho, S. W., Nguyen, M. L., Rubin, A. J., Granja, J. M., Kazane, K. R., et al. (2017) · Nature Genetics

Genomics and Chromatin DynamicsGenetic Associations and Epidemiology

Cited by 490

Chromatin and gene-regulatory dynamics of the developing human cerebral cortex at single-cell resolution

Trevino, A. E., Müller, F., Andersen, J., Sundaram, L., Kathiria, A., Shcherbina, A., Farh, K., Chang, H. Y., Pașca, A. M., Kundaje, A., et al. (2021) · Cell

Single-cell and spatial transcriptomicsGenomics and Chromatin Dynamics

Cited by 478

Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions

Schep, A. N., Buenrostro, J. D., Denny, S. K., Schwartz, K., Sherlock, G., & Greenleaf, W. J. (2015) · Genome Research

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 375

Single-cell epigenomic analyses implicate candidate causal variants at inherited risk loci for Alzheimer’s and Parkinson’s diseases

Corces, M. R., Shcherbina, A., Kundu, S., Gloudemans, M. J., Frésard, L., Granja, J. M., Louie, B. H., Eulalio, T., Shams, S., Bagdatli, S. T., et al. (2020) · Nature Genetics

Genetic Associations and EpidemiologyGenomics and Chromatin Dynamics

Cited by 358

Coupled Single-Cell CRISPR Screening and Epigenomic Profiling Reveals Causal Gene Regulatory Networks

Rubin, A. J., Parker, K. R., Satpathy, A. T., Qi, Y., Wu, B., Ong, A. J., Mumbach, M. R., Ji, A. L., Kim, D. S., Cho, S. W., et al. (2019) · Cell

Genomics and Chromatin DynamicsCRISPR and Genetic Engineering

Cited by 314

Discovery of stimulation-responsive immune enhancers with CRISPR activation

Simeonov, D. R., Gowen, B. G., Boontanrart, M., Roth, T. L., Gagnon, J. D., Mumbach, M. R., Satpathy, A. T., Lee, Y., Bray, N. L., Chan, A. Y., et al. (2017) · Nature

Genomics and Chromatin DynamicsCRISPR and Genetic Engineering

Cited by 297

Lineage-specific dynamic and pre-established enhancer-promoter contacts cooperate in terminal differentiation

Rubin, A. J., Barajas, B. C., Furlan-Magaril, M., Lopez-Pajares, V., Mumbach, M. R., Howard, I., Kim, D. S., Boxer, L. D., Cairns, J., Spivakov, M., et al. (2017) · Nature Genetics

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 293

Epigenomics of human CD8 T cell differentiation and aging

Moskowitz, D. M., Zhang, D. W., Hu, B., Le Saux, S., Yanes, R. E., Ye, Z., Buenrostro, J. D., Weyand, C. M., Greenleaf, W. J., & Goronzy, J. J. (2017) · Science Immunology

T-cell and B-cell ImmunologyGenomics and Chromatin Dynamics

Cited by 252

Chromatin accessibility dynamics in a model of human forebrain development

Trevino, A. E., Sinnott-Armstrong, N., Andersen, J., Yoon, S.-J., Huber, N., Pritchard, J. K., Chang, H. Y., Greenleaf, W. J., & Pașca, S. P. (2020) · Science

Genomics and Chromatin DynamicsNeurogenesis and neuroplasticity mechanisms

Cited by 251