Ren, Bing

DNA Methylation Atlas of the Mouse Brain at Single-Cell Resolution

Liu, H., Zhou, J., Tian, W., Luo, C., Bartlett, A., Aldridge, A., Lucero, J., Osteen, J. K., Nery, J. R., Chen, H., et al. (2020) · Nature

Single-cell and spatial transcriptomicsEpigenetics and DNA Methylation

Cited by 290

DNA methylation atlas of the mouse brain at single-cell resolution

Liu, H., Zhou, J., Tian, W., Luo, C., Bartlett, A., Aldridge, A., Lucero, J., Osteen, J. K., Nery, J. R., Chen, H., et al. (2021) · Nature

Single-cell and spatial transcriptomicsEpigenetics and DNA Methylation

Cited by 289

Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation

Kubo, N., Ishii, H., Xiong, X., Bianco, S., Meitinger, F., Hu, R., Hocker, J. D., Conte, M., Gorkin, D., Yu, M., et al. (2021) · Nature Structural & Molecular Biology

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 289

A tiling-deletion-based genetic screen for cis-regulatory element identification in mammalian cells

Diao, Y., Fang, R., Li, B., Meng, Z., Yu, J., Qiu, Y., Lin, K. C., Huang, H., Liu, T., Marina, R. J., et al. (2017) · Nature Methods

Genomics and Chromatin DynamicsCRISPR and Genetic Engineering

Cited by 259

Characterizing cis-regulatory elements using single-cell epigenomics

Preissl, S., Gaulton, K. J., & Ren, B. (2023) · Nature Reviews Genetics

Genomics and Chromatin DynamicsEpigenetics and DNA Methylation

Cited by 251

CRISPR Reveals a Distal Super-Enhancer Required for Sox2 Expression in Mouse Embryonic Stem Cells

Li, Y., Rivera, C. M., Ishii, H., Jin, F., Selvaraj, S., Lee, A. Y., Dixon, J. R., & Ren, B. (2014) · PLoS ONE

Pluripotent Stem Cells ResearchGenomics and Chromatin Dynamics

Cited by 212

CTCF mediates dosage- and sequence-context-dependent transcriptional insulation by forming local chromatin domains

Huang, H., Zhu, Q., Jussila, A., Han, Y., Bintu, B., Kern, C., Conte, M., Zhang, Y., Bianco, S., Chiariello, A. M., et al. (2021) · Nature Genetics

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 187

An Atlas of Gene Regulatory Elements in Adult Mouse Cerebrum

Li, Y. E., Preissl, S., Hou, X., Zhang, Z., Zhang, K., Fang, R., Qiu, Y., Poirion, O., Li, B., Liu, H., et al. (2020) · Nature

Genomics and Chromatin DynamicsSingle-cell and spatial transcriptomics

Cited by 187

A fast, scalable and versatile tool for analysis of single-cell omics data

Zhang, K., Zemke, N. R., Armand, E. J., & Ren, B. (2024) · Nature Methods

Single-cell and spatial transcriptomicsCell Image Analysis Techniques

Cited by 185

An atlas of gene regulatory elements in adult mouse cerebrum

Li, Y. E., Preissl, S., Hou, X., Zhang, Z., Zhang, K., Qiu, Y., Poirion, O. B., Li, B., Chiou, J., Liu, H., et al. (2021) · Nature

Genomics and Chromatin DynamicsSingle-cell and spatial transcriptomics

Cited by 185

Analysis of Genetically Diverse Macrophages Reveals Local and Domain-wide Mechanisms that Control Transcription Factor Binding and Function

Link, V. M., Duttke, S. H., Chun, H. B., Holtman, I. R., Westin, E., Hoeksema, M. A., Abe, Y., Skola, D., Romanoski, C. E., Tao, J., et al. (2018) · Cell

Genomics and Chromatin DynamicsGenetic Associations and Epidemiology

Cited by 182

A comparative atlas of single-cell chromatin accessibility in the human brain

Li, Y. E., Preissl, S., Miller, M., Johnson, N. D., Wang, Z., Jiao, H., Zhu, C., Wang, Z., Xie, Y., Poirion, O., et al. (2023) · Science

Genomics and Chromatin DynamicsSingle-cell and spatial transcriptomics

Cited by 173

The human noncoding genome defined by genetic diversity

di Iulio, J., Bartha, I., Wong, E. H. M., Yu, H.-C., Lavrenko, V., Yang, D., Jung, I., Hicks, M. A., Shah, N., Kirkness, E. F., et al. (2018) · Nature Genetics

Genetic Associations and EpidemiologyGenomics and Phylogenetic Studies

Cited by 161

Single-cell DNA methylation and 3D genome architecture in the human brain

Tian, W., Zhou, J., Bartlett, A., Zeng, Q., Liu, H., Castanon, R. G., Kenworthy, M., Altshul, J., Valadon, C., Aldridge, A., et al. (2023) · Science

Epigenetics and DNA MethylationSingle-cell and spatial transcriptomics

Cited by 154

Single-cell DNA methylome and 3D multi-omic atlas of the adult mouse brain

Liu, H., Zeng, Q., Zhou, J., Bartlett, A., Wang, B.-A., Berube, P., Tian, W., Kenworthy, M., Altshul, J., Nery, J. R., et al. (2023) · Nature

Epigenetics and DNA MethylationSingle-cell and spatial transcriptomics

Cited by 139

A new class of temporarily phenotypic enhancers identified by CRISPR/Cas9-mediated genetic screening

Diao, Y., Li, B., Meng, Z., Jung, I., Lee, A. Y., Dixon, J., Maliskova, L., Guan, K.-L., Shen, Y., & Ren, B. (2016) · Genome Research

Genomics and Chromatin DynamicsCRISPR and Genetic Engineering

Cited by 122

MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments

Juric, I., Yu, M., Abnousi, A., Raviram, R., Fang, R., Zhao, Y., Zhang, Y., Qiu, Y., Yang, Y., Li, Y., et al. (2019) · PLOS Computational Biology

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 121

Genome-wide prediction of transcription factor binding sites using an integrated model

Won, K.-J., Ren, B., & Wang, W. (2010) · Genome Biology

Genomics and Chromatin DynamicsGenomics and Phylogenetic Studies

Cited by 116

Comparative analyses of CTCF and BORIS occupancies uncover two distinct classes of CTCF binding genomic regions

Pugacheva, E. M., Rivero-Hinojosa, S., Espinoza, C. A., Méndez-Catalá, C. F., Kang, S., Suzuki, T., Kosaka-Suzuki, N., Robinson, S., Nagarajan, V., Ye, Z., et al. (2015) · Genome biology

Genomics and Chromatin DynamicsEpigenetics and DNA Methylation

Cited by 110

Single-cell epigenome analysis reveals age-associated decay of heterochromatin domains in excitatory neurons in the mouse brain

Zhang, Y., Amaral, M. L., Zhu, C., Grieco, S. F., Hou, X., Lin, L., Buchanan, J., Tong, L., Preissl, S., Xu, X., et al. (2022) · Cell Research

Genomics and Chromatin DynamicsEpigenetics and DNA Methylation

Cited by 89

SALL1 enforces microglia-specific DNA binding and function of SMADs to establish microglia identity

Fixsen, B. R., Han, C. Z., Zhou, Y., Spann, N. J., Saisan, P., Shen, Z., Balak, C., Sakai, M., Cobo, I., Holtman, I. R., et al. (2023) · Nature Immunology

Neuroinflammation and Neurodegeneration MechanismsTGF-β signaling in diseases

Cited by 87

ZNF143 mediates CTCF-bound promoter–enhancer loops required for murine hematopoietic stem and progenitor cell function

Zhou, Q., Yu, M., Tirado-Magallanes, R., Li, B., Kong, L., Guo, M., Tan, Z. H., Lee, S., Chai, L., Numata, A., et al. (2021) · Nature Communications

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 79

Droplet-based single-cell joint profiling of histone modifications and transcriptomes

Xie, Y., Zhu, C., Wang, Z., Tastemel, M., Chang, L., Li, Y. E., & Ren, B. (2023) · Nature Structural & Molecular Biology

Single-cell and spatial transcriptomicsGenomics and Chromatin Dynamics

Cited by 69

FIREcaller: Detecting frequently interacting regions from Hi-C data

Crowley, C., Yang, Y., Qiu, Y., Hu, B., Abnousi, A., Lipiński, J., Plewczyński, D., Wu, D., Won, H., Ren, B., et al. (2021) · Computational and Structural Biotechnology Journal

Genomics and Chromatin DynamicsBioinformatics and Genomic Networks

Cited by 37