Dixon, Jesse R.

Topological domains in mammalian genomes identified by analysis of chromatin interactions

Dixon, J. R., Selvaraj, S., Yue, F., Kim, A., Li, Y., Shen, Y., Hu, M., Liu, J. S., & Ren, B. (2012) · Nature

Genomics and Chromatin DynamicsChromosomal and Genetic Variations

Cited by 6,829

Integrative analysis of 111 reference human epigenomes

Roadmap Epigenomics Consortium, Kundaje, A., Meuleman, W., Ernst, J., Bilenky, M., Yen, A., Heravi-Moussavi, A., Kheradpour, P., Zhang, Z., Wang, J., et al. (2015) · Nature

Genomics and Chromatin DynamicsEpigenetics and DNA Methylation

Cited by 6,368

Chromatin architecture reorganization during stem cell differentiation

Dixon, J. R., Jung, I., Selvaraj, S., Shen, Y., Antosiewicz-Bourget, J. E., Lee, A. Y., Ye, Z., Kim, A., Rajagopal, N., Xie, W., et al. (2015) · Nature

Genomics and Chromatin DynamicsEpigenetics and DNA Methylation

Cited by 1,646

A map of the cis-regulatory sequences in the mouse genome

Shen, Y., Yue, F., McCleary, D. F., Ye, Z., Edsall, L., Kuan, S., Wagner, U., Dixon, J., Lee, L., Lobanenkov, V. V., et al. (2012) · Nature

Genomics and Chromatin DynamicsChromosomal and Genetic Variations

Cited by 1,361

A high-resolution map of the three-dimensional chromatin interactome in human cells

Jin, F., Li, Y., Dixon, J. R., Selvaraj, S., Ye, Z., Lee, A. Y., Yen, C.-A., Schmitt, A. D., Espinoza, C. A., & Ren, B. (2013) · Nature

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 1,208

Chromatin Domains: The Unit of Chromosome Organization

Dixon, J. R., Gorkin, D. U., & Ren, B. (2016) · Molecular Cell

Genomics and Chromatin DynamicsNuclear Structure and Function

Cited by 811

Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells

Zuin, J., Dixon, J. R., van der Reijden, M. I. J. A., Ye, Z., Kolovos, P., Brouwer, R. W. W., van de Corput, M. P. C., van de Werken, H. J. G., Knoch, T. A., van IJcken, W. F. J., et al. (2014) · Proceedings of the National Academy of Sciences

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 779

Integrative detection and analysis of structural variation in cancer genomes

Dixon, J. R., Xu, J., Dileep, V., Zhan, Y., Song, F., Le, V. T., Yardımcı, G. G., Chakraborty, A., Bann, D. V., Wang, Y., et al. (2018) · Nature Genetics

Genomic variations and chromosomal abnormalitiesCancer Genomics and Diagnostics

Cited by 452

Simultaneous profiling of 3D genome structure and DNA methylation in single human cells

Lee, D.-S., Luo, C., Zhou, J., Chandran, S., Rivkin, A., Bartlett, A., Nery, J. R., Fitzpatrick, C., O’Connor, C., Dixon, J. R., et al. (2019) · Nature Methods

Genomics and Chromatin DynamicsEpigenetics and DNA Methylation

Cited by 340

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

Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer

Akdemir, K. C., Le, V. T., Chandran, S., Li, Y., Verhaak, R. G., Beroukhim, R., Campbell, P. J., Chin, L., Dixon, J. R., Futreal, P. A., et al. (2020) · Nature Genetics

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 283

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

Robust single-cell Hi-C clustering by convolution- and random-walk-based imputation

Zhou, J., Ma, J., Chen, Y., Cheng, C., Bao, B., Peng, J., Sejnowski, T. J., Dixon, J. R., & Ecker, J. R. (2019) · Proceedings of the National Academy of Sciences

Genomics and Chromatin DynamicsSingle-cell and spatial transcriptomics

Cited by 180

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

Incorporation of a nucleoside analog maps genome repair sites in postmitotic human neurons

Reid, D. A., Reed, P. J., Schlachetzki, J. C. M., Nitulescu, I. I., Chou, G., Tsui, E. C., Jones, J. R., Chandran, S., Lu, A. T., McClain, C. A., et al. (2021) · Science

DNA Repair MechanismsDNA and Nucleic Acid Chemistry

Cited by 121

Coming full circle: On the origin and evolution of the looping model for enhancer–promoter communication

Popay, T. M., & Dixon, J. R. (2022) · Journal of Biological Chemistry

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 94

Genome-wide in vivo dynamics of cohesin-mediated loop extrusion and its role in transcription activation

Popay, T. M., Pant, A., Munting, F., Black, M. E., Haghani, N., & Dixon, J. R. (2024) · Nature Genetics

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 15