Bernstein, Bradley E.

Model-based Analysis of ChIP-Seq (MACS)

Zhang, Y., Liu, T., Meyer, C. A., Eeckhoute, J., Johnson, D. S., Bernstein, B. E., Nusbaum, C., Myers, R. M., Brown, M., Li, W., et al. (2008) · Genome Biology

Genomics and Chromatin DynamicsGenomics and Phylogenetic Studies

Cited by 18,386

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

Lieberman-Aiden, E., van Berkum, N. L., Williams, L., Imakaev, M., Ragoczy, T., Telling, A., Amit, I., Lajoie, B. R., Sabo, P. J., Dorschner, M. O., et al. (2009) · Science

Genomics and Chromatin DynamicsChromosomal and Genetic Variations

Cited by 8,898

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

A bivalent chromatin structure marks key developmental genes in embryonic stem cells

Bernstein, B. E., Mikkelsen, T. S., Xie, X., Kamal, M., Huebert, D. J., Cuff, J., Fry, B., Meissner, A., Wernig, M., Plath, K., et al. (2006) · Cell

Epigenetics and DNA MethylationGenomics and Chromatin Dynamics

Cited by 5,361

Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma

Patel, A. P., Tirosh, I., Trombetta, J. J., Shalek, A. K., Gillespie, S. M., Wakimoto, H., Cahill, D. P., Nahed, B. V., Curry, W. T., Martuza, R. L., et al. (2014) · Science

Single-cell and spatial transcriptomicsGlioma Diagnosis and Treatment

Cited by 5,063

Genome-wide maps of chromatin state in pluripotent and lineage-committed cells

Mikkelsen, T. S., Ku, M., Jaffe, D. B., Issac, B., Lieberman, E., Giannoukos, G., Alvarez, P., Brockman, W., Kim, T.-K., Koche, R. P., et al. (2007) · Nature

Genomics and Chromatin DynamicsEpigenetics and DNA Methylation

Cited by 4,129

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

Guttman, M., Amit, I., Garber, M., French, C., Lin, M. F., Feldser, D., Huarte, M., Zuk, O., Carey, B. W., Cassady, J. P., et al. (2009) · Nature

Cancer-related molecular mechanisms researchGenomics and Chromatin Dynamics

Cited by 4,098

Mapping and analysis of chromatin state dynamics in nine human cell types

Ernst, J., Kheradpour, P., Mikkelsen, T. S., Shoresh, N., Ward, L. D., Epstein, C. B., Zhang, X., Wang, L., Issner, R., Coyne, M., et al. (2011) · Nature

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 2,898

Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression

Khalil, A. M., Guttman, M., Huarte, M., Garber, M., Raj, A., Rivea Morales, D., Thomas, K., Presser, A., Bernstein, B. E., van Oudenaarden, A., et al. (2009) · Proceedings of the National Academy of Sciences

Cancer-related molecular mechanisms researchGenomics and Chromatin Dynamics

Cited by 2,872

Single-Cell Transcriptomic Analysis of Primary and Metastatic Tumor Ecosystems in Head and Neck Cancer

Puram, S. V., Tirosh, I., Parikh, A. S., Patel, A. P., Yizhak, K., Gillespie, S., Rodman, C., Luo, C. L., Mroz, E. A., Emerick, K. S., et al. (2017) · Cell

Single-cell and spatial transcriptomicsCancer Cells and Metastasis

Cited by 2,557

Genome-scale DNA methylation maps of pluripotent and differentiated cells

Meissner, A., Mikkelsen, T. S., Gu, H., Wernig, M., Hanna, J., Sivachenko, A., Zhang, X., Bernstein, B. E., Nusbaum, C., Jaffe, D. B., et al. (2008) · Nature

Epigenetics and DNA MethylationGenomics and Chromatin Dynamics

Cited by 2,536

Active Genes Are Tri-Methylated at K4 of Histone H3

Santos-Rosa, H., Schneider, R., Bannister, A. J., Sherriff, J., Bernstein, B. E., Emre, N. C. T., Schreiber, S. L., Mellor, J., & Kouzarides, T. (2002) · Nature

Genomics and Chromatin DynamicsEpigenetics and DNA Methylation

Cited by 2,138

The Mammalian Epigenome

Bernstein, B. E., Meissner, A., & Lander, E. S. (2007) · Cell

Epigenetics and DNA MethylationGenomics and Chromatin Dynamics

Cited by 2,086

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

Landt, S. G., Marinov, G. K., Kundaje, A., Kheradpour, P., Pauli, F., Batzoglou, S., Bernstein, B. E., Bickel, P., Brown, J. B., Cayting, P., et al. (2012) · Genome Research

Genomics and Chromatin DynamicsGenomics and Phylogenetic Studies

Cited by 2,033

Genetic and epigenetic fine mapping of causal autoimmune disease variants

Farh, K. K.-H., Marson, A., Zhu, J., Kleinewietfeld, M., Housley, W. J., Beik, S., Shoresh, N., Whitton, H., Ryan, R. J. H., Shishkin, A. A., et al. (2015) · Nature

Genetic Associations and EpidemiologyGenomics and Chromatin Dynamics

Cited by 1,956

The NIH Roadmap Epigenomics Mapping Consortium

Bernstein, B. E., Stamatoyannopoulos, J. A., Costello, J. F., Ren, B., Milosavljevic, A., Meissner, A., Kellis, M., Marra, M. A., Beaudet, A. L., Ecker, J. R., et al. (2010) · Nature Biotechnology

Epigenetics and DNA MethylationGenomics and Chromatin Dynamics

Cited by 1,892

Cohesin Loss Eliminates All Loop Domains

Rao, S. S. P., Huang, S.-C., Glenn St Hilaire, B., Engreitz, J. M., Perez, E. M., Kieffer-Kwon, K.-R., Sanborn, A. L., Johnstone, S. E., Bascom, G. D., Bochkov, I. D., et al. (2017) · Cell

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 1,883

Charting a dynamic DNA methylation landscape of the human genome

Ziller, M. J., Gu, H., Müller, F., Donaghey, J., Tsai, L. T.-Y., Kohlbacher, O., De Jager, P. L., Rosen, E. D., Bennett, D. A., Bernstein, B. E., et al. (2013) · Nature

Epigenetics and DNA MethylationGenomics and Chromatin Dynamics

Cited by 1,357

Epigenetic plasticity and the hallmarks of cancer

Flavahan, W. A., Gaskell, E., & Bernstein, B. E. (2017) · Science

Epigenetics and DNA MethylationChromatin Remodeling and Cancer

Cited by 1,340

Insulator dysfunction and oncogene activation in IDH mutant gliomas

Flavahan, W. A., Drier, Y., Liau, B. B., Gillespie, S. M., Venteicher, A. S., Stemmer-Rachamimov, A. O., Suvà, M. L., & Bernstein, B. E. (2016) · Nature

Glioma Diagnosis and TreatmentChromatin Remodeling and Cancer

Cited by 1,288

Single-Cell RNA-Seq Reveals AML Hierarchies Relevant to Disease Progression and Immunity

van Galen, P., Hovestadt, V., Wadsworth II, M. H., Hughes, T. K., Griffin, G. K., Battaglia, S., Verga, J. A., Stephansky, J., Pastika, T. J., Lombardi Story, J., et al. (2019) · Cell

Acute Myeloid Leukemia ResearchSingle-cell and spatial transcriptomics

Cited by 1,164

Charting histone modifications and the functional organization of mammalian genomes

Zhou, V. W., Goren, A., & Bernstein, B. E. (2011) · Nature Reviews Genetics

Genomics and Chromatin DynamicsEpigenetics and DNA Methylation

Cited by 1,147

Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types

Finucane, H. K., Reshef, Y. A., Anttila, V., Slowikowski, K., Gusev, A., Byrnes, A., Gazal, S., Loh, P.-R., Lareau, C., Shoresh, N., et al. (2018) · Nature Genetics

Genetic Associations and EpidemiologyBioinformatics and Genomic Networks

Cited by 1,097

Alzheimer's disease: early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci

De Jager, P. L., Srivastava, G., Lunnon, K., Burgess, J., Schalkwyk, L. C., Yu, L., Eaton, M. L., Keenan, B. T., Ernst, J., McCabe, C., et al. (2014) · Nature Neuroscience

Epigenetics and DNA MethylationDementia and Cognitive Impairment Research

Cited by 956