Ernst, Jason

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

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

STEM: a tool for the analysis of short time series gene expression data

Ernst, J., & Bar-Joseph, Z. (2006) · BMC Bioinformatics

Gene expression and cancer classificationBioinformatics and Genomic Networks

Cited by 1,703

A high-resolution map of human evolutionary constraint using 29 mammals

Broad Institute Sequencing Platform and Whole Genome Assembly Team, Lindblad-Toh, K., Baylor College of Medicine Human Genome Sequencing Center Sequencing Team, Genome Institute at Washington University, Garber, M., Zuk, O., Lin, M. F., Parker, B. J., Washietl, S., Kheradpour, P., et al. (2011) · Nature

Genomics and Phylogenetic StudiesChromosomal and Genetic Variations

Cited by 1,108

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

Chromosome conformation elucidates regulatory relationships in developing human brain

Won, H., de la Torre-Ubieta, L., Stein, J. L., Parikshak, N. N., Huang, J., Opland, C. K., Gandal, M. J., Sutton, G. J., Hormozdiari, F., Lu, D., et al. (2016) · Nature

Genomics and Chromatin DynamicsGenomic variations and chromosomal abnormalities

Cited by 584

Cooperative Binding of Transcription Factors Orchestrates Reprogramming

Chronis, C., Fiziev, P., Papp, B., Butz, S., Bonora, G., Sabri, S., Ernst, J., & Plath, K. (2017) · Cell

Pluripotent Stem Cells ResearchGenomics and Chromatin Dynamics

Cited by 555

Intracellular crowding defines the mode and sequence of substrate uptake by Escherichia coli and constrains its metabolic activity

Beg, Q. K., Vazquez, A., Ernst, J., de Menezes, M. A., Bar-Joseph, Z., Barabási, A.-L., & Oltvai, Z. N. (2007) · Proceedings of the National Academy of Sciences

Microbial Metabolic Engineering and BioproductionGene Regulatory Network Analysis

Cited by 368

Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells

Ram, O., Goren, A., Amit, I., Shoresh, N., Yosef, N., Ernst, J., Kellis, M., Gymrek, M., Issner, R., Coyne, M., et al. (2011) · Cell

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 331

Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay

Kheradpour, P., Ernst, J., Melnikov, A., Rogov, P., Wang, L., Zhang, X., Alston, J., Mikkelsen, T. S., & Kellis, M. (2013) · Genome Research

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 315

Long-Range Chromatin Contacts in Embryonic Stem Cells Reveal a Role for Pluripotency Factors and Polycomb Proteins in Genome Organization

Denholtz, M., Bonora, G., Chronis, C., Splinter, E., de Laat, W., Ernst, J., Pellegrini, M., & Plath, K. (2013) · Cell Stem Cell

Genomics and Chromatin DynamicsPluripotent Stem Cells Research

Cited by 274

Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions

Ernst, J., Melnikov, A., Zhang, X., Wang, L., Rogov, P., Mikkelsen, T. S., & Kellis, M. (2016) · Nature Biotechnology

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 162

DNA methylation networks underlying mammalian traits

Haghani, A., Li, C. Z., Robeck, T. R., Zhang, J., Lu, A. T., Ablaeva, J., Acosta-Rodríguez, V. A., Adams, D. M., Alagaili, A. N., Almunia, J., et al. (2023) · Science

Epigenetics and DNA MethylationGenetic Syndromes and Imprinting

Cited by 128

Impact of the solvent capacity constraint on E. coli metabolism

Vazquez, A., Beg, Q. K., deMenezes, M. A., Ernst, J., Bar-Joseph, Z., Barabási, A.-L., Boros, L. G., & Oltvai, Z. N. (2008) · BMC Systems Biology

Microbial Metabolic Engineering and BioproductionGene Regulatory Network Analysis

Cited by 124

Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration

Wu, W., Cheng, Y., Keller, C. A., Ernst, J., Kumar, S. A., Mishra, T., Morrissey, C., Dorman, C. M., Chen, K.-B., Drautz, D., et al. (2011) · Genome Research

Genomics and Chromatin DynamicsEpigenetics and DNA Methylation

Cited by 118

An integrative approach for fine-mapping chromatin interactions

Jaroszewicz, A., & Ernst, J. (2020) · Bioinformatics

Genomics and Chromatin DynamicsChromosomal and Genetic Variations

Cited by 7