Hughes, Jim R.

Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment

Hughes, J. R., Roberts, N., McGowan, S., Hay, D., Giannoulatou, E., Lynch, M., De Gobbi, M., Taylor, S., Gibbons, R., & Higgs, D. R. (2014) · Nature Genetics

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 461

A genome-editing strategy to treat β-hemoglobinopathies that recapitulates a mutation associated with a benign genetic condition

Traxler, E. A., Yao, Y., Wang, Y.-D., Woodard, K. J., Kurita, R., Nakamura, Y., Hughes, J. R., Hardison, R. C., Blobel, G. A., Li, C., et al. (2016) · Nature Medicine

Hemoglobinopathies and Related DisordersCRISPR and Genetic Engineering

Cited by 366

A blood atlas of COVID-19 defines hallmarks of disease severity and specificity

Ahern, D. J., Ai, Z., Ainsworth, M., Allan, C., Allcock, A., Angus, B., Ansari, M. A., Arancibia-Cárcamo, C. V., Aschenbrenner, D., Attar, M., et al. (2022) · Cell

COVID-19 Clinical Research StudiesSARS-CoV-2 and COVID-19 Research

Cited by 328

Multiplexed analysis of chromosome conformation at vastly improved sensitivity

Davies, J. O. J., Telenius, J. M., McGowan, S. J., Roberts, N. A., Taylor, S., Higgs, D. R., & Hughes, J. R. (2016) · Nature Methods

Genomics and Chromatin DynamicsChromosomal and Genetic Variations

Cited by 268

Intragenic Enhancers Act as Alternative Promoters

Kowalczyk, M. S., Hughes, J. R., Garrick, D., Lynch, M. D., Sharpe, J. A., Sloane-Stanley, J. A., McGowan, S. J., De Gobbi, M., Hosseini, M., Vernimmen, D., et al. (2012) · Molecular Cell

RNA Research and SplicingGenomics and Chromatin Dynamics

Cited by 267

Tissue-specific CTCF-cohesin-mediated chromatin architecture delimits enhancer interactions and function in vivo

Hanssen, L. L. P., Kassouf, M. T., Oudelaar, A. M., Biggs, D., Preece, C., Downes, D. J., Gosden, M., Sharpe, J. A., Sloane-Stanley, J. A., Hughes, J. R., et al. (2017) · Nature Cell Biology

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 219

Globin gene activation during haemopoiesis is driven by protein complexes nucleated by GATA‐1 and GATA‐2

Anguita, E., Hughes, J., Heyworth, C., Blobel, G. A., Wood, W. G., & Higgs, D. R. (2004) · The EMBO Journal

Genomics and Chromatin DynamicsHemoglobinopathies and Related Disorders

Cited by 207

Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains

Oudelaar, A. M., Davies, J. O. J., Hanssen, L. L. P., Telenius, J. M., Schwessinger, R., Liu, Y., Brown, J. M., Downes, D. J., Chiariello, A. M., Bianco, S., et al. (2018) · Nature Genetics

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 196

DNA methylation of intragenic CpG islands depends on their transcriptional activity during differentiation and disease

Jeziorska, D. M., Murray, R. J. S., De Gobbi, M., Gaentzsch, R., Garrick, D., Ayyub, H., Chen, T., Li, E., Telenius, J., Lynch, M., et al. (2017) · Proceedings of the National Academy of Sciences

Epigenetics and DNA MethylationGenomics and Chromatin Dynamics

Cited by 166

Nrf2 controls iron homoeostasis in haemochromatosis and thalassaemia via Bmp6 and hepcidin

Lim, P. J., Duarte, T. L., Arezes, J., Garcia-Santos, D., Hamdi, A., Pasricha, S.-R., Armitage, A. E., Mehta, H., Wideman, S., Santos, A. G., et al. (2019) · Nature Metabolism

Iron Metabolism and DisordersGenomics, phytochemicals, and oxidative stress

Cited by 147

Comparative analysis of three-dimensional chromosomal architecture identifies a novel fetal hemoglobin regulatory element

Huang, P., Keller, C. A., Giardine, B., Grevet, J. D., Davies, J. O. J., Hughes, J. R., Kurita, R., Nakamura, Y., Hardison, R. C., & Blobel, G. A. (2017) · Genes & Development

Genomics and Chromatin DynamicsHemoglobinopathies and Related Disorders

Cited by 127

Dynamics of the 4D Genome during in Vivo Lineage Specification and Differentiation

Oudelaar, A. M., Beagrie, R. A., Gosden, M., de Ornellas, S., Georgiades, E., Kerry, J., Hidalgo, D., Carrelha, J., Shivalingam, A., El-Sagheer, A. H., et al. (2020) · Nature Communications

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 119

Absolute Quantification of Transcription Factors Reveals Principles of Gene Regulation in Erythropoiesis

Gillespie, M. A., Palii, C. G., Sanchez-Taltavull, D., Shannon, P., Longabaugh, W. J. R., Downes, D. J., Sivaraman, K., Espinoza, H. M., Hughes, J. R., Price, N. D., et al. (2020) · Molecular Cell

Gene Regulatory Network AnalysisGenomics and Chromatin Dynamics

Cited by 110

Adventitious changes in long-range gene expression caused by polymorphic structural variation and promoter competition

Lower, K. M., Hughes, J. R., De Gobbi, M., Henderson, S., Viprakasit, V., Fisher, C., Goriely, A., Ayyub, H., Sloane-Stanley, J., Vernimmen, D., et al. (2009) · Proceedings of the National Academy of Sciences

Genomics and Chromatin DynamicsHemoglobinopathies and Related Disorders

Cited by 92

A revised model for promoter competition based on multi-way chromatin interactions at the α-globin locus

Oudelaar, A. M., Harrold, C. L., Hanssen, L. L. P., Telenius, J. M., Higgs, D. R., & Hughes, J. R. (2019) · Nature Communications

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 80

A tissue-specific self-interacting chromatin domain forms independently of enhancer-promoter interactions

Brown, J. M., Roberts, N. A., Graham, B., Waithe, D., Lagerholm, C., Telenius, J. M., De Ornellas, S., Oudelaar, A. M., Scott, C., Szczerbal, I., et al. (2018) · Nature Communications

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 72

Sasquatch: predicting the impact of regulatory SNPs on transcription factor binding from cell- and tissue-specific DNase footprints

Schwessinger, R., Suciu, M. C., McGowan, S. J., Telenius, J., Taylor, S., Higgs, D. R., & Hughes, J. R. (2017) · Genome Research

Genomics and Chromatin DynamicsGenetic Associations and Epidemiology

Cited by 35

Between form and function: the complexity of genome folding

Oudelaar, A. M., Hanssen, L. L. P., Hardison, R. C., Kassouf, M. T., Hughes, J. R., & Higgs, D. R. (2017) · Human Molecular Genetics

Genomics and Chromatin DynamicsNuclear Structure and Function

Cited by 16

Chromatin remodeller Chd7 is developmentally regulated in the neural crest by tissue-specific transcription factors

Williams, R. M., Taylor, G., Ling, I. T. C., Candido-Ferreira, I., Fountain, D. M., Mayes, S., Ateş-Kalkan, P. S., Haug, J. O., Price, A. J., McKinney, S. A., et al. (2024) · PLOS Biology

Developmental Biology and Gene RegulationCongenital Ear and Nasal Anomalies

Cited by 12