Publications

Aljahani, A.; Hua, P.; Karpinska, M. A.; Quililan, K.; Davies, J. O. J.; Oudelaar, A. M.: Analysis of sub-kilobase chromatin topology reveals nano-scale regulatory interactions with variable dependence on cohesin and CTCF. Nature Communications 13, 2139 (2022)

Downes, D. J.; Smith, A. L.; Karpinska, M. A.; Velychko, T.; Rue-Albrecht, K.; Sims, D.; Milne, T. A.; Davies, J. O. J.; Oudelaar, A. M.; Hughes, J. R.: Capture-C: a modular and flexible approach for high-resolution chromosome conformation capture. Nature Protocols 17 (2), pp. 445 - 475 (2022)

King, A. J.; Songdej, D.; Downes, D. J.; Beagrie, R. A.; Liu, S.; Buckley, M.; Hua, P.; Suciu, M. C.; Oudelaar, A. M.; Hanssen, L. L. P. et al.; Jeziorska, D.; Roberts, N.; Carpenter, S. J.; Francis, H.; Telenius, J.; Olijnik, A.-A.; Sharpe, J. A.; Sloane-Stanley, J.; Eglinton, J.; Kassouf, M. T.; Orkin, S. H.; Pennacchio, L. A.; Davies, J. O. J.; Hughes, J. R.; Higgs, D. R.; Babbs, C.: Reactivation of a developmentally silenced embryonic globin gene. Nature Communications 12, 4439 (2021)

Bozhilov, Y. K.; Downes, D. J.; Telenius, J.; Oudelaar, A. M.; Olivier, E. N.; Mountford, J. C.; Hughes, J. R.; Gibbons, R. J.; Higgs, D. R.: A gain-of-function single nucleotide variant creates a new promoter which acts as an orientation-dependent enhancer-blocker. Nature Communications 12, 3806 (2021)

Hua, P.; Badat, M.; Hanssen, L. L. P.; Hentges, L. D.; Crump, N.; Downes, D. J.; Jeziorska, D. M.; Oudelaar, A. M.; Schwessinger, R.; Taylor, S. et al.; Milne, T. A.; Hughes, J. R.; Higgs, D. R.; Davies, J. O. J.: Defining genome architecture at base-pair resolution. Nature, In Press (2021)

Oudelaar, A. M.; Beagrie, R. A.; Kassouf, M. T.; Higgs, D. R.: The mouse alpha-globin cluster: A paradigm for studying genome regulation and organization. Current Opinion in Genetics and Development 67, pp. 18 - 24 (2021)

Larke, M. S. C.; Schwessinger, R.; Nojima, T.; Telenius, J.; Beagrie, R. A.; Downes, D. J.; Oudelaar, A. M.; Truch, J.; Graham, B.; Bender, M. A. et al.; Proudfoot, N. J.; Higgs, D. R.; Hughes, J. R.: Enhancers predominantly regulate gene expression during differentiation via transcription initiation. Molecular Cell 81 (5), pp. 983 - 997.e7 (2021)

Downes, D. J.; Beagrie, R. A.; Gosden, M. E.; Telenius, J.; Carpenter, S. J.; Nussbaum, L.; Ornellas, S. D.; Sergeant, M.; Eijsbouts, C. Q.; Schwessinger, R. et al.; Kerry, J.; Roberts, N.; Shivalingam, A.; El-Sagheer, A.; Oudelaar, A. M.; Brown, T.; Buckle, V. J.; Davies, J. O. J.; Hughes, J. R.: High-resolution targeted 3C interrogation of cis-regulatory element organization at genome-wide scale. Nature Communications 12, 531(2021) (2021)

Oudelaar, A. M.; Higgs, D. R.: The relationship between genome structure and function. Nature Reviews Genetics, In Press (2020)

Schwessinger, R.; Gosden, M.; Downes, D.; Brown, R. C.; Oudelaar, A. M.; Telenius, J.; Teh, Y. W.; Lunter, G.; Hughes, J. R.: DeepC: predicting 3D genome folding using megabase-scale transfer learning. Nature Methods 17 (11), pp. 1118 - 1124 (2020)

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.; Telenius, J. M.; Brown, T.; Buckle, V. J.; Socolovsky, M.; Higgs, D. R.; Hughes, J. R.: Dynamics of the 4D genome during in vivo lineage specification and differentiation. Nature Communications 11, 2722 (2020)

Chiariello, A. M.; Bianco, S.; Oudelaar, A. M.; Esposito, A.; Annunziatella, C.; Fiorillo, L.; Conte, M.; Corrado, A.; Prisco, A.; Larke, M. S. C. et al.; Telenius, J. M.; Sciarretta, R.; Musella, F.; Buckle, V. J.; Higgs, D. R.; Hughes, J. R.; Nicodemi, M.: A dynamic folded hairpin conformation is associated with α-globin activation in erythroid cells. Cell Reports 30 (7), pp. 2125 - 2135.e1-e5 (2020)

Oudelaar, A. M.; Harrold, C. L.; Hanssen, L. L. P.; Telenius, J. M.; Higgs, D. R.; Hughes, J. R.: A revised model for promoter competition based on multi-way chromatin interactions at the α-globin locus. Nature Coummunications 10, 5412 (2019)

Godfrey, L.; Crump, N. T.; Thorne, R.; Lau, I.-J.; Repapi, E.; Dimou, D.; Smith, A. L.; Harman, J. R.; Telenius, J. M.; Oudelaar, A. M. et al.; Downes, D. J.; Vyas, P.; Hughes, J. R.; Milne, T. A.: DOT1L inhibition reveals a distinct subset of enhancers dependent on H3K79 methylation. Nature Communications 10, 2803 (2019)

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.; Nicodemi, M.; Buckle, V. J.; Dekker, J.; Higgs, D. R.; Hughes, J. R.: Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains. Nature Genetics 50 (12), pp. 1744 - 1751 (2018)

Brown, J. M.; Roberts, N. A.; Graham, B.; Waithe, D.; Lagerholm, C.; Telenius, J. M.; Ornellas, S. D.; Oudelaar, A. M.; Scott, C.; Szczerbal, I. et al.; Babbs, C.; Kassouf, M. T.; Hughes, J. R.; Higgs, D. R.; Buckle, V. J.: A tissue-specific self-interacting chromatin domain forms independently of enhancer-promoter interactions. Nature Communications 9, 3849 (2018)

Oudelaar, A. M.; Davies, J. O. J.; Downes, D. J.; Higgs, D. R.; Hughes, J. R.: Robust detection of chromosomal interactions from small numbers of cells using low-input Capture-C. Nuceic Acids Research 45 (22), e184 (2017)

Oudelaar, A. M.; Downes, D. J.; Davies, J. O. J.; Hughes, J. R.: Low-input Capture-C: A chromosome conformation capture assay to analyze chromatin architecture in small numbers of cells. Bio-Protocol 7 (23), e2645 (2017)

Oudelaar, A. M.; Hanssen, L. L. P.; Hardison, R. C.; Kassouf, M. T.; Hughes, J. R.; Higgs, D. R.: Between form and function: The complexity of genome folding. Human Molecular Genetics 26 (R2), pp. R208 - R215 (2017)

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.; Davies, B.; Higgs, D. R.: Tissue-specific CTCF–cohesin-mediated chromatin architecture delimits enhancer interactions and function in vivo. Nature Cell Biology 19 (8), pp. 952 - 961 (2017)