SELECTED PUBLICATIONS

Recent papers

Brierley CK, Yip BH, Orlando G, Wen J, Wen S, Goyal H, Levine M, Jakobsdottir GM, Tapinos A, Cornish AJ, Rodriguez-Romera A, Rodriguez-Meira A, Bashton M, Hamblin A, Clark SA, Hamley JC, Fox O, Giurgiu M, O’Sullivan J, Murphy L, Adamo A, Olijnik AA, Cotton A, Hendrix E, Narina S, Pruett-Miller SM, Enshaei A, Harrison C, Drummond M, Knapper S, Tefferi A, Antony-Debré I, Davies J, Henssen AG, Thongjuea S, Wedge DC, Constantinescu S, Papaemmanuil E, Psaila B, Crispino JD, Mead AJ ‘Chromothripsis-associated chromosome 21 amplification orchestrates transformation to blast-phase MPN through targetable overexpression of DYRK1A’ Nature Genetics 2025

Preston AE, Frost JN, Teh MR, Badat M, Armitage AE, Norfo R, Wideman SK, Hanifi M, White N, Roy NBA, Babbs C, Ghesquiere B, Davies J, Howden AJM, Sinclair LV, Hughes JR, Kassouf M, Beagrie R, Higgs DR, Drakesmith H ‘Ancient genomic linkage of α-globin and Nprl3 couples metabolism with erythropoiesis’ Nature Communications 2025 (16) 2749

Badat M and Davies J ‘Clinical applications of gene editing and therapy’ Hoffbrand’s Post Graduate Haematology 2025 96-105

Jonker AH, Tataru EA, Graessner H, Dimmock D, Jaffe A, Baynam A, Davies JO, Mitkus S, Iliach O, Horgan R, Augustine EF, Bateman-House A, Pasmooij AMG, Yu T, Synofzik M, Douville J, Lapteva L, Brooks PJ, O’Connor D, Aartsma-Rus A, N-of-1 Task Force of the International Rare Diseases Research Consortium (IRDiRC) ‘The state-of-the-art of N-of-1 therapies and the IRDiRC N-of-1 development roadmap’, Nature Reviews Drug Discovery 2025 24 (1), 40-56

Rahman S, Bloye G, Farah N, Demeulemeester J, Costa JR, O'Connor D, Pocock R, Rapoz-D'Silva T, Turna A, Wang L, Wah Lee S, Fielding AK, Roels J, Jaksik R, Dawidowska M, Van Vlierberghe P, Hadjur S, Hughes JR, Davies JO, Gutierrez A, Kelliher M, Van Loo P, Dawson MA, Mansour MR ‘Focal deletions of a promoter tether activate the IRX3 oncogene in T-cell acute lymphoblastic leukemia’, Blood 2024 2024024300

Jim R Hughes and James OJ Davies 'Single-cell technologies meet Hi-C' Nature Genetics 2024 56 (8), 1542-1543

Turkalj S, Jakobsen NA, Groom A, Metzner M, Riva SG, Gür ER, Usukhbayar B, Angulo Salazar M, Hentges LD, Mickute G, Clark K, Sopp P, Davies JO, Hughes JR, Paresh Vyas ‘GTAC enables parallel genotyping of multiple genomic loci with chromatin accessibility profiling in single cells’ Cell Stem Cell 2023 722-740

Maresca M, van den Brand T, Li H, Teunissen H, Davies JO, de Wit E ‘Pioneer activity distinguishes activating from non‐activating SOX2 binding sites’ EMBO J 2023 42, e113150

Crump NT, Smith AL, Godfrey L, Dopico-Fernandez AM, Denny N, Harman JR, Hamley JC, Jackson NE, Chahrour C, Riva S, Rice S, Kim J, Basrur V, Fermin D, Elenitoba-Johnson K, Roeder RG, Allis CD, Roberts I, Roy A, Geng H, Davies JO, Milne TA ‘MLL-AF4 cooperates with PAF1 and FACT to drive high-density enhancer interactions in leukemia‘ Nature Communications 2023 14, 5208

Robbe P, Ridout KE, Vavoulis DV, Dréau H, Kinnersley B, Denny N, Chubb D, Appleby N, Cutts A, Cornish AJ, Lopez-Pascua L, Clifford R, Burns A, Stamatopoulos B, Cabes M, Alsolami R, Antoniou P, Oates M, Cavalieri D, Gibson J, Prabhu AV, Schwessinger R, Jennings D, James T, Maheswari U, Duran-Ferrer M, Carninci P, Knight SJL, Månsson R, Hughes J, Davies JO, Ross M, Bentley D, Strefford JC, Devereux S, Pettitt AR, Hillmen P, Caulfield MJ, Houlston RS, Martín-Subero JI, Schuh A ‘Whole-genome sequencing of chronic lymphocytic leukemia identifies subgroups with distinct biological and clinical features’ Nature Genetics 2022 54:1675–1689

Downes DJ, Smith AL, Karpinska MA, Velychko T, Rue-Albrecht K, Sims D, Milne TA, Davies JO, Oudelaar AM, Hughes JR, ‘Capture-C: a modular and flexible approach for high-resolution chromosome conformation capture’ Nature Protocols 2022 17 (2), 445-475

Badat M, Ejaz A, Hua P, Rice S, Zhang W, Hentges LD, Fisher CA, Denny N, Schwessinger R, Yasara N, Roy NBA, Issa F, Roy A, Telfer P, Hughes J, Mettananda S, Higgs DR and Davies JO ‘Direct correction of haemoglobin E β-thalassaemia using base editors’ Nature Communications 2023 14, 2238

Hamley JC, Li H, Denny N, Downes D and Davies JO ‘Determining chromatin architecture with Micro Capture-C’ Nature Protocols 2023 18, 1687-1711

Abrar Aljahani, Peng Hua, Magdalena A Karpinska, Kimberly Quililan, James OJ Davies* and A Marieke Oudelaar* ‘Analysis of sub-kilobase chromatin topology reveals nano-scale regulatory interactions with variable dependence on cohesin and CTCF’ Nature Communications 2022 13:1-13 *Joint corresponding

Peng Hua, Mohsin Badat, Lars LP Hanssen, Lance D Hentges, Nicholas Crump, Damien J Downes, Danuta M Jeziorska, A Marieke Oudelaar, Ron Schwessinger, Stephen Taylor, Thomas A Milne, Jim R Hughes, Doug R Higgs and James OJ Davies ‘Defining genome architecture at base-pair resolution’ Nature 2021 ; 595(7865):125-129

Downes DJ, Cross AR, Hua P, Roberts N, Schwessinger R, Cutler AJ, Munis AM, Brown J, Mielczarek O, de Andrea CE, COMBAT Consortium, Gill DR, Hyde SC, Knight JC, Todd JA, Sansom SN, Issa F, Davies JO* and Hughes JR* ‘Identification of LZTFL1 as the likely effector gene at a severe COVID-19 risk locus.’ Nature genetics 2021 53 (11), 1606-1615 (* joint corresponding)

Mohsin Badat, James OJ Davies, Christopher A Fisher, Damien J Downes, Anna Rose, Andreas B Glenthøj, Eduard J van Beers, Cornelis L Harteveld, Douglas R Higgs ‘A remarkable case of HbH disease illustrates the relative contributions of the α-globin enhancers to gene expression’ Blood 2021; 137, 572-575;

Damien J Downes, Robert A Beagrie, Matthew E Gosden, Jelena Telenius, Stephanie J Carpenter, Lea Nussbaum, Sara De Ornellas, Martin Sergeant, Chris Q Eijsbouts, Ron Schwessinger, Jon Kerry, Nigel Roberts, Arun Shivalingam, Afaf El-Sagheer, A Marieke Oudelaar, Tom Brown, Veronica J Buckle, James OJ Davies, Jim R Hughes ‘High-resolution targeted 3C interrogation of cis-regulatory element organization at genome-wide scale’ Nature Communications 2021; 12, 1-15;

Nicholas T Crump, Erica Ballabio, Laura Godfrey, Ross Thorne, Emmanouela Repapi, Jon Kerry, Marta Tapia, Peng Hua, Christoffer Lagerholm, Panagis Filippakopoulos, James OJ Davies, Thomas A Milne ‘BET inhibition disrupts transcription but retains enhancer-promoter contact’ Nature Communications 2021; 12, 1-15;

Peng Hua, Joanna Hester, George Adigbli, Rong Li, Bethan Psaila, Anindita Roy, Carole JR Bataille, Graham M Wynne, Thomas Jackson, Thomas A Milne, Angela J Russell, James Davies, Irene Roberts, Fadi Issa, Suzanne M Watt ‘The BET inhibitor CPI203 promotes ex vivo expansion of cord blood long-term repopulating HSCs and megakaryocytes’ Blood 2020; 21, 2410-2415;

Hannah K Long, Marco Osterwalder, Ian C Welsh, Karissa Hansen, James OJ Davies, Yiran E Liu, Mervenaz Koska, Alexander T Adams, Robert Aho, Neha Arora, Kazuya Ikeda, Ruth M Williams, Tatjana Sauka-Spengler, Matthew H Porteus, Tim Mohun, Diane E Dickel, Tomek Swigut, Jim R Hughes, Douglas R Higgs, Axel Visel, Licia Selleri, Joanna Wysocka 'Loss of extreme long-range enhancers in human neural crest drives a craniofacial disorder’ Cell stem cell 2020; 27 765-783

van Bemmel J.G., Galupa R., Gard C., Servant N., Picard C., Davies J., Szempruch A.J., Zhan Y., Żylicz J.J., Nora E.P., Lameiras S., de Wit E., Gentien D., Baulande S., Giorgetti L., Guttman M., Hughes J.R., Higgs D.R., Gribnau J., Heard E. ‘The bipartite TAD organization of the X-inactivation center ensures opposing developmental regulation of Tsix and Xist’ Nature Genetics 2019; 51, 1024-1034

A Marieke Oudelaar, James OJ Davies, Lars LP Hanssen, Jelena M Telenius, Ron Schwessinger, Yu Liu, Jill M Brown, Damien J Downes, Andrea M Chiariello, Simona Bianco, Mario Nicodemi, Veronica J Buckle, Job Dekker, Douglas R Higgs, Jim R Hughes ‘Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains’ Nature Genetics 2018; 50, 1744-55

Davies J.O.J., Hart A.C., De La Fuente J., Bain B.J. ‘Macrophage activation syndrome and post‐transplant microangiopathy following haploidentical bone marrow transplantation for sickle cell anemia’ American journal of hematology 2018; 93 (4), 588-589

Yan T., Ooi W.F., Qamra A., Cheung A., Ma D., Sundaram G.M., Xu C., Xing M., Poon L., Wang J., Loh Y.P., Jie Ho J.H., Quan Ng J.J., Ramlee M.K., Aswad L., Rozen S.G., Ghosh S., Bard F.A., Sampath P., Tergaonkar V., Davies J.O.J., Hughes J.R., Goh E., Bi X., Fullwood M.J., Tan P., Li S. ‘HoxC5 and miR-615-3p target newly evolved genomic regions to repress hTERT and inhibit tumorigenesis’ Nature communications 2018; 9 (1), 100

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’ Nucleic Acid Research 2017, doi: 10.1093/nar/gkx1194

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 2017; 7 (23)

Yao X., Tan J., Lim K.J., Koh J., Ooi W.F., Li Z., Huang D., Xing M., Chan Y.S., Qu J.Z., Tay S.T., Wijaya G., Lam Y.N., Hong J.H., Lee-Lim A.P., Guan P., Ng M.S.W., He C.Z., Lin J.S., Qamra T.A., Xu C., Myint S.S., Davies J.O.J, Goh J.Y., Loh G., Tan B.C., Rozen S.G., Yu Q., Tan I.B.H., Cheng C.W.S., Li S., Chang K.T.E., Tan P.H., Silver D.L., Lezhava A., Steger G., Hughes J.R., The B.T., Tan P., ‘VHL deficiency drives enhancer activation of oncogenes in clear cell renal cell carcinoma’, Cancer Discovery 2017; CD-17-0375

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. ‘Comparative analysis of three-dimensional chromosomal architecture identifies a novel fetal hemoglobin regulatory element’ Genes and Development 2017; 31(16): 1704-1713

Badat M. and Davies J.O.J. ‘Gene Therapy in a Patient with Sickle Cell Disease’ New England Journal of Medicine 2017; 376(21):2093-4

Davies J.O.J., Oudelaar A.M., Higgs D.R. and Hughes J.R. ‘How best to identify chromosomal interactions: a comparison of approaches’, Nature Methods 2017; 14 (2), 125-134

Hay D., Hughes J.R., Babbs C., Davies J.O.J., Graham B.J., Hanssen L., T. Kassouf M.T, Oudelaar A.M., Sharpe J.A., Suciu M.C., Telenius J., Williams R., Rode C., Li P., Pennacchio L.A., Sauka-Spengler T., Sloane-Stanley J.A., Ayyub H., Butler S., Gibbons R.J., Smith A.J.H., Wood W.G., Higgs D.R. ‘Testing the Super-Enhancer Concept by In-Vivo Dissection’, Nature Genetics 2016; 48(8):895-903

Paralkar V.R., Taborda C.C., Huang P., Yao Y., Kossenkov A.V., Prasad R., Luan J., Davies J.O.J., Hughes J.R., Hardison R.C., Blobel G.A., Weiss M.J. ‘Unlinking an lncRNA from Its Associated cis Element’ Molecular Cell. 2016; 7:62(1):104-10

Ooi W.F., Xing M., Xu C., Lin S.J., Yao X., Qamra A., Irwanto A., Nandi T., Lim K., Lee-Lim A.P., Chan Y.S., Tay S.T., Lee M., Davies J., Wong W.K., Soo K., Chan W.H., Ong H.S., Chow P., Wong C.Y., Rha S.Y., Pr Liu J., Hillmer A., Hughes J., Rozen S., Teh B.T., Ramlee M., Lim M.C., Cao F., Babu D., Qu Z.J., Fullwood M., Li S., Poon L. ‘Epigenomic Profiling of Primary Gastric Adenocarcinoma Reveals Super Enhancer Heterogeneity’, Nature Communications. 2016; 7; 12983

Godfrey L., Kerry J., Thorne R., Repapi E., Davies J.O.J, Tapia M., Ballabio E., Hughes J.R., Geng H., Konopleva M., Milne T.A. ‘MLL-AF4 binds directly to a BCL-2 specific enhancer and modulates H3K27 acetylation’, Experimental Haematology. 2016; doi:10.1016/j.exphem.2016.11.003

Brackley C.A., Brown J.M., Waithe D., Babbs C., Davies J.O.J., Hughes J.R., Buckle V.J., Marenduzzo D. ‘Predicting the three-dimensional folding of cis-regulatory regions in mammalian genomes using bioinformatic data and polymer models’, Genome Biology 2016; Mar 31;17(1):59

Platt J.L., Salama R., Smythies J., Choudhry H., Davies J.O.J., Hughes J.R., Ratcliffe P.J., Mole D.R. ‘Capture-C reveals preformed chromatin interactions between HIF-binding sites and distant promoters’, EMBO reports 2016; 17, 1410-21

Davies J.O.J., Telenius J.M., McGowan S., Roberts N.A., Taylor S., Higgs D.R. and Hughes J.R. ‘Multiplexed analysis of chromosome conformation at vastly improved sensitivity’, Nature Methods 2016; 13, 74-80

Shanavas M., Popat U., Michaelis L.C., Fauble V., McLornan D., Klisovic R., Mascarenhas J., Tamari R., Arcasoy M.O., Davies J.O.J., Gergis U., Ukaegbu O.C., Kamble R.T., Storring J.M., Majhail N.S., Romee R., Verstovsek S., Pagliuca A., Vasu S., Ernst B., Atenafu E.G., Hanif A., Champlin R., Hari P., Gupta V. ‘Outcomes of Allogeneic Hematopoietic Cell Transplantation in Patients with Myelofibrosis with Prior Exposure to Janus Kinase 1/2 Inhibitors’, Biology of Blood and Bone Marrow Transplantation 2016; 22(3), 432–440

Davies J.O.J., Stringaris K., Barrett J.A. and Rezvani K. ‘Opportunities and limitations of natural killer cells as adoptive therapy for malignant disease’, Cytotherapy 2014;16(11):1453-1466

I-Jun Lau, Joe R Harman, Alastair L Smith, Nicholas Denny, Nicole E Jackson, Joseph C Hamley, Paresh Vyas, James OJ Davies, Jim R Hughes, Nicholas T Crump, Thomas A Milne 'Sustained MYB activity drives emergent enhancer activation and precise enhancer-promoter interactions' bioRxiv 2025 2025.04. 16.649256

Jelena M Telenius, Damien Downes, Martin Sergeant, A Marieke Oudelaar, Simon McGowan, Jon Kerry, Lars LP Hanssen, Ron Schwessinger, Chris Q Eijsbouts, James OJ Davies, Stephen Taylor, Jim R Hughes ‘CaptureCompendium: a comprehensive toolkit for 3C analysis’ BioRxiv 2020

Damien J Downes, Ron Schwessinger, Stephanie J Hill, Lea Nussbaum, Caroline Scott, Matthew E Gosden, Priscila P Hirschfeld, Jelena M Telenius, Chris E Eijsbouts, Simon J McGowan, Antony J Cutler, Jon Kerry, Jessica L Davies, Calliope A Dendrou, Jamie RJ Inshaw, Martin SC Larke, A Marieke Oudelaar, Yavor Bozhilov, Andrew King, Richard C Brown, Maria C Suciu, James OJ Davies, Philip Hublitz, Chris Fisher, Ryo Kurita, Yukio Nakamura, Stephen Taylor, Veronica J Buckle, John A Todd, Douglas R Higgs, Jim R Hughes ‘An integrated platform to systematically identify causal variants and genes for polygenic human traits’ BioRxiv 2019

Davies Lab Blogs

Marieke Oudelaar "DNA origami how to fold a genome"

James Davies "GM humans are possible, but do we really want them?" The Conversation

Rhys Blakley "DNA edited to treat sickle cell disease" The Times

Jack Elsom "Hope for thousands of patients with sickle cell disease" Mail online

MRC Weatherall Institute of Molecular Medicine, Oxford University

We're always keen to hear from people who are interested in working with us