Recent papers
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 in press (* 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
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’ Biorxiv 2021 https://www.biorxiv.org/content/10.1101/2021.08.10.455796v1 *Joint corresponding
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
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
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