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DAVIES LAB PUBLICATIONS

SELECTED PUBLICATIONS

Recent papers

PREPRINTS

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

Nicholas T Crump, Erica Ballabio, Laura Godfrey, Ross Thorne, Emmanouela Repapi, Jon Kerry, Marta Tapia, Peng Hua, Panagis Filippakopoulos, James OJ Davies, Thomas A Milne ‘BET inhibition disrupts transcription but retains enhancer-promoter contact’ BioRxiv 2019

PUBLICATIONS

Peng Hua, Noemi Roy, Josu de la Fuente, Guanlin Wang, Supat Thongjuea, Kevin Clark, Anindita Roy, Bethan Psaila, Neil Ashley, Yvonne Harrington, Claus Nerlov, Suzanne M Watt, Irene Roberts, James OJ Davies, ‘Single cell analysis of bone marrow derived CD34+ cells from children with sickle cell disease and thalassemia.’ Blood 2019; 134, 2111-2115;

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

BLOGS

Davies Lab Blogs

Marieke Oudelaar "DNA origami how to fold a genome"

MEDIA

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

CONTACT

MRC Weatherall Institute of Molecular Medicine, Oxford University

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Oxford, UK
Phone: +44 01865 222419