Low-input Capture-C: A Chromosome Conformation Capture Assay to Analyze Chromatin Architecture in Small Numbers of Cells

le Oudelaar, Marieke A., Downes, Damien J., Davies, James O.J., Hughes, Jim R.
Foilsithe in Bio Protoc (2017)

Multi Locus View: an extensible web-based tool for the analysis of genomic data.

le Sergeant, Martin J., Hughes, Jim R., Hentges, Lance, Lunter, Gerton, Downes, Damien J., Taylor, Stephen
Foilsithe in Commun Biol (2021)

Robust detection of chromosomal interactions from small numbers of cells using low-input Capture-C

le Oudelaar, A. Marieke, Davies, James O.J., Downes, Damien J., Higgs, Douglas R., Hughes, Jim R.
Foilsithe in Nucleic Acids Res (2017)

Between form and function: the complexity of genome folding

le Oudelaar, A. Marieke, Hanssen, Lars L.P., Hardison, Ross C., Kassouf, Mira T., Hughes, Jim R., Higgs, Douglas R.
Foilsithe in Hum Mol Genet (2017)

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

le Schwessinger, Ron, Suciu, Maria C., McGowan, Simon J., Telenius, Jelena, Taylor, Stephen, Higgs, Doug R., Hughes, Jim R.
Foilsithe in Genome Res (2017)

High-Throughput Genotyping of CRISPR/Cas Edited Cells in 96-Well Plates

le Nussbaum, Lea, Telenius, Jelena M., Hill, Stephanie, Hirschfeld, Priscila P., Suciu, Maria C., Downes, Damien J., Hughes, Jim R.
Foilsithe in Methods Protoc (2018)

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

le Oudelaar, A. Marieke, Harrold, Caroline L., Hanssen, Lars L. P., Telenius, Jelena M., Higgs, Douglas R., Hughes, Jim R.
Foilsithe in Nat Commun (2019)

Genome-wide identification of TAL1's functional targets: Insights into its mechanisms of action in primary erythroid cells

le Kassouf, Mira T., Hughes, Jim R., Taylor, Stephen, McGowan, Simon J., Soneji, Shamit, Green, Angela L., Vyas, Paresh, Porcher, Catherine
Foilsithe 2010

Predicting the three-dimensional folding of cis-regulatory regions in mammalian genomes using bioinformatic data and polymer models

le Brackley, Chris A., Brown, Jill M., Waithe, Dominic, Babbs, Christian, Davies, James, Hughes, Jim R., Buckle, Veronica J., Marenduzzo, Davide
Foilsithe in Genome Biol (2016)

Multiplexed analysis of chromosome conformation at vastly improved sensitivity

le Davies, James O.J., Telenius, Jelena M., McGowan, Simon, Roberts, Nigel A., Taylor, Stephen, Higgs, Douglas R., Hughes, Jim R.
Foilsithe in Nat Methods (2015)

Capture‐C reveals preformed chromatin interactions between HIF‐binding sites and distant promoters

le Platt, James L, Salama, Rafik, Smythies, James, Choudhry, Hani, Davies, James OJ, Hughes, Jim R, Ratcliffe, Peter J, Mole, David R
Foilsithe in EMBO Rep (2016)

DeepC: predicting 3D genome folding using megabase-scale transfer learning

le Schwessinger, Ron, Gosden, Matthew, Downes, Damien, Brown, Richard C, Oudelaar, A. Marieke, Telenius, Jelena, Teh, Yee Whye, Lunter, Gerton, Hughes, Jim R.
Foilsithe in Nat Methods (2020)

Functional characterisation of cis-regulatory elements governing dynamic Eomes expression in the early mouse embryo

le Simon, Claire S., Downes, Damien J., Gosden, Matthew E., Telenius, Jelena, Higgs, Douglas R., Hughes, Jim R., Costello, Ita, Bikoff, Elizabeth K., Robertson, Elizabeth J.
Foilsithe in Development (2017)

Annotation of cis-regulatory elements by identification, subclassification, and functional assessment of multispecies conserved sequences

le Hughes, Jim R., Cheng, Jan-Fang, Ventress, Nicki, Prabhakar, Shyam, Clark, Kevin, Anguita, Eduardo, De Gobbi, Marco, de Jong, Pieter, Rubin, Eddy, Higgs, Douglas R.
Foilsithe 2005

Causes and Consequences of Chromatin Variation between Inbred Mice

le Hosseini, Mona, Goodstadt, Leo, Hughes, Jim R., Kowalczyk, Monika S., de Gobbi, Marco, Otto, Georg W., Copley, Richard R., Mott, Richard, Higgs, Douglas R., Flint, Jonathan
Foilsithe 2013

ATRX Plays a Key Role in Maintaining Silencing at Interstitial Heterochromatic Loci and Imprinted Genes

le Voon, Hsiao P.J., Hughes, Jim R., Rode, Christina, De La Rosa-Velázquez, Inti A., Jenuwein, Thomas, Feil, Robert, Higgs, Douglas R., Gibbons, Richard J.
Foilsithe in Cell Rep (2015)

MLL-AF4 binds directly to a BCL-2 specific enhancer and modulates H3K27 acetylation

le Godfrey, Laura, Kerry, Jon, Thorne, Ross, Repapi, Emmanouela, Davies, James O.J., Tapia, Marta, Ballabio, Erica, Hughes, Jim R., Geng, Huimin, Konopleva, Marina, Milne, Thomas A.
Foilsithe in Exp Hematol (2017)

A gain-of-function single nucleotide variant creates a new promoter which acts as an orientation-dependent enhancer-blocker

le Bozhilov, Yavor K., Downes, Damien J., Telenius, Jelena, Marieke Oudelaar, A., Olivier, Emmanuel N., Mountford, Joanne C., Hughes, Jim R., Gibbons, Richard J., Higgs, Douglas R.
Foilsithe in Nat Commun (2021)

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

le Huang, Peng, Keller, Cheryl A., Giardine, Belinda, Grevet, Jeremy D., Davies, James O.J., Hughes, Jim R., Kurita, Ryo, Nakamura, Yukio, Hardison, Ross C., Blobel, Gerd A.
Foilsithe in Genes Dev (2017)

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

le Traxler, Elizabeth A., Yao, Yu, Wang, Yong-Dong, Woodard, Kaitly J., Kurita, Ryo, Nakamura, Yukio, Hughes, Jim R., Hardison, Ross C., Blobel, Gerd A., Li, Chunliang, Weiss, Mitchell J.
Foilsithe in Nat Med (2016)