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

per Oudelaar, Marieke A., Downes, Damien J., Davies, James O.J., Hughes, Jim R.
Publicat a Bio Protoc (2017)

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

per Sergeant, Martin J., Hughes, Jim R., Hentges, Lance, Lunter, Gerton, Downes, Damien J., Taylor, Stephen
Publicat a Commun Biol (2021)

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

per Oudelaar, A. Marieke, Davies, James O.J., Downes, Damien J., Higgs, Douglas R., Hughes, Jim R.
Publicat a Nucleic Acids Res (2017)

Between form and function: the complexity of genome folding

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

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

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

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

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

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

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

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

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

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

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

Multiplexed analysis of chromosome conformation at vastly improved sensitivity

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

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

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

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

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

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

per 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.
Publicat a Development (2017)

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

per 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.
Publicat 2005

Causes and Consequences of Chromatin Variation between Inbred Mice

per 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
Publicat 2013

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

per 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.
Publicat a Cell Rep (2015)

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

per 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.
Publicat a Exp Hematol (2017)

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

per 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.
Publicat a Nat Commun (2021)

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

per 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.
Publicat a Genes Dev (2017)

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

per 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.
Publicat a Nat Med (2016)