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

Por Oudelaar, Marieke A., Downes, Damien J., Davies, James O.J., Hughes, Jim R.
Publicado no Bio Protoc (2017)

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

Por Oudelaar, A. Marieke, Davies, James O.J., Downes, Damien J., Higgs, Douglas R., Hughes, Jim R.
Publicado no Nucleic Acids Res (2017)

Between form and function: the complexity of genome folding

Por Oudelaar, A. Marieke, Hanssen, Lars L.P., Hardison, Ross C., Kassouf, Mira T., Hughes, Jim R., Higgs, Douglas R.
Publicado no Hum Mol Genet (2017)

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

Por Schwessinger, Ron, Suciu, Maria C., McGowan, Simon J., Telenius, Jelena, Taylor, Stephen, Higgs, Doug R., Hughes, Jim R.
Publicado no Genome Res (2017)

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

Por Nussbaum, Lea, Telenius, Jelena M., Hill, Stephanie, Hirschfeld, Priscila P., Suciu, Maria C., Downes, Damien J., Hughes, Jim R.
Publicado no Methods Protoc (2018)

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

Por Oudelaar, A. Marieke, Harrold, Caroline L., Hanssen, Lars L. P., Telenius, Jelena M., Higgs, Douglas R., Hughes, Jim R.
Publicado no Nat Commun (2019)

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

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

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

Por Brackley, Chris A., Brown, Jill M., Waithe, Dominic, Babbs, Christian, Davies, James, Hughes, Jim R., Buckle, Veronica J., Marenduzzo, Davide
Publicado no Genome Biol (2016)

Multiplexed analysis of chromosome conformation at vastly improved sensitivity

Por Davies, James O.J., Telenius, Jelena M., McGowan, Simon, Roberts, Nigel A., Taylor, Stephen, Higgs, Douglas R., Hughes, Jim R.
Publicado no Nat Methods (2015)

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

Por Platt, James L, Salama, Rafik, Smythies, James, Choudhry, Hani, Davies, James OJ, Hughes, Jim R, Ratcliffe, Peter J, Mole, David R
Publicado no EMBO Rep (2016)

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

Por Schwessinger, Ron, Gosden, Matthew, Downes, Damien, Brown, Richard C, Oudelaar, A. Marieke, Telenius, Jelena, Teh, Yee Whye, Lunter, Gerton, Hughes, Jim R.
Publicado no Nat Methods (2020)

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

Por 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.
Publicado no Development (2017)

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

Por 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.
Publicado em 2005

Causes and Consequences of Chromatin Variation between Inbred Mice

Por 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
Publicado em 2013

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

Por 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.
Publicado no Cell Rep (2015)

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

Por 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.
Publicado no Exp Hematol (2017)

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

Por 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.
Publicado no Genes Dev (2017)

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

Por 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.
Publicado no Nat Med (2016)

Capture-C: A modular and flexible approach for high-resolution chromosome conformation capture

Por Downes, Damien J., Smith, Alastair L., Karpinska, Magdalena A., Velychko, Taras, Rue-Albrecht, Kevin, Sims, David, Milne, Thomas A., Davies, James O.J., Oudelaar, A. Marieke, Hughes, Jim R.
Publicado no Nat Protoc (2022)

High-resolution analysis of cis-acting regulatory networks at the α-globin locus

Por Hughes, Jim R., Lower, Karen M., Dunham, Ian, Taylor, Stephen, De Gobbi, Marco, Sloane-Stanley, Jacqueline A., McGowan, Simon, Ragoussis, Jiannis, Vernimmen, Douglas, Gibbons, Richard J., Higgs, Douglas R.
Publicado em 2013