Jim R Hughes (Jim Hughes)

Publication Activity (10 Years)

Years Active: 2016-2024
Publications (10 Years): 37

Top Topics

Chronic Lymphocytic Leukemia

Gene Expression

Top Venues

Nature communications

Genome research

Nature genetics

Nature protocols

This page only lists publications with an associated author ORCID identifier.

Publications

Jim R Hughes, James O J Davies
Single-cell technologies meet Hi-C. Nature genetics 56 (8) (2024)
Guanjue Xiang, Xi He, Belinda M Giardine, Kathryn J Isaac, Dylan J Taylor, Rajiv C McCoy, Camden Jansen, Cheryl A Keller, Alexander Q Wixom, April Cockburn, Amber Miller, Qian Qi, Yanghua He, Yichao Li, Jens Lichtenberg, Elisabeth F Heuston, Stacie M Anderson, Jing Luan, Marit W Vermunt, Feng Yue, Michael E G Sauria, Michael C Schatz, James Taylor, Berthold Göttgens, Jim R Hughes, Douglas R Higgs, Mitchell J Weiss, Yong Cheng, Gerd A Blobel, David M Bodine, Yu Zhang, Qunhua Li, Shaun Mahony, Ross Cameron Hardison
Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes. Genome research 34 (7) (2024)
Guanjue Xiang, Xi He, Belinda M Giardine, Kathryn J Isaac, Dylan J Taylor, Rajiv C McCoy, Camden Jansen, Cheryl A Keller, Alexander Q Wixom, April Cockburn, Amber Miller, Qian Qi, Yanghua He, Yichao Li, Jens Lichtenberg, Elisabeth F Heuston, Stacie M Anderson, Jing Luan, Marit W Vermunt, Feng Yue, Michael E G Sauria, Michael C Schatz, James Taylor, Berthold Göttgens, Jim R Hughes, Douglas R Higgs, Mitchell J Weiss, Yong Cheng, Gerd A Blobel, David M Bodine, Yu Zhang, Qunhua Li, Shaun Mahony, Ross Cameron Hardison
Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes. Genome research 34 (7) (2024)
Guanjue Xiang, Xi He, Belinda M Giardine, Kathryn J Isaac, Dylan J Taylor, Rajiv C McCoy, Camden Jansen, Cheryl A Keller, Alexander Q Wixom, April Cockburn, Amber Miller, Qian Qi, Yanghua He, Yichao Li, Jens Lichtenberg, Elisabeth F Heuston, Stacie M Anderson, Jing Luan, Marit W Vermunt, Feng Yue, Michael E G Sauria, Michael C Schatz, James Taylor, Berthold Göttgens, Jim R Hughes, Douglas R Higgs, Mitchell J Weiss, Yong Cheng, Gerd A Blobel, David M Bodine, Yu Zhang, Qunhua Li, Shaun Mahony, Ross Cameron Hardison
Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes. Genome research (2024)
Guanjue Xiang, Xi He, Belinda M Giardine, Kathryn J Isaac, Dylan J Taylor, Rajiv C McCoy, Camden Jansen, Cheryl A Keller, Alexander Q Wixom, April Cockburn, Amber Miller, Qian Qi, Yanghua He, Yichao Li, Jens Lichtenberg, Elisabeth F Heuston, Stacie M Anderson, Jing Luan, Marit W Vermunt, Feng Yue, Michael E G Sauria, Michael C Schatz, James Taylor, Berthold Göttgens, Jim R Hughes, Douglas R Higgs, Mitchell J Weiss, Yong Cheng, Gerd A Blobel, David M Bodine, Yu Zhang, Qunhua Li, Shaun Mahony, Ross Cameron Hardison
Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes. Genome research (2024)
Jim R Hughes, James O J Davies
Single-cell technologies meet Hi-C. Nature genetics (2024)
Guanjue Xiang, Xi He, Belinda M Giardine, Kathryn J Isaac, Dylan J Taylor, Rajiv C McCoy, Camden Jansen, Cheryl A Keller, Alexander Q Wixom, April Cockburn, Amber Miller, Qian Qi, Yanghua He, Yichao Li, Jens Lichtenberg, Elisabeth F Heuston, Stacie M Anderson, Jing Luan, Marit W Vermunt, Feng Yue, Michael E G Sauria, Michael C Schatz, James Taylor, Berthold Göttgens, Jim R Hughes, Douglas R Higgs, Mitchell J Weiss, Yong Cheng, Gerd A Blobel, David M Bodine, Yu Zhang, Qunhua Li, Shaun Mahony, Ross Cameron Hardison
Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes. Genome research (2024)
Mohsin Badat, Ayesha Ejaz, Peng Hua, Siobhan Rice, Weijiao Zhang, Lance D Hentges, Christopher A Fisher, Nicholas D R Denny, Ron Schwessinger, Nirmani Yasara, Noemi B A Roy, Fadi Issa, Anindita Roy, Paul Telfer, Jim R Hughes, Sachith Mettananda, Douglas R Higgs, James O J Davies
Direct correction of haemoglobin E β-thalassaemia using base editors. Nature communications 14 (1) (2023)
Damien J Downes, Alastair L Smith, Magdalena A Karpińska, Taras Velychko, Kevin Christophe Rue-Albrecht, David Sims, Thomas A Milne, James O J Davies, A Marieke Oudelaar, Jim R Hughes
Author Correction: Capture-C: a modular and flexible approach for high-resolution chromosome conformation capture. Nature protocols (2023)
Guanjue Xiang, Xi He, Belinda M Giardine, Kathryn J Weaver, Dylan J Taylor, Rajiv C McCoy, Camden Jansen, Cheryl A Keller, Alexander Q Wixom, April Cockburn, Amber Miller, Qian Qi, Yanghua He, Yichao Li, Jens Lichtenberg, Elisabeth F Heuston, Stacie M Anderson, Jing Luan, Marit W Vermunt, Feng Yue, Michael E G Sauria, Michael C Schatz, James Taylor, Berthold Göttgens, Jim R Hughes, Douglas R Higgs, Mitchell J Weiss, Yong Cheng, Gerd A Blobel, David Bodine, Yu Zhang, Qunhua Li, Shaun Mahony, Ross Cameron Hardison
Cross-species regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes. bioRxiv : the preprint server for biology (2023)
Dominic D G Owens, Giorgio Anselmi, A Marieke Oudelaar, Damien J Downes, Alessandro Cavallo, Joe R Harman, Ron Schwessinger, Akin Bucakci, Lucas Greder, Sara de Ornellas, Danuta Jeziorska, Jelena Telenius, Jim R Hughes, Marella F T R de Bruijn
Dynamic Runx1 chromatin boundaries affect gene expression in hematopoietic development. Nature communications 13 (1) (2022)
Julia Truch, Damien J Downes, Caroline Scott, E Ravza Gür, Jelena M Telenius, Emmanouela Repapi, Ron Schwessinger, Matthew E Gosden, Jill M Brown, Stephen Taylor, Pak Leng Cheong, Jim R Hughes, Douglas R Higgs, Richard J Gibbons
The chromatin remodeller ATRX facilitates diverse nuclear processes, in a stochastic manner, in both heterochromatin and euchromatin. Nature communications 13 (1) (2022)
Damien J Downes, Alastair L Smith, Magdalena A Karpińska, Taras Velychko, Kevin Christophe Rue-Albrecht, David Sims, Thomas A Milne, James O J Davies, A Marieke Oudelaar, Jim R Hughes
Capture-C: a modular and flexible approach for high-resolution chromosome conformation capture. Nature protocols 17 (2) (2022)
Pauline Robbe, Kate E Ridout, Dimitrios V Vavoulis, Helene Dréau, Ben Kinnersley, Nicholas D R Denny, Daniel Chubb, Niamh Appleby, Anthony Cutts, Alex J Cornish, Laura Lopez-Pascua, Ruth Clifford, Adam Burns, Basile Stamatopoulos, Maite Cabes, Reem Alsolami, Pavlos Antoniou, Melanie Oates, Doriane Cavalieri, null null, null null, Jane Gibson, Anika V Prabhu, Ron Schwessinger, Daisy Jennings, Terena James, Uma Maheswari, Martí Duran-Ferrer, Piero Carninci, Samantha J L Knight, Robert Månsson, Jim R Hughes, James Davies, Mark Ross, David Bentley, Jonathan C Strefford, Stephen Devereux, Andrew R Pettitt, Peter Hillmen, Mark J Caulfield, Richard S Houlston, José I Martín-Subero, Anna Schuh
Whole-genome sequencing of chronic lymphocytic leukemia identifies subgroups with distinct biological and clinical features. Nature genetics 54 (11) (2022)
Lance D Hentges, Martin J Sergeant, Christopher B Cole, Damien J Downes, Jim R Hughes, Stephen Taylor
LanceOtron: a deep learning peak caller for genome sequencing experiments. Bioinformatics (Oxford, England) 38 (18) (2022)
Ioanna Pavlaki, Michael Shapiro, Giuseppina Pisignano, Stephanie M E Jones, Jelena Telenius, Silvia Muñoz-Descalzo, Robert J Williams, Jim R Hughes, Keith W Vance
Chromatin interaction maps identify Wnt responsive cis-regulatory elements coordinating Paupar-Pax6 expression in neuronal cells. PLoS genetics 18 (6) (2022)
Damien J Downes, Amy R Cross, Peng Hua, Nigel A Roberts, Ron Schwessinger, Antony J Cutler, Altar M Munis, Jill M Brown, Olga Mielczarek, Carlos E de Andrea, Ignacio Melero, null null, Deborah R Gill, Stephen C Hyde, Julian C Knight, John A Todd, Stephen N Sansom, Fadi Issa, James O J Davies, Jim R Hughes
Identification of LZTFL1 as a candidate effector gene at a COVID-19 risk locus. Nature genetics 53 (11) (2021)
Andrew J King, Duantida Songdej, Damien J Downes, Robert A Beagrie, Siyu Liu, Megan Buckley, Peng Hua, Maria C Suciu, A Marieke Oudelaar, Lars L P Hanssen, Danuta Jeziorska, Nigel A Roberts, Stephanie J Carpenter, Helena S Francis, Jelena Telenius, Aude-Anais Olijnik, Jacqueline A Sharpe, Jacqueline Sloane-Stanley, Jennifer Eglinton, Mira T Kassouf, Stuart H Orkin, Len A Pennacchio, James O J Davies, Jim R Hughes, Douglas R Higgs, Christian Babbs
Reactivation of a developmentally silenced embryonic globin gene. Nature communications 12 (1) (2021)
Peng Hua, Mohsin Badat, Lars L P Hanssen, Lance D Hentges, Nicholas T Crump, Damien J Downes, Danuta M Jeziorska, A Marieke Oudelaar, Ron Schwessinger, Stephen Taylor, Thomas A Milne, Jim R Hughes, Douglas R Higgs, James O J Davies
Defining genome architecture at base-pair resolution. Nature 595 (7865) (2021)
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 A Roberts, Arun Shivalingam, Afaf Helmy El-Sagheer, A Marieke Oudelaar, Tom Brown, Veronica J Buckle, James O J Davies, Jim R Hughes
High-resolution targeted 3C interrogation of cis-regulatory element organization at genome-wide scale. Nature communications 12 (1) (2021)
Yavor K Bozhilov, Damien J Downes, Jelena Telenius, A Marieke Oudelaar, Emmanuel N Olivier, Joanne C Mountford, Jim R Hughes, Richard J Gibbons, Douglas R Higgs
A gain-of-function single nucleotide variant creates a new promoter which acts as an orientation-dependent enhancer-blocker. Nature communications 12 (1) (2021)
Martin J Sergeant, Jim R Hughes, Lance D Hentges, Gerton Lunter, Damien J Downes, Stephen Taylor
Multi Locus View: an extensible web-based tool for the analysis of genomic data. Communications biology 4 (1) (2021)
Guanjue Xiang, Cheryl A Keller, Elisabeth F Heuston, Belinda M Giardine, Lin An, Alexander Q Wixom, Amber Miller, April Cockburn, Michael E G Sauria, Kathryn Weaver, Jens Lichtenberg, Berthold Göttgens, Qunhua Li, David Bodine, Shaun Mahony, James Taylor, Gerd A Blobel, Mitchell J Weiss, Yong Cheng, Feng Yue, Jim R Hughes, Douglas R Higgs, Yu Zhang, Ross Cameron Hardison
An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis. Genome research 30 (3) (2020)
Ron Schwessinger, Matthew E Gosden, Damien Downes, Richard C Brown, A Marieke Oudelaar, Jelena Telenius, Yee Whye Teh, Gerton Lunter, Jim R Hughes
DeepC: predicting 3D genome folding using megabase-scale transfer learning. Nature methods 17 (11) (2020)
A Marieke Oudelaar, Robert A Beagrie, Matthew E Gosden, Sara De Ornellas, Emily Georgiades, Jon Kerry, Daniel Hidalgo, Joana Carrelha, Arun Shivalingam, Afaf Helmy El-Sagheer, Jelena M Telenius, Tom Brown, Veronica J Buckle, Merav Socolovsky, Douglas R Higgs, Jim R Hughes
Dynamics of the 4D genome during in vivo lineage specification and differentiation. Nature communications 11 (1) (2020)
Joke G van Bemmel, Rafael Galupa, Chris Gard, Nicolas Servant, Christel Picard, James O J Davies, Anthony James Szempruch, Yinxiu Zhan, Jan Jakub Żylicz, Elphѐge P Nora, Sonia Lameiras, Elzo de Wit, David Gentien, Sylvain Baulande, Luca Giorgetti, Mitchell Guttman, Jim R Hughes, Douglas R Higgs, Joost Gribnau, Edith Heard
The bipartite TAD organization of the X-inactivation center ensures opposing developmental regulation of Tsix and Xist. Nature genetics 51 (6) (2019)
A Marieke Oudelaar, Caroline L Harrold, Lars L P Hanssen, Jelena M Telenius, Douglas R Higgs, Jim R Hughes
A revised model for promoter competition based on multi-way chromatin interactions at the α-globin locus. Nature communications 10 (1) (2019)
Laura C Godfrey, Nicholas T Crump, Ross Thorne, I-Jun Lau, Emmanouela Repapi, Dimitra Dimou, Alastair L Smith, Joe R Harman, Jelena M Telenius, A Marieke Oudelaar, Damien J Downes, Paresh Vyas, Jim R Hughes, Thomas A Milne
DOT1L inhibition reveals a distinct subset of enhancers dependent on H3K79 methylation. Nature communications 10 (1) (2019)
TingDong Yan, Wen Fong Ooi, Aditi Qamra, Alice Cheung, DongLiang Ma, Gopinath Meenakshi Sundaram, Chang Xu, Manjie Xing, LaiFong Poon, Jing Wang, Yan Ping Loh, Jess Hui Jie Ho, Joscelyn Jun Quan Ng, Muhammad Khairul Ramlee, Luay Aswad, Steven G Rozen, Sujoy Ghosh, Frederic A Bard, Prabha Sampath, Vinay Tergaonkar, James O J Davies, Jim R Hughes, Eyleen L K Goh, Xuezhi Bi, Melissa Jane Fullwood, Patrick Tan, Shang Li
HoxC5 and miR-615-3p target newly evolved genomic regions to repress hTERT and inhibit tumorigenesis. Nature communications 9 (1) (2018)
Jill M Brown, Nigel A Roberts, Bryony Graham, Dominic Waithe, Christoffer Lagerholm, Jelena M Telenius, Sara De Ornellas, A Marieke Oudelaar, Caroline Scott, Izabela Szczerbal, Christian Babbs, Mira T Kassouf, Jim R Hughes, Douglas R Higgs, Veronica J Buckle
A tissue-specific self-interacting chromatin domain forms independently of enhancer-promoter interactions. Nature communications 9 (1) (2018)
A Marieke Oudelaar, James O J Davies, Lars L P 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 50 (12) (2018)
Lars L P Hanssen, Mira T Kassouf, A Marieke Oudelaar, Daniel Biggs, Chris Preece, Damien J Downes, Matthew Gosden, Jacqueline A Sharpe, Jacqueline A Sloane-Stanley, Jim R Hughes, Benjamin Davies, Douglas R Higgs
Tissue-specific CTCF-cohesin-mediated chromatin architecture delimits enhancer interactions and function in vivo. Nature cell biology 19 (8) (2017)
Ron Schwessinger, Maria C Suciu, Simon J McGowan, Jelena Telenius, Stephen Taylor, Douglas R Higgs, Jim R Hughes
Sasquatch: predicting the impact of regulatory SNPs on transcription factor binding from cell- and tissue-specific DNase footprints. Genome research 27 (10) (2017)
James O J Davies, A Marieke Oudelaar, Douglas R Higgs, Jim R Hughes
How best to identify chromosomal interactions: a comparison of approaches. Nature methods 14 (2) (2017)
Sant-Rayn Pasricha, Pei Jin Lim, Tiago L Duarte, Carla Casu, Dorenda Oosterhuis, Katarzyna Mleczko-Sanecka, Maria Suciu, Ana Rita Da Silva, Kinda Al-Hourani, João Arezes, Kirsty McHugh, Sarah Gooding, Joe N Frost, Katherine Wray, Ana Santos, Graça Porto, Emmanouela Repapi, Nicki Gray, Simon J Draper, Neil Ashley, Elizabeth Soilleux, Peter Olinga, Martina U Muckenthaler, Jim R Hughes, Stefano Rivella, Thomas A Milne, Andrew E Armitage, Hal Drakesmith
Hepcidin is regulated by promoter-associated histone acetylation and HDAC3. Nature communications 8 (1) (2017)
Sachith Mettananda, Chris A Fisher, Deborah Hay, Mohsin Badat, Lynn Quek, Kevin Clark, Philip Hublitz, Damien Downes, Jon Kerry, Matthew Gosden, Jelena Telenius, Jackie A Sloane-Stanley, Paula Faustino, Andreia Coelho, Jessica Doondeea, Batchimeg Usukhbayar, Paul Sopp, Jacqueline A Sharpe, Jim R Hughes, Paresh Vyas, Richard J Gibbons, Douglas R Higgs
Editing an α-globin enhancer in primary human hematopoietic stem cells as a treatment for β-thalassemia. Nature communications 8 (1) (2017)
Wen Fong Ooi, Manjie Xing, Chang Xu, Xiaosai Yao, Muhammad Khairul Ramlee, Mei Chee Lim, Fan Cao, Kevin Lim, Deepak Babu, Lai-Fong Poon, Joyce Lin Suling, Aditi Qamra, Astrid Irwanto, James Qu Zhengzhong, Tannistha Nandi, Ai Ping Lee-Lim, Yang Sun Chan, Su Ting Tay, Ming Hui Lee, James O J Davies, Wai Keong Wong, Khee Chee Soo, Weng Hoong Chan, Hock Soo Ong, Pierce Chow, Chow Yin Wong, Sun Young Rha, Jianjun Liu, Axel Maximilian Hillmer, Jim R Hughes, Steven G Rozen, Bin Tean Teh, Melissa Jane Fullwood, Shang Li, Patrick Tan
Epigenomic profiling of primary gastric adenocarcinoma reveals super-enhancer heterogeneity. Nature communications 7 (2016)