Jim R. Hughes MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine University of Oxford Biography Publications Institution JoVE Articles Jim R. Hughes has not added a biography. If you are Jim R. Hughes and would like to personalize this page please email our Author Liaison for assistance. Publications Inferring Causal Genes at Type 2 Diabetes GWAS Loci Through Chromosome Interactions in Islet Cells Wellcome Open Research. 2023 | Pubmed ID: 37736013 Author Correction: Capture-C: a Modular and Flexible Approach for High-resolution Chromosome Conformation Capture Nature Protocols. Jun, 2023 | Pubmed ID: 37369851 GTAC Enables Parallel Genotyping of Multiple Genomic Loci with Chromatin Accessibility Profiling in Single Cells Cell Stem Cell. May, 2023 | Pubmed ID: 37146586 Assessment of Multiway Interactions with Tri-C Methods in Molecular Biology (Clifton, N.J.). 2022 | Pubmed ID: 35867247 LanceOtron: a Deep Learning Peak Caller for Genome Sequencing Experiments Bioinformatics (Oxford, England). Sep, 2022 | Pubmed ID: 35866989 The Chromatin Remodeller ATRX Facilitates Diverse Nuclear Processes, in a Stochastic Manner, in Both Heterochromatin and Euchromatin Nature Communications. Jun, 2022 | Pubmed ID: 35710802 Chromatin Interaction Maps Identify Wnt Responsive Cis-regulatory Elements Coordinating Paupar-Pax6 Expression in Neuronal Cells PLoS Genetics. Jun, 2022 | Pubmed ID: 35709096 Natural and Experimental Rewiring of Gene Regulatory Regions Annual Review of Genomics and Human Genetics. Aug, 2022 | Pubmed ID: 35472292 Dynamic Runx1 Chromatin Boundaries Affect Gene Expression in Hematopoietic Development Nature Communications. Feb, 2022 | Pubmed ID: 35140205 Capture-C: a Modular and Flexible Approach for High-resolution Chromosome Conformation Capture Nature Protocols. Feb, 2022 | Pubmed ID: 35121852 Making Connections: Enhancers in Cellular Differentiation Trends in Genetics : TIG. Apr, 2022 | Pubmed ID: 34753603 Identification of LZTFL1 As a Candidate Effector Gene at a COVID-19 Risk Locus Nature Genetics. Nov, 2021 | Pubmed ID: 34737427 Reactivation of a Developmentally Silenced Embryonic Globin Gene Nature Communications. Jul, 2021 | Pubmed ID: 34290235 A Gain-of-function Single Nucleotide Variant Creates a New Promoter Which Acts As an Orientation-dependent Enhancer-blocker Nature Communications. Jun, 2021 | Pubmed ID: 34155213 Defining Genome Architecture at Base-pair Resolution Nature. Jul, 2021 | Pubmed ID: 34108683 Multi Locus View: an Extensible Web-based Tool for the Analysis of Genomic Data Communications Biology. May, 2021 | Pubmed ID: 34035422 Enhancers Predominantly Regulate Gene Expression During Differentiation Via Transcription Initiation Molecular Cell. Mar, 2021 | Pubmed ID: 33539786 High-resolution Targeted 3C Interrogation of Cis-regulatory Element Organization at Genome-wide Scale Nature Communications. Jan, 2021 | Pubmed ID: 33483495 Genetic and Functional Insights into CDA-I Prevalence and Pathogenesis Journal of Medical Genetics. Mar, 2021 | Pubmed ID: 32518175 DeepC: Predicting 3D Genome Folding Using Megabase-scale Transfer Learning Nature Methods. Nov, 2020 | Pubmed ID: 33046896 Loss of Extreme Long-Range Enhancers in Human Neural Crest Drives a Craniofacial Disorder Cell Stem Cell. Nov, 2020 | Pubmed ID: 32991838 Dynamics of the 4D Genome During in Vivo Lineage Specification and Differentiation Nature Communications. Jun, 2020 | Pubmed ID: 32483172 Absolute Quantification of Transcription Factors Reveals Principles of Gene Regulation in Erythropoiesis Molecular Cell. Jun, 2020 | Pubmed ID: 32330456 A Dynamic Folded Hairpin Conformation Is Associated with α-Globin Activation in Erythroid Cells Cell Reports. Feb, 2020 | Pubmed ID: 32075757 A Revised Model for Promoter Competition Based on Multi-way Chromatin Interactions at the α-globin Locus Nature Communications. Nov, 2019 | Pubmed ID: 31776347 Nrf2 Controls Iron Homeostasis in Haemochromatosis and Thalassaemia Via Bmp6 and Hepcidin Nature Metabolism. 05, 2019 | Pubmed ID: 31276102 DOT1L Inhibition Reveals a Distinct Subset of Enhancers Dependent on H3K79 Methylation Nature Communications. Jun, 2019 | Pubmed ID: 31243293 The Bipartite TAD Organization of the X-inactivation Center Ensures Opposing Developmental Regulation of Tsix and Xist Nature Genetics. 06, 2019 | Pubmed ID: 31133748 High-Throughput Genotyping of CRISPR/Cas Edited Cells in 96-Well Plates Methods and Protocols. Aug, 2018 | Pubmed ID: 31164571 Single-allele Chromatin Interactions Identify Regulatory Hubs in Dynamic Compartmentalized Domains Nature Genetics. Dec, 2018 | Pubmed ID: 30374068 Low-input Capture-C: A Chromosome Conformation Capture Assay to Analyze Chromatin Architecture in Small Numbers of Cells Bio-protocol. Dec, 2017 | Pubmed ID: 29270442 Robust Detection of Chromosomal Interactions from Small Numbers of Cells Using Low-input Capture-C Nucleic Acids Research. Dec, 2017 | Pubmed ID: 29186505 Between Form and Function: the Complexity of Genome Folding Human Molecular Genetics. Oct, 2017 | Pubmed ID: 28977451 Editing an α-globin Enhancer in Primary Human Hematopoietic Stem Cells As a Treatment for β-thalassemia Nature Communications. Sep, 2017 | Pubmed ID: 28871148 Hepcidin is Regulated by Promoter-associated Histone Acetylation and HDAC3 Nature Communications. Sep, 2017 | Pubmed ID: 28864822 Tissue-specific CTCF-cohesin-mediated Chromatin Architecture Delimits Enhancer Interactions and Function in Vivo Nature Cell Biology. Aug, 2017 | Pubmed ID: 28737770 Functional Characterisation of -regulatory Elements Governing Dynamic Expression in the Early Mouse Embryo Development (Cambridge, England). Apr, 2017 | Pubmed ID: 28174238 MLL-AF4 Binds Directly to a BCL-2 Specific Enhancer and Modulates H3K27 acetylation Experimental Hematology. Mar, 2017 | Pubmed ID: 27856324 Capture-C Reveals Preformed Chromatin Interactions Between HIF-binding Sites and Distant Promoters EMBO Reports. Oct, 2016 | Pubmed ID: 27506891 ATRX Plays a Key Role in Maintaining Silencing at Interstitial Heterochromatic Loci and Imprinted Genes Cell Reports. Apr, 2015 | Pubmed ID: 25865896 MIG: Multi-Image Genome Viewer Bioinformatics (Oxford, England). Oct, 2013 | Pubmed ID: 23842811 Causes and Consequences of Chromatin Variation Between Inbred Mice PLoS Genetics. Jun, 2013 | Pubmed ID: 23785304 Nprl3 is Required for Normal Development of the Cardiovascular System Mammalian Genome : Official Journal of the International Mammalian Genome Society. Apr, 2012 | Pubmed ID: 22538705 Intragenic Enhancers Act As Alternative Promoters Molecular Cell. Feb, 2012 | Pubmed ID: 22264824 An Interspecies Analysis Reveals a Key Role for Unmethylated CpG Dinucleotides in Vertebrate Polycomb Complex Recruitment The EMBO Journal. 2011 | Pubmed ID: 22056776 Generation of Bivalent Chromatin Domains During Cell Fate Decisions Epigenetics & Chromatin. Jun, 2011 | Pubmed ID: 21645363 CATCH-UP: A High-Throughput Upstream-Pipeline for Bulk ATAC-Seq and ChIP-Seq Data Simone G. Riva1,2, Emily Georgiades1,2, E. Ravza Gur1,2, Matthew Baxter1,2,3, Jim R. Hughes1,2 1MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, 2MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, 3Division of Cardiovascular Medicine, Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford JoVE 65633 遗传学
CATCH-UP: A High-Throughput Upstream-Pipeline for Bulk ATAC-Seq and ChIP-Seq Data Simone G. Riva1,2, Emily Georgiades1,2, E. Ravza Gur1,2, Matthew Baxter1,2,3, Jim R. Hughes1,2 1MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, 2MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, 3Division of Cardiovascular Medicine, Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford JoVE 65633 遗传学