Publications by authors named "Jim Hughes"

73Publications

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

Nat Methods 2020 Oct 12. Epub 2020 Oct 12.

MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.

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http://dx.doi.org/10.1038/s41592-020-0960-3DOI Listing
October 2020

Loss of Extreme Long-Range Enhancers in Human Neural Crest Drives a Craniofacial Disorder.

Cell Stem Cell 2020 Sep 22. Epub 2020 Sep 22.

Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2020.09.001DOI Listing
September 2020

Predictions of Systemic, Intracellular, and Lung Concentrations of Azithromycin With Different Dosing Regimens Used in COVID-19 Clinical Trials.

CPT Pharmacometrics Syst Pharmacol 2020 08 15;9(8):435-443. Epub 2020 Jul 15.

Pfizer Global Research and Development, Groton, Connecticut, USA.

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http://dx.doi.org/10.1002/psp4.12537DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7300789PMC
August 2020

Absolute Quantification of Transcription Factors Reveals Principles of Gene Regulation in Erythropoiesis.

Mol Cell 2020 06 23;78(5):960-974.e11. Epub 2020 Apr 23.

Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON K1H8L6, Canada; Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H8L6, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2020.03.031DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7344268PMC
June 2020

A Dynamic Folded Hairpin Conformation Is Associated with α-Globin Activation in Erythroid Cells.

Cell Rep 2020 02;30(7):2125-2135.e5

Dipartimento di Fisica, Università degli Studi di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, 80126 Naples, Italy; Berlin Institute of Health (BIH), MDC-Berlin, 13125 Berlin, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2020.01.044DOI Listing
February 2020

Relationship between vemurafenib plasma concentrations and survival outcomes in patients with advanced melanoma.

Cancer Chemother Pharmacol 2020 Mar 30;85(3):615-620. Epub 2019 Nov 30.

Department of Clinical Pharmacology, College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Australia.

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http://dx.doi.org/10.1007/s00280-019-04002-1DOI Listing
March 2020

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

Nat Commun 2019 11 27;10(1):5412. Epub 2019 Nov 27.

MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.

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http://dx.doi.org/10.1038/s41467-019-13404-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6881440PMC
November 2019

Reconstruction of the Global Neural Crest Gene Regulatory Network In Vivo.

Dev Cell 2019 10;51(2):255-276.e7

University of Oxford, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK. Electronic address:

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http://dx.doi.org/10.1016/j.devcel.2019.10.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6838682PMC
October 2019

Development of a physiologically based pharmacokinetic model for intravenous lenalidomide in mice.

Cancer Chemother Pharmacol 2019 11 6;84(5):1073-1087. Epub 2019 Sep 6.

School of Pharmacy and Medical Sciences, University of South Australia, North Terrace, Adelaide, 5001, Australia.

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http://dx.doi.org/10.1007/s00280-019-03941-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7375688PMC
November 2019

Optimising time samples for determining area under the curve of pharmacokinetic data using non-compartmental analysis.

J Pharm Pharmacol 2019 Nov 14;71(11):1635-1644. Epub 2019 Aug 14.

School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, SA, Australia.

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http://dx.doi.org/10.1111/jphp.13154DOI Listing
November 2019

DOT1L inhibition reveals a distinct subset of enhancers dependent on H3K79 methylation.

Nat Commun 2019 06 26;10(1):2803. Epub 2019 Jun 26.

MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK.

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http://dx.doi.org/10.1038/s41467-019-10844-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6594956PMC
June 2019

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

Methods Protoc 2018 Aug 1;1(3). Epub 2018 Aug 1.

MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford OX3 9DU, UK.

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http://dx.doi.org/10.3390/mps1030029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6481090PMC
August 2018

Population pharmacokinetics of lenalidomide in patients with B-cell malignancies.

Br J Clin Pharmacol 2019 05 27;85(5):924-934. Epub 2019 Feb 27.

Australian Centre for Pharmacometrics, School of Pharmacy and Medical Sciences, Division of Health Sciences, University of South Australia, Australia.

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http://dx.doi.org/10.1111/bcp.13873DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6475687PMC
May 2019

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

Bio Protoc 2017 Dec;7(23)

Medical Research Council (MRC) Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom.

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http://dx.doi.org/10.21769/BioProtoc.2645DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5736099PMC
December 2017

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

Nucleic Acids Res 2017 Dec;45(22):e184

Medical Research Council (MRC) Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.

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http://dx.doi.org/10.1093/nar/gkx1194DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5728395PMC
December 2017

Between form and function: the complexity of genome folding.

Hum Mol Genet 2017 10;26(R2):R208-R215

MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS, UK.

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http://dx.doi.org/10.1093/hmg/ddx306DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5886466PMC
October 2017

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

Genome Res 2017 10 13;27(10):1730-1742. Epub 2017 Sep 13.

MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford OX3 9DS, United Kingdom.

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http://dx.doi.org/10.1101/gr.220202.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5630036PMC
October 2017

DNA methylation of intragenic CpG islands depends on their transcriptional activity during differentiation and disease.

Proc Natl Acad Sci U S A 2017 09 21;114(36):E7526-E7535. Epub 2017 Aug 21.

Division of Medical Sciences and Graduate Entry Medicine, School of Medicine, University of Nottingham, Royal Derby Hospital, Derby DE22 3DT, United Kingdom;

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http://dx.doi.org/10.1073/pnas.1703087114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5594649PMC
September 2017

Comparison of non-compartmental and mixed effect modelling methods for establishing bioequivalence for the case of two compartment kinetics and censored concentrations.

J Pharmacokinet Pharmacodyn 2017 06 13;44(3):233-244. Epub 2017 Feb 13.

School of Pharmacy and Medical Sciences, Australian Centre for Pharmacometrics and Sansom Institute, University of South Australia, Adelaide, SA, 5000, Australia.

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http://dx.doi.org/10.1007/s10928-017-9511-7DOI Listing
June 2017

How best to identify chromosomal interactions: a comparison of approaches.

Nat Methods 2017 01;14(2):125-134

Medical Research Council (MRC) Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, United Kingdom.

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http://dx.doi.org/10.1038/nmeth.4146DOI Listing
January 2017

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

Exp Hematol 2017 03 14;47:64-75. Epub 2016 Nov 14.

Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, University of Oxford, Headington, Oxford, UK. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S0301472X163070
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http://dx.doi.org/10.1016/j.exphem.2016.11.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5333536PMC
March 2017

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

EMBO Rep 2016 10 8;17(10):1410-1421. Epub 2016 Aug 8.

Henry Wellcome Building for Molecular Physiology, University of Oxford, Oxford, UK

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http://dx.doi.org/10.15252/embr.201642198DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5048371PMC
October 2016

Unlinking an lncRNA from Its Associated cis Element.

Mol Cell 2016 Apr 31;62(1):104-10. Epub 2016 Mar 31.

Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2016.02.029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4877494PMC
April 2016

Multiplexed analysis of chromosome conformation at vastly improved sensitivity.

Nat Methods 2016 Jan 23;13(1):74-80. Epub 2015 Nov 23.

Medical Research Council, Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, UK.

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http://dx.doi.org/10.1038/nmeth.3664DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4724891PMC
January 2016

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

Cell Rep 2015 Apr 9;11(3):405-18. Epub 2015 Apr 9.

MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2015.03.036DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4410944PMC
April 2015

Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment.

Nat Genet 2014 Feb 12;46(2):205-12. Epub 2014 Jan 12.

Medical Research Council (MRC) Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, UK.

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http://dx.doi.org/10.1038/ng.2871DOI Listing
February 2014

The worm has turned: unexpected similarities between the transcription of enhancers and promoters in the worm and mammalian genomes.

Bioessays 2014 Feb 5;36(2):157-62. Epub 2013 Dec 5.

MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, The John Radcliffe Hospital, Oxford, United Kingdom.

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http://dx.doi.org/10.1002/bies.201300105DOI Listing
February 2014

MIG: Multi-Image Genome viewer.

Bioinformatics 2013 Oct 10;29(19):2477-8. Epub 2013 Jul 10.

Computational Biology Research Group and Molecular Haemotology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Headington, Oxford OX3 9DS, UK.

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http://dx.doi.org/10.1093/bioinformatics/btt406DOI Listing
October 2013

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

Philos Trans R Soc Lond B Biol Sci 2013 6;368(1620):20120361. Epub 2013 May 6.

MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford OX3 9DS, UK.

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http://dx.doi.org/10.1098/rstb.2012.0361DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3682726PMC
December 2013

Analysis of sequence variation underlying tissue-specific transcription factor binding and gene expression.

Hum Mutat 2013 Aug 18;34(8):1140-8. Epub 2013 Jun 18.

MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, UK.

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http://dx.doi.org/10.1002/humu.22343DOI Listing
August 2013

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

Genome Res 2010 Aug 21;20(8):1064-83. Epub 2010 Jun 21.

MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford University, Oxford OX3 9DS, United Kingdom.

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http://dx.doi.org/10.1101/gr.104935.110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2909570PMC
August 2010

Adventitious changes in long-range gene expression caused by polymorphic structural variation and promoter competition.

Proc Natl Acad Sci U S A 2009 Dec 3;106(51):21771-6. Epub 2009 Dec 3.

Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, The John Radcliffe Hospital, Headington, Oxford, OX3 9DS, United Kingdom.

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http://dx.doi.org/10.1073/pnas.0909331106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2799829PMC
December 2009

Alternative Runx1 promoter usage in mouse developmental hematopoiesis.

Blood Cells Mol Dis 2009 Jul-Aug;43(1):35-42. Epub 2009 May 21.

MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK.

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http://dx.doi.org/10.1016/j.bcmd.2009.03.011DOI Listing
September 2009

Association between active genes occurs at nuclear speckles and is modulated by chromatin environment.

J Cell Biol 2008 Sep;182(6):1083-97

Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford OX3 9DS, England, UK.

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http://dx.doi.org/10.1083/jcb.200803174DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2542471PMC
September 2008

Tissue-specific histone modification and transcription factor binding in alpha globin gene expression.

Blood 2007 Dec 22;110(13):4503-10. Epub 2007 Aug 22.

Medical Research Council, Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, UK.

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http://dx.doi.org/10.1182/blood-2007-06-097964DOI Listing
December 2007

Using genomics to study how chromatin influences gene expression.

Annu Rev Genomics Hum Genet 2007 ;8:299-325

MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headington, Oxford OX3 9DS, United Kingdom.

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http://dx.doi.org/10.1146/annurev.genom.8.080706.092323DOI Listing
December 2007

Manipulating the mouse genome to engineer precise functional syntenic replacements with human sequence.

Cell 2007 Jan;128(1):197-209

Institute for Stem Cell Research, University of Edinburgh, King's Buildings, West Mains Road, Edinburgh EH9 3JQ, United Kingdom.

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http://dx.doi.org/10.1016/j.cell.2006.11.044DOI Listing
January 2007

A regulatory SNP causes a human genetic disease by creating a new transcriptional promoter.

Science 2006 May;312(5777):1215-7

Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, OX3 9DS, UK.

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http://dx.doi.org/10.1126/science.1126431DOI Listing
May 2006

How transcriptional and epigenetic programmes are played out on an individual mammalian gene cluster during lineage commitment and differentiation.

Biochem Soc Symp 2006 (73):11-22

MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK.

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http://dx.doi.org/10.1042/bss0730011DOI Listing
May 2006

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

Proc Natl Acad Sci U S A 2005 Jul 5;102(28):9830-5. Epub 2005 Jul 5.

Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headington, Oxford OX3 9DS, United Kingdom.

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http://dx.doi.org/10.1073/pnas.0503401102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1174996PMC
July 2005

Globin gene activation during haemopoiesis is driven by protein complexes nucleated by GATA-1 and GATA-2.

EMBO J 2004 Jul 24;23(14):2841-52. Epub 2004 Jun 24.

MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, UK.

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http://emboj.embopress.org/cgi/doi/10.1038/sj.emboj.7600274
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http://dx.doi.org/10.1038/sj.emboj.7600274DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC514941PMC
July 2004

Heterogeneity of the 7q36 breakpoints in the t(7;12) involving ETV6 in infant leukemia.

Genes Chromosomes Cancer 2003 Oct;38(2):191-200

MRC Molecular Haematology Unit, Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, United Kingdom.

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http://dx.doi.org/10.1002/gcc.10258DOI Listing
October 2003

De novo deletion within the telomeric region flanking the human alpha globin locus as a cause of alpha thalassaemia.

Br J Haematol 2003 Mar;120(5):867-75

MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, UK.

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http://dx.doi.org/10.1046/j.1365-2141.2003.04197.xDOI Listing
March 2003