Publications by authors named "David R Westhead"

73Publications

Ibrutinib induces chromatin reorganisation of chronic lymphocytic leukaemia cells.

Oncogenesis 2019 May 10;8(5):32. Epub 2019 May 10.

Section of Experimental Haematology, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK.

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May 2019

Parsimonious Gene Correlation Network Analysis (PGCNA): a tool to define modular gene co-expression for refined molecular stratification in cancer.

NPJ Syst Biol Appl 2019 11;5:13. Epub 2019 Apr 11.

1Section of Experimental Haematology, Leeds Institute of Medical Research, University of Leeds, Leeds, LS9 7TF UK.

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April 2020

Cut-and-Run: A Distinct Mechanism by which V(D)J Recombination Causes Genome Instability.

Mol Cell 2019 05 21;74(3):584-597.e9. Epub 2019 Mar 21.

School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK. Electronic address:

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May 2019

The Role of SurA PPIase Domains in Preventing Aggregation of the Outer-Membrane Proteins tOmpA and OmpT.

J Mol Biol 2019 03 1;431(6):1267-1283. Epub 2019 Feb 1.

Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK. Electronic address:

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March 2019

Growth Factor-like Gene Regulation Is Separable from Survival and Maturation in Antibody-Secreting Cells.

J Immunol 2019 02 14;202(4):1287-1300. Epub 2019 Jan 14.

Section of Experimental Haematology, Leeds Institute of Medical Research, St. James's University Hospital, University of Leeds, Leeds LS9 7TF, United Kingdom;

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February 2019

Simulation of heterogeneous tumour genomes with HeteroGenesis and in silico whole exome sequencing.

Bioinformatics 2019 08;35(16):2850-2852

Leeds Institute of Medical Research at St James's, St James's University Hospital, Leeds, UK.

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August 2019

A PQM-1-Mediated Response Triggers Transcellular Chaperone Signaling and Regulates Organismal Proteostasis.

Cell Rep 2018 06;23(13):3905-3919

School of Molecular and Cell Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK. Electronic address:

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June 2018

Flexible model-based clustering of mixed binary and continuous data: application to genetic regulation and cancer.

Nucleic Acids Res 2017 04;45(7):e53

School of Molecular and Cellular Biology, University of Leeds, Leeds, West Yorkshire LS2 9JT, UK.

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April 2017

Cancer somatic mutations cluster in a subset of regulatory sites predicted from the ENCODE data.

Mol Cancer 2016 11 25;15(1):76. Epub 2016 Nov 25.

School of Molecular and Cellular Biology, Garstang Building, University of Leeds, Leeds, LS2 9JT, UK.

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November 2016

A validated microRNA profile with predictive potential in glioblastoma patients treated with bevacizumab.

Mol Oncol 2016 10 1;10(8):1296-304. Epub 2016 Jul 1.

Leeds Institute of Cancer and Pathology, St James's University Hospital, Leeds LS9 7TF, UK.

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October 2016

Network Analysis Identifies Proinflammatory Plasma Cell Polarization for Secretion of ISG15 in Human Autoimmunity.

J Immunol 2016 08 29;197(4):1447-59. Epub 2016 Jun 29.

Section of Experimental Haematology, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds LS9 7TF, United Kingdom;

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August 2016

Gene expression meta-analysis reveals immune response convergence on the IFNγ-STAT1-IRF1 axis and adaptive immune resistance mechanisms in lymphoma.

Genome Med 2015 Sep 11;7:96. Epub 2015 Sep 11.

Section of Experimental Haematology, Wellcome Trust Brenner Building, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, LS9 7TF, UK.

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September 2015

Transferring genomics to the clinic: distinguishing Burkitt and diffuse large B cell lymphomas.

Genome Med 2015 1;7(1):64. Epub 2015 Jul 1.

School of Molecular and Cellular Biology, Garstang Building, University of Leeds, Leeds, LS2 9JT UK.

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July 2015

SPIB and BATF provide alternate determinants of IRF4 occupancy in diffuse large B-cell lymphoma linked to disease heterogeneity.

Nucleic Acids Res 2014 Jul 29;42(12):7591-610. Epub 2014 May 29.

Section of Experimental Haematology, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK Haematological Malignancy Diagnostic Service, Leeds Cancer Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK

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July 2014

A crucial role for the ubiquitously expressed transcription factor Sp1 at early stages of hematopoietic specification.

Development 2014 Jun 21;141(12):2391-401. Epub 2014 May 21.

School of Cancer Sciences, Institute of Biomedical Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK

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June 2014

Using common variants to indicate cancer genes.

Int J Cancer 2015 Jan 14;136(1):241-5. Epub 2014 May 14.

Leeds Institute of Cancer and Pathology, University of Leeds, St James's University Hospital, Leeds, United Kingdom.

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January 2015

A microarray platform-independent classification tool for cell of origin class allows comparative analysis of gene expression in diffuse large B-cell lymphoma.

PLoS One 2013 12;8(2):e55895. Epub 2013 Feb 12.

Section of Experimental Haematology, Leeds Institute of Molecular Medicine, University of Leeds, Leeds, United Kingdom.

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August 2013

In vitro generation of long-lived human plasma cells.

J Immunol 2012 Dec 16;189(12):5773-85. Epub 2012 Nov 16.

Section of Experimental Haematology, Leeds Institute of Molecular Medicine, University of Leeds, Leeds LS9 7TF, United Kingdom.

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December 2012

Simple sequence-based kernels do not predict protein-protein interactions.

Bioinformatics 2010 Oct 27;26(20):2610-4. Epub 2010 Aug 27.

School of Computer Science and Technology, Harbin Institute of Technology, Harbin 150001, China.

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October 2010

MetNetMaker: a free and open-source tool for the creation of novel metabolic networks in SBML format.

Bioinformatics 2010 Sep 29;26(18):2352-3. Epub 2010 Jul 29.

Faculty of Biological Sciences, University of Leeds, Leeds, UK.

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September 2010

KvDB; mining and mapping sequence variants in voltage-gated potassium channels.

Hum Mutat 2010 Aug;31(8):908-17

University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK.

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August 2010

An extended set of PRDM1/BLIMP1 target genes links binding motif type to dynamic repression.

Nucleic Acids Res 2010 Sep 26;38(16):5336-50. Epub 2010 Apr 26.

Section of Experimental Haematology, Leeds Institute of Molecular Medicine, University of Leeds, Leeds LS9 7TF, UK.

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September 2010

PlasmoPredict: a gene function prediction website for Plasmodium falciparum.

Trends Parasitol 2010 Mar 19;26(3):107-10. Epub 2010 Jan 19.

Institute of Molecular and Cellular Biology, University of Leeds, Leeds, UK.

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March 2010

GO-At: in silico prediction of gene function in Arabidopsis thaliana by combining heterogeneous data.

Plant J 2010 Feb 27;61(4):713-21. Epub 2009 Nov 27.

Institute of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK.

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February 2010

From gene expression to gene regulatory networks in Arabidopsis thaliana.

BMC Syst Biol 2009 Sep 3;3:85. Epub 2009 Sep 3.

School of Computing, University of Leeds, Leeds, UK.

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September 2009

The transcriptional regulation of protein complexes; a cross-species perspective.

Genomics 2009 Dec 18;94(6):369-76. Epub 2009 Aug 18.

Institute of Cellular and Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.

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December 2009

Prediction of horizontal gene transfers in eukaryotes: approaches and challenges.

Biochem Soc Trans 2009 Aug;37(Pt 4):792-5

Institute of Molecular and Cellular Biology, University of Leeds, Leeds, West Yorkshire LS2 9JT, UK.

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August 2009

Small RNA analysis in Petunia hybrida identifies unusual tissue-specific expression patterns of conserved miRNAs and of a 24mer RNA.

RNA 2009 Jun 15;15(6):1012-20. Epub 2009 Apr 15.

Institute of Molecular and Cellular Biology, The University of Leeds, Leeds LS29JT, United Kingdom.

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June 2009

The transferome of metabolic genes explored: analysis of the horizontal transfer of enzyme encoding genes in unicellular eukaryotes.

Genome Biol 2009 15;10(4):R36. Epub 2009 Apr 15.

Institute of Molecular and Cellular Biology, University of Leeds, Leeds, West Yorkshire, LS2 9JT, UK.

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September 2009

metaTIGER: a metabolic evolution resource.

Nucleic Acids Res 2009 Jan 25;37(Database issue):D531-8. Epub 2008 Oct 25.

Institute of Molecular and Cellular Biology, Garstang Building, University of Leeds, Leeds, W. Yorks, LS2 9JT, UK.

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January 2009

Bioinformatic approaches to biological systems.

SEB Exp Biol Ser 2008 ;61:1-16

Institute of Molecular and Cellular Biology, University of Leeds, UK.

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July 2011

Heat stress enhances the accumulation of polyadenylated mitochondrial transcripts in Arabidopsis thaliana.

PLoS One 2008 Aug 6;3(8):e2889. Epub 2008 Aug 6.

Center for Plant Sciences, University of Leeds, Leeds, United Kingdom.

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August 2008

Metabolic reconstruction and analysis for parasite genomes.

Trends Parasitol 2007 Nov 22;23(11):548-54. Epub 2007 Oct 22.

Faculty of Life Sciences, The University of Manchester, Oxford Road, Manchester, UK.

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November 2007

A primer on learning in Bayesian networks for computational biology.

PLoS Comput Biol 2007 Aug;3(8):e129

School of Computing, University of Leeds, Leeds, United Kingdom.

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August 2007

Bayesian refinement of protein functional site matching.

BMC Bioinformatics 2007 Jul 17;8:257. Epub 2007 Jul 17.

Department of Statistics, University of Leeds, Leeds, UK.

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July 2007

A consensus algorithm to screen genomes for novel families of transmembrane beta barrel proteins.

Proteins 2007 Oct;69(1):8-18

Institute of Cellular and Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom.

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October 2007

Modelling the pH-dependent properties of Kv1 potassium channels.

J Mol Biol 2007 Apr 22;368(2):328-35. Epub 2007 Feb 22.

Cardiovascular Research Group, School of Medicine, University of Manchester, Core Technology Facility, 46 Grafton Street, Manchester M13 9NT, UK.

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April 2007

Deleterious SNP prediction: be mindful of your training data!

Bioinformatics 2007 Mar 18;23(6):664-72. Epub 2007 Jan 18.

Institute of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK and School of Computing, University of Leeds, Leeds, LS2 9JT, UK.

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March 2007

Conservation, convergence, and divergence of light-responsive, circadian-regulated, and tissue-specific expression patterns during evolution of the Arabidopsis GATA gene family.

Plant Physiol 2007 Feb 5;143(2):941-58. Epub 2007 Jan 5.

Centre for Plant Sciences, Institute for Integrative and Comparative Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, United Kingdom.

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February 2007

Predicting the effect of missense mutations on protein function: analysis with Bayesian networks.

BMC Bioinformatics 2006 Sep 6;7:405. Epub 2006 Sep 6.

School of Computing, University of Leeds, Leeds, LS2 9JT, UK.

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September 2006

Insights into protein-protein interfaces using a Bayesian network prediction method.

J Mol Biol 2006 Sep 21;362(2):365-86. Epub 2006 Jul 21.

Institute of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK.

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September 2006

metaSHARK: a WWW platform for interactive exploration of metabolic networks.

Nucleic Acids Res 2006 Jul;34(Web Server issue):W725-8

Faculty of Biological Sciences, University of Leeds, Clarendon Way, Leeds LS2 9JT, UK.

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July 2006

Inference in Bayesian networks.

Nat Biotechnol 2006 Jan;24(1):51-3

School of Computing, University of Leeds, Leeds, LS2 9JT, UK.

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January 2006

TmaDB: a repository for tissue microarray data.

BMC Bioinformatics 2005 Sep 1;6:218. Epub 2005 Sep 1.

Academic Unit of Pathology, University of Leeds, Leeds, LS1 3EX, UK.

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September 2005

Differential expression and extent of fungal/plant and fungal/bacterial chitinases of Aspergillus fumigatus.

Arch Microbiol 2005 Oct 3;184(1):78-81. Epub 2005 Nov 3.

School of Biochemistry & Microbiology, University of Leeds, LS2 9JT, Leeds, UK.

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October 2005

TMB-Hunt: a web server to screen sequence sets for transmembrane beta-barrel proteins.

Nucleic Acids Res 2005 Jul;33(Web Server issue):W188-92

School of Biochemistry and Microbiology, University of Leeds, Leeds LS2 9JT, UK.

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July 2005

TMB-Hunt: an amino acid composition based method to screen proteomes for beta-barrel transmembrane proteins.

BMC Bioinformatics 2005 Mar 15;6:56. Epub 2005 Mar 15.

School of Biochemistry and Microbiology, University of Leeds, Leeds, LS2 9JT, UK.

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March 2005

Improved prediction of protein-protein binding sites using a support vector machines approach.

Bioinformatics 2005 Apr 21;21(8):1487-94. Epub 2004 Dec 21.

School of Biochemistry and Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.

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April 2005

Annotating the Plasmodium genome and the enigma of the shikimate pathway.

Trends Parasitol 2004 Feb;20(2):60-5

Faculty of Biological Sciences, University of Leeds, Clarendon Way, LS2 9JT, Leeds, UK.

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February 2004

TOPS: an enhanced database of protein structural topology.

Nucleic Acids Res 2004 Jan;32(Database issue):D251-4

School of Biochemistry and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.

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January 2004

Beta edge strands in protein structure prediction and aggregation.

Protein Sci 2003 Oct;12(10):2348-59

School of Biochemistry and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.

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October 2003

Asymmetric mutation rates at enzyme-inhibitor interfaces: implications for the protein-protein docking problem.

Protein Sci 2003 Sep;12(9):2099-103

School of Biochemistry and Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.

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September 2003

Calculation of helix packing angles in protein structures.

Bioinformatics 2003 Jul;19(10):1298-9

School of Biochemistry and Molecular Biology, University of Leeds, Leeds, West Yorkshire LS2 9JT, UK.

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July 2003

Ligand binding: functional site location, similarity and docking.

Curr Opin Struct Biol 2003 Jun;13(3):389-95

School of Biochemistry and Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.

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June 2003

The fibril_one on-line database: mutations, experimental conditions, and trends associated with amyloid fibril formation.

Protein Sci 2002 Jul;11(7):1862-6

School of Biochemistry and Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.

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July 2002