Publications by authors named "David R Westhead"

73Publications

Comparative analysis of gene expression platforms for cell-of-origin classification of diffuse large B-cell lymphoma shows high concordance.

Authors:
Sophia Ahmed Paul Glover Jan Taylor Chulin Sha Matthew A Care Reuben Tooze Andrew Davies David R Westhead Peter W M Johnson Catherine Burton Sharon L Barrans

Br J Haematol 2020 Nov 29. Epub 2020 Nov 29.

Haematological Malignancy Diagnostic Service, St James' University Hospital, Leeds, UK.

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November 2020

Distinct genetic changes reveal evolutionary history and heterogeneous molecular grade of DLBCL with MYC/BCL2 double-hit.

Authors:
Francesco Cucco Sharon Barrans Chulin Sha Alexandra Clipson Simon Crouch Rachel Dobson Zi Chen Joe Sneath Thompson Matthew A Care Thomas Cummin Josh Caddy Hongxiang Liu Anne Robinson Anna Schuh Jude Fitzgibbon Daniel Painter Alexandra Smith Eve Roman Reuben Tooze Catherine Burton Andrew J Davies David R Westhead Peter W M Johnson Ming-Qing Du

Leukemia 2020 05 16;34(5):1329-1341. Epub 2019 Dec 16.

Department of Pathology, University of Cambridge, Cambridge, UK.

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May 2020

Identification of gene specific cis-regulatory elements during differentiation of mouse embryonic stem cells: An integrative approach using high-throughput datasets.

Authors:
M S Vijayabaskar Debbie K Goode Nadine Obier Monika Lichtinger Amber M L Emmett Fatin N Zainul Abidin Nisar Shar Rebecca Hannah Salam A Assi Michael Lie-A-Ling Berthold Gottgens Georges Lacaud Valerie Kouskoff Constanze Bonifer David R Westhead

PLoS Comput Biol 2019 11 4;15(11):e1007337. Epub 2019 Nov 4.

School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom.

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November 2019

Ibrutinib induces chromatin reorganisation of chronic lymphocytic leukaemia cells.

Authors:
Katie B Holmes Ildar I Sadreev Andy C Rawstron Tal Munir David R Westhead Peter Hillmen Pascal F Lefevre

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.

Authors:
Matthew A Care David R Westhead Reuben M Tooze

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

Gene-expression profiling of bortezomib added to standard chemoimmunotherapy for diffuse large B-cell lymphoma (REMoDL-B): an open-label, randomised, phase 3 trial.

Authors:
Andrew Davies Thomas E Cummin Sharon Barrans Tom Maishman Christoph Mamot Urban Novak Josh Caddy Louise Stanton Shamim Kazmi-Stokes Andrew McMillan Paul Fields Christopher Pocock Graham P Collins Richard Stephens Francesco Cucco Alexandra Clipson Chulin Sha Reuben Tooze Matthew A Care Gareth Griffiths Ming-Qing Du David R Westhead Catherine Burton Peter W M Johnson

Lancet Oncol 2019 05 1;20(5):649-662. Epub 2019 Apr 1.

Cancer Research UK Centre, University of Southampton, Southampton, UK. Electronic address:

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May 2019

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

Authors:
Christopher M Kirkham James N F Scott Xiaoling Wang Alastair L Smith Adam P Kupinski Anthony M Ford David R Westhead Peter G Stockley Roman Tuma Joan Boyes

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.

Authors:
Julia R Humes Bob Schiffrin Antonio N Calabrese Anna J Higgins David R Westhead David J Brockwell Sheena E Radford

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.

Authors:
Sophie Stephenson Matthew A Care Im Fan Alexandre Zougman David R Westhead Gina M Doody Reuben M Tooze

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.

Authors:
Georgette Tanner David R Westhead Alastair Droop Lucy F Stead

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

Molecular High-Grade B-Cell Lymphoma: Defining a Poor-Risk Group That Requires Different Approaches to Therapy.

Authors:
Chulin Sha Sharon Barrans Francesco Cucco Michael A Bentley Matthew A Care Thomas Cummin Hannah Kennedy Joe S Thompson Rahman Uddin Lisa Worrillow Rebecca Chalkley Moniek van Hoppe Sophia Ahmed Tom Maishman Josh Caddy Anna Schuh Christoph Mamot Catherine Burton Reuben Tooze Andrew Davies Ming-Qing Du Peter W M Johnson David R Westhead

J Clin Oncol 2019 01 3;37(3):202-212. Epub 2018 Dec 3.

1 University of Leeds, Leeds, United Kingdom.

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January 2019

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

Authors:
Daniel O'Brien Laura M Jones Sarah Good Jo Miles M S Vijayabaskar Rebecca Aston Catrin E Smith David R Westhead Patricija van Oosten-Hawle

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.

Authors:
Fatin N Zainul Abidin David R Westhead

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.

Authors:
Nisar A Shar M S Vijayabaskar David R Westhead

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.

Authors:
Josie Hayes Helene Thygesen Walter Gregory David R Westhead Pim J French Martin J Van Den Bent Sean E Lawler Susan C Short

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.

Authors:
Matthew A Care Sophie J Stephenson Nicholas A Barnes Im Fan Alexandre Zougman Yasser M El-Sherbiny Edward M Vital David R Westhead Reuben M Tooze Gina M Doody

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

Dynamic Gene Regulatory Networks Drive Hematopoietic Specification and Differentiation.

Authors:
Debbie K Goode Nadine Obier M S Vijayabaskar Michael Lie-A-Ling Andrew J Lilly Rebecca Hannah Monika Lichtinger Kiran Batta Magdalena Florkowska Rahima Patel Mairi Challinor Kirstie Wallace Jane Gilmour Salam A Assi Pierre Cauchy Maarten Hoogenkamp David R Westhead Georges Lacaud Valerie Kouskoff Berthold Göttgens Constanze Bonifer

Dev Cell 2016 Mar 25;36(5):572-87. Epub 2016 Feb 25.

Institute of Cancer end Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham B152TT, UK. Electronic address:

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March 2016

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

Authors:
Matthew A Care David R Westhead Reuben M Tooze

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

Chronic FLT3-ITD Signaling in Acute Myeloid Leukemia Is Connected to a Specific Chromatin Signature.

Authors:
Pierre Cauchy Sally R James Joaquin Zacarias-Cabeza Anetta Ptasinska Maria Rosaria Imperato Salam A Assi Jason Piper Martina Canestraro Maarten Hoogenkamp Manoj Raghavan Justin Loke Susanna Akiki Samuel J Clokie Stephen J Richards David R Westhead Michael J Griffiths Sascha Ott Constanze Bonifer Peter N Cockerill

Cell Rep 2015 Aug 23;12(5):821-36. Epub 2015 Jul 23.

School of Immunity and Infection, College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, UK. Electronic address:

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August 2015

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

Authors:
Chulin Sha Sharon Barrans Matthew A Care David Cunningham Reuben M Tooze Andrew Jack David R Westhead

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

Identification of a dynamic core transcriptional network in t(8;21) AML that regulates differentiation block and self-renewal.

Authors:
Anetta Ptasinska Salam A Assi Natalia Martinez-Soria Maria Rosaria Imperato Jason Piper Pierre Cauchy Anna Pickin Sally R James Maarten Hoogenkamp Dan Williamson Mengchu Wu Daniel G Tenen Sascha Ott David R Westhead Peter N Cockerill Olaf Heidenreich Constanze Bonifer

Cell Rep 2014 Sep 18;8(6):1974-1988. Epub 2014 Sep 18.

School of Cancer Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, UK. Electronic address:

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September 2014

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

Authors:
Matthew A Care Mario Cocco Jon P Laye Nicholas Barnes Yuanxue Huang Ming Wang Sharon Barrans Ming Du Andrew Jack David R Westhead Gina M Doody Reuben M Tooze

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.

Authors:
Jane Gilmour Salam A Assi Ulrike Jaegle Divine Kulu Harmen van de Werken Deborah Clarke David R Westhead Sjaak Philipsen Constanze Bonifer

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.

Authors:
Lucy F Stead Helene Thygesen David R Westhead Pamela Rabbitts

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.

Authors:
Matthew A Care Sharon Barrans Lisa Worrillow Andrew Jack David R Westhead Reuben M Tooze

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.

Authors:
Mario Cocco Sophie Stephenson Matthew A Care Darren Newton Nicholas A Barnes Adam Davison Andy Rawstron David R Westhead Gina M Doody Reuben M Tooze

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

RUNX1 reshapes the epigenetic landscape at the onset of haematopoiesis.

Authors:
Monika Lichtinger Richard Ingram Rebecca Hannah Dorothee Müller Deborah Clarke Salam A Assi Michael Lie-A-Ling Laura Noailles M S Vijayabaskar Mengchu Wu Daniel G Tenen David R Westhead Valerie Kouskoff Georges Lacaud Berthold Göttgens Constanze Bonifer

EMBO J 2012 Nov 12;31(22):4318-33. Epub 2012 Oct 12.

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

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November 2012

Whole genome expression profiling based on paraffin embedded tissue can be used to classify diffuse large B-cell lymphoma and predict clinical outcome.

Authors:
Sharon L Barrans Simon Crouch Matthew A Care Lisa Worrillow Alex Smith Russell Patmore David R Westhead Reuben Tooze Eve Roman Andrew S Jack

Br J Haematol 2012 Nov 13;159(4):441-53. Epub 2012 Sep 13.

Haematological Malignancy Diagnostic Service, St. James's Institute of Oncology, Leeds, UK.

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November 2012

Two distinct auto-regulatory loops operate at the PU.1 locus in B cells and myeloid cells.

Authors:
Mathias Leddin Chiara Perrod Maarten Hoogenkamp Saeed Ghani Salam Assi Sven Heinz Nicola K Wilson George Follows Jörg Schönheit Lena Vockentanz Ali M Mosammam Wei Chen Daniel G Tenen David R Westhead Berthold Göttgens Constanze Bonifer Frank Rosenbauer

Blood 2011 Mar 14;117(10):2827-38. Epub 2011 Jan 14.

Max Delbrück Center for Molecular Medicine, Berlin, Germany.

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March 2011

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

Authors:
Jiantao Yu Maozu Guo Chris J Needham Yangchao Huang Lu Cai David R Westhead

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

Gene function prediction using semantic similarity clustering and enrichment analysis in the malaria parasite Plasmodium falciparum.

Authors:
Philip M R Tedder James R Bradford Chris J Needham Glenn A McConkey Andrew J Bulpitt David R Westhead

Bioinformatics 2010 Oct 6;26(19):2431-7. Epub 2010 Aug 6.

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

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October 2010

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

Authors:
Thomas Forth Glenn A McConkey David R Westhead

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.

Authors:
Lucy F Stead Ian C Wood David R Westhead

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.

Authors:
Gina M Doody Matthew A Care Nicholas J Burgoyne James R Bradford Maria Bota Constanze Bonifer David R Westhead Reuben M Tooze

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.

Authors:
Philip M R Tedder James R Bradford Glenn A McConkey Andy J Bulpitt David R Westhead

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.

Authors:
James R Bradford Chris J Needham Philip Tedder Matthew A Care Andrew J Bulpitt David R Westhead

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.

Authors:
Chris J Needham Iain W Manfield Andrew J Bulpitt Philip M Gilmartin David R Westhead

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

Alio intuitu: the automated reconstruction of the metabolic networks of parasites.

Authors:
John W Whitaker David R Westhead Glenn A McConkey

Trends Parasitol 2009 Sep 28;25(9):396-7. Epub 2009 Aug 28.

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September 2009

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

Authors:
Elizabeth C Webb David R Westhead

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.

Authors:
John W Whitaker Glenn A McConkey David R Westhead

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.

Authors:
Philip Tedder Elena Zubko David R Westhead Peter Meyer

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.

Authors:
John W Whitaker Glenn A McConkey David R Westhead

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.

Authors:
John W Whitaker Ivica Letunic Glenn A McConkey David R Westhead

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.

Authors:
David R Westhead Iain W Manfield Christopher J Needham

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.

Authors:
Alessio Adamo John W Pinney Andrea Kunova David R Westhead Peter Meyer

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.

Authors:
John W Pinney Balázs Papp Christopher Hyland Lillian Wambua David R Westhead Glenn A McConkey

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.

Authors:
Chris J Needham James R Bradford Andrew J Bulpitt David R Westhead

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.

Authors:
Kanti V Mardia Vysaul B Nyirongo Peter J Green Nicola D Gold David R Westhead

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.

Authors:
Andrew G Garrow David R Westhead

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.

Authors:
Binbin Liu David R Westhead Mark R Boyett Jim Warwicker

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!

Authors:
Matthew A Care Chris J Needham Andrew J Bulpitt David R Westhead

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.

Authors:
Iain W Manfield Paul F Devlin Chih-Hung Jen David R Westhead Philip M Gilmartin

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.

Authors:
Chris J Needham James R Bradford Andrew J Bulpitt Matthew A Care David R Westhead

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.

Authors:
James R Bradford Chris J Needham Andrew J Bulpitt David R Westhead

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

Identification of the REST regulon reveals extensive transposable element-mediated binding site duplication.

Authors:
Rory Johnson Richard J Gamblin Lezanne Ooi Alexander W Bruce Ian J Donaldson David R Westhead Ian C Wood Richard M Jackson Noel J Buckley

Nucleic Acids Res 2006 9;34(14):3862-77. Epub 2006 Aug 9.

Institute of Membrane and Systems Biology, University of Leeds, Leeds LS2 9JT, UK.

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September 2006

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

Authors:
Christopher Hyland John W Pinney Glenn A McConkey David R Westhead

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

Arabidopsis Co-expression Tool (ACT): web server tools for microarray-based gene expression analysis.

Authors:
Iain W Manfield Chih-Hung Jen John W Pinney Ioannis Michalopoulos James R Bradford Philip M Gilmartin David R Westhead

Nucleic Acids Res 2006 Jul;34(Web Server issue):W504-9

Centre for Plant Sciences, University of Leeds, West Yorkshire, LS2 9JT, UK.

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July 2006

The Arabidopsis co-expression tool (ACT): a WWW-based tool and database for microarray-based gene expression analysis.

Authors:
Chih-Hung Jen Iain W Manfield Ioannis Michalopoulos John W Pinney William G T Willats Philip M Gilmartin David R Westhead

Plant J 2006 Apr;46(2):336-48

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

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April 2006

Inference in Bayesian networks.

Authors:
Chris J Needham James R Bradford Andrew J Bulpitt David R Westhead

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.

Authors:
Archana Sharma-Oates Philip Quirke David R Westhead

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.

Authors:
Mariam Taib John W Pinney David R Westhead Kenneth J McDowall David J Adams

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.

Authors:
Andrew G Garrow Alison Agnew David R Westhead

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

Natural antisense transcripts with coding capacity in Arabidopsis may have a regulatory role that is not linked to double-stranded RNA degradation.

Authors:
Chih-Hung Jen Ioannis Michalopoulos David R Westhead Peter Meyer

Genome Biol 2005 1;6(6):R51. Epub 2005 Jun 1.

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

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August 2006

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

Authors:
Andrew G Garrow Alison Agnew David R Westhead

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

metaSHARK: software for automated metabolic network prediction from DNA sequence and its application to the genomes of Plasmodium falciparum and Eimeria tenella.

Authors:
John W Pinney Martin W Shirley Glenn A McConkey David R Westhead

Nucleic Acids Res 2005 3;33(4):1399-409. Epub 2005 Mar 3.

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

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March 2005

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

Authors:
James R Bradford David R Westhead

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.

Authors:
Glenn A McConkey John W Pinney David R Westhead Kirsten Plueckhahn Teresa B Fitzpatrick Peter Macheroux Barbara Kappes

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.

Authors:
Ioannis Michalopoulos Gilleain M Torrance David R Gilbert David R Westhead

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.

Authors:
Jennifer A Siepen Sheena E Radford David R Westhead

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.

Authors:
James R Bradford David R Westhead

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.

Authors:
James A R Dalton Ioannis Michalopoulos David R Westhead

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.

Authors:
Stephen J Campbell Nicola D Gold Richard M Jackson David R Westhead

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.

Authors:
Jennifer A Siepen David R Westhead

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