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

Cucco F, Barrans S, Sha C, Clipson A, Crouch S, Dobson R, Chen Z, Thompson JS, Care MA, Cummin T, Caddy J, Liu H, Robinson A, Schuh A, Fitzgibbon J, Painter D, Smith A, Roman E, Tooze R, Burton C, Davies AJ, Westhead DR, Johnson PWM, Du MQ.

Leukemia. 2019 Dec 16. doi: 10.1038/s41375-019-0691-6. [Epub ahead of print]


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

Vijayabaskar MS, Goode DK, Obier N, Lichtinger M, Emmett AML, Abidin FNZ, Shar N, Hannah R, Assi SA, Lie-A-Ling M, Gottgens B, Lacaud G, Kouskoff V, Bonifer C, Westhead DR.

PLoS Comput Biol. 2019 Nov 4;15(11):e1007337. doi: 10.1371/journal.pcbi.1007337. eCollection 2019 Nov.


Ibrutinib induces chromatin reorganisation of chronic lymphocytic leukaemia cells.

Holmes KB, Sadreev II, Rawstron AC, Munir T, Westhead DR, Hillmen P, Lefevre PF.

Oncogenesis. 2019 May 10;8(5):32. doi: 10.1038/s41389-019-0142-2.


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

Care MA, Westhead DR, Tooze RM.

NPJ Syst Biol Appl. 2019 Apr 11;5:13. doi: 10.1038/s41540-019-0090-7. eCollection 2019.


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

Davies A, Cummin TE, Barrans S, Maishman T, Mamot C, Novak U, Caddy J, Stanton L, Kazmi-Stokes S, McMillan A, Fields P, Pocock C, Collins GP, Stephens R, Cucco F, Clipson A, Sha C, Tooze R, Care MA, Griffiths G, Du MQ, Westhead DR, Burton C, Johnson PWM.

Lancet Oncol. 2019 May;20(5):649-662. doi: 10.1016/S1470-2045(18)30935-5. Epub 2019 Apr 1.


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

Kirkham CM, Scott JNF, Wang X, Smith AL, Kupinski AP, Ford AM, Westhead DR, Stockley PG, Tuma R, Boyes J.

Mol Cell. 2019 May 2;74(3):584-597.e9. doi: 10.1016/j.molcel.2019.02.025. Epub 2019 Mar 21.


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

Humes JR, Schiffrin B, Calabrese AN, Higgins AJ, Westhead DR, Brockwell DJ, Radford SE.

J Mol Biol. 2019 Mar 15;431(6):1267-1283. doi: 10.1016/j.jmb.2019.01.032. Epub 2019 Feb 1.


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

Stephenson S, Care MA, Fan I, Zougman A, Westhead DR, Doody GM, Tooze RM.

J Immunol. 2019 Feb 15;202(4):1287-1300. doi: 10.4049/jimmunol.1801407. Epub 2019 Jan 14.


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

Tanner G, Westhead DR, Droop A, Stead LF.

Bioinformatics. 2019 Aug 15;35(16):2850-2852. doi: 10.1093/bioinformatics/bty1063.


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

Sha C, Barrans S, Cucco F, Bentley MA, Care MA, Cummin T, Kennedy H, Thompson JS, Uddin R, Worrillow L, Chalkley R, van Hoppe M, Ahmed S, Maishman T, Caddy J, Schuh A, Mamot C, Burton C, Tooze R, Davies A, Du MQ, Johnson PWM, Westhead DR.

J Clin Oncol. 2019 Jan 20;37(3):202-212. doi: 10.1200/JCO.18.01314. Epub 2018 Dec 3. Erratum in: J Clin Oncol. 2019 Apr 20;37(12):1035.


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

O'Brien D, Jones LM, Good S, Miles J, Vijayabaskar MS, Aston R, Smith CE, Westhead DR, van Oosten-Hawle P.

Cell Rep. 2018 Jun 26;23(13):3905-3919. doi: 10.1016/j.celrep.2018.05.093.


Chromatin Accessibility-Based Characterization of the Gene Regulatory Network Underlying Plasmodium falciparum Blood-Stage Development.

Toenhake CG, Fraschka SA, Vijayabaskar MS, Westhead DR, van Heeringen SJ, Bártfai R.

Cell Host Microbe. 2018 Apr 11;23(4):557-569.e9. doi: 10.1016/j.chom.2018.03.007.


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

Zainul Abidin FN, Westhead DR.

Nucleic Acids Res. 2017 Apr 20;45(7):e53. doi: 10.1093/nar/gkw1270.


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

Shar NA, Vijayabaskar MS, Westhead DR.

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


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

Hayes J, Thygesen H, Gregory W, Westhead DR, French PJ, Van Den Bent MJ, Lawler SE, Short SC.

Mol Oncol. 2016 Oct;10(8):1296-304. doi: 10.1016/j.molonc.2016.06.004. Epub 2016 Jul 1.


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

Care MA, Stephenson SJ, Barnes NA, Fan I, Zougman A, El-Sherbiny YM, Vital EM, Westhead DR, Tooze RM, Doody GM.

J Immunol. 2016 Aug 15;197(4):1447-59. doi: 10.4049/jimmunol.1600624. Epub 2016 Jun 29.


Dynamic Gene Regulatory Networks Drive Hematopoietic Specification and Differentiation.

Goode DK, Obier N, Vijayabaskar MS, Lie-A-Ling M, Lilly AJ, Hannah R, Lichtinger M, Batta K, Florkowska M, Patel R, Challinor M, Wallace K, Gilmour J, Assi SA, Cauchy P, Hoogenkamp M, Westhead DR, Lacaud G, Kouskoff V, Göttgens B, Bonifer C.

Dev Cell. 2016 Mar 7;36(5):572-87. doi: 10.1016/j.devcel.2016.01.024. Epub 2016 Feb 25.


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

Cauchy P, James SR, Zacarias-Cabeza J, Ptasinska A, Imperato MR, Assi SA, Piper J, Canestraro M, Hoogenkamp M, Raghavan M, Loke J, Akiki S, Clokie SJ, Richards SJ, Westhead DR, Griffiths MJ, Ott S, Bonifer C, Cockerill PN.

Cell Rep. 2015 Aug 4;12(5):821-36. doi: 10.1016/j.celrep.2015.06.069. Epub 2015 Jul 23.


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

Sha C, Barrans S, Care MA, Cunningham D, Tooze RM, Jack A, Westhead DR.

Genome Med. 2015 Jul 1;7(1):64. doi: 10.1186/s13073-015-0187-6. eCollection 2015.


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

Ptasinska A, Assi SA, Martinez-Soria N, Imperato MR, Piper J, Cauchy P, Pickin A, James SR, Hoogenkamp M, Williamson D, Wu M, Tenen DG, Ott S, Westhead DR, Cockerill PN, Heidenreich O, Bonifer C.

Cell Rep. 2014 Sep 25;8(6):1974-1988. doi: 10.1016/j.celrep.2014.08.024. Epub 2014 Sep 18.


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

Care MA, Cocco M, Laye JP, Barnes N, Huang Y, Wang M, Barrans S, Du M, Jack A, Westhead DR, Doody GM, Tooze RM.

Nucleic Acids Res. 2014 Jul;42(12):7591-610. doi: 10.1093/nar/gku451. Epub 2014 May 29.


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

Gilmour J, Assi SA, Jaegle U, Kulu D, van de Werken H, Clarke D, Westhead DR, Philipsen S, Bonifer C.

Development. 2014 Jun;141(12):2391-401. doi: 10.1242/dev.106054. Epub 2014 May 21.


Using common variants to indicate cancer genes.

Stead LF, Thygesen H, Westhead DR, Rabbitts P.

Int J Cancer. 2015 Jan 1;136(1):241-5. doi: 10.1002/ijc.28951. Epub 2014 May 14.


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

Care MA, Barrans S, Worrillow L, Jack A, Westhead DR, Tooze RM.

PLoS One. 2013;8(2):e55895. doi: 10.1371/journal.pone.0055895. Epub 2013 Feb 12.


In vitro generation of long-lived human plasma cells.

Cocco M, Stephenson S, Care MA, Newton D, Barnes NA, Davison A, Rawstron A, Westhead DR, Doody GM, Tooze RM.

J Immunol. 2012 Dec 15;189(12):5773-85. doi: 10.4049/jimmunol.1103720. Epub 2012 Nov 16.


RUNX1 reshapes the epigenetic landscape at the onset of haematopoiesis.

Lichtinger M, Ingram R, Hannah R, Müller D, Clarke D, Assi SA, Lie-A-Ling M, Noailles L, Vijayabaskar MS, Wu M, Tenen DG, Westhead DR, Kouskoff V, Lacaud G, Göttgens B, Bonifer C.

EMBO J. 2012 Nov 14;31(22):4318-33. doi: 10.1038/emboj.2012.275. Epub 2012 Oct 12.


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

Barrans SL, Crouch S, Care MA, Worrillow L, Smith A, Patmore R, Westhead DR, Tooze R, Roman E, Jack AS.

Br J Haematol. 2012 Nov;159(4):441-53. doi: 10.1111/bjh.12045. Epub 2012 Sep 13.


Depletion of RUNX1/ETO in t(8;21) AML cells leads to genome-wide changes in chromatin structure and transcription factor binding.

Ptasinska A, Assi SA, Mannari D, James SR, Williamson D, Dunne J, Hoogenkamp M, Wu M, Care M, McNeill H, Cauchy P, Cullen M, Tooze RM, Tenen DG, Young BD, Cockerill PN, Westhead DR, Heidenreich O, Bonifer C.

Leukemia. 2012 Aug;26(8):1829-41. doi: 10.1038/leu.2012.49. Epub 2012 Feb 20.


KvSNP: accurately predicting the effect of genetic variants in voltage-gated potassium channels.

Stead LF, Wood IC, Westhead DR.

Bioinformatics. 2011 Aug 15;27(16):2181-6. doi: 10.1093/bioinformatics/btr365. Epub 2011 Jun 17.


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

Leddin M, Perrod C, Hoogenkamp M, Ghani S, Assi S, Heinz S, Wilson NK, Follows G, Schönheit J, Vockentanz L, Mosammam AM, Chen W, Tenen DG, Westhead DR, Göttgens B, Bonifer C, Rosenbauer F.

Blood. 2011 Mar 10;117(10):2827-38. doi: 10.1182/blood-2010-08-302976. Epub 2011 Jan 14. Erratum in: Blood. 2011 May 26;117(21):5783.


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

Yu J, Guo M, Needham CJ, Huang Y, Cai L, Westhead DR.

Bioinformatics. 2010 Oct 15;26(20):2610-4. doi: 10.1093/bioinformatics/btq483. Epub 2010 Aug 27.


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

Tedder PM, Bradford JR, Needham CJ, McConkey GA, Bulpitt AJ, Westhead DR.

Bioinformatics. 2010 Oct 1;26(19):2431-7. doi: 10.1093/bioinformatics/btq450. Epub 2010 Aug 6.


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

Forth T, McConkey GA, Westhead DR.

Bioinformatics. 2010 Sep 15;26(18):2352-3. doi: 10.1093/bioinformatics/btq425. Epub 2010 Jul 29.


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

Stead LF, Wood IC, Westhead DR.

Hum Mutat. 2010 Aug;31(8):908-17. doi: 10.1002/humu.21295.


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

Doody GM, Care MA, Burgoyne NJ, Bradford JR, Bota M, Bonifer C, Westhead DR, Tooze RM.

Nucleic Acids Res. 2010 Sep;38(16):5336-50. doi: 10.1093/nar/gkq268. Epub 2010 Apr 26.


PlasmoPredict: a gene function prediction website for Plasmodium falciparum.

Tedder PM, Bradford JR, McConkey GA, Bulpitt AJ, Westhead DR.

Trends Parasitol. 2010 Mar;26(3):107-10. doi: 10.1016/ Epub 2010 Jan 19.


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

Bradford JR, Needham CJ, Tedder P, Care MA, Bulpitt AJ, Westhead DR.

Plant J. 2010 Feb;61(4):713-21. doi: 10.1111/j.1365-313X.2009.04097.x. Epub 2009 Nov 27.


From gene expression to gene regulatory networks in Arabidopsis thaliana.

Needham CJ, Manfield IW, Bulpitt AJ, Gilmartin PM, Westhead DR.

BMC Syst Biol. 2009 Sep 3;3:85. doi: 10.1186/1752-0509-3-85.


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

Whitaker JW, Westhead DR, McConkey GA.

Trends Parasitol. 2009 Sep;25(9):396-7. doi: 10.1016/ Epub 2009 Aug 28. No abstract available.


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

Webb EC, Westhead DR.

Genomics. 2009 Dec;94(6):369-76. doi: 10.1016/j.ygeno.2009.08.003. Epub 2009 Aug 18.


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

Whitaker JW, McConkey GA, Westhead DR.

Biochem Soc Trans. 2009 Aug;37(Pt 4):792-5. doi: 10.1042/BST0370792. Review. Erratum in: Biochem Soc Trans. 2009 Oct;37(Pt 5):1145.


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

Tedder P, Zubko E, Westhead DR, Meyer P.

RNA. 2009 Jun;15(6):1012-20. doi: 10.1261/rna.1517209. Epub 2009 Apr 15.


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

Whitaker JW, McConkey GA, Westhead DR.

Genome Biol. 2009;10(4):R36. doi: 10.1186/gb-2009-10-4-r36. Epub 2009 Apr 15.


A unique dual activity amino acid hydroxylase in Toxoplasma gondii.

Gaskell EA, Smith JE, Pinney JW, Westhead DR, McConkey GA.

PLoS One. 2009;4(3):e4801. doi: 10.1371/journal.pone.0004801. Epub 2009 Mar 11.


Combining the interactome and deleterious SNP predictions to improve disease gene identification.

Care MA, Bradford JR, Needham CJ, Bulpitt AJ, Westhead DR.

Hum Mutat. 2009 Mar;30(3):485-92. doi: 10.1002/humu.20917.


metaTIGER: a metabolic evolution resource.

Whitaker JW, Letunic I, McConkey GA, Westhead DR.

Nucleic Acids Res. 2009 Jan;37(Database issue):D531-8. doi: 10.1093/nar/gkn826. Epub 2008 Oct 25.


Bioinformatic approaches to biological systems.

Westhead DR, Manfield IW, Needham CJ.

SEB Exp Biol Ser. 2008;61:1-16. Review. No abstract available.


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

Adamo A, Pinney JW, Kunova A, Westhead DR, Meyer P.

PLoS One. 2008 Aug 6;3(8):e2889. doi: 10.1371/journal.pone.0002889.


Metabolic reconstruction and analysis for parasite genomes.

Pinney JW, Papp B, Hyland C, Wambua L, Westhead DR, McConkey GA.

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


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