Statistical Bioinformatics Group

@Informatics, Edinburgh

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2014-present

Heil􏰐 KF, Wysocka􏰐 EM, Sorokina O, Kotaleski JH, Simpson TI, Armstrong JD, Sterratt DC. Analysis of proteins in computational models of synaptic plasticity (Submitted)2017

Qiu J, Dando O, Baxter P, Hasel P, Heron S, Simpson TI, Hardingham GE. Mixed-species RNA-seq for elucidating non cell-autonomous control of gene transcription (Submitted) 2017

Hasel P, Dando O, Jiwaji Z, Todd A, Heron S, Márkus NM, Baxter P, McQueen J, Hampton DW, Torvell M, Tiwari SS, McKay S, Chandran S, Wyllie DJA, Simpson TI and Hardingham GE. Neurons and neuronal activity control gene expression in astrocytes to regulate their development and metabolism. Nature Communications 2017 8:15132. doi:10.1038/ncomms15132

Qiu J, McQueen J, Bilican B, Dando O, Magnani D, Punovuori K, Selvaraj B, Livesey M, Haghi G, Heron S, Burr K, Patani R, Rajan R, Sheppard O, Kind PC, Simpson TI, Tybulewicz VL, Fisher E, Wyllie DJ, Lowell S, Chandran S, Hardingham GE. Evidence for evolutionary divergence of activity-dependent gene expression in developing neurons. eLife 2016 10.7554/eLife.20337. doi:10.7554/eLife.20337

Dora NJ, Crookshanks AJF, Leung KKY, Simpson TI, Mason JO, Price DJ, and West JD. Analysis of compound heterozygotes reveals that the mouse floxed Pax6 tm1Ued allele produces abnormal eye phenotypes. Transgenic Research 2016 25:679–692. doi:10.1007/s11248-016-9962-4

Hindle MM, Le Bihan T, Krahmer J, Martin SF, Noordally ZB, Simpson TI, Millar AJ. qpMerge: Merging different peptide isoforms using a motif centric strategy. BioRxiv 2016. doi:10.1101/047100

Inberg S, Jacob E, Elkobi A, Edry E, Rapoport A, Simpson TI, Armstrong  JD, Shomron N, Pasmanik-Chor M, Rosenblum K. Fluid consumption and taste novelty determines transcription temporal dynamics in the gustatory cortex. Molecular Brain 2016 9:13. doi:10.1186/s13041-016-0188-4

Mclean C, He X, Simpson TI and Armstrong JD. Improved Functional Enrichment Analysis of Biological Networks using Scalable Modularity Based Clustering. Journal of Proteomics & Bioinformatics. 2016 9:009-018. doi:10.4172/jpb.1000383

Márkus NM, Hasel P, Qiu J, Bell KFS, Heron S, Kind PWC, Dando O, Simpson TI, Hardingham GE. Expression of mRNA encoding Mcu and other mitochondrial calcium regulatory genes depends on cell type, neuronal subtype, and Ca2+ signaling. PLoS One 2016 11(2): e0148164. doi: 10.1371/journal.pone.0148164

Sanhueza M,  Chai A, Smith C, McCray BA, Simpson TI, Taylor JP, Pennetta G. Network analyses reveal novel aspects of ALS pathogenesis. PLoS Genetics. 2015 11(3). doi:10.1371/journal.pgen.1005107

Hindle MM, Martin SF, Noordally ZB, van Ooijen G, Barrios-Llerena ME, Simpson TI, Le Bihan T, Millar AJ. The reduced kinome of Ostreococcus tauri: core eukaryotic signalling components in a tractable model species. BMC. Genomics. 2014 15:644. doi:10.1186/1471-2164-15-640

Pai B, Siripornmongcolchai T, Berentsen B, Pakzad A, Vieuille C, Pallesen S, Pajak M,Simpson TI, Armstrong J, Wibrand K and Bramham CR. NMDA receptor-dependent regulation of miRNA expression and association with Argonaute during LTP in vivo. Front. Cell. Neurosci. 2014 7:285. doi:10.3389/fncel.2013.00285

2008-2013

Mi D, Carr CB, Georgala PA, Huang YT, Manuel MN, Jeanes E, Niisato E, Sansom SN, Livesey FJ, Theil T, Hasenpusch-Theil K, Simpson TI, Mason JO, Price DJ. Pax6 Exerts Regional Control of Cortical Progenitor Proliferation via Direct Repression of Cdk6 and Hypophosphorylation of pRb. Neuron 2013 78(2):269-284.  doi:10.1016/j.neuron.2013.02.012

Gal-Ben-Ari S, Kenney JW, Ounalla-Saad H, Taha E, David O, Levitan D, Gildish I, Panja D, Pai B, Wibrand K, Simpson TI, Proud CG, Bramham CR, Armstrong JD and Rosenblum K. Consolidation and Translation Regulation. Learning and Memory 2012 19: 410-422.  doi:10.1101/lm.026849.112

Gallone G, Simpson TI, Armstrong JD, Jarman AP. Bio::Homology::InterologWalk--a Perl module to build putative protein-protein interaction networks through interolog mapping. BMC Bioinformatics. 2011 Jul 18;12:289. doi:10.1186/1471-2105-12-289

zur Lage P, Simpson TI and Jarman AP. Linking specification to differentiation: from proneural genes to the regulation of ciliogenesis. Fly 2011; Oct 1;5(4). doi: 10.4161/fly.5.4.16159

Simpson TI, Cachero S, zur Lage PI, Ma L, Newton FG, Holohan E, Armstrong JD, Jarman AP. The gene regulatory cascade linking proneural specification with differentiation in Drosophila sensory neurons. PLoS Biology 2011;9(1):e1000568.  doi:10.1371/journal.pbio.1000568

Simpson TI, Armstrong JD and Jarman AP. Merged consensus clustering to assess and improve class discovery with microarray data. BMC Bioinformatics 2010, 11:590. doi:10.1186/1471-2105-11-590

Simpson TI, Pratt T, Mason JO and Price DJ. Normal ventral telencephalic expression of Pax6 is required for normal development of thalamocortical axons in embryonic mice. Neural Dev. 2009 Jun 5;4(1):19. doi:10.1186/1749-8104-4-19

2002-2007

Manuel M, Georgala PA, Carr CB, Chanas S, Kleinjan DA, Martynoga B, Mason JO, Molinek M, Pinson J, Pratt T, Quinn JC, Simpson TI, Tyas DA, van Heyningen V, West JD and Price DJ. Controlled over-expression of Pax6 in vivo negatively auto-regulates the Pax6 locus and causes cell autonomous defects of late cortical progenitor proliferation but has little effect on cortical arealization. Development 2007 ;134(3):545-555. doi:10.1242/dev.02764

Zaki PA, Collinson, MC, Simpson TI, Price DJ and Quinn JC. Compound heterozygosity for mutations in Pax6 and Gli3 results in severe anterior segment and retinal abnormalities in the mouse eye. BMC Dev Biol. 2006 Oct 9;6:46. doi:10.1186/1471-213X-6-46

Kleinjan DA, Seawright A, Mella S, Carr CB, Tyas DA, Simpson TI, Mason JO, Price DJ and van Heyningen V. Long-range downstream enhancers are essential for Pax6 expression. Dev Biol. 2006 Nov 15;299(2):563-81. doi:10.1016/j.ydbio.2006.08.060

Pinson J, Simpson TI, Mason JO and Price DJ. Positive auto-regulation of the transcription factor Pax6 in response to increased levels of either of its major isoforms, Pax6 or Pax6(5a), in cultured cells. BMC Dev Biol. 2006 May 25;6:25. doi:10.1186/1471-213X-6-25

Tyas DA, Simpson TI, Carr CB, Kleinjan DA, van Heyningen V, Mason JO and Price DJ. Functional conservation of Pax6 regulatory elements in humans and mice demonstrated with a novel transgenic reporter mouse. BMC Dev Biol. 2006 May 4;6:21. doi:10.1186/1471-213X-6-21

Pinson J, Mason JO, Simpson TI and Price DJ. Regulation of the Pax6 : Pax6(5a) mRNA ratio in the developing mammalian brain. BMC Dev Biol. 2005 Jul 19;5:13. doi:10.1186/1471-213X-5-13

Yap CT, Simpson TI, Pratt T, Price DJ and Maciver SK. The motility of glioblastoma tumour cells is modulated by intracellular cofilin expression in a concentration-dependent manner. Cell Motil Cytoskeleton. 2005 Mar;60(3):153-65. doi:10.1002/cm.20053

Pratt T, Tian NM, Simpson TI, Mason JO and Price DJ. The winged helix transcription factor Foxg1 facilitates retinal ganglion cell axon crossing of the ventral midline in the mouse. Development. 2004 Aug;131(15):3773-84. Epub 2004 Jul 7. doi:10.1242/dev.01246

Tyas DA, Pratt T, Simpson TI, Mason JO and Price DJ. Identifying GFP-transgenic animals by flashlight. Biotechniques. 2003 Mar;34(3):474-6.

Simpson TI and Price DJ. Pax6; a pleiotropic player in development. Bioessays. 2002 Nov;24(11):1041-51. doi:10.1002/bies.10174

Tyas DA, Kleinjan DA, Simpson TI, van Heyningen V, Mason JO and Price DJ. Generation of a ‘Pax6 GFP reporter’ transgenic mouse. Mol. Biol. Cell. 2002 Nov;13:519A:292

Pratt T, Quinn JC, Simpson TI, West JD, Mason JO and Price DJ. Disruption of early events in thalamocortical tract formation in mice lacking the transcription factors Pax6 or Foxg1. J Neurosci. 2002 Oct 1;22(19):8523-31.