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<title>Statistical Bioinformatics Group by statbio</title>
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<h1><a href="https://statbio.github.io/">Statistical Bioinformatics Group</a></h1>
<p>@Informatics, Edinburgh</p>
<p class="view"><a href="https://github.com/statbio">View Our GitHub Profile</a></p>
<p class="view"><a href="http://www.twitter.com/tisimpson">Twitter</a></p>
<p class="view"><a href="http://statbio.github.io/research.html">Research</a></p>
<p class="view"><a href="http://statbio.github.io/people.html">People</a></p>
<p class="view"><a href="http://statbio.github.io/publications.html">Publications</a></p>
<p class="view"><a href="mailto:ian.simpson@ed.ac.uk">Contact (e-mail)</a></p>
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<section>
<h3>
<a id="publications" class="anchor" href="#publications" aria-hidden="true"><span class="octicon octicon-link"></span></a>Group publications
</h3>
<p>Our publications at
<a href="http://www.ncbi.nlm.nih.gov/pubmed?term=simpson_ti%5BAU%5D%20AND%202002%5BPDAT%5D%20%3A%202050%5BPDAT%5D&cmd=DetailsSearch">Pubmed</a>,
<a href="http://scholar.google.com/citations?hl=en&user=rmKe2dYAAAAJ">GoogleScholar</a> and
<a href="http://www.researcherid.com/rid/B-4722-2011">ResearcherID</a>
</p>
<p><strong>2014-present</strong></p>
<p>Tomas G, Moir N, Kitchen RR, Pearce DA, Taciroglu A, Dixon JM, <u>Simpson TI</u>, Sims AH. Subtype-aware batch correction retains biological signal of integrated breast cancer datasets (<b>Submitted</b>) 2018.</p>
<p>Qiu J, Dando O, Baxter PS, Hasel P, Heron S, <u>Simpson TI</u>, Hardingham GE. Mixed-species RNA-seq for elucidation of non-cell-autonomous control of gene transcription. <b>Nature Protocols</b> 2018 Sep 24. <a href='https://doi.org/10.1038/s41596-018-0029-2'>doi.org/10.1038/s41596-018-0029-2</a></p>
<p>Noordally ZB, M. Hindle MM, Martin SF, Seaton D, Simpson TI, Le Bihan T, Millar AJ. Circadian protein regulation in the green lineage I. A phospho-dawn anticipates light onset before proteins peak in daytime <b>BioRxiv Pre-Print</b> 2018. <a href="http://biorxiv.org/cgi/content/short/287862v1">doi.org/10.1101/287862</a></p>
<p>Heil KF, Wysocka EM, Sorokina O, Kotaleski JH, <u>Simpson TI</u>, Armstrong JD, Sterratt DC. Analysis of proteins in computational models of synaptic plasticity <b>BioRxiv Pre-Print</b> 2018. <a href="https://doi.org/10.1101/254094">doi.org/10.1101/254094</a></p>
<p>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, <u>Simpson TI</u> and Hardingham GE. Neurons and neuronal activity control gene expression in astrocytes to regulate their development and metabolism. <b>Nature Communications </b> 2017 8:15132. <a href='http://dx.doi.org/doi:10.1038/ncomms15132'>doi:10.1038/ncomms15132</a></p>
<p>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, <u>Simpson TI</u>, Tybulewicz VL, Fisher E, Wyllie DJ, Lowell S, Chandran S, Hardingham GE. Evidence for evolutionary divergence of activity-dependent gene expression in developing neurons. <b>eLife</b> 2016 10.7554/eLife.20337. <a href="http://dx.doi.org/10.7554/eLife.20337">doi:10.7554/eLife.20337</a></p>
<p>Dora NJ, Crookshanks AJF, Leung KKY, <u>Simpson TI</u>, Mason JO, Price DJ, and West JD. Analysis of compound heterozygotes reveals that the mouse floxed Pax6 tm1Ued allele produces abnormal eye phenotypes. <b>Transgenic Research</b> 2016 25:679–692. <a href="http://dx.doi.org/10.1007/s11248-016-9962-4">doi:10.1007/s11248-016-9962-4</a></p>
<p>Hindle MM, Le Bihan T, Krahmer J, Martin SF, Noordally ZB, <u>Simpson TI</u>, Millar AJ. qpMerge: Merging different peptide isoforms using a motif centric strategy. <b>BioRxiv</b> 2016. <a href="http://dx.doi.org/10.1101/047100">doi:10.1101/047100</a></p>
<p>Inberg S, Jacob E, Elkobi A, Edry E, Rapoport A, <u>Simpson TI</u>, Armstrong JD, Shomron N, Pasmanik-Chor M, Rosenblum K. Fluid consumption and taste novelty determines transcription temporal dynamics in the gustatory cortex. <b>Molecular Brain</b> 2016 9:13. <a href="http://dx.doi.org/10.1186/s13041-016-0188-4">doi:10.1186/s13041-016-0188-4</a></p>
<p>Mclean C, He X, <u>Simpson TI</u> and Armstrong JD. Improved Functional Enrichment Analysis of Biological Networks using Scalable Modularity Based Clustering. <b>Journal of Proteomics & Bioinformatics</b>. 2016 9:009-018. <a href='http://dx.doi.org/doi:10.4172/jpb.1000383'>doi:10.4172/jpb.1000383</a></p>
<p>Márkus NM, Hasel P, Qiu J, Bell KFS, Heron S, Kind PWC, Dando O, <u>Simpson TI</u>, Hardingham GE. Expression of mRNA encoding Mcu and other mitochondrial calcium regulatory genes depends on cell type, neuronal subtype, and Ca2+ signaling. <b>PLoS One</b> 2016 11(2): e0148164. <a href="http://dx.doi.org/doi:10.1371/journal.pone.0148164">doi: 10.1371/journal.pone.0148164</a></p>
<p>Sanhueza M, Chai A, Smith C, McCray BA, <u>Simpson TI</u>, Taylor JP, Pennetta G. Network analyses reveal novel aspects of ALS pathogenesis. <b>PLoS Genetics</b>. 2015 11(3). <a href="http://dx.doi.org/doi:10.1371/journal.pgen.1005107">doi:10.1371/journal.pgen.1005107</a></p>
<p>Hindle MM, Martin SF, Noordally ZB, van Ooijen G, Barrios-Llerena ME, <u>Simpson TI</u>, Le Bihan T, Millar AJ. The reduced kinome of Ostreococcus tauri: core eukaryotic signalling components in a tractable model species. <b>BMC. Genomics</b>. 2014 15:644. <a href="http://dx.doi.org/doi:10.1186/1471-2164-15-640">doi:10.1186/1471-2164-15-640</a></p>
<p>Pai B, Siripornmongcolchai T, Berentsen B, Pakzad A, Vieuille C, Pallesen S, Pajak M,<u>Simpson TI</u>, Armstrong J, Wibrand K and Bramham CR. NMDA receptor-dependent regulation of miRNA expression and association with Argonaute during LTP in vivo. <b>Front. Cell. Neurosci.</b> 2014 7:285. <a href="http://dx.doi.org/10.3389/fncel.2013.00285">doi:10.3389/fncel.2013.00285</a></p>
<p><strong>2008-2013</strong></p>
<p>Mi D, Carr CB, Georgala PA, Huang YT, Manuel MN, Jeanes E, Niisato E, Sansom SN, Livesey FJ, Theil T, Hasenpusch-Theil K, <u>Simpson TI</u>, Mason JO, Price DJ. Pax6 Exerts Regional Control of Cortical Progenitor Proliferation via Direct Repression of Cdk6 and Hypophosphorylation of pRb. <b>Neuron</b> 2013 78(2):269-284. <a href="http://dx.doi.org/10.1016/j.neuron.2013.02.012">doi:10.1016/j.neuron.2013.02.012</a></p>
<p>Gal-Ben-Ari S, Kenney JW, Ounalla-Saad H, Taha E, David O, Levitan D, Gildish I, Panja D, Pai B, Wibrand K, <u>Simpson TI</u>, Proud CG, Bramham CR, Armstrong JD and Rosenblum K. Consolidation and Translation Regulation. <b>Learning and Memory</b> 2012 19: 410-422. <a href="http://dx.doi.org/10.1101/lm.026849.112">doi:10.1101/lm.026849.112</a></p>
<p>Gallone G, <u>Simpson TI</u>, Armstrong JD, Jarman AP. Bio::Homology::InterologWalk--a Perl module to build putative protein-protein interaction networks through interolog mapping. <b>BMC Bioinformatics</b>. 2011 Jul 18;12:289. <a href="http://dx.doi.org/10.1186/1471-2105-12-289">doi:10.1186/1471-2105-12-289</a></p>
<p>zur Lage P, <u>Simpson TI</u> and Jarman AP. Linking specification to differentiation: from proneural genes to the regulation of ciliogenesis. <b>Fly</b> 2011; Oct 1;5(4). <a href="http://dx.doi.org/10.4161/fly.5.4.16159">doi: 10.4161/fly.5.4.16159</a></p>
<p><u>Simpson TI</u>, 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. <b>PLoS Biology</b> 2011;9(1):e1000568. <a href="http://dx.doi.org/10.1371/journal.pbio.1000568">doi</a><a href="http://dx.doi.org/10.1371/journal.pbio.1000568">:10.1371/journal.pbio.1000568</a></p>
<p><u>Simpson TI</u>, Armstrong JD and Jarman AP. Merged consensus clustering to assess and improve class discovery with microarray data. <b>BMC Bioinformatics</b> 2010, 11:590. <a href="http://dx.doi.org/10.1186/1471-2105-11-590">doi:10.1186/1471-2105-11-590</a></p>
<p><u>Simpson TI</u>, Pratt T, Mason JO and Price DJ. Normal ventral telencephalic expression of Pax6 is required for normal development of thalamocortical axons in embryonic mice. <b>Neural Dev.</b> 2009 Jun 5;4(1):19. <a href="http://dx.doi.org/10.1186/1749-8104-4-19">doi:10.1186/1749-8104-4-19</a></p>
<p><strong>2002-2007</strong></p>
<p>Manuel M, Georgala PA, Carr CB, Chanas S, Kleinjan DA, Martynoga B, Mason JO, Molinek M, Pinson J, Pratt T, Quinn JC, <u>Simpson TI</u>, 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. <b>Development</b> 2007 ;134(3):545-555. <a href="http://dx.doi.org/10.1242/dev.02764">doi:10.1242/dev.02764</a></p>
<p>Zaki PA, Collinson, MC, <u>Simpson TI</u>, 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. <b>BMC Dev Biol.</b> 2006 Oct 9;6:46. <a href="http://dx.doi.org/10.1186/1471-213X-6-46">doi:10.1186/1471-213X-6-46</a></p>
<p>Kleinjan DA, Seawright A, Mella S, Carr CB, Tyas DA, <u>Simpson TI</u>, Mason JO, Price DJ and van Heyningen V. Long-range downstream enhancers are essential for Pax6 expression. <b>Dev Biol.</b> 2006 Nov 15;299(2):563-81. <a href="http://dx.doi.org/10.1016/j.ydbio.2006.08.060">doi:10.1016/j.ydbio.2006.08.060</a></p>
<p>Pinson J, <u>Simpson TI</u>, 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. <b>BMC Dev Biol.</b> 2006 May 25;6:25. <a href="http://dx.doi.org/10.1186/1471-213X-6-25">doi:10.1186/1471-213X-6-25</a></p>
<p>Tyas DA, <u>Simpson TI</u>, 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. <b>BMC Dev Biol.</b> 2006 May 4;6:21. <a href="http://dx.doi.org/10.1186/1471-213X-6-21">doi:10.1186/1471-213X-6-21</a></p>
<p>Pinson J, Mason JO, <u>Simpson TI</u> and Price DJ. Regulation of the Pax6 : Pax6(5a) mRNA ratio in the developing mammalian brain. <b>BMC Dev Biol.</b> 2005 Jul 19;5:13. <a href="http://dx.doi.org/10.1186/1471-213X-5-13">doi:10.1186/1471-213X-5-13</a></p>
<p>Yap CT, <u>Simpson TI</u>, Pratt T, Price DJ and Maciver SK. The motility of glioblastoma tumour cells is modulated by intracellular cofilin expression in a concentration-dependent manner. <b>Cell Motil Cytoskeleton.</b> 2005 Mar;60(3):153-65. <a href="http://dx.doi.org/10.1002/cm.20053">doi:10.1002/cm.20053</a></p>
<p>Pratt T, Tian NM, <u>Simpson TI</u>, Mason JO and Price DJ. The winged helix transcription factor Foxg1 facilitates retinal ganglion cell axon crossing of the ventral midline in the mouse. <b>Development.</b> 2004 Aug;131(15):3773-84. Epub 2004 Jul 7. <a href="http://dx.doi.org/10.1242/dev.01246">doi:10.1242/dev.01246</a></p>
<p>Tyas DA, Pratt T, <u>Simpson TI</u>, Mason JO and Price DJ. Identifying GFP-transgenic animals by flashlight. <b>Biotechniques</b>. 2003 Mar;34(3):474-6.</p>
<p><u>Simpson TI</u> and Price DJ. Pax6; a pleiotropic player in development. <b>Bioessays.</b> 2002 Nov;24(11):1041-51. <a href="http://dx.doi.org/10.1002/bies.10174">doi:10.1002/bies.10174</a></p>
<p>Tyas DA, Kleinjan DA, <u>Simpson TI</u>, van Heyningen V, Mason JO and Price DJ. Generation of a ‘Pax6 GFP reporter’ transgenic mouse. <b>Mol. Biol. Cell.</b> 2002 Nov;13:519A:292</p>
<p>Pratt T, Quinn JC, <u>Simpson TI</u>, West JD, Mason JO and Price DJ. Disruption of early events in thalamocortical tract formation in mice lacking the transcription factors Pax6 or Foxg1. <b>J Neurosci.</b> 2002 Oct 1;22(19):8523-31.</p>
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