Ryan B, Marioni RE, Simpson TI. Multi-Omic Graph Diagnosis (MOGDx) : A data integration tool to perform classification tasks for heterogeneous diseases. Bioinformatics 2024 https://doi.org/10.1093/bioinformatics/btae523.

Lee C, Simpson TI, Posma JM, Lain AD. Comparative Analyses of Multilingual Drug Entity Recognition Systems for Clinical Case Reports In Cardiology. CUE@MultiCardioNER submission at CLEF 2024 https://ceur-ws.org/Vol-3740/

Zimmermann J, Wiktorek D, Meusburger T, Monge-Dalmau M, Fabregat A, Jarasch A, Schmidt G, Reis-Filho JS, Simpson TI. The Ontoverse: Democratising Access to Knowledge Graph-based Data Through a Cartographic Interface. arXiv:2408.03339v1 2024. https://doi.org/10.48550/arXiv.2408.03339 [pre-print]

Gema AP, Lee C, Minervini P, Daines L, Simpson TI, and Alex B. Edinburgh Clinical NLP at MEDIQA-CORR 2024: Guiding Large Language Models with Hints. arXiv:2405.18028 2024. https://doi.org/10.48550/arXiv.2405.18028 [pre-print]

Ryan B, Marioni RE, Simpson TI. An Integrative Network Approach for Longitudinal Stratification in Parkinson’s Disease. medRxiv 2024. https://doi.org/10.1101/2024.01.25.24301595 [pre-print]

Wood A, Mackaness W, Simpson TI, Armstrong JD. Improved prediction of hiking speeds using a data driven approach. PLoS ONE 2023 18(12): e0295848. https://doi.org/10.1371/journal.pone.0295848

Kim H, Kim C, Sohn J, Beck T, Rei M, Kim S, Simpson, TI, Posma JM, Lain A, Sung M, Kang J. Advancing Phenotype Named Entity Recognition and Normalization for Dysmorphology Physical Examination Reports. KU AIGEN ICL EDI@BC8 Track 3: Proceedings of the Biocreative VIII Challenge and Workshop 2023: Curation and Evaluation in the Era of Generative Models. AMIA 2023 Annual Symposium, New Orleans, USA. https://doi.org/10.5281/zenodo.10104804

Ryan B, Marioni RE, Simpson TI. Multi-Omic Graph Diagnosis (MOGDx) : A data integration tool to perform classification tasks for heterogeneous diseases. medRxiv 2023. https://doi.org/10.1101/2023.07.09.23292410 [pre-print]

Wood A, Mackaness W, Simpson TI, Armstrong JD. Improved prediction of hiking speeds using a data driven approach. arXiv 2023. https://doi.org/10.48550/arXiv.2303.16065 [pre-print]

McLean C, Sorokin A, Simpson TI, Armstrong JD, Sorokina O. BioNAR: an integrated biological network analysis package in bioconductor, Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad137, https://doi.org/10.1093/bioadv/vbad137

McLean C, Sorokin A, Simpson TI, Armstrong JD, Sorokina O. BioNAR: An Integrated Biological Network Analysis Package in Bioconductor. bioRxiv 2023. https://doi.org/10.1101/2023.02.08.527636 [pre-print]

Noordally ZB, Hindle MM, Martin SF, Seaton DD, Simpson TI, Le Bihan T, Millar AJ. A phospho-dawn of protein modification anticipates light onset in the picoeukaryote O. tauri. Journal of Experimental Botany, 2023;, erad290, https://doi.org/10.1093/jxb/erad290

Wysocka EM, Page M, Snowden J, Simpson TI. Comparison of rule- and ordinary differential equation-based dynamic model of DARPP-32 signalling network. PeerJ 2022 10:e14516. https://doi.org/10.7717/peerj.14516

Lain A, Yoon W, Kim H, Kang J, Simpson TI. KU_ED at SocialDisNER: Extracting Disease Mentions in Tweets Written in Spanish Proceedings of the Seventh Social Media Mining for Health Applications (#SMM4H) Workshop & Shared Task 2022. https://aclanthology.org/2022.smm4h-1.23

Navarro Torres-Arpi M, and Simpson TI. SFARI Genes and where to find them; modelling Autism Spectrum Disorder specific gene expression dysregulation with RNA-seq data.Scientific Reports 2022 12:10158. https://doi.org/10.1038/s41598-022-14077-1

Yates TM, Lain A, Campbell J, FitzPatrick DR, Simpson TI. Creation and evaluation of full-text literature-derived, feature- weighted disease models of genetically determined developmental disorders. Database 2022 Vol.2022:article ID baac038. https://doi.org/10.1093/database/baac038

Wysocka EM, Page M, Snowden J, Simpson TI. Comparison of rule- and ordinary differential equation-based dynamic model of DARPP-32 signalling network. bioRxiv 2022. https://dx.doi.org//10.1101/2022.03.26.485918 [pre-print]

Yates TM, Lain A, Campbell J, FitzPatrick DR, Simpson TI. Creation and evaluation of full-text literature-derived, feature- weighted disease models of genetically determined developmental disorders. medRxiv 2021. https://dx.doi.org/10.1101/2021.11.04.21265878 [pre-print]

Dagleish MP, Flockhart AF, Baily JL, Hall AJ, Simpson TI and Longbottom D. Presence of DNA from Chlamydia-like organisms in the nasal cavities of grey seal pups (Halichoerus grypus) and three different substrates present in a breeding colony. BMC Veterinary Research 2021 17,328. https://dx.doi.org/10.1186/s12917-021-03032-3

Sorokina O, McLean C, Croning MDR, Heil KF, Wysocka E, He X, Sterratt DC, Grant S, Simpson TI, Armstrong JD. A unified resource and configurable model of the synapse proteome and its role in disease. Scientific Reports 2021. https://doi.org/10.1038/s41598-021-88945-7

Navarro M and Simpson TI. SFARI Genes and where to find them; classification modelling to identify genes associated with Autism Spectrum Disorder from RNA-seq data. bioRxiv 2021. https://doi.org/10.1101/2021.01.29.428754 [pre-print]

Sorokina O, McLean C, Croning MDR, Heil KF, Wysocka E, He X, Sterratt DC, Grant S, Simpson TI, Armstrong JD. A configurable model of the synaptic proteome reveals the molecular mechanisms of disease co-morbidity. bioRxiv 2020. https://doi.org/10.1101/2020.10.27.356899 [pre-print]

Berentsen B, Patil S, Rønnestad K, Goff KM, Pajak M, Simpson TI, Wibrand K, Bramham CR. MicroRNA-34a Acutely Regulates Synaptic Efficacy in the Adult Dentate Gyrus In Vivo. Molecular Neurobiology 2020 57:1432–1445 https://doi.org/10.1007/s12035-019-01816-1

Qiu J, Dando O, Baxter PS, Hasel P, Heron S, Simpson TI, Hardingham GE. Mixed-species RNA-seq for elucidation of non-cell-autonomous control of gene transcription. Nature Protocols 2018 Sep 24. https://doi.org/10.1038/s41596-018-0029-2

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 BioRxiv 2018. https://doi.org/10.1101/287862 [pre-print]

Heil KF, Wysocka EM, Sorokina O, Kotaleski JH, Simpson TI, Armstrong JD, Sterratt DC. Analysis of proteins in computational models of synaptic plasticity bioRxiv 2018. https://doi.org/10.1101/254094 [pre-print]

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 https://doi.org/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 https://doi.org/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 https://doi.org/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 https://doi.org/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 https://doi.org/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 https://doi.org/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 https://doi.org/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) https://doi.org/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 https://doi.org/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 https://doi.org/10.3389/fncel.2013.00285

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 https://doi.org/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 https://doi.org/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 https://doi.org/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) https://doi.org/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 https://doi.org/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 https://doi.org/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 https://doi.org/10.1186/1749-8104-4-19

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 https:doi.org/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 https://doi.org/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 https://doi.org/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 https://doi.org/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 https://doi.org/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 https://doi.org/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 https://doi.org/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 https://doi.org/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 https://doi.org/10.2144/03343bm04

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

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 https://doi.org/10.1523/JNEUROSCI.22-19-08523.2002