Staff Profile

Roles and Responsibilities

I joined the Bioinformatics Support Unit at Newcastle in February 2014 to apply my range of skills to assist in bioinformatics, data analysis, modelling and teaching in the Faculty of Medical Sciences.

Previous Positions

Research Associate, Institute for Ageing and Health, University of Newcastle upon Tyne, 2008-13

Head of Protein-Protein Interactions Group, Biosystems Informatics Institute, Newcastle upon Tyne, 2005-07

Research Fellow, Cancer Research UK London Research Institute, 2000-04

Postdoctoral Research Assistant, Laboratory of Molecular Biophysics, University of Oxford, 1995-2000

Qualifications

PhD in Physics (Edinburgh, 1995)

BSc in Natural Sciences (Cambridge, 1990)

Memberships of Professional Organisations

Biochemical Society

Other information

Google Scholar 

ORCID entry

Main Expertise

Analysis of Next-generation sequencing data (RNA-Seq, ChIP-Seq). Wide range of bioinformatics techniques including interpretation of gene lists in term of pathways. Statistical analysis with R/Bioconductor.

Other Expertise and Interests

Kinetic modelling of metabolic and signalling pathways with Ordinary Differential Equations. Ageing. Modelling of the cardiovascular system, with application to the investigation of orthostatic symptoms in Chronic Fatigue Syndrome. Structural aspects of biomolecular interactions, especially protein-protein interactions. Homology modelling. The computational prediction of the structure and affinity of protein-protein complexes using docking and electrostatics calculations. Molecular Dynamics simulation.

• Articles

  • Dalgliesh C, Aldalaqan S, Atallah C, Best A, Scott E, Ehrmann I, Merces G, Mannion J, Badurova B, Sandher R, Illing Y, Wirth B, Wells S, Codner G, Teboul L, Smith GR, Hedley A, Herbert M, de Rooij DG, Miles C, Reynard LN, Elliott DJ. An ultra-conserved poison exon in the Tra2b gene encoding a splicing activator is essential for male fertility and meiotic cell division. EMBO Journal 2025, 44, 877-902.
  • Wibowo CS, Susilo R, Ernawan R, Apriyanto A, Alshaharni MO, Smith GR, Gatehouse AM, Edwards MG. Molecular basis of resistance to leaf spot disease in oil palm. Frontiers in Plant Science 2024, 15, 1458346.
  • Moya-Molina M, Dorgau B, Flood E, Letteboer SJF, Lorentzen E, Coxhead J, Smith G, Roepman R, Nagaraja Grellscheid S, Armstrong L, Lako M. Deciphering the impact of PROM1 alternative splicing on human photoreceptor development and maturation. Cell Death & Disease 2024, 15(10), 721.
  • Siachisumo C, Luzzi S, Aldalaqan S, Hysenaj G, Dalgliesh C, Cheung K, Gazzara M, Yonchev ID, James K, Kheirollahi Chadegani M, Ehrmann I, Smith GR, Cockell SJ, Munkley J, Barash Y, Wilson SA, Elliott DJ. An anciently diverged family of RNA binding proteins maintain correct splicing of a class of ultra-long exons through cryptic splice site repression. eLife 2024, 12, RP89705.
  • Adamson B, Brittain N, Walker L, Duncan R, Luzzi S, Rescigno P, Smith GR, McGill S, Burchmore RJS, Willmore E, Hickson I, Robson CN, Bogdan D, Jimenez-Vacas JM, Paschalis A, Welti J, Yuan W, McCracken SR, Heer R, Sharp A, de Bono J, Gaughan L. The catalytic subunit of DNA-PK regulates transcription and splicing of AR in advanced prostate cancer. Journal of Clinical Investigation 2023, 133(22), e169200.
  • Gee LMV, Barron-Millar B, Leslie J, Richardson C, Zaki MYW, Luli S, Burgoyne RA, Cameron RIT, Smith GR, Brain JG, Innes B, Jopson L, Dyson JK, McKay KRC, Pechlivanis A, Holmes E, Berlinguer-Palmini R, Victorelli S, Mells GF, Sandford RN, Palmer J, Kirby JA, Kiourtis C, Mokochinski J, Hall Z, Bird TG, Borthwick LA, Morris CM, Hanson PS, Jurk D, Stoll EA, LeBeau FEN, Jones DEJ, Oakley F. Anti–Cholestatic Therapy with Obeticholic Acid Improves Short-Term Memory in Bile Duct–Ligated Mice. American Journal of Pathology 2023, 193(1), 11-26.
  • Jones DEJ, Wetten A, Barron-Millar B, Ogle L, Mells G, Flack S, Sandford R, Kirby J, Palmer J, Brotherston S, Jopson L, Brain J, Smith GR, Rushton S, Jones R, Rushbrook S, Thorburn D, Ryder SD, Hirschfield G, Dyson JK. The relationship between disease activity and UDCA response criteria in primary biliary cholangitis: A cohort study. eBioMedicine 2022, 80, 104068.
  • Isaacs JD, Brockbank S, Pedersen AW, Hilkens C, Anderson A, Stocks P, Lendrem D, Tarn J, Smith GR, Allen B, Casement J, Diboll J, Harry R, Cooles FAH, Cope AP, Simpson G, Toward R, Noble H, Parke A, Wu W, Clarke F, Scott D, Scott IC, Galloway J, Lempp H, Ibrahim F, Schwank S, Molyneux G, Lazarov T, Geissmann F, Goodyear CS, McInnes IB, Donnelly I, Gilmour A, Virlan AT, Porter D, Ponchel F, Emery P, El-Jawhari J, Parmar R, McDermott MF, Fisher BA, Young SP, Jones P, Raza K, Filer A, Pitzalis C, Barnes MR, Watson DS, Henkin R, Thorborn G, Fossati-Jimack L, Kelly S, Humby F, Bombardieri M, Rana S, Jia Z, Goldmann K, Lewis M, Ng S, Barbosa-Silva A, Tzanis E, Gallagher-Syed A, John CR, Ehrenstein MR, Altobelli G, Martins S, Nguyen D, Ali H, Ciurtin C, Buch M, Symmons D, Worthington J, Bruce IN, Sergeant JC, Verstappen SMM, Stirling F, Hughes-Morley A, Tom B, Farewell V, Zhong Y, Taylor PC, Buckley CD, Keidel S, Cuff C, Levesque M, Long A, Liu Z, Lipsky S, Harvey B, Macoritto M, Hong F, Kaymakcalan S, Tsuji W, Sabin T, Ward N, Talbot S, Padhji D, Sleeman M, Finch D, Herath A, Lindholm C, Jenkins M, Ho M, Hollis S, Marshall C, Parker G, Page M, Edwards H, Cuza A, Gozzard N, Pandis I, Rowe A, Capdevila FB, Loza MJ, Curran M, Verbeeck D, Dan Baker, Mela CM, Vranic I, Mela CT, Wright S, Rowell L, Vernon E, Joseph N, Payne N, Rao R, Binks M, Belson A, Ludbrook V, Hicks K, Tipney H, Ellis J, Hasan S, Didierlaurent A, Burny W, Haynes A, Larminie C, Harris R, Dastros-Pitei D, Carini C, Kola B, Jelinsky S, Hodge M, Maciejewski M, Ziemek D, Schulz-Knappe P, Zucht H-D, Budde P, Coles M, Butler JA, Read S. RA-MAP, molecular immunological landscapes in early rheumatoid arthritis and healthy vaccine recipients. Scientific Data 2022, 9(1), 196.
  • Kataura T, Otten EG, Rabanal-Ruiz Y, Adriaenssens E, Urselli F, Scialo F, Fan L, Smith GR, Dawson WM, Chen X, Yue WW, Bronowska AK, Carroll B, Martens S, Lazarou M, Korolchuk VI. NDP52 acts as a redox sensor in PINK1/Parkin-mediated mitophagy. EMBO Journal 2022, 42, 1-16.
  • Cooles FAH, Tarn J, Lendrem DW, Naamane N, Lin CMA, Millar B, Maney NJ, Anderson AE, Thalayasingam N, Diboll J, Bondet V, Duffy D, Barnes MR, Smith GR, Ng S, Watson D, Henkin R, Cope AP, Reynard LN, Pratt AG, Isaacs JD. Interferon-α-mediated therapeutic resistance in early rheumatoid arthritis implicates epigenetic reprogramming. Annals of the Rheumatic Diseases 2022, 81(9), 1214-1223.
  • Shmarov F, Smith GR, Weatherhead SC, Reynolds NJ, Zuliani P. Individualised computational modelling of immune mediated disease onset, flare and clearance in psoriasis. PLoS Computational Biology 2022, 18(9), e1010267.
  • Addison R, Weatherhead SC, Pawitri A, Smith GR, Rider A, Grantham HJ, Cockell SJ, Reynolds NJ. Therapeutic wavelengths of ultraviolet B radiation activate apoptotic, circadian rhythm, redox signalling and key canonical pathways in psoriatic epidermis. Redox Biology 2021, 41, 101924.
  • Barron-Millar B, Ogle L, Mells G, Flack S, Badrock J, Sandford R, Kirby J, Palmer J, Jopson L, Brain J, Smith GR, Rushton S, Hegade VS, Jones R, Rushbrook S, Thorburn D, Ryder S, Hirschfield G, Dyson JK, Jones DEJ. The Serum Proteome and Ursodeoxycholic Acid Response in Primary Biliary Cholangitis. Hepatology 2021, 74(6), 3269-3283.
  • Worrell J, Leslie J, Smith GR, Zaki M, Paish H, Knox A, James ML, Cartwright TN, OReily S, Kania G, Distler O, Distler J, Herrick A, Jeziorska M, Borthwick LA, Fisher AJ, Mann J, Mann DA, Oakley F. cRel expression regulates distinct transcriptional and functional profiles driving fibroblast matrix production in systemic sclerosis. Rheumatology 2020, 59(12), 3939-3951.
  • Anderson AE, Maney NJ, Nair N, Lendrem DW, Skelton AJ, Diboll J, Brown PM, Smith GR, Carmody RJ, Barton A, Isaacs JD, Pratt AG. Expression of STAT3-regulated genes in circulating CD4+ T cells discriminates rheumatoid arthritis independently of clinical parameters in early arthritis. Rheumatology 2019, 58(7), 1250-1258.
  • Carroll B, Otten E, Manni D, Stefanatos R, Menzies F, Smith G, Jurk D, Kenneth N, Wilkinson S, Passos J, Attems J, Veal E, Teyssou E, Seilhean D, Millecamps S, Eskelinen E-L, Bronowska A, Rubinsztein DC, Sanz A, Korolchuk V. Oxidation of SQSTM1/p62 mediates the link between redox state and protein homeostasis. Nature Communications 2018, 9, 256.
  • Paish HL, Kalson NS, Smith GR, del Carpio Pons A, Baldock TE, Smith N, Swist-Szulik K, Weir DJ, Bardgett M, Deehan DJ, Mann DA, Borthwick LA. Fibroblasts Promote Inflammation and Pain via IL-1α Induction of the Monocyte Chemoattractant Chemokine (C-C Motif) Ligand 2. American Journal of Pathology 2018, 188(3), 696-714.
  • Proctor CJ, Smith GR. Computer simulation models as a tool to investigate the role of microRNAs in osteoarthritis. PLoS ONE 2017, 12(11), 0187568.
  • Tomalin LE, Day AM, Underwood ZE, Smith GR, Dalle Pezze P, Rallis C, Patel W, Dickinson BC, Bähler J, Brewer TF, Chang CJ-L, Shanley DP, Veal EA. Increasing extracellular H₂O₂ produces a bi-phasic response in intracellular H₂O₂with peroxiredoxin hyperoxidation only triggered once the cellular H₂O₂-buffering capacity is overwhelmed. Free Radicals in Biology and Medicine 2016, 95, 333-348.
  • Carroll B, Maetzel D, Maddocks ODK, Otten G, Ratcliff M, Smith GR, Dunlop EA, Passos JF, Davies OR, Jaenisch R, Tee AR, Sarkar S, Korolchuk VI. Control of TSC2-Rheb signaling axis by arginine regulates mTORC1 activity. eLife 2016, 5, e11058.
  • Wilson CL, Jurk D, Fullard N, Banks P, Page A, Luli S, Elsharkawy AM, Gieling RG, Bagchi-Chakraborty J, Fox C, Richardson C, Callaghan K, Blair GE, Fox N, Lagnado A, Passos JF, Moore AJ, Smith GR, Tiniakos DG, Mann J, Oakley F, Mann DA. NFkB1 is a suppressor of neutrophil-driven hepatocellular carcinoma. Nature Communications 2015, 6, 6818.
  • Barter MJ, Tselepi M, Gomez R, Woods S, Hui W, Smith GR, Shanley DP, Clark IM, Young DA. Genome-wide microRNA and gene analysis of mesenchymal stem cell chondrogenesis identifies an essential role and multiple targets for miR-140-5p. Stem Cells 2015, 33(11), 3266-3280.
  • Dolan D, Nelson G, Zupanic A, Smith G, Shanley D. Systems Modelling of NHEJ Reveals the Importance of Redox Regulation of Ku70/80 in the Dynamics of DNA Damage Foci. PLoS One 2013, 8(2), e55190.
  • Smith GR, Shanley DP. Computational modelling of the regulation of Insulin signalling by oxidative stress. BMC Systems Biology 2013, 7, 41.
  • Smith GR, Shanley DP. Modelling the Response of FOXO Transcription Factors to Multiple Post-Translational Modifications Made by Ageing-Related Signalling Pathways. PLoS ONE 2010, 5(6), e11092.
  • Pellicane G, Smith GR, Sarkisov L. Molecular Dynamics Characterization of Protein Crystal Contacts in Aqueous Solutions. Physical Review Letters 2008, 101(24), 248102.

• Conference Proceedings (inc. Abstract)

  • Moran-Salvador E, Paoli PP, Smith GR, Page A, Howarth RM, Oakley F, Mann J, Mann D. MeCP2 exerts global control over the myofibroblast transcriptome and reveals new regulators of fibrosis. In: The Liver Meeting 2015: 66th Annual Meeting of the American Association for the Study of Liver Diseases. 2015, San Francisco: John Wiley & Sons, Inc.