My Research & Papers

From 2008 till 2011, I completed a PhD in Assoc. Prof Timothy Bailey's group at the Institute for Molecular Bioscience, at The University of Queensland, Australia. This focused on developing tools and methods to better under transcription factor binding and gene expression. One key focus of my PhD was on integrating epigenetic (and particularly, histone modification) data into in silico methods of predicting transcription factor binding. This both greatly improves accuracy (less false positives), and allows these methods to be tissue-specific.

Following this, until 2019, I was undertaking research and development for a start-up company that co-founded, DoseMe Pty Ltd, producing a software product that more accurately assists in determining the individually optimum dose of a given drug to give to a patient to reach a desired therapeutic range. We predominantly gave talks and published posters at conferences all over the world. Since DoseMe was acquired in 2019, and throughout the time of DoseMe's journey I also published the odd paper in bioinformatics as well.

You can view a list of papers and posters I have published and presented below. I also link to software tools developed in these posters. My PhD thesis is also available for download.

Papers:

• Evaluation of amikacin use and comparison of the models implemented in two Bayesian forecasting software packages to guide dosing.
  Ryan A, Carland JE, McLeay RC, Lau C, Marriot DJE, Day RO, Stocker SL. British Journal of Clinical Pharmacology. 2021. 87(3), 1422-1431.
• Voriconazole: An audit of hospital dosing and monitoring and evaluation of the predictive performance of a dose prediction software.
  Chaudri K, Stocker SL, Williams KM, McLeay RC, Marriot DJE, Di Tanna GL, Day RO, Carland JE. Journal of Antimicrobial Chemotherapy. 2020. 75(7), 1981-1984.
• Critique of Vancomycin Dose‐Optimizing Software Review
  McLeay RC. Pharmacotherapy. 2019 May;39(5):619. doi: 10.1002/phar.2264.
• Clinically proven drug targets differentially expressed in the prefrontal cortex of schizophrenia patients. Voisey J, Mehta D, McLeay R, Morris, C. P., Wockner, L. F., Noble, E. P., Lawford, B. R., & Young, R. M. Brain Behav Immun. 2017;61:259‐265. doi:10.1016/j.bbi.2016.12.006
• Expression and Methylation of BDNF in Human Schizophrenia Brain.
  Cheah SY, McLeay R, Wockner LF, Lawford BR, Young RM, Morris CP, Voisey J. World J Biol Psychiatry. 2016 Oct 7:1-29.
• NFIB-mediated repression of the epigenetic factor Ezh2 regulates cortical development.
  Piper M, Barry G, Harvey TJ, McLeay R, Smith AG, Harris L, Mason S, Stringer BW, Day BW, Wray NR, Gronostajski RM, Bailey TL, Boyd AW, Richards LJ. J Neurosci. 2014 Feb 19;34(8):2921-30. doi: 10.1523/JNEUROSCI.2319-13.2014.
• Expression of nuclear factor one A and -B in the olfactory bulb.
  Plachez C, Cato K, McLeay RC, Heng YH, Bailey TL, Gronostasjki RM, Richards LJ, Puche AC, Piper M. J Comp Neurol. 2012 Oct 1;520(14):3135-49. doi: 10.1002/cne.23081.
• NFIX Regulates Neural Progenitor Cell Differentiation During Hippocampal Morphogenesis.
  Heng YH, McLeay RC, Harvey TJ, Smith AG, Barry G, Cato K, Plachez C, Little E, Mason S, Dixon C, Gronostajski RM, Bailey TL, Richards LJ, Piper M. Cereb Cortex. 2012 Oct 4.
• Genome-wide in silico prediction of gene expression.
  McLeay RC, Lesluyes T, Cuellar Partida G, Bailey TL. Bioinformatics. 2012 Nov 1;28(21):2789-96. doi:10.1093/bioinformatics/bts529.
• Epigenetic priors for identifying active transcription factor binding sites.
  Cuellar Partida, G, Buske F. A., McLeay, R.C., Whitington, T, Noble, W.S., Bailey, T.L. (2011). Bioinformatics, doi: 10.1093/bioinformatics/btr614
• Tissue-specific prediction of directly regulated genes.
  McLeay, R. C., Leat, C. J., and Bailey, T. L. (2011). Bioinformatics, 27 (17): 2354-2360, doi: 10.1093/bioinformatics/btr399
• Motif enrichment analysis: A unified framework and an evaluation on ChIP data.
  McLeay, R. C. and Bailey, T. L. (2010). BMC Bioinformatics, 11, 165, doi:10.1186/1471-2105-11-165

PhD Thesis:

• McLeay RC. Predicting Tissue-Specific Transcription Factor Binding and Gene Expression in silico. 2011. Abstract | Full Thesis

Recent Notable Posters:

• Predictive Ability and Bias of Vancomycin Population PK Models in an Obese Adult Population.
  Sabourenkov PE, McLeay RC. Open Forum Infect Dis. 2019 Oct; 6(Suppl 2): S575. (Presented at IDWeek 2019).
• AUC24 Vancomycin Bayesian-Based Dosing: Increasing Therapeutic Target Attainment with Decreased TDM Cost.
  Sabourenkov PE, McLeay RC. Open Forum Infect Dis. 2019 Oct; 6(Suppl 2): S583. (Presented at IDWeek 2019).
• Application of Bayesian modelling with infliximab to determine optimal patient-specific regimens.
  Ritter TE, Sarles HE, McLeay RC, Van Anglen LJ, Schroeder CP, Hardin TC. Journal of Crohn's and Colitis. 2019. 13:S1, S271–S272. (Presented at ECCO 2019).
• Application of Bayesian modelling with infliximab to determine optimal patient-specific regimens.
  Ritter TE, Sarles HE, McLeay RC, Van Anglen LJ, Schroeder CP, Hardin TC. Gastroenterology. 2019. 156:6, S-267. (Presented at Digestive Diseases Week 2019).

Software Tools on External Sites:

• AME & RAMEN - Motif enrichment analysis. Find transcription factor motifs over-represented in a set of genes. AME is now maintained in the MEME Suite, and porting RAMEN is in progress.
• DR Gene - Identify promoters bound by a given transcription factor in a tissue-specific manner (i.e. find Directly Regulated Genes).
• WigShrink - Reduce the size of a "wiggle" file by removing unnecessary runs of zeros.
• Genome-wide gene expression modelling - Supplementary data and scripts for gene expression modelling (for a submitted paper).