Gordon Smyth Home

Research Students

Current Students

• Shama Deb, Master of Science, University of Melbourne
  Supervisors: Gordon Smyth, Lizhong Chen
  Bias-corrected deviances and empirical Bayes for analysis of DNA methylation data
• Mahdieh Mahdavi, Master of Philosophy (Science), University of Melbourne
  Supervisors: Nadia Davidson, Gordon Smyth
  Advancing long-read data analysis of the transcriptome
• Lei Qin, PhD (Medical Biology), University of Melbourne
  Supervisors: Yunshun Chen, Gordon Smyth, Lizhong Chen
  Novel statistical strategies and bioinformatics software tools for processing and analysis of spatial data
• Melody Jin, PhD (Medical Biology), University of Melbourne
  Supervisors: Belinda Phipson, Gordon Smyth, Marie-Liesse Labat
  New statistical methods for analysing spatially resolved genomics data
• Junli Nie, PhD (Medical Biology), University of Melbourne
  Supervisors: Stephen Nutt, Julie Tellier, Gordon Smyth
  Understanding the mechanisms of gene regulation in B cells

Completed students

PhD

1. Jinming Cheng, PhD (Medical Biology), University of Melbourne, September 2024
   Supervisors: Gordon Smyth and Yunshun Chen
   Exploring mammary gland developmental stages and breast cancer heterogeneity using single-cell technologies
2. Mengbo Li, PhD (Medical Biology), University of Melbourne, July 2024 (awarded October 2024)
   Supervisors: Gordon Smyth, Andrew Webb and Yunshun Chen
   Linear models and empirical Bayes methods for mass spectrometry-based label-free proteomics data
3. Yue You, PhD (Medical Biology), University of Melbourne, May 2023 (awarded October 2023)
   Supervisors: Matt Ritchie, Peter Hickey, Charity Law and Gordon Smyth
   Benchmarking and methods development for single cell analysis
4. Xueyi Dong, PhD (Medical Biology), University of Melbourne, December 2022 (awarded June 2023)
   Supervisors: Matt Ritchie, Charity Law and Gordon Smyth
   Benchmarking long-read RNA-seq analysis methods
5. Ilariya Tarasova, PhD (Medical Biology), University of Melbourne, December 2022 (awarded June 2023)
   Supervisors: Gordon Smyth and Phil Hodgkin
   Deconvolving gene expression changes associated with time and cell division following B cell activation
6. Aaron Tin Long Lun, PhD (Medical Biology), University of Melbourne, August 2015 (awarded January 2016)
   Supervisors: Gordon Smyth and Stephen Nutt
   Statistical analyses of high-throughput sequencing data to study chromatin structure and organisation
7. Yunshun (Andy) Chen, PhD (Medical Biology), University of Melbourne, October 2013 (awarded January 2014)
   Supervisors: Gordon Smyth and Terry Speed
   Differential expression analysis of complex RNA-seq experiments
8. Eugene Kapp, PhD (Medical Biology), University of Melbourne, May 2013
   Supervisors: Terry Speed and Gordon Smyth
   Improved bioinformatics tools for the analysis of mass spectrometry and proteomics data
9. Joshy George, PhD (Biochemistry and Molecular Biology), University of Melbourne, March 2013
   Supervisors: David Bowtell and Gordon Smyth
   Integrated analysis of distinct molecular profiles of tumour data
10. Belinda Phipson, PhD (Mathematics and Statistics), University of Melbourne, March 2013
    Supervisors: Gordon Smyth and Peter Hall
    Empirical Bayes modelling of expression profiles and their associations
11. Charity Law, PhD (Medical Biology), University of Melbourne, January 2013
    Supervisors: Gordon Smyth and Terry Speed
    Precision weights for gene expression analysis
12. Di Wu, PhD (Medical Biology), University of Melbourne, January 2011
    Supervisors: Gordon Smyth and Terry Speed
    Finding hidden relationships between expression profiles with application to breast cancer biology
13. Carolyn de Graaf, PhD (Medical Biology), University of Melbourne, October 2010
    Supervisors: Doug Hilton, Gordon Smyth and Li Wu
    Genetic regulation of hematopoiesis
14. Tobias J Sargeant, PhD (Medical Biology), University of Melbourne, October 2008
    Supervisors: Terry Speed and Gordon Smyth
    Studying the evolution of apicomplexa. New methods for species tree inference using protein domains.
15. Mark Robinson, PhD (Medical Biology), University of Melbourne, October 2008
    Supervisors: Terry Speed, Gordon Smyth and Tom Brodnicki
    Methods for the analysis of gas chromatography-mass spectrometry data
16. Penelope Bryant, PhD (Paediatrics), University of Melbourne, May 2008.
    Supervisors: Nigel Curtis, Roy Robins-Browne and Gordon Smyth
    The use of global gene expression analysis and the investigation of the pathogenesis of rheumatic fever
17. Catherine Carmichael, PhD (Medical Biology), University of Melbourne, February 2008.
    Supervisors: Hamish Scott and Gordon Smyth
    Investigation into genetic predispositions to haematopoietic malignancies
18. Matthew Ritchie, PhD (Medical Biology), University of Melbourne, May 2005
    Supervisors: Gordon Smyth and Terry Speed
    Quantitative quality control and background correction for two-colour microarray data
19. Natalie Thorne, PhD (Mathematics and Statistics), University of Melbourne, May 2004.
    Supervisors: Terry Speed, Gordon Smyth, Simon Foote and Ian Gordon
    Single-channel normalisation and analysis of two-colour cDNA microarray data
20. Peter Dunn, PhD (Mathematics), University of Queensland, December 2001
    Supervisors: Gordon Smyth
    Likelihood-based inference for Tweedie generalized linear models
21. Heather Podlich, PhD (Mathematics), University of Queensland 1999.
    Supervisors: Gordon Smyth and Malcolm Faddy
    Extended Poisson process models for count data
22. William Dixon, PhD (Chemistry), University of Queensland 1997.
    Supervisors: Barry Chiswell and Gordon Smyth.
    The spatial optimization of water quality monitoring programs by simulated annealing [Published version]

Honours and Masters

1. Mai Tam Pham, MSc (Bioinformatics), University of Melbourne, June 2024
   Supervisors: Yunshun Chen, Gordon Smyth
   Detecting alternative splicing by incorporating internal exon and junction reads
2. Soroor Hediyeh Zadeh, MSc (Mathematics and Statistics), University of Melbourne, May 2019 (awarded July 2019)
   Supervisors: Gordon Smyth, Melissa Davis and Yunshun Chen
   Statistical methods for transcript differential expression analysis from RNA-seq data
3. Jiaping Liu, MPhil (Paediatrics), University of Melbourne, February 2019 (awarded May 2019)
   Supervisors: Ken Pang, Gordon Smyth, Lesley Cheng and John Christodoulou
   Identifying biomarkers in Autism Spectrum Disorder and Rett Syndrome
4. Chengzhong Ye, MRes (Medical Biology), University of Melbourne, July 2018 (awarded October 2018)
   Supervisors: Terry Speed and Gordon Smyth
   Some statistical and analytical problems with single cell RNA-seq
5. Guido Pacini, Masters of Statistical Sciences (Project), University of Bologna, July 2015
   Supervisors: Angela Montanari and Gordon Smyth
   Simulation analyses on ROMER, a rotation-based gene set testing method
6. Stephanie Ana Conos, Honours (Medical Biology), University of Melbourne 2012
   Supervisors: Paul Ekert and Gordon Smyth
   miR-150 antagonises Hoxb8 dependent immortalisation of myeloid cells
7. Davis McCarthy, Honours (Mathematics and Statistics), University of Melbourne 2009
   Supervisors: Gordon Smyth
   Accounting for biological variation in digital gene expression experiments
8. Ella Wilkins, Honours (Medical Biology), University of Melbourne 2005
   Supervisors: Hamish Scott and Gordon Smyth
   Identification of genes involved in differentiation, proliferation and developmental networks
9. Michael Lazzarini, Honours (Mathematics), University of Queensland 1998.
   Keeping indigenous people out of custody: generalized linear modelling of arrests data from the NATSIS
10. Douglas Lincoln, Honours (Mathematics), University of Queensland 1998.
    Smoothing splines in statistical Analysis: application to malaria vaccine trials
11. Leighton Ayre, Honours (Mathematics), University of Queensland 1997.
    Regression graphics and applications
12. Murray Keir, Honours (Mathematics), University of Queensland 1997.
    An empirical Bayes approach to random effects models
13. Michael Larner, Honours (Mathematics), University of Queensland 1997.
    Using modified time series methods to model sales and labour data at Pizza Hut
14. Geoff Mallon, Honours (Mathematics), University of Queensland 1994.
    Mixed linear models and applications
15. Jeremy O'Reilly, Honours (Mathematics), University of Queensland 1994.
    Point processes and the analysis of environmental data
16. Joseph Ting, Bachelor of Medicine (Child Health), University of Queensland 1992
    Supervisors: John Vance and Gordon Smyth
    The relationship between gastro-oesophageal reflux and sleeping position in infants (implication to Sudden Infant Death Syndrome)
17. Sharon Raiteri, Honours (Mathematics), University of Queensland 1991.
    Methods of analysing Taguchi experiments
18. Robert G Clark, Honours (Mathematics), University of Queensland 1990.
    Non-standard generalized linear models and algorithms
19. Joanne White, Honours (Mathematics), University of Queensland 1989.
    Nonlinear estimation, with application to the rate-reducing resistance of Stylosanthes scabra
20. Sumit Roy, Master of Arts (Statistics & Applied Probability), University of California, Santa Barbara 1988.
    Supervisors: SR Jammalamadaka, RC Tiwari and Gordon Smyth
    Algorithms for computation of the likelihood function

Undergraduate Research Projects

1. Soroor Hediyeh Zadeh, Science Research Project, Department of Mathematics and Statistics, University of Melbourne, March-June 2015
   Supervisors: Gordon Smyth
   Differential expression analysis of RNA-seq data
2. Lynn Wang, UROP 2013-2014
3. Davis McCarthy, UROP 2006-2009
4. Yifang Hu, UROP 2007