Students and postdoctoral researchers I have supervised or sponsored, from 2002 to the present. See my publications, projects and talks for related work.

Current doctoral students

  • Haoyuan Huang — PhD, School of Biological Sciences, University of Auckland (since April 2026)
  • Yuan Xu — PhD, School of Biological Sciences, University of Auckland (since March 2025)
  • Eva Li — PhD, School of Biological Sciences, University of Auckland (since March 2025)
  • Yao Xiao — PhD, School of Biological Sciences, University of Auckland (since March 2024)
  • Sophie Yang — PhD, School of Computer Science, University of Auckland (since July 2023)

Postdoctoral researchers

  • Dr Kylie Chen — Research Fellow, School of Biological Sciences, University of Auckland (2023–2025)
  • Dr Jonathan Klawitter — Research Fellow, School of Computer Science, University of Auckland (2022–2025)
  • Dr Fábio Mendes — Research Fellow, School of Biological Sciences, University of Auckland (2018–2021)
  • Dr Tim Vaughan — Research Fellow, Massey University and Department of Computer Science, University of Auckland (2011–2017)
  • Dr Remco Bouckaert — Research Fellow, Department of Computer Science, University of Auckland (2010–2017)
  • Dr Georgianne Griffiths — Research Fellow, School of Biological Sciences, University of Auckland (2012–2017)
  • Dr Alex Gavryushkin — Research Fellow, Department of Computer Science, University of Auckland (2014–2016)
  • Dr Joseph Heled — Research Fellow, Department of Computer Science, University of Auckland (2011–2014)
  • Dr Michael Defoin-Platel — Research Fellow, Department of Computer Science, University of Auckland (2007–2008)

Former doctoral students

  • Cinthy Jimenez-Silva — PhD, School of Computer Science, University of Auckland (2020–2024)
  • Kylie Chen — PhD, School of Computer Science, University of Auckland (2018–2022). Dean's List for PhD thesis, 2022
  • Rong Zhang — PhD, Department of Computer Science, University of Auckland (2017–2021)
  • Jordan Douglas — PhD, Department of Computer Science, University of Auckland (2016–2020)
  • Roman Oliynyk — PhD, Department of Computer Science, University of Auckland (2017–2020)
  • Alexandra Gavryushkina — PhD, Department of Computer Science, University of Auckland (2013–2018). Best paper in department
  • Andrew Dopheide — PhD, School of Biological Sciences, University of Auckland (2012–2018), co-supervisor
  • Ben Potter — PhD, School of Biological Sciences, University of Auckland (2010–2018), co-supervisor
  • Jing Yang — PhD, Department of Computer Science, University of Auckland (2017–2018), external supervisor during a year abroad from her degree in Beijing
  • Huw Ogilvie — PhD, Research School of Biology, Australian National University (2014–2017), co-supervisor
  • Jessie Wu — PhD, Departments of Computer Science and Statistics, University of Auckland (2010–2015). Best Doctoral Thesis in Department, 2014
  • Denise Kühnert — PhD, Department of Computer Science, University of Auckland (2009–2014). Best Doctoral Thesis in Department, 2013
  • Sibon Li — PhD, Department of Computer Science, University of Auckland (2006–2014)
  • Joseph Heled — PhD, Department of Computer Science, University of Auckland (2006–2012). Dean's List for PhD research and Vice-Chancellor's Award for Best Doctoral Thesis, 2011
  • Helen (Yulong) Gu — PhD, Department of Computer Science, University of Auckland (2006–2011), co-supervisor
  • Simon Ho — PhD, Department of Zoology, University of Oxford (2004–2005)
  • Jan Strugnell — PhD, Department of Zoology, University of Oxford (2002–2005), advisor
  • Jennifer Jackson — PhD, Department of Zoology, University of Oxford (2002–2005), advisor

Former masters and honours students

  • Jasmine Saghafifar — MSc, School of Computer Science, University of Auckland (2025–2026)
  • Sinuo He — MSc, School of Computer Science, University of Auckland (2025–2026)
  • Ming Yang — MSc, School of Computer Science, University of Auckland (2025–2026)
  • Clementine Yan — MSc, School of Biological Sciences, University of Auckland (2024–2025)
  • Jessie Wu — BSc(Hons), Bioinformatics Institute, University of Auckland (2009)
  • Sebastian Höhna — MSc, Department of Computer Science, University of Auckland (2008)
  • Melanie Hayr — BSc(Hons), Bioinformatics Institute, University of Auckland (2008); undergraduate research (2007)
  • Thomas Lopdell — BSc(Hons), Bioinformatics Institute, University of Auckland (2007)
  • Mohsen Khorshid — MSc, Bioinformatics Institute, University of Auckland (2007), co-supervisor
  • Peter den Harder — MSc, Department of Bioinformatics, Vrije Universiteit, Netherlands (2007)
  • Nicolas Derian — MSc, Université de Rennes 1, France (2007)
  • Helen Shearman — MSc, Bioinformatics Institute, University of Auckland (2006), co-supervisor
  • Blake Gwilt — MSc, Bioinformatics Institute, University of Auckland (2006)
  • Ben Curran — MSc, Bioinformatics Institute, University of Auckland (2006)
  • Joseph Heled — BSc(Hons), Department of Computer Science, University of Auckland (2005)
  • Nasser Giacaman and Elias Billeh — final year project, Department of Computer Science, University of Auckland (2005)
  • Pavan Cheruvu — MSc, Department of Computer Science, University of Oxford (2004)
  • Lucy Beaumont — MSc, Bioinformatics, University of York (2003), external supervisor