Dr Matthieu Vignes PhD, DEA

Contact details

• Ph: +64(0)6 951 7654 (direct) or +64(0)6 356 9099; ext. 84654
  Location: B3.06, Science Tower B
  Campus: Turitea

Qualifications

• Doctor of Philosophy - Joseph Fourier University (2007)
• Diplôme d'Études approfondies en mathématiques - Université Claude Bernard Lyon 1 (2002)

Certifications and Registrations

• Licence, Supervisor, Massey University

Research Interests

My research is motivated by the understanding of the structure(s) which govern(s) the behaviour of complex systems. Mostly, I have been working with high-throughput data generated by biological organims, regarded as layers of components of different natures which interact with each other possibly fulfilling different goals.
To this end, I am interested in probabilistic graphical modelling as a convenient way of representing the system under study and how its constituting elements interact. I am often faced with high-dimensional data posing both statistical and computational challenges. Missingness in the data sets at hand can also be a hindrance. Data sets are heterogeneous (e.g. mixing discrete and continuous data), sampling is certainly not independent and identically distributed and off-equilibrium and measurements noisy.
Recently, I am moving towards a causal interpretation of learnt relationships, hopefully revealing realistic mechanisms which explain the inner functioning of the system.
I have also been involved in the study of epidemiological models at different scales.

Thematics

Future Food Systems

Area of Expertise

Field of research codes
Applied Mathematics (010200): Applied Statistics (010401):
Artificial Intelligence and Image Processing (080100):
Biological Mathematics (010202): Biostatistics (010402):
Information And Computing Sciences (080000):
Mathematical Sciences (010000): Numerical and Computational Mathematics (010300): Optimisation (010303):
Pattern Recognition and Data Mining (080109):
Statistical Theory (010405): Statistics (010400): Stochastic Analysis and Modelling (010406)

Keywords

• Probabilistic graphical models (Bayesian networks, GGM...)
• High-dimensional (biological) data
• Gene network inference
• Causality
• Data integration
• Computational statistics

Languages

• English
  Last used: today
  Spoken ability: Excellent
  Written ability: Excellent
• French
  Last used: today
  Spoken ability: Excellent
  Written ability: Excellent
• German
  Last used: few years ago
  Spoken ability: Average
  Written ability: Average
• Spanish
  Last used: Today
  Spoken ability: Needs work
  Written ability: Needs work

Teaching Statement

Papers taught: (at Massey)

• 161.200 Statistical Modelling (with Martin Hazelton)
• 161.331 Biostatistics (with Geoff Jones)
• 161.704 Bayesian statistics (with Mark Bebbington)
• 161.705 Statistical Inference (with Mark Bebbington)
• 161.729 Topics in Applied Statistics (with Chris Jewell)
• 161.744 Statistical Genetics (with Patrick Biggs)

Old teaching:

• Statistics and learning at SupAero (with Emmanuel Rachelson) and Probability (with Jeremie Bigot) at ISAE SupAero, Toulouse, France, 2012-2014.
• Statistics: basics to advanced subjects to undergraduates in Biology or Economics (2002-2006), to PhD students and scientists from research institutes (2007-2008).
• General mathematics: Algebra and Analysis to undergraduates in Mathematics and Physics (2003-2005).
• General science courses to high-school pupils (2005-2006).

Student supervision:

• Co-supervision of Luca Panizzi
• Co-supervision of Thilini Warusawithana
• Co-supervision of Olivia Angelin-Bonnet (2017-2021, Massey University), "Investigation of genotype and phenotype interactions using computational statistics"
• Co-supervision of Magali Champion PhD (2011-2014, Universite Paul Sabatier Toulouse 3), "Contribution to the modelling and inference of gene regulatory networks"

Graduate Supervision Statement

Please have a look at my research interest, and feel free to contact me, if you would like to do a project with us on the study of data generated from a complex system to decipher its structure. Note that projects range from quite applied to quite theoretical.

Current Doctoral Supervision

Main Supervisor of:

• James Bristow - Doctor of Philosophy
  Identifying novel integration methods for spatiotemporal climate and genetic data to advance epidemiological insights: Applications for animal influenza and salmonella
• Doris Benig - Doctor of Philosophy
  The Resilience of Species to Climate Change is Dependent on Their Adaptive Capacity
• Mario Prado Lara - Doctor of Philosophy
  An evaluation of statistical classification tools for microbiome and multiomic data
• Padmini Parthasarathy - Doctor of Philosophy
  Unravelling the Hidden Mysteries of Facial Eczema in Sheep

Co-supervisor of:

• Patricia Soh - Doctor of Philosophy
  Protein intake and protein quality in vegan diets

Completed Doctoral Supervision

Main Supervisor of:

• 2021 - Olivia Angelin-Bonnet - Doctor of Philosophy
  Investigation of genotype and phenotype interactions using computational statistics

Co-supervisor of:

• 2024 - Thilini Warusawithana - Doctor of Philosophy
  Gene duplication fate in a genetic pathway context: An examination of the trichome initiation pathway in the allopolyploid genus Pachycladon (Brassicaceae)
• 2024 - Luca Panizzi - Doctor of Philosophy
  Biomarker profiling of biologic fluids and tissues from horses with induced carpal osteoarthritis

Other Links

• INRAE Research Fellow website - (detached position)