About Me

For the past five years my research has focused on plant-fungal interactions. In my current postdoctoral position, I am investigating the genetic basis of the interaction between Phytophthora agathidicida and kauri (Agathis australis), a native tree of New Zealand having major social importance for Māori. Phytophthora agathidicida is an oomycete pathogen similar to the potato blight agent, Phytophthora infestans which caused the Irish Great Famine in 1845 killing over 1 million people. The goal of this research is to identify candidate effectors (small secreted proteins often essential for disease) using population genetics data, whole genome comparisons and transcriptomic analyses.

My previous research focused on the association between the fungal endophyte Epichloë festucae and perennial ryegrass, a key pasture grass in New Zealand, using bioinformatics and next generation sequencing approaches. These associations play an important role in forage improvement as the fungus protects its host against a wide range of pests (insects and pathogenic fungi), and enhances host drought tolerance. My research encompassed three main areas: lateral gene transfer between plant-associated fungi, host transcriptomic responses to endophyte infection, and transcriptomic comparison of mutualistic and pathogenic Epichloë-grass interactions. The study of lateral gene transfer between plant-associated fungi (pathogens, endophytes, mycorrhiza) was based on a genomic comparison of different fungi and started with the annotation of the gene models of Epichloë festucae and perennial ryegrass. My work on host responses to endophyte infection identified transcriptomic and metabolomic signatures of endophyte infection. The comparison of mutualistic and pathogenic interactions was performed on different mutant Epichloë strains that display a switch from a mutualistic to pathogen-like behaviour. A transcriptomic study comparing three of these mutants to the original wild-type association was performed and led to the discovery of a key set of fungal genes involved in symbiosis.

Personal details

Date of Birth24/04/1984
NationalityFrench
ResidencyNew Zealand

Contact Details

Dr. Pierre-Yves Dupont
Institute of Fundamental Sciences
Massey University
Private Bag 11 222
Palmerston North 4442
New Zealand

Work

Massey University - New Zealand

Postdoctoral researcher 2016 - now

Time to fight back: harnessing molecular determinants of virulence and adaptation in kauri dieback pathogens - Massey University & the Bio-Protection Research Centre

Postdoctoral researcher 2012 - 2016

Lateral gene transfer in fungi: Identifying the cross-species toolbox for metabolic innovation - Massey University & the Bio-Protection Research

Education

INRA - France

PhD studentship 2008 - 2011

INRA is the French National Agronomy Research Institute. Thesis on developing bioinformatics tools to combine information from metabolomics, transcriptomics and promotor studies to characterize metabolic pathways involved in liver cancers. This was in collaboration with the Polytechnic school (Palaiseau, France) and a IT startup company, Solusciences (Clermont-Ferrand, France) to develop software for biological pathway modelling and biochemical dynamics analysis.

Bordeaux University - France

Masters in Computational Biology 2008

During my Masters, I worked on two different projects:
•  Evaluation of a docking software (Autodock v.4) and development of an automatic procedure to compute docking of multiple ligands on kinase receptors using a computation cluster
•  Development of software for visualization and detection of internal movements in biomolecules

Bachelor in Computer Sciences 2007

I did this diploma in parallel with my first year of Masters

Bachelor in Biology, Geology and Earth Sciences 2005

Diploma to become High School biology and geology teacher

Awards

Massey University Team Research Medal 2015

Medal given to the Massey Bio-Protection Research Team for our research on "Decoding the molecular basis of fungal-plant interactions". Rosie Bradshaw, Murray Cox, Pierre-Yves Dupont, Carla Eaton, Austen Ganley and Barry Scott

Publications

Articles

Evolution of polyketide synthesis in a Dothideomycete forest pathogenOzturk IK, Chettri P, Dupont PY, Barnes I, McDougal RL, Moore GG, Sim A Bradshaw RE  Fungal Genetics and Biology  2017 • In press

Genomic data quality impacts automatic detection of lateral gene transfer in fungiDupont PY and Cox MP  Genes | Genomes | Genetics  2017

Fungal endophyte infection of ryegrass reprogrammes host metabolism and alters developmentDupont PY, Eaton CJ, Wargent JJ, Fechtner S, Solomon P, Schmid J, Day RC, Scott B, Cox MP  New Phytologist  2015

A core gene set describes the molecular basis of mutualism and antagonism in EpichloĆ« spp.Eaton CJ, Dupont PY, Solomon P, Clayton W, Scott B, Cox MP  Molecular Plant-Microbe Interactions  2015

HyLiTE: accurate and flexible analysis of gene expression in allopolyploid speciesDuchemin W, Dupont PY, Campbell MA, Ganley A, Cox MP  BMC Bioinformatics  2015

Genomes of plant-associated clavicipitaceaeSchardl CL, Young CA, Moore N, Krom N, Dupont PY, Pan J, Farman ML  Advances in Botanical Research  2014

Computational identification of transcriptionally co-regulated genes, validation with the four ANT isoform genesDupont PY, Guttin A, Issartel JP, Stepien G  BMC Genomics  2012

Computational analysis of the transcriptional regulation of the adenine nucleotide translocator isoform 4 gene and its role in spermatozoid glycolytic metabolismDupont PY, Stepien G  Gene  2011

Description and assessment of a model for GSK-3β database virtual screening Ventimila N, Dupont PY, Laguerre M, Dessolin J  Journal of Enzyme Inhibition and Medicinal Chemistry  2010

Conferences

Time to fight back: Harnessing molecular determinants of virulence and adaptation in kauri dieback pathogens2017 Healthy Trees Healthy Future Symposium  Scion Rotorua  2017  Oral presentation

Time to fight back: Harnessing molecular determinants of virulence and adaptation in kauri dieback pathogensFungal effectors symposium  Massey University  2016  Oral presentation

Insights into the molecular mechanisms underlying grass-endophyte symbiosisPlant-fungal interactions symposium  The Samuel Roberts Noble Foundation  March 2015  Oral presentation

Fungal endophyte infection of ryegrass reprograms host metabolism and alters development28th Fungal Genetics Conference  March 2015  Poster

Endophyte infection of ryegrass alters metabolism, development and response to stressQueenstown Molecular Biology Conference   August 2014  Two oral presenations (plant satellite and main meeting)

Workshops

Cold Spring Harbor Laboratory, Computational & Comparative Genomics workshopCold Spring Harbor Laboratory   February 2015

Work experience

Teaching

I have been involved in teaching to both undergraduate students and academic staff. I have been in charge of teaching Microarray analysis to third year students at Massey University in 2015 and to medical students in Clermont-Ferrand University, France in 2010 and 2011. I also created an introductory course to Unix and Python programming for Massey University staff (2013-2014). I have also given numerous tutorials on a variety of computer-related topics including SVN and GIT, Ruby on Rails and Lisp. Finally, I am train and mentor PhD students and confirmed researchers for statistical analyses and the use of bioinformatics tools in the space or transcriptomics, phylogenetics, next-generation sequencing and comparative genomics.

Databases

Epichloë gene models database

This database is a Ruby on Rails web application linked to a MySQL server. It contains the results of automatic annotations for 9000 Epichloë festucae genes models as well as transcriptomics results and manual annotations. It is used both by national and international researchers. It was publically announced in Eaton et al. (2015).

Perennial Ryegrass gene models database

This database is based on the same framework as the Epichloë festucae database and contains automatic annotations of about 50.000 gene models. It was publically announced in Dupont et al. (2015).

Software

Hybrid Lineage Transcriptome Explorer (HyLiTE)

HyLiTE is a software allowing the analysis of high-throughput transcriptome data from allopolyploid species

Geneprom

Geneprom is a Ruby on Rails web application developped during my PhD. It allowed me to study regultory elements present in gene promoters.

MPSA (Metabolic Pathway Software Analyzer)

It is a Java plugin for VANTED. It allows the integration of data from different biological analysis methods to have a better understanding of metabolic pathways and their regulation.


Some more of my work, including the slides of my teaching, can be found in my Sourceforge and Github personal pages.

I also worked on the developement of a propriatary information system for academic research (written in C++) during my PhD.

Skills

Bioinformatics skills

Phylogeny
Neighbor Joining, Maximum Likelihood (PHYLIP, PhyML, RAxML), supertrees, consensus trees. Multiple sequence alignments with mafft, clustal, kalign, muscle, etc. Analysis libraries: ETE toolkit (Python) and phangorn (R)
Next Generation Sequencing
Expert in NGS data analysis. RNA-Seq (Illumina) data analysis from raw read data to complex statistical analysis of the results and experimental condition comparison. Genomic (Illumina and 454) de novo assembly, genomic comparison and SNP calling.
Statistics
Good understanding of statistics, Markov chains and Monte Carlo statistics. Principal and Independent Component Analysis, clustering. Commonly build statistical pipeline for analysing biological data. Common use of Python and R for adanced data analysis
Protein structure analysis and visualisation
AutoDock, GOLD, VMD

Computer Sciences skills

Development environments
Daily usage of Emacs and SublimeText 3. Good practice of Eclipse and NetBeans
Operating systems
Daily use of Windows 7 and 10 computers as well as Linux (Fedora, Ubuntu and Mint). Good command of Mac OS X. Common use of high performance computing (OpenMP, MPI, Torque and OpenPBS)
Languages and Libraries
Good command of languages Ruby, Python (Pandas, Matplotlib, Plotly, ScikitLearn) and Java. Common practice of C++, R (BioConductor) and Perl (BioPerl, EnsEMBL libraries). Good understanding of Agent-Based Models and Petri Nets and their implementation
Web technologies
Advanced knowledge of Ruby on Rails. Good practice of HTML5, CSS3 and Javascript (including JQuery, Underscorejs, ...) and SQL (MySQL, PostgreSQL)

Programming

  • 100%

    Python + BioPython
  • 90%

    R + Bioconductor
  • 80%

    HTML5 / CSS3
  • 80%

    SQL
  • 70%

    Ruby on Rails
  • 70%

    Java
  • 60%

    C++

Get In Touch.

Address

Dr. Pierre-Yves Dupont
Institute of Fundamental Sciences
Massey University
Private Bag 11 222
Palmerston North 4442
New Zealand

Phone

+64-6-356 9099 X 85734

Email

p.y.dupont@massey.ac.nz
pierreyves.dupont@gmail.com