The lab was established at the Hawkesbury Institute for the Environment (HIE) in 2015 and works on the crux of biosecurity, genomics and evolutionary biology, creating novel capability to address real world problems.
Alexie heads the lab which basically means he spends 50% of his time on administrivia. Otherwise, Alexie is a genome bioinformatician working on ecological and economically important species, such as the Heliconius butterflies, the megapest Heliothine moths, invasive Tephritid fruit flies, C4 grasses, eucalyptus trees and marine species such as oysters and anemones.
Before becoming faculty at the HIE (Lecturer, the Australian equivalent to the American Assistant Professor), Alexie was a post-doctoral fellow at the CSIRO Entomology/Ecosystem Sciences/Land & Water (the department rebranded every two years), a research associate at the University of Exeter in Cornwall, UK and completed his PhD at the Max Planck Institute for Chemical Ecology, Jena, Germany.
Alexie’s work aims to blend the frontiers of molecular biology and computer science to secure Australia’s agricultural and natural ecosystems in the face of a changing climate. His main research interest is developing bioinformatics capability to address evolutionary questions such as how organisms adapt to a changing or novel environment. His main teaching activities focus on empowering researchers to analyse their own data and helping post-docs develop the soft skills needed for furthering their academic or industrial careers.
A post-doctoral member of the ARC Centre of Excellence for Translational Photosynthesis, Alex joined the HIE July 2015 and is working with us and Oula Ghannoum on dissecting the mechanism for C4 & C3 photosynthesis in model species and Australian native grasses. Alex completed his PhD at the University of Southampton on the transgenerational effects of elevated CO2 on plants.
Yagiz is currently undertaking his PhD with Chris Cazzonelli, David Tissue, and Alexie. He is seeking to further decypher the carotenoid biosynthesis pathway (the pigment that gives plants certain colours but also triggers growth responses). He is also working on identifying new RNA regulatory switches in the 5′ UTR of plants that can control physiological traits in a heritable manner.
Eric is a molecular biologist working on understanding how plants respond to stresses such as touch, temperature, and herbivory responses using a molecular, potentially inherited, mechanism. Co-supervised by Chris Cazzonelli and Alexie, Eric is taking a multi-omic approach using RNA, DNA, LC-MS and methylation to generate a new model for this mechanism.
Brendan joined HIE in 2016 as a graduate PhD student supervised by A/Prof Jeff Powell and Alexie. He is currently developing his evolutionary biology thesis on the exciting topic of the interaction between beneficial and pathogenic fungi that can co-exist in plant roots.
MD Golam Sarwer
Sarwer joined us in 2018 to create a new approach for studying aquatic pathogens with a focus on oysters. Supervised by Alexie, Sarwer is currently completing his Confirmation of Candidature developing a project that seeks to close the life cycle of the Martelia sydneyi protozoan – the agent of the QX oyster disease – and understand how it affects the molecular responses of two its hosts, an oyster and a polychaete worm.
Kay Jutamat Anantanawat
Joining us in July 2015 as a visiting post-doctoral fellow for 2 years, Kay is a molecular biologist in the School of Veterinary and Life Sciences in Murdoch University based at SARDI. She is now at the Next Gen Sequencing Facility of the Western Sydney University. While with us, she was spearheading the effort of developing new transcriptomic methods and using them to understand how environmentally stressed insects trigger and inhibit apoptosis.
Kay completed her PhD through the University of Adelaide working on transgenerational immune memory in insects in response to pesticide. Kay’s PhD work included identifying genes using RNASeq that might be involved in this immune response pathway. Subsequently, she worked at Adelaide in the area of entomovectoring (using insects to deliver biological control in vineyards) and at SARDI developing assays for the detection of fungal plant pathogens.
Elaine was an undergraduate research assistant in the lab during 2017 where she developed and executed a really cool investigation of the effects of capsicum on the midgut of the polyphagous herbivore Helicoverpa armigera.
Kaitao joined us in June 2015 after completing his PhD at the University of Queensland on crop genomics and bioinformatics. He is now at the CSIRO. At the HIE, Kaitao was involved in driving a research project on pangenomes (i.e. “is the reference genome really a reference?”) and discovering variation within honey bee ecotypes. He was also the lead developer of the TaxaCloud system, an elastic cloud computing system for taxonomic analytics of metagenomic amplicon data with QIIME (Quantitative Insights Into Microbial Ecology), and supporting our metagenomics collaborators in the HIE.
Daniel was completing his computer science WSU undergraduate degree when he was hired as an undegraduate assistant. He worked with us as a second year undergraduate research project student and summer scholar learning about bioinformatics and developing new techniques with SVMs and kmer databases. Working with Paul Greenfield (CSIRO) and Alexie, his work was instrumental in facilitating on jump-starting a research project on the environmental degradation of RNAi biopesticides.
Emily was a second year undergraduate student of biological/biomedical sciences at WSU. She is working with us as an undergraduate scholar on understanding how Culex pipiens f molestus mosquitoes can lay eggs without requiring the blood meal that most other mosquitoes need. She is learning about RNA biology while undertaking her own mosquito transcriptome project.
Penny came to us from the University of Melbourne to undertake a summer project prior to her Honours in forensic science. She helped us build material for our MSc in Data Science by creating new protocols for our the oral microbiome project we teach.
Interested in joining or working with us?
Contact the Stressed Fruit Fly Lab: