People

Professor Mathew G. Lewsey completed his PhD in Molecular Virology at the University of Cambridge with John Carr. He conducted postdoctoral research at the Salk Institute (La Jolla, USA) with Joe Ecker and at the Centro Nacional de Biotecnología (Madrid, Spain) with Roberto Solano. Mat joined AgriBio in April 2016 to further his interests in genomics, systems biology and plant science. In 2017 became Director of the La Trobe Genomics Platform, which is based at AgriBio. In 2019 he became Co-Deputy Director of the ARC Research Hub for Medicinal Agriculture. In 2022 he became the La Trobe University Node Leader of the ARC Centre of Excellence in Plants For Space.

Muluneh Tamiru Oli obtained his PhD from Georg-August-University Göttingen in Germany studying the genetic diversity in yam (Dioscorea spp.) in Ethiopia. He was awarded the Japan Society for the Promotion of Science (JSPS) Fellowship and conducted postdoctoral research in rice molecular genetics and genomics at Iwate Biotechnology Research Centre (Japan). Muluneh joined AgriBio in November 2016 to work on maximizing yields of agricultural and horticultural plants using controlled environment growth experiments, plant molecular biology, high-throughput sequencing, biochemistry and agronomy.

Marta Peirats-Llobet obtained her PhD in Plant Molecular Biology and Biotechnology at IBMCP in Spain studying how drought stress hormone, ABA, is connected with chromatin remodeling machinery. Marta joined AgriBio in 2018 as a postdoc to study seed germination with high-throughput sequencing techniques at the opposite side of the world! Marta's project is in collaboration with PepsiCo and she is based primarily in the lab of Prof Jim Whelan.

Diego Lozano is a creative PhD student at La Trobe University with a strong background in technical activities related to telecommunication systems, image processing and machine learning technology in both private and public sectors. His diverse professional experience has led to development of an almost unique skill set as well as excellent communication and problem-solving skills. Diego is applying these to hardware and software development for the La Trobe High-Throughput Phenomics Platform. He believes the breakthroughs in plant phenotyping will come as a result of interdisciplinary collaboration of plant biologists, engineers and computer scientists. His research aims to develop an automated phenotyping system that helps plant researchers to identify, measure and analyze quantitative plant parameters. It would have the advantages of increased repeat accuracy and throughput coupled with decreased hands-on time. Moreover, it would be able to create prediction models for plant diseases, morphological and physiological patterns. Diego is co-supervised by Prof Jim Whelan, Dr Eddie Custovic and Dr Dennis Deng. He joined us in late 2016.

Lingling Yin is a PhD student in the lab. She previously completed her Master’s degree in Horticulture at Zhejiang University in China with Prof Jingquan Yu, studying the mechanism of Mi-1-mediated resistance to Meloidogyne incognita. In 2015, she was awarded a national scholarship. Her current research focuses on analysing regulatory networks of hormone-responsive transcription factors using 'omic data.

Asha Haslem coordinates and conducts a range of next generation sequencing technical services for the Genomics Platform. She completed her Bachelor of Science degree at La Trobe University in 2000, majoring in Microbiology and Genetics. In 2006 Asha moved to Darwin to study the potentially fatal disease Melioidosis caused by the bacterium Burkholderia pseudomallei at Menzies School of Health Research. After returning to Melbourne, she began working at the Royal Children's Hospital establishing and validating molecular tests for the monitoring of minimal residual disease in leukaemia patients before moving to the Australian Genome Research Facility working in the Next-Generation Sequencing division. In 2016 Asha joined the Genomics Platform at AgriBio.

Neha Patel won a competitive PhD scholarship from Council of Scientific and Industrial Research (CSIR), India and completed her PhD at National Chemical Laboratory, India in 2014. Thereafter, she moved to Australia to join Australian National University as an Endeavour Research Fellow in 2015. She continued working as a Postdoctoral Fellow at ANU on identifying plant peptide hormones regulating plant root architecture by applying plant molecular biology, mass spectrometry and plant biotechnology techniques. She has developed a novel approach for in vivo identification of secretory peptide hormones from cultured plant root exudates. She is currently working as a Research Officer on CSIRO SIEF STEM+ Business Fellowship program at La Trobe University and her project aims at developing herbicide resistant field crops.

Uyen Hong is a PhD student at La Trobe University. She joined our group in April 2019 after obtaining her master’s degree in Plant science from Tel Aviv University, Israel under the supervision of Prof. Nir Ohad. Her previous research focused on genetics and epigenetics, especially understand the role of some specific genes involved in the DNA methylation establishment in moss (Physcomitrella patens). In our lab, she aims to broaden knowledge of genetic and biochemical regulation of the alkaloid biosynthetic pathway.

James Lancaster is a Masters student at La Trobe University studying the epigenetic phenomenon known as paramutation in Pisum sativum, the common pea. He aims to identify the causal locus of the ‘rogue’ phenotype, and the mechanisms involved in paramutation at this locus. His project involves utilising bioinformatic analysis, phenomics, and epigenomics to identify and characterise the rogue paramutation.

Esmaeil Ebrahimie is the lead expert bioinformatician in the La Trobe Genomics Platform and an Adjunct Associate Professor at La Trobe University. Esmaeil completed his PhD in Plant Breeding – Molecular Genetics & Genetic Engineering at The University of Tehran. He has 10 years’ postdoctoral research experience in statistical analysis and bioinformatics at The University of Adelaide and The University of South Australia. Esmaeil is an Honorary Associate Professor at The University of Adelaide and is an Accredited Statistician with the Statistical Society of Australia (SSA). Esmaeil joined La Trobe University in 2019. His interest is the application of machine learning algorithms for pattern discovery in cutting edge sciences such as single cell, circular RNA, and alternative splicing fields.

Bhavna Hurgobin obtained her PhD in applied bioinformatics focusing on crop genomics from the University of Queensland. She was based in Prof. David Edwards lab and her main research topic revolved around pangenomics of plant species. During this time, she constructed and analysed the first pangenome for the important oilseed crop, Brassica napus. After her PhD, she decided to explore other applications of bioinformatics, especially in the context of medical research. Consequently, she took up a research officer role at the Telethon Kids Institute in Perth, working in the areas of systems immunology and translational genomics. Bhavna is now based at AgriBio, La Trobe University in A/Prof. Mathew Lewsey’s group where she will applies her bioinformatics skills to assist with the genomic improvement of agricultural plants.

Sophia Ng is a research assistant in biochemistry and molecular biology. Sophia obtained her PhD from the University of Western Australia in 2013. She then continued her post-doctoral training in Australia, China and France. Her past research has focused on the understanding of (1) how nuclear genes encoding mitochondrial proteins are regulated under abiotic stresses and (2) how plants respond to phosphate starvation at a molecular level. Sophia's current project is to utilize several deep-sequencing approaches to understand and modify regulatory networks in crop plants.

Joe (Changyu Yi) completed his Masters degree in horticulture in China where he studied the effects of CO2 enrichment on salt tolerance in tomato. For this work, he received the 2014 Zhejiang University Meritorious Student Award, Outstanding Graduate Student. Joe joined Agribio, La Trobe University, in December of 2015 as a Ph.D student in Prof. Jim Whelan’s lab. He worked on identifying modulators that involved in phosphate starvation response in Arabidopsis using RNA sequencing and GWAS during his Ph.D. Joe joined the Lewsey lab in September of 2019 as a bioinformatician to study the mechanisms of beta-glucans accumulation in oats using high-throughput sequencing.

Mary Khodayari obtained her PhD in Plant Breeding – Molecular Genetics & Genetic Engineering in 2014, University of Tehran, investigating the effect of elicitors on expression of genes involved in secondary metabolism in cell suspension cultures. After PhD completion, Mary worked at a private agricultural research company, setting up a plant tissue culture laboratory there and working with different governmental and private research groups. She developed several projects on plant tissue culture and gene transformation for research and commercial purposes. Mary joined the Lewsey lab in Jan 2020 to develop her interests in plant tissue culture.

Lee Conneely is a PhD student. He completed his Master’s by research at Southern Cross University in 2020 investigating glandular trichome proteomics. He completed his Master’s by research and coursework in biological sciences (plant science) at the University of Amsterdam in 2019. In 2016 graduated from University college Dublin with a Bachelor of Science degree, majoring in genetics. During his Bachelor of Science degree, he was awarded an Erasmus student grant to undertake his Bachelor of Science research project in collaboration with the University of Copenhagen, where he joined the DNA repair and disease mechanisms research group. Lee joined the team in 2020 as a PhD student with the aim of furthering our understanding of glandular trichomes and pursuing his interests in epigenetics and functional genomics.

Manijeh Mohammadi-Dehcheshmeh is a bioinformatician in the La Trobe Genomics Platform since 2019. She received her PhD from The University of Adelaide in 2014. Her PhD research focused on uncovering the function of GmbHLHm1 as an enhancing transcription factor in both rhizobium and arbuscular mycorrhiza symbioses. As a part-time Postdoctoral Research Fellow at the School of Animal and Veterinary Science at The University of Adelaide, she worked on microbiome profiling and analysis of the impact of diets and antibiotics in a range of wild and production animals. Manijeh is also experienced in full genome sequencing and genome assembly of bacteria and viruses.

Lab alumni

Quentin Gouil joined the Lewsey group for a postdoctoral project on the gene networks that govern germination in Arabidopsis. He obtained his PhD from the University of Cambridge, studying tomato epigenetics in the Baulcombe lab. Quentin has now moved to the lab of Matt Ritchie at WEHI, but we continue to collaborate on epigenomics and single cell sequencing projects.

Junji Miyazaki completed his PhD at Curtin University (Perth, WA) working on the plant-microbe interactions. After completion of PhD, he worked with various research groups at the Department of Agriculture and Food (WA), The University of Adelaide, CSIRO Agriculture (Narrabri, NSW), The Australian National University (Canberra, ACT) and The University of Melbourne. Junji joined the Lewsey lab in July 2017 to develop his interests in molecular plant-insect interactions. He is also a tutor for third year laboratory project students.

Akanksha Sharma completed her PhD in Agricultural Sciences at The University of Melbourne with Prof Prem Bhalla and Prof Mohan Singh, studying grass pollen allergens using Brachypodium distachyon as a model system. After submitting her PhD thesis, she has worked on generating biotic stress tolerant crop plants (Brassica) that control pests without the need for pesticides, for 6 months in the same lab. During her time in the Lewsey lab, Akanksha worked on improving economic benefits of plants through genetic tolerance to herbicides using plant molecular biology and biotechnology approaches.

Maddison Browne completed her bachelor of agricultural science at La Trobe University, and conducted an honours degree with in the lab. Maddison investigated the function of candidate transcription factors in Arabidopsis seed dormancy and germination.

Long Chen was a bioinformatics expert in the La Trobe Genomics Platform. He has expertise across multiple data-types and species.

Yinan Wang completed her PhD in Bioinformatics at Institute of Developmental and Genetics Biology, Chinese Academy of Sciences in 2012. She then worked as a research assistant at Shanghai Jiao Tong University while also working as a NGS specialist at Shanghai Genome Pilot Technology Inc. In 2014, she was employed at Institute for Applied Ecology, University of Canberra. Yinan's role at La Trobe was to provide bioinformatics support for Genomics Platform. Her specialties included RNA-Seq, ChIP-Seq, genotyping and variant calling.

Sarah was a research fellow with the Australian Research Council Centre of Excellence in Plant Energy Biology and the Australian Centre for Robotic Vision at the Australian National University (ANU). She joined the lab as a research visitor in Feb. 2017, studying plant phenomics. Sarah was a PhD student at the ANU and National Information Communications Technology Australia, during 2012 to 2016. Her PhD thesis was on "Scene Parsing using Multiple Modalities". She also studied the potential of multi-spectral imaging and Near Infrared (NIR) data in particular, in outdoor scene understanding that led to receiving a grant fund from Toyota-US to work on "Multi-spectral and Infrared Imaging for Driving Hazard Awareness" during her PhD. She worked on Genotype/Phenotype classification using deep plant features and their temporal behaviour to find the relations between genes and plant phenotypes.

Michael Dodt was a multidisciplinary postdoc working on optimising crop growth and establishment. He completed his PhD at the Centre for Tropical Crops and Biocommodities (QUT) in Brisbane, QLD, on improving drought tolerance of pulse crops by modifying root systems architecture. Michael has a diverse research background spanning neuroscience, biomedical science and plant abiotic stress tolerance. He was a scholarship recipient of the Massachusetts Institute of Technology for entrepreneurship and remains passionate about applying science to real-world problems.

Lim Chee Liew completed her PhD in Plant Genetics at the University of Tasmania with A/Prof Jim Weller investigating the control of flowering and photoperiodism in garden pea. She was awarded a McKenzie Postdoctoral Fellowship at the University of Melbourne to conduct research on the circadian clock and flowering time regulation on soybean with Prof Prem Bhalla and Prof Mohan Singh. Lim Chee joined Agribio, La Trobe University, to further her interests in molecular genetics and plant science. Her projects investigated tissue specific regulation of gene expression in barley seeds using laser capture micro dissection and high throughput chromatin sequencing approaches. Lim Chee is now a member of Prof Jim Whelan's laboratory and we continue to collaborate on seed 'omics projects.