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Helen Gunter is a Senior Postdoctoral Fellow at the Australian Institute for Bioengineering and Nanotechnology. Dr. Gunter is partnering with Oxford Nanopore Technologies and the BASE Facility to benchmark a comprehensive test of mRNA vaccine quality. Helen has authored 25 publications, with 10 as first author, one as senior author, and 14 as middle author. She has published in influential journals such as Nature, Nature Communications and Translational Psychiatry. Helen’s work has attracted >$2M in funding from Oxford Nanopore (2023), the Genome Innovation Hub (2021), Deutesche Forschungsgemeinschaft (2011), a Zukunftskolleg Fellowship (2008) and from the University of Konstanz (2013).

Professor Emma Hamilton-Williams’ career focuses on understanding how immune tolerance is disrupted leading to the development of the autoimmune disease type 1 diabetes. She received her PhD from the Australian National University in 2001, followed by postdoctoral training in Germany and the Scripps Research Institute in the USA.

In 2012, she started a laboratory at the Frazer Institute, University of Queensland where she investigates the gut microbiota as a potential trigger or therapy target for type 1 diabetes, as well as developing an immunotherapy for type 1 diabetes. The overall aim of her research is to find new ways to prevent or treat the underlying immune dysfunction causing autoimmunity.

She is Chief Scientific Officer for an Australia-wide pregnancy-birth cohort study of children at increased risk of type 1 diabetes, which aims to uncover the environmental drivers of this disease. Her laboratory uses big-data approaches including proteomics, metabolomics and metagenomics to understand the function of the gut microbiota linked to disease.

She recently conducted a clinical trial of a microbiome-targeting biotherapy aimed at restoring a healthy microbiome and immune tolerance, with an ultimate aim of preventing type 1 diabetes.

Dr Pingping Han currently leads the Epigenetic Nanodiagnostics and Therapeutics Group within the Centre for Orofacial Regeneration, Reconstruction and Rehabilitation (COR3) at the UQ School of Dentistry. She received her PhD in Biomedical Engineering from the Queensland University of Technology (QUT) in 2014.

Dr Han’s current research focuses on three main areas: (a) salivary diagnostics for periodontal disease and (b) “cell-free” regenerative therapies for periodontal tissue engineering.

Dr April Hastwell is a plant molecular biologist with the School of Agriculture and Food Science at The University of Queensland, Australia. The focus of her research group is on roles of short signalling peptides in root development including in molecular networks controlling the beneficial legume-rhizobia symbiosis and nodule development.

Alesha Hatton is a postdoctoral research fellow specializing in statistical genetics and genetic epidemiology at the Institute for Molecular Bioscience, University of Queensland. Currently, her research focuses on understanding the genetic and environmental aetiology underlying complex traits through use of Mendelian randomization and statistical genetics methodologies. Her PhD was in systems genomics, applying quantitative genetics methods to investigate the role of DNA methylation in complex trait variation. Alesha has a bachelor’s degree in medical mathematics from the University of Wollongong and previously was employed as a statistician at the South Australian health and Medical Research Institute.

Professor Lee Hickey is a plant breeder and crop geneticist within the Queensland Alliance for Agriculture and Food Innovation at The University of Queensland, Australia. He is an ARC Future Fellow and Director of the ARC Training Centre in Predictive Breeding. His own research group specialises in plant breeding innovation to support development of more productive crops, including cereals, legumes, sugarcane, as well as horticultural and fibre crops. He has a strong interest in the integration of breeding technologies, such as genomic prediction, AI, speed breeding and genome editing. His advice for speed breeding crops is sought internationally and the technology is now adopted by plant breeding programs worldwide, which is fast-tracking development of improved crop varieties for farmers. His research outcomes have featured in >100 refereed publications, including articles in high profile journals Nature Plants, Nature Protocols and Nature Biotechnology. Lee is a prolific science communicator and his research outcomes have appeared in mainstream media such as BBC World News, National Geographic, and the New York Times. He is passionate about training the next generation of plant breeders and currently mentors 18 PhD students, while 20 of his previous graduates now work for leading plant breeding companies and high-profile research institutes around the globe.

Check out the ARC Training Centre in Predictive Breeding website here

Follow Professor Lee Hickey on X: @DrHikov

Research interests

• Speed breeding techniques to reduce the length of breeding cycles
• Understanding the genetics of physiological traits that support yield in different environments
• Integrating breeding technologies to accelerate genetic gain in breeding programs
• Innovative genomic selection methodologies
• Identifying novel sources of disease resistance

Queensland Brain Institute

Dr Massimo A. Hilliard received his PhD in Biological Chemistry and Molecular Biology in 2001 from the University of Naples, Italy. His experimental work, performed at the Institute of Genetics and Biophysics of the CNR (Italian National Council of Research), was aimed at understanding the neuronal and genetic basis of aversive taste behavior (bitter taste) in C. elegans.

During his first postdoc at the University of California, San Diego, using the Ca2+ indicator Cameleon he published the first direct visualisation of chemosensory activity in C. elegans neurons. In his second postdoctoral work at the University of California, San Francisco and at The Rockefeller University, he switched from neuronal function to neuronal development, focusing in particular on how neurons establish and orient their polarity with respect to extracellular cues.

From September 2007, he is at the Queensland Brain Institute where he established an independent laboratory.

Valentin was awarded a PhD from the French National Institute of Higher Education in Agricultural Sciences and the University of Montpellier (France) in 2018. His thesis focused on methodological developments for genetic differentiation analysis in the Next Generation Sequencing era in a neutral and adaptive context. Since 2019, he works as a post-doctoral researcher at the University of Queensland in the Program in Complex Trait Genomics group under the supervision of Professor Peter Visscher. His current research focuses on studying the within and between-population genetic variation in human complex traits.

The research interests of the Hume Laboratory centre on the biology of macrophages and osteoclasts. These are cells of haematopoietic origin that are closely related to each other but have distinctly different activities.

David Hume was a group leader at the Institute for Molecular Bioscience (1988-2007) and subsequently Director of the Roslin Institute at the University of Edinburgh in Scotland from 2007-2017. He is currently a Professorial Research Fellow at the Mater Research Institute-UQ, located at the Translational Research Institute

Dr Daniel Liang-Dar Hwang is a genetic epidemiologist and statistical geneticist by training. His research interests include sensory nutrition, causal modelling, and personalized nutrition. Dr Hwang applies statistical models to big data to understand genetic and environmental factors contributing to individual differences in taste and olfactory perception and their relationship with dietary behaviour and chronic conditions (See his research on taste perception in The Conversation). He develops methods for increasing statistical power for gene discovery, estimating intergenerational causal relationships, and personalized intervention. He also works with clinicians to investigate impaired chemosensory perception in cancer patients and COVID-19.

Daniel has a B.Sc from the National Taiwan University, majoring in Biochemical Science and Technology, and an M.Biotech from the University of Pennsylvania. Following graduation, he worked as a research technician in Danielle Reed's lab at the Monell Chemical Senses Center, where he first developed a keen interest in genetics and chemosensory perception. Later, he was awarded scholarships to complete an M.Sc in Nutrition at the University of Washington, under the supervision of Glen Duncan, and a PhD in Genetic Epidemiology at the QIMR Berghofer Medical Research Institute, under the supervision of Nicholas Martin and Margaret Wright. He then joined David Evans's group as a postdoc at the University of Queensland Diamantina Institute (now the Frazer Institute). Dr Hwang is an ARC DECRA Fellow at the Institute for Molecular Bioscience. He is also an Affiliated Scientist at the Monell Chemical Senses Center.

Dr Hwang has published more than 50 peer-reviewed publications. His work has been referred to in international health policy guidelines and a WHO report for the intervention of childhood obesity and in a global patent for personalized wine selection. He is on the editorial boards of BMC Medicine and Twin Research and Human Genetics. Dr Hwang is a Leadership Team member of the Global Consortium for Chemosensory Research, a global initiative to understand the relationship between smell loss and COVID-19 and foster the advancement of chemosensory science. He currently drives an international collaborative project to investigate the impact of COVID-19 vaccinations on long-COVID symptoms. Dr Hwang is a member of the National Committee for Nutrition of the Australian Academy of Science. He contributes to implementing the decadal plan for the science of nutrition in Australia.

Clara Jiang is a postdoctoral research fellow at the Institute for Molecular Bioscience, the University of Queensland. Clara’s research focuses on using genomic and transcriptomic analysis to investigate the genetic basis of cardiovascular and psychiatric disorders, with a particular focus on female health, as well as using statistical genomic approaches to explore possible opportunities for drug repurposing. Clara graduated from the University of Queensland with Bachelor of Advanced Science (First Class Honours) in 2017, and was awarded the University Medal. Clara was awarded her PhD at the University of Queensland in 2021, where she utilised bioinformatic approaches and molecular experiments to decipher the genetic aetiology of breast cancer, specifically the regulatory role of transposons or ‘jumping genes’ in modulating the transcriptional landscape in the cancer state. Clara is also a UQ Wellness ambassador and an advocate for promoting equity, diversity and inclusion in academia.

Prof. David Jordan is a sorghum breeder and geneticist with more than 20 years experience working in both the public and private sector.

For the last decade he has led the public sorghum pre-breeding program in Australia which is a partnership between the University of Queensland (UQ), The Queensland Department of Agriculture and Fisheries (DAF) and the Grains research and Develop Corporation (GRDC). This is a long running and successful research effort with a reputation for integrating across disciplines and linking research efforts from the strategic to the applied. Breeding lines from this program are widely used commercially in Australia and internationally with 100% of the commercial sorghum grown in Australia having genetics from the program. At the same time the research group continues to produce research papers at the forefront of sorghum research.

In recent years he had led projects focused on improving the lives of resource poor farmers in Africa that rely on sorghum.

I am a computational biologist with a centre-wide research role in the ARC Centre of Excellence for Plant Success in Nature and Agriculture, based here at UQ. I spend my time researching new computational techniques for predicting complex quantitative traits by integrating multiple layers of 'omics data (amongst dozens of other things!).

Areas of interest:

• Machine Learning, AI and high performance computing to learn and exploit functional connectivity in biological data
• Gene Expressions networks
• Multiplex networks, information propagation and perturbation
• Genomic Prediction

My goal is to aid crop and forestry breeders in selecting parental lines more accurately, which gives us a pathway to improving certain plant species. I also spend time developing new data analysis techniques that are being applied to human disease and conditions such as Autism and substance addiction.

David completed his PhD at Australian National University in 2017, focusing on the genome-wide basis of foliar terpene variation in Eucalyptus. He then undertook a postdoc at Oak Ridge National Laboratory, a US Dept of Energy lab with a focus on big data. After a stint as a staff scientist at Oak Ridge, David arrived at the Centre of Excellence in 2023 in the role of a Senior Research Fellow.

Dr Kemper is a postdoctoral fellow in statistical genetics. She joined UQ in 2016 after obtaining a PhD and postdoctoral experience at the University of Melbourne (2006-2016). Her expertise and research interests span a range of topics in quantitative genetics, including genomic prediction, modelling the epidemiological consequences of genetic change in disease and population genetics. Current research areas include:

• genetic analysis of longitudinal traits
• estimation of non-additive genetic effects
• genomic prediction in admixed populations

I am a developmental neuroscientist and bioinformatician interested in the molecular evolution of the mammalian brain. I completed a PhD on the molecular development of vasculature in the primate retina at the Australian National University, followed by a postdoctoral position at the Institut de la Vision in France that was supported by a NHMRC CJ Martin fellowship, where I investigated the role of guidance factors in the formation of commissural neurons within the mammalian hindbrain. My current research focuses on the development and evolution of the mammalian forebrain, in particular understanding the regulatory mechanisms and molecular evolutionary processes that control specification of cortical neuron subtypes.

Dr Snehlata Kumari is a group leader and the head of the Skin Inflammation and Immunity Laboratory at the Frazer Institute, University of Queensland, in Brisbane, Australia. Her international career and academic training spanned Germany, India, and Australia. She is a board member of the Australasian Society for Dermatology Research (ASDR) and a councillor on the International Psoriasis Council.

She has discovered novel signalling mechanisms that regulate the balance between homeostasis and inflammation in the skin. These findings highlight new mechanisms by which inflammatory diseases are initiated and propagated via NF-κB, TNF, IL-20 family cytokines, and necroptotic and apoptotic signalling pathways. Her research work has been published in top-tier journals, including Nature (3x), Nature Communications, Cell Metabolism, and Immunity.

Her scientific contributions have received international recognitions and honours, including the German National Academy of Sciences, the German Research Foundation (DFG), the European Society for Dermatological Research, the Japanese Society for Investigative Dermatology, and the Young Women Investigators Award from the International Cytokine and Interferon Society.

Overall aims and research focus

- Immunomodulatory mechanisms regulating inflammation and immunity.

- Cellular and cell-soluble factor interactions in inflammatory diseases, including Psoriasis, Hidradenitis Suppurative, and Atopic Dermatitis.

Dr. Joan Li is a Senior Lecturer and a Research Fellow with an established national and international reputation at The University of Queensland. She holds both an MD and a PhD, blending clinical and scientific expertise, which provides her with a unique perspective on research and education. While establishing an emerging profile in medical education, she maintains engagement in discipline-related biomedical research through collaboration and supervision.

With over seven years of teaching experience, Joan has actively engaged in face-to-face teaching in biomedical science and medicine courses, contributed to curriculum design, development, and course coordination for both undergraduate and postgraduate programs. She brings her strong analytical skills and critical thinking abilities, honed through her medical and biomedical research background, to her teaching practices. Driven by a genuine passion for teaching, Joan continuously strives for excellence, with specific interests in assessment, curriculum design, development and student learning experience. She has implemented innovative teaching methods, designed diverse and inclusive curricula, created new learning activities, and fostered student engagement as learning partners, with a consistent goal of improving curriculum quality and enhancing student learning outcomes.

Leveraging her medical knowledge, extensive experience in biomedical research, and growing understanding of medical education, Joan is committed to developing medical students into critical thinkers and lifelong learners with a genuine appreciation for medical practice and medical research, enabling them to better serve an ever-changing society. Drawing upon her extensive experience in developmental biology and physiology, particularly in cardiac and renal research, Joan actively supervises higher degree research students and continues to make significant contributions to discipline-related research through publications and collaborations.

Dr. Joan Li is a versatile academic professional with a rich background in biomedical research and an emerging presence in medical education research. Her dedication to teaching and learning, combined with her impressive track record in both disciplines, makes her a valuable asset to The University of Queensland and the broader academic community.

Bio

Dr. Yang Liu is an evolutionary geneticist, currently working at the University of Queensland (UQ) as a Research Fellow. Prior to UQ, he obtained a PhD from the University of British Columbia (UBC) and worked in research as a postdoc at UBC and University of Cambridge. He is broadly interested in the eco-evolutionary dynamics of plant populations that have undergone environmental heterogeneity over spatiotemporal scales. The goal of his research is to increase our understanding of the impacts of major episodes in plant demography and life histories on trait evolution and to foster sustainability. He tackles research questions at the interface between ecology and evolutionary biology with the integration of population genetics and quantitative genomics to elucidate the ecological and genetic basis of phenotypic traits and biological adaptation.

Currently, he leverages available Arabidopsis natural accessions across its geographic distribution range, coupled with their genomic data, to perform common-garden and divergent selection experiments. From these he aims to dissect features of the genetic architecture of traits and to reveal their relationships to environmental conditions. He is focusing on the shoot branching phenotype and its associated traits including flowering timing.

ECO-EVO-GENOMICS TEAM

Three PhD positions available in 2023-2025

Ongoing Projects

Project 1: Unification of selection and inheritance informs adaptive potential for generations to come (Applications open in 2023; CLOSED)

Natural selection acts on phenotypes and produces immediate phenotypic effects within a generation. In this short-term process, some phenotypes are more successful than others. Use of single traits for selection analysis could generate opposing outcomes and cannot predict how selection operates on an organism. In contrast, multivariate selection in trait combinations utilizes the attribute of functional integrations to reveal how selection works in a multi-dimensional trait space. Selection is an important force driving evolution but not equal to evolution; the latter leads to changes in genetic variation. Only through assessment of the evolutionary responses of phenotypes can we understand the transmission of such selection from one generation to the next. How does selection occurring within a generation affect evolution across generations? In the project, we aim to address the question by unifying the two processes to forecast evolutionary potential in relation to selection. To that end, we partition genetic variance into components based on an experimental design, employ experimental evolution to estimate additive genetic variance-covariances (G) on quantitative scales and evaluate G-matrix evolution. We eventually hope to elucidate how populations subjected to artificial selection move along evolutionary trajectories and whether there are genetic constraints making the fitness optimum evolutionarily inaccessible.

Project 2: Genetic and ecological bases of shoot branching divergence across Arabidopsis species-wide accessions (Applications open in 2024; CLOSED)

Spatial patterns of genetic variation are shaped by environmental factors, topological features, and dispersal barriers. As a result, we often can identify population genetic structure stratified by geographic locations or ecological niches, the drivers of population isolation by distance or the environment, clinal genetic variation over space in alignment with gradually varying environment gradients, and adaptive genetic variation in relation to environmental variables. At the ecological level, assembly rules uncover the coordination of phenotypic traits along environmental clines. Tradeoffs between traits represent the consequence of environmental filters and reflect adaptation to environmental heterogeneity. For example, three fundamental adaptive strategies are delineated by a CSR theory, that is, Competitors, Stress-tolerators, and Ruderals. As such, ways of genetic and phenotypic assemblage over space and throughout time point to a role for natural selection driven by spatially varying environmental conditions to maintain genetic variation that confers natural variation in phenotypes. In this project, we focus on an important agronomic trait – shoot branching – due to its important contribution to the overall shoot architecture of a plant and being a potential target for yield optimization. We aim to dissect features of the genetic architecture of the trait and to reveal its relationships to environmental conditions. We integrate geographic, environmental, and genomic data from the 1001 Arabidopsis Genomes Project, coupled with the branching phenotype measured in selected accessions and then forecasted for the rest of the 1001 accessions using machine-learning models, to investigate the ecological relevance and genetic underpinnings of branching divergence across the Arabidopsis species-wide accessions. Our study has implications for enhancing our understanding of the genetic and ecological basis of shoot branching divergence and the potential for generating novel knowledge for improving phenotypic predictability.

Project 3: Dimensionality, modularity, and integration: Insights from the architecture features of pan-genomes, pan-transcriptome, pan-epigenomes, and pan-chromatin (applications open in 2025) Application Portal ALSO ACCEPTING EXPRESSION OF INTEREST FROM INTERNATIONAL APPLICANTS

Organisms are functionally integrated systems, where interactions among phenotypic traits make the whole more than the sum of its parts. How is a suite of traits assembled into an adaptive module? How is an intramodule rewired to form a regulatory network? What is the persistence and stability of a module under exposures to perturbations triggered by altered interactions between the response to disparate environmental conditions or between the responses of multiple traits to the same environment? What constrains modules to vary independently, reflecting the integration and canalization of evolutionary trajectories? In this project, we utilize a compilation of pan-genomes, pan-transcriptome, pan-epigenomes, and pan-chromatin resources of Arabidopsis thaliana to uncover how dimensionality, modularity, and integration are organized at different omics levels including genetic polymorphisms, structural variants, RNA isoforms, expression abundance, epigenetic imprinting, and chromatin accessibility. Ultimately, we apply such functional elements to multivariate genomic selection, in the hope of enhancing multilayered omics-enabled prediction.