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Research officer, Medical Genomics

QIMR Berghofer Medical Research Institute

Noorul Amin is SAAFE CRC's foundational Postdoctoral Research Fellow in the data analytics program. His research focuses on advanced computational techniques in biological data, including omics data analysis and tools development. With a background in applying machine learning and data mining approaches to biological challenges, Noorul's current work centres on the intersection of data analytics and antimicrobial resistance, particularly in agribusiness, food security, and the environment.

He is seeking Honours and PhD students interested in applying machine learning, cloud computing, and big data approaches to biological research problems.

Prof David Ascher is currently an NHMRC Investigator and Director of the Biotechnology Program at the University of Queensland. He is also Head of Computational Biology and Clinical Informatics at the Baker Institute.

David’s research focus is in modelling biological data to gain insight into fundamental biological processes. One of his primary research interests has been developing tools to unravel the link between genotype and phenotype, using computational and experimental approaches to understand the effects of mutations on protein structure and function. His group has developed a platform of over 40 widely used programs for assessing the molecular consequences of coding variants (>7 million hits/year).

Working with clinical collaborators in Australia, Brazil and UK, these methods have been translated into the clinic to guide the diagnosis, management and treatment of a number of hereditary diseases, rare cancers and drug resistant infections.

David has a B.Biotech from the University of Adelaide, majoring in Biochemistry, Biotechnology and Pharmacology and Toxicology; and a B.Sci(Hon) from the University of Queensland, majoring in Biochemistry, where he worked with Luke Guddat and Ron Duggleby on the structural and functional characterization of enzymes in the branched-chain amino acid biosynthetic pathway. David then went to St Vincent’s Institute of Medical Research to undertake a PhD at the University of Melbourne in Biochemistry. There he worked under the supervision of Michael Parker using computational, biochemical and structural tools to develop small molecules drugs to improve memory.

In 2013 David went to the University of Cambridge to work with Sir Tom Blundell on using fragment based drug development techniques to target protein-protein interactions; and subsequently on the structural characterisation of proteins involved in non-homologous DNA repair. He returned to Cambridge in 2014 to establish a research platform to characterise the molecular effects of mutations on protein structure and function- using this information to gain insight into the link between genetic changes and phenotypes. He was subsequently recruited as a lab head in the Department of Biochemistry and Molecular Biology at the University of Melbourne in 2016, before joining the Baker Institute in 2019 and the University of Queensland in 2021.

He is an Associate Editor of PBMB and Fronteirs in Bioinformatics, and holds honorary positions at Bio21 Institute, Cambridge University, FIOCRUZ, and the Tuscany University Network.

Dr Melinda Ashcroft is a Research Fellow on Infectious Disease Epidemiology (Climate Change) in the Faculty of Medicine at The University of Queensland (UQ). Her current research focus is on Nontuberculous mycobacteria (NTM) and how NTM infections are associated with climate change and major weather events. Previously Melinda has worked at Monash University as a Research Fellow on the Sero-epidemiology of Klebsiella spp., at the University of Melbourne as a Postdoctoral Research Fellow on the Genomic Epidemiology of Neisseria gonorrhoeae and as a Research Associate at UQ on the genomics and epigenomics of extraintestinal pathogenic Escherichia coli. Melinda was awarded a Bachelor of Applied Science (Biotechnology/Biochemistry) in 2004 from Queensland University of Technology and a Master of Biotechnology in 2013 from UQ. She then switched fields to Microbial Genomics and was awarded a PhD from UQ in 2019 for her thesis: Evolution and function of mobile genetic elements and DNA methyltransferases in extraintestinal pathogenic Escherichia coli.

Evan Bailey is a postdoctoral researcher in the Molecular and Systems Medicine Group at the School of Biomedical Sciences and Queensland Brain Institute. His current work focuses on the interplay between innate immune signaling and cellular metabolism in neurodegenerative diseases utilising his skills and experience in molecular genetics, cellular physiology and computational biology.

Evan started his career as a Research Assistant in the lab of Dr. Natasha Kumar at UNSW, Sydney, studying functional plasticity in chemoreceptive brainstem neurons in response to chronic hypercapnia (elevated CO2) before moving to UQ to pursue a PhD in evolutionary-developmental neuroscience. His PhD work under the supervision of Dr. Laura Fenlon and Dr. Rodrigo Suarez focused on the evolution of cellular mechanisms controlling neuronal differentiation and fate specification in the neocortex of marsupial and placental mamals, resulting in publications in Nature Communications and PNAS. Throughout his research career, Evan has had a keen interest in how cells establish and maintain their functional identity across a wide range of contexts and how homesostatic programs (e.g. energy metabolism) influence cell identity and phenotypic transitions.

Mikael Bodén has a PhD in Computer Science and statistical machine learning from the University of Exeter (UK) but has spent the last decade and a half in biological research environments, including the Institute for Molecular Bioscience/ARC Centre of Excellence in Bioinformatics and the School of Chemistry and Molecular Biosciences, where he is currently located. He is the director of UQ’s postgraduate program in bioinformatics. Mikael Bodén has supervised 7 postdocs from funding he received from both ARC and NHMRC; he has been the primary advisor for 11 PhD and 3 MPhil graduates; he is currently supervising another 6 PhD students in bioinformatics and computational biology. Mikael Bodén collaborates with researchers in neuroscience, developmental biology, protein engineering and bioeconomy to mention but a few, and contributes expertise in the processing, analysis and integration of biological data; this is exemplified by recent publications in Science, Nature Catalysis, Nature Communications, Cell Systems, Nucleic Acids Research and Bioinformatics.

Dr Sandra Brosda is a Research Fellow within the Surgical Oncology group led by Professor Andrew Barbour.

Dr Brosda was awarded a PhD in bioinformatics and cancer genetics from the University of Queensland in November 2020. Her research focused on biomarker discovery and intra-tumour heterogeneity and tumour evolution in oesophageal adenocarcinoma (OAC). In 2021, Dr Brosda was awarded a Cure Cancer Australia PdCCRS grant and an MSH project grant to further investigate tumour evolution to improve precision medicine in OAC.

She has been involved in research projects covering genetics, epigenetics, spatial transcriptomics, radiomics, ctDNA and quality of life assessments in the context of cancer. Overall, her research applies bioinformatics tools and approaches to cancer genomics to improve precision medicine and health outcomes for patients with melanoma, oesophago-gastric cancer and pancreatic cancer.

Dr Chan has a PhD in Genomics and Computational Biology from UQ. He underwent postdoctoral training at Rutgers University (USA) in algal genomics and evolution. He returmed to UQ in late 2011 as one of the inaugural Great Barrier Reef Foundation Bioinformatics Fellows.

Dr Chan joined the School of Chemistry and Molecular Biosciences in 2020 as a group leader at the Australian Centre for Ecogenomics (ACE). His group uses advanced computational approaches to study genome evolution and develop scalable approaches for comparative genomics.

Dr Seth Cheetham is an ARC Discovery Early Career Award Fellow and group leader at the Australian Institute for Bioengineering and Nanotechnology. He is also the Deputy Director of the BASE facility, Australia's leading mRNA manufacturing hub. He completed his PhD at the University of Cambridge, supported by the Herchel Smith Research Studentship. Seth is a molecular biologist and geneticist with a focus on mRNA drugs, synthetic biology and epigenetics. He has authored 22 publications, including twelve as a first author and four as a corresponding author. He has published in some of the most influential molecular biology journals including Science, Molecular Cell, Nature Reviews Genetics , Genome Biology and Nature Structural and Molecular Biology. His work has attracted > $10M in funding from an ARC DECRA (2022), NHMRC Fellowship (2019), MRFF grants, UQ HERA Grant, a Cancer Australia Grant (2021), Mater Foundation seeding grant (2019), a UQ ECR grant (2019) and the UQ Genome Innovation Hub (2020). In 2021 Seth was awarded the Genetics Society of Australasia Alan Wilton ECR awarded for his research in the field of RNA and epigenetics.

Evolutionary and ecological genomics of marine invertebrate animals.

Animals evolve because their genomes need to respond to the constantly changing environment presented by both their external habitat and their internal microbial symbionts. Over evolutionary time, these different factors interact during development, when the animal body plan is being established, to generate the extraordinary animal diversity that graces our planet. In ecological time, early life history stages must detect and respond to the precise nature of their environment to generate a locally-adapted functional phenotype. Using coral reef invertebrates from phyla that span the animal kingdom, we study these gene-environment interactions using genomic, molecular and cellular approaches combined with behavioural ecology in natural populations. We work mostly with embryonic and larval life history stages of indirect developers, as these are crucial to the survival, connectivity, and evolution of marine populations. When not immersed in the molecular or computer lab, we are lucky enough to be immersed in the ocean, often in beautiful places!

Paul Dennis leads an exciting research group that applies cutting-edge technologies to understand the roles of microorganisms and their responses to environmental change.

He is also a passionate educator and public speaker who advocates for the importance of biological diversity and evidence-based environmental awareness. He has talked about his research on ABC Radio and a range of other media outlets.

His teaching covers aspects of ecology, microbiology, plant and soil science, and climatology. He considers these topics to be of fundamental importance for the development of more sustainable societies and takes pride in helping others to obtain the knowledge and skills they need to build a better future.

Paul's research has taken him to Antarctica, the Amazon Rainforest, high mountains and oceans. The approaches used in his lab draw on a wide range of expertise in molecular biology, ecology, statistics, computer science, advanced imaging and soil science. He applies these skills to a wide-range of topics and systems including plant-microbe interactions, Antarctic marine and terrestrial ecology, biogeography, pollution and human health.

Plant viruses and horticultural crop improvement

Dr Dietzgen is internationally recognised for his work on plant virus characterisation, detection and engineered resistance. Before joining UQ, Dr Dietzgen was a Science Leader in Agri-Science in the Queensland Department of Employment, Economic Development and Innovation. He previously held research positions at the University of Adelaide, University of California, Cornell University and University of Kentucky. Dr Dietzgen’s research interests are in molecular virus-plant-insect interactions, virus biodiversity and evolution, and disease resistance mechanisms. His focus is on the biology of RNA viruses in the family Rhabdoviridae and the molecular protein interactions of plant-adapted rhabdoviruses and tospoviruses. He has published extensively on plant virus characterisation and genetic variability, RNAi- mediated virus resistance and diagnostic technologies with 20 review articles and book chapters and over 65 peer-reviewed publications.

Birgitta Ebert’s research focuses on developing biotechnology concepts to address critical challenges such as pollution, climate change and overexploitation of natural resources.

She specializes in improving microbial catalysts for eco-friendly chemical and material production by leveraging metabolic engineering, synthetic biology, systems analysis, and modelling. Her goal is to create microbial cell factories that convert renewable resources and waste into valuable products, reducing reliance on petrochemicals. She collaborates closely with chemists and chemical engineers to enhance the integration of chemical and biological processes for improved efficiency and sustainability.

Birgitta has a background in Chemical Engineering and a PhD in Systems Biotechnology from TU Dortmund University (Germany). She led a research group in Systems Metabolic Engineering at the Institute of Applied Microbiology at RWTH Aachen University (Germany) from 2012 to 2019. In 2016, she expanded her expertise in Synthetic Biology by joining the Keasling lab at the University of California in Berkeley and the Joint BioEnergy Institute in Emeryville (USA).

Since April 2019, she has been at the Australian Institute for Bioengineering and Nanotechnology at the University of Queensland, applying her expertise to engineer microbial cell factories for fermentation-based manufacturing.

Dr Daniel Edge-Garza is a horticulture and crop geneticist at the Queensland Alliance for Agriculture and Food Innovation at the University of Queensland, Australia. His research interests are to develop and translate tools using genome-wide DNA information for breeders and growers to make meaningful decisions. Daniel’s PhD awarded by the University of Queensland in 2024 focused on identifying global G x E patterns to assist with improved germplasm-environment matching for commercial deployment. Before joining QAAFI, he obtained his Bachelor's Degree in Biological Sciences in 2005 and Master's Degree in Biotechnology in 2009 both at California State University, Fresno. From 2008, he worked as a faculty associate in research for tree fruit breeding at Washington State University becoming recognized worldwide for his efforts to streamline the deployment of DNA tests for pome and stone fruit breeding programs. He has also collaborated with the Genome Database for Rosaceae since 2018 to curate genomics data and train breeders on how to upload and access their data on the Breeding Information Management System.

Dr. Forutan is an internationally recognized Researcher. Her research area includes understanding the bovine genome and epigenome, discovering causative mutation underlying economic important traits such as fertility, understanding the way genes turn on and off, investigating different methodologies to improve the accuracy of genomic prediction, and optimizing methods for predicting genetic diversity and inbreeding. Her future research career vision is to make a significant contribution to creating new knowledge in the field of quantitative genetics that can help to improve efficiency and resilience in Livestock.

The molecular evolution of cytochrome P450 Enzymes: biological catalysts of unprecedented versatility.

Cytochrome P450 enzymes (CYPs, P450s) especially those responsible for drug metabolism in humans, are the unifying theme of the research in our lab. These fascinating enzymes are catalysts of exceptional versatility, and functional diversity. In humans they are principally responsible for the clearance of a practically unlimited variety of chemicals from the body, but are also critical in many important physiological processes. In other organisms (plants, animals, bacteria, fungi, almost everything!) they carry out an unprecedented range of functions, such as defense, chemical communication, neural development and even pigmentation. P450s are involved in the biosynthesis of an unequalled range of potent, biologically active natural products in microbes, plants and animals, including many antibiotics, plant and animal hormones, signalling molecules, toxins, flavours and fragrances. We are studying how P450s have evolved to deal with novel substrates by reconstructing ancestral precursors and evolutionary pathways, to answer such questions as how did the koala evolve to live on eucalyptus leaves, a toxic diet for most mammals.

The capabilities of P450s are only just coming to be fully recognized and structural studies on P450s should yield critical insights into how enzyme structure determines function. For example, recently we discovered that P450s are present within cells in the Fe(II) form, a finding that has led to a radical revision of the dogma concerning the P450 catalytic cycle, and has implications for the control of uncoupling of P450 activity in cells. Importantly, the biotechnological potential of P450s remains yet to be exploited. All of the specific research themes detailed below take advantage of our recognized expertise in the expression of recombinant human cytochrome P450 enzymes in bacteria. Our group is interested in finding out how P450s work and how they can be made to work better.

Artificial evolution of P450s for drug development and bioremediation: a way of exploring the sequence space and catalytic potential of P450s. The demonstrated catalytic diversity of P450 enzymes makes them the ideal starting material for engineering sophisticated chemical reagents to catalyse difficult chemical transformations. We are using artificial (or directed) evolution to engineer enzymes that are more efficient, robust and specialized than naturally occurring enzymes with the aim of selecting for properties that are commercially useful in the areas of drug discovery and development and bioremediation of pollutants in the environment. The approach we are using also allows us to explore the essential sequence and structural features that underpin all ~12000 known P450s so as to determine how they work.

Synthetic biology of enzymes for clean, green, solar-powered chemistry in drug development, bioremediation and biosensors. We have identified ancestral enzymes that are extremely thermostable compared to their modern counterparts, making them potentially very useful in industry, since they can withstand long incubations at elevated temperatures. They can be used as ‘off the shelf’ reagents to catalyse useful chemistry, such as in in drug discovery and development, fine chemicals synthesis, and cleaning up the environment. Working with drug companies, we are exploring how they can be best deployed in chemical processes and what structural features make them efficient, robust and specialized. We are also immobilizing P450s in virus-like-particles as ‘designer’ reagents that can be recovered from reactions and reused. To make such processes cheaper and more sustainable, we are using photosynthesis to power P450 reactions for clean, green biocatalysis in microalgae.

Biosketch:

After graduating from UQ with first class Honours in Biochemistry, Elizabeth took up a Royal Commission for the Exhibition of 1851 Overseas Scholarship to pursue doctoral work at Oxford University then undertook postdoctoral work at the Center in Molecular Toxicology and Department of Biochemistry at Vanderbilt University School of Medicine with Prof. F.P. Guengerich. She returned to UQ in 1993 to take up a position in Pharmacology and joined the School of Chemistry and Molecular Biosciences in 2009 as a Professor of Biochemistry.

Associate 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.

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.

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.