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.
My current research at UQ is as Professor in this School (teaching AGRC3040 Crop Physiology) and as an Affiliate Professor of QAAFI. Since 2020, with full-time appointment at UQ, my research portfolio has included multiple projects in applications of machine learning and artificial intelligence into the ag domain. This area is developing rapidly and across UQ, I am engaging with faculty in multiple schools (ITEE, Maths and Physics, Mining and Mech Engineering) as well as in the Research Computing Centre to develop new projects and training opportunities at the interface of field agriculture and these new digital analytics.
My career research has been around genetic and environment effects on physiology of field crops, particularly where drought dominates. Application of quantitative approaches (crop simulation and statistical methods) and phenotyping (aerial imaging, canopy monitoring) to integrate the understanding of interactions of genetics, growth and development and the bio-physical environment on crop yield. In recent years, this work has expanded more generally into various applications in digital agriculture from work on canopy temperature sensing for irrigation decisions (CSIRO Entrepreneurship Award 2022) through to applications of deep-learning to imagery to assist breeding programs.
Much of this research was undertaken with CSIRO since 1996. Building on an almost continuous collaboration with UQ over that time, including as an Adjunct Professor to QAAFI, Prof Chapman was jointly appointed (50%) as a Professor in Crop Physiology in the UQ School of Agriculture and Food Sciences from 2017 to 2020, and at 100% with UQ from Sep 2020. He has led numerous research projects that impact local and global public and private breeding programs in wheat, sorghum, sunflower and sugarcane; led a national research program on research in ‘Climate-Ready Cereals’ in the early 2010s; and was one of the first researchers to deploy UAV technologies to monitor plant breeding programs. Current projects include a US DoE project with Purdue University, and multiple projects with CSIRO, U Adelaide, La Trobe, INRA (France) and U Tokyo. With > 8500 citations, Prof Chapman is currently in the top 1% of authors cited in the ESI fields of Plant and Animal Sciences and in Agricultural Sciences.
We are using the genetic model organism, C. elegans, do investigate the genetic basis of both normal and disordered behaviour. Our current interests are identifying the genes responsible for anxiety and depression as well as the genes for eating disoders and addiction. Using C. elegans as a model organism will also allow us to study gene function as it relates to behaviour.
Molecular mechanisms of phosphine resistance (other research)
Genetic mapping of oxidative stress resistance genes. The fumigant phosphine disrupts oxidative metabolism, resulting in the production of reactive oxygen intermediates. This causes the premature ageing and death of targeted pests. Insect pests of stored grain in Australia now exhibit resistance to phosphine at levels more than 200 times the normal lethal dose.
We have genetically mappedf and identified the genes responsible for phosphine resistance in tall major insect pests of stored grain. We are using a systems biology approach in the model organism C. elegans to understand the molecular basis of phosphine action. Our genetic studies have recently shown that resistance to phosphine is associated with an extension of lifespan
David Evans is an NHMRC Leadership Fellow and Professor of Statistical Genetics at the University of Queensland Institute for Molecular Bioscience. He is a winner of the NHMRC Marshall and Warren Award.
He completed his PhD in Statistical Genetics at the University of Queensland in 2003, before undertaking a four-year post-doctoral fellowship at the Wellcome Trust Centre for Human Genetics, University of Oxford where he worked as part of the The International HapMap Consortium and co-led the analysis of four diseases within the first Wellcome Trust Case Control Consortium. In 2007 he moved to take up a Senior Lecturer position at the University of Bristol where he led much of the genome-wide association studies work in the Avon Longitudinal Study of Parents and Children (ALSPAC). In 2013 he returned to take up a chair at the University of Queensland whilst continuing to lead an MRC Programme in statistical genetics at the University of Bristol.
His research interests include the genetic mapping of complex traits and diseases (including birthweight and other perinatal traits, osteoporosis, ankylosing spondylitis, sepsis, laterality) and the development of statistical methodologies in genetic epidemiology including approaches for gene mapping, individual risk prediction, causal modelling and dissecting the genetic architecture of complex traits. He has a particular interest in Mendelian randomization and has used it and other causal methods to investigate the Developmental Origins of Health and Disease (DOHaD)- the idea that adverse intrauterine exposures lead to increased risk of disease in later life.
He is Academic Codirector at the NIH funded International Workshop on Statistical Genetics Methods and is faculty on the European Programme in Educational Epidemiology.
He is Associate Editor at the International Journal of Epidemiology and Behavior Genetics journals.
Queensland Alliance for Agriculture and Food Innovation
Availability:
Available for supervision
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.
After completing his BSc and MSc (Hons) at the University of Canterbury (NZ), Dylan worked for five years as a Research Scientist at Antisoma Research Limited (London, UK), developing antibody-enzyme fusion proteins for cancer therapy. He returned to New Zealand to carry out his PhD research into antidepressant pharmacogenomics at the University of Otago. Afterwards, he continued working at the University of Otago as a Research Fellow, studying the biological function of genes involved with inflammatory bowel disease. Dylan moved to the United States in 2009 to perform postdoctoral training, researching the functional genetics of the VEGF-pathway and its relationship with cancer at the University of Chicago and, subsequently, the University of North Carolina, Chapel Hill.
In 2013, Dylan began working at QIMR Berghofer and has undertaken the functional follow-up of large-scale genetic studies of breast, endometrial and ovarian cancer to identify the likely causal variants and genes that mediate associations with cancer risk and survival. He has been awarded both internal and NHMRC grant funding to support these studies. Since 2019, Dylan has held an Honorary Associate Professorship at UQ
As of early 2021, Dylan has authored one conference report, two editorials, two book chapters, six reviews and 31 original research articles. He is first or last author on 20 of these publications and 27 of his publications have been cited at least 10 times. According to CiteScore, since 2010, 53% of his articles have been published in journals ranked in the top 10% and 19% of hispublications are in the 10% most cited publications worldwide.
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.
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.
Dr Hwang has published more than 40 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.
Queensland Alliance for Agriculture and Food Innovation
Availability:
Available for supervision
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 completed a PhD in Neuroscience with Jack Pettigrew (FRS) at Vision, Touch & Hearing Research Centre followed by an NHMRC Clinical Research Fellowship at Alfred Health & Monash University.
Back in QLD I'm continuing a transdisciplinary research & innovation program to Bring Discoveries of the Brain to Life!
I'm currently focused on developing novel MedTech Biotech diagnostics & therapeutics for enhancing human performance, recovery & resilience with the following projects:
[1] Precision Pain Medicine — the largest genetic study of persistent (chronic) pain in Australia, in collaboration with QIMR Berghofer & Monash University, aims to identify pharmacogenomics causal pathways for the design of personalised therapeutics & effective early intervention approaches (e.g., screening, education, prevention).
[2] Brain Switcha — A digital transdiagnostic biomarker and cloud-based large-scale population phenotyping & analytics platform to improve early intervention strategies in sleep & mental health conditions (esp. at-risk youth cohorts) and recruitment screening for Defence forces.
[3] VCS — vestibulocortical stimulation: A simple, inexpensive, non-invasive & non-pharmacologic neurotherapeutic treatment technique for fibromyalgia (with US colleagues) and other centralised pain syndromes, sleep apnoea, dementia & mental health conditions (e.g., depression, PTSD, bipolar disorder).
I also have >5 years professional services experience providing specialist research performance evaluation, consultation, reporting & training workshops that successfully delivered several major strategic priorities to a large internal & external client base — such as organisational unit leaders/managers at multiple levels (e.g., Centre/Department) and senior executive business missions for national/international strategic partnerships. This work includes mapping, monitoring & benchmarking of research capacity, capabilities/strengths, gaps & collaboration networks (e.g., clinical, corporate & government) across diverse disciplines for Annual & Septennial Departmental Reviews (e.g., patent, policy & clinical guideline citations; external stakeholder engagement including media); ARC Engagement & Impact assessments; and workforce capability development (e.g., recruitment for senior leadership positions and ranking of NHMRC/ARC funding applicants).
In particular, I enjoy meeting & connecting people with a shared vision & commitment towards building innovative & sustainable public-private partnerships to deliver meaningful solutions for the wider community.
Dr Quan Nguyen is a Group Leader at the Institute for Molecular Bioscience (IMB), The University of Queensland. He is leading the Genomics and Machine Learning (GML) lab to study neuroinflammation and cancer-immune cells at single-cell resolution and within spatial morphological tissue context. His research interest is about revealing gene and cell regulators that determine the states of the complex cancer and neuronal ecosystems. Particularly, he is interested in quantifying cellular diversity and the dynamics of cell-cell interactions within the tissues to find ways to improve cancer diagnosis or cell-type specific treatments or the immunoinflammation responses that cause neuronal disease.
Using machine learning and genomic approaches, his group are integrating single-cell spatiotemporal sequencing data with tissue imaging data to find causal links between cellular genotypes, tissue microenvironment, and disease phenotypes. GML lab is also developing experimental technologies that enable large-scale profiling of spatial gene and protein expression (spatial omics) in a range of cancer tissues (focusing on brain and skin cancer) and in mouse brain and spinal cord.
Dr Quan Nguyen completed a PhD in Bioengineering at the University of Queensland in 2013, postdoctoral training in Bioinformatics at RIKEN institute in Japan in 2015, a CSIRO Office of Chief Executive (OCE) Research Fellowship in 2016, an IMB Fellow in 2018, an Australian Research Council DECRA fellowship (2019-2021), and is currently a National Health and Medical Research Council leadership fellow (EL2). He has published in top-tier journals, including Cell, Cell Stem Cell, Nature Methods, Nature Protocols, Nature Communications, Genome Research, Genome Biology and a prize-winning paper in GigaScience. In the past three years, he has contributed to the development of x8 open-source software, x2 web applications, and x4 databases for analysis of single-cell data and spatial transcriptomics. He is looking for enthusiastic research students and research staff to join his group.
Dr Sathish Periyasamy is a Research Fellow at a Queensland Brain Institute and Senior Scientist at Queensland Centre for Mental Health Research. He is currently building and focusing on Systems/Genomic Medicine and conducting research in the interface of systems genetics and psychiatry. He is involved in studying the mechanisms of (patho-)physiological processes in psychiatric disorders using a unique combination of educational experience coupled with over twenty-five years of computer programming and eleven years of computational biology experience in biomedicine. Over the past 20 years, his experience working in chemical, biological and medical domains has enabled him to focus on the interface of basic and clinical research and contribute to translational research. From 2011 to 2014, he was involved in cancer genetics research at King Abdullah International Medical Research Centre, KSA. As the bioinformatics lead, with interdisciplinary skills and expertise at the interface of computational intelligence, systems biology, and quantitative/psychiatric genetics, He has been contributing to psychiatric genetics research since 2014 in Professor Bryan Mowry’s lab.
His current research areas include:
Bioinformatics, Systems Biology and Statistical Genetics - Developing and applying GWAS, post-GWAS bioinformatics, cross-population genetic association and systems genetics approaches.
Psychiatric Genomics
Common and rare variant association studies in schizophrenia using data generated from DNA microarray and whole-exome/whole-genome sequencing technologies.
Post-GWAS bioinformatics approaches to characterise risk variants discovered in schizophrenia GWAS.
Cross-population genetic association approaches in schizophrenia.
Computational Intelligence – Developing conventional and visible deep learning models for biomedicine.
Developing genetic resources for Indigenous Oceanic populations
My group's research uses large-scale genomic data to address knowledge gaps in disease, with a particular focus on cardiovascular disease.
Research programme
1. Cardiovascular disease research using big-data and genomics: with the goal of improving prevention and treatment of cardiovascular disease. By focusing on underrepresented groups, including women, my research aims to also address inequity in cardiovascular outcomes. I am the lead of the South Asian Genes and Health in Australia (SAGHA) study, which aims to increase representation of Australian South Asians in cardiovascular and genomics research. See saghaus.org for further details.
2. Drug genomics: I'm interested in using genomic approaches to predict drug effects, including identification of drug repurposing opportunities as well as identifying unknown adverse effects of medication.
3. Liver transplant research: In this collaboration with the QLD Liver Transplant Unit, we are using genomics to understand the effect of normo-thermic perfusion (a new organ storage method) on liver function, with the long-term goal of improving our ability to predict transplant outcomes.
Career summary: I was awarded my PhD from University College London (UK) in cardiovascular genetics. I began my post-doctoral fellowship under the mentorship of Prof Peter Visscher at the Queensland Brain Institute in 2013. Between 2016-2018, I was the lead analyst for the International Heart Failure Genetics Consortium (HERMES). In 2018, I was awarded an NHMRC Early Career Researcher Fellowship to investigate the relationship between cardiovascular and brain-related disorders using large-scale genetic and genomic data, under the mentorship of Prof Naomi Wray. I currently hold a National Heart Foundation Future Leader Fellowship.
Recognition:
2024 Australian Academy of Science Ruth Stephens Gani Medal for outstanding contribution to genetics research
2023 1 of 5 global finalists for the Nature Inspiring Women in Science (Scientific Achievement Award)
2023 Lifesciences QLD Rose-Anne Kelso Award
2023: Named in Australia's Top 25 Women in Science by Newscorp
2022 Queensland Young Tall Poppy Award
2022 UQ Foundation Research Excellence Award
2021/2022 Australian Superstar of STEM,
2020 Genetic Society of Australasia Early Career Award
2020 Women in Technology Rising Star Science Award
Dr Nicole Warrington is a NHMRC Emerging Leadership Fellow at the University of Queensland Institute for Molecular Bioscience. She has a strong background in statistical genetics and has been actively working towards understanding the genetic determinants of early life growth. Dr Warrington studied a Bachelor of Science at Victoria University in Wellington, New Zealand, majoring in Mathematical Statistics and Psychology. She then completed an honours degree at The University of Western Australia, where she developed a keen interest for genetics, and was subsequently awarded an Australian Postgraduate Award to complete her PhD in statistical genetics and life-course epidemiology. During her PhD she spent time at the University of Toronto to gain experience in statistical modelling methods for longitudinal growth trajectories and conducted the first genome-wide association study of longitudinal growth trajectories over childhood. After completing her PhD, Dr Warrington started at the University of Queensland and focused on using genetics to inform about the relationship between birth weight and cardio-metabolic diseases in later life. She pioneered a new statistical method to partition genetic effects on birth weight into maternal and fetal components, and combined this method with a causal modelling approach, Mendelian randomization. This method was instrumental in demonstrating the relationship between birth weight and adult hypertension is driven by genetic effects, over-turning 30 years of research into the effects of intrauterine programming. More recently, her research focus has broadened to determine whether rapid weight growth across early life, including fetal development, childhood and adolescence, causally increases risk of cardio-metabolic disease and in doing so, hopes to identify optimal times across the life-course where interventions could reduce the incidence of cardio-metabolic diseases.
Dr Jian Zeng is a statistical geneticist and NHMRC Emerging Leadership Fellow at the Institute for Molecular Bioscience (IMB) at the University of Queensland (UQ). He received his PhD in animal breeding and genetics at Iowa State University and joined the Program in Complex Trait Genomics (PCTG) at UQ in 2016. His research focuses on the development and application of innovative statistical methods for estimating the genetic architecture and evolutionary signals in complex traits, identifying genetic variants, genes and other molecular intermediates associated with phenotype variation, and predicting trait phenotypes using genome sequence data. In 2019, he was awarded an NHMRC Investigator Emerging Leadership Grant to develop statistical methods and software tools for best predict an individual’s disease risk using genomic and omics data. He was an invited speaker at the prestigious Gordon Research Conference in 2019.
