Management Committee
Professor Mark Ragan (Chair), Institute for Molecular Biology
Dr David Hansen, e-Health Research Centre, CSIRO
Elizabeth Shannon, Tourism, Regional Development and Industry Department, Queensland Government
Professor Gillian Bushell, Griffith University
Associate Professor James Hogan, QUT
Dr Ralf G.Dietzgen, Qld Department of Primary Industries and Fisheries
Jeremy Barker, CEO, QFAB
Executive Management
Jeremy Barker, CEO
Dr Dominique Gorse, Technical Manager
Operational Team
Matthew Bryant
Pierre-Alain Chaumeil
Melissa Davis
Mhairi Marshall
Amanda Miotto
Nick Rhodes
Cas Simons
David Wood
Professor Mark Ragan, IMB
Mark Ragan is founding head of the Division of Genomics and Computational Biology at the Institute for Molecular Bioscience of The University of Queensland, a Professor in UQ's School of Information Technology and Electrical Engineering, and Director of the Australian Research Council Centre of Excellence in Bioinformatics. He co-chaired ISMB-2003 and was General Chair of APBC 2003 and GIW 2008. Mark is a Fellow of the Linnean Society of London, and serves on six editorial board and seven management and advisory boards in molecular bioscience, informatics and e-research. Before coming to Australia in 2000 he was a Fellow of the Canadian Institute for Advanced Research, co-chief Investigator on the first Canadian whole genome-sequencing project, co-founder and host of the Canadian Bioinformatics Resource, and an active participant in Genome Canada and Genome Atlantic. He has more than 160 peer-reviewed publications and research interests that include comparative, computational and evolutionary genomics, high-throughput bioinformatics, high-performance computing, and technologies for management and integration of large datasets.
David Hansen
David is the Theme Leader for e-Health and a Principal Research Scientist at the CSIRO Australian e-Health Research Centre. The e-Health theme aims to create new ICT-based technologies that can securely and seamlessly acquire, manipulate, interpret and present data relevant to healthcare professionals, from a variety of sources. Research projects in this theme are in the areas of biomedical imaging, remote monitoring, health data integration and clinical terminologies. Prior to this, David was the Development Manager for SRS at LION Bioscience, Ltd in Cambridge, UK. SRS is the leading genomic data and tool integration software, and is used by pharmaceutical and biotechnology companies, such as Glaxo Kline-Smith, Celera and Affymetrix, as well as academic institutes, such as The European Bioinformatics Institute. Before joining LION, David did a Bachelor of Science at the University of Queensland in Chemistry and Computer Science and then a PhD (Theoretical Chemistry) at the Australian National University.
Elizabeth Shannon
Professor Gillian Bushell, Griffith University
Professor Gillian Bushell is the Dean of the Faculty of Science at Griffith University and a member of the cell biology program and the Eskitis Institute for Cell and Molecular Therapies. Gillian has many years experience in cell and molecular biology, having worked on a variety of projects, including malaria vaccines, connective tissue disorders, and cell signalling processes. Gillian's current research interests include the development of biosensors, molecular modeling, novel methods of drug delivery, and the role of Sin 1 in cell signalling processes.
Associate Professor James Hogan, QUT
James Hogan is a senior lecturer in the School of Software Engineering and Data Communications at QUT. His research interests are centred upon machine learning and its application to cognitive science and bioinformatics problems, with subsidiary interests in software engineering. In particular, his work is concerned with learning in visual domains with associated text, in the tradition of the Berkeley L0 project. His most significant contribution in this area is a connectionist synthesis of bottom-up and top-down attentional systems as a model of spatial relations acquisition and processing. Additional contributions in the field of visual processing have centred on the classification of facial expressions through the use of novel neural network receptive fields - and subsequently within the support vector machine framework. Within the pure textprocessing domain, Dr. Hogan is active in the development of a Hidden Markov Model approach to authorship attribution, with conceptually related work in the use of novel kernels for the identification of promoter motifs with bacterial genomes. More recently, he has taken a leading role in the development of software internationalisation work within Australia.
Dr Ralf G.Dietzgen, Qld Department of Primary Industries and Fisheries
Dr Ralf G. Dietzgen is Science Leader, Molecular Bioscience Technologies, in the Emerging Technologies R&D Delivery unit of the Queensland Department of Primary Industries and Fisheries (DPI&F). Ralf also holds an adjunct appointment as Associate Professor with the University of Queensland's School of Molecular and Microbial Sciences. He obtained his PhD in Microbiology from the University of Tuebingen, Germany and worked at the University of Cambridge, Cornell University, University of California at Berkeley and Davis and the University of Adelaide before joining DPI&F. His research interests are in gene discovery and biodiversity in viruses, plants and insects and he has published extensively on plant virus characterisation and genetic variability, diagnostic technologies and RNAi- mediated virus resistance.
Jeremy Barker, CEO
Jeremy Barker has a track record of establishing or growing a number of organisations in the life sciences sector including his own management consultancy. He took a leading role in establishing the Australian Genome Research Facility Ltd, including it's specialist bioinformatics service, and is a director and shareholder in ESPDATA Pty Ltd, which provides pre-clinical and clinical trials capability. As Chief Operating Officer at AGRF Ltd he was responsible for all corporate affairs activity covering operational, financial, legal and commercialisation activities.
Mr Barker holds postgraduate science and commercial qualifications, is a Member of the Australian Institute of Company Directors and a Fellow of the Australian Institute of Management. He has been actively involved as member and Chair of the Queensland Branch of AusBiotech Ltd, the peak body for Australian Biotechnology, and is currently the deputy chair of the Queensland Branch of Chartered Secretaries Australia, the governance professional's institute.
Dr Dominique Gorse, Technical Manager
Dominique Gorse is Technical Manager at QFAB since June 2007. In this role, he is leading the development of QFAB’s platform for integrated and accessible bioinformatics which is designed to support large multi-institution research projects. Dominique has over 18 years' experience in software development, information management, data mining and data modelling applied to life science applications. Prior to joining QFAB, Dominique was Head of informatics & computational chemistry with Bio-Layer where he designed and developed a full hardware and software system for collection, management, search and tracking of experimental data, including molecular structures, biological and analytical data. From 1997 to 2001, Dominique was team leader at Synt:em, a French biopharmaceutical company focused on the discovery of drug candidates for Central Nervous System diseases. He led the development of Synt:em proprietary software, Diverser, specifically design for molecular diversity analysis and compound library design in the context of Combinatorial Chemistry and High-Throughput Screening. Prior Synt:em, Dominique Gorse was ARC Postdoctoral Research Fellow at the Department of Biochemistry of the University of Sydney and then at the John Curtin School of Medical Research in Canberra. During these two years, he developed a computation method based on molecular dynamics simulations to determine binding mode and free energy of binding of potential inhibitors of the dihydrofolate reductase. Dominique received his Ph.D. in computational chemistry from the University of Bordeaux, France in 1993 where he developed a computer program for the interactive study and visualisation of molecular systems in interactions.
Matthew Bryant
Matthew Bryant has worked for the University of Queensland in Brisbane for over 6 years in a high performance computing environment, supplying expertise in computing and storage solutions utilizing the latest in storage and processing technology. This includes resources such as large SMP machines, distributed clusters, SAN storage, backup and virtualization solutions. Before this, Matthew worked with Williams Lea in London, programming a personnel information system to facilitate employee interactions from geographically dispersed offices. Matthew used his Perl, Linux, Apache and C skills to deploy a flexible system that meet the employee's needs. Prior to this Matthew worked for over 6 years as a Senior System Engineer for GBST in Brisbane where he worked on stockbrokers’ sites to plan, install and manage high availability systems and networks responsible for 40% of all trades on the Australian Stock Market. Matthew also participated in, then managed the central support team to maintain these system on a 24/7 basis. Matthew has a Bachelor of Electrical Engineering specializing in Computer Systems from the University of Queensland.
Pierre-Alain Chaumeil
Pierre-Alain Chaumeil is a recent graduate from the University of Bordeaux (France) with a Bachelor of Science majoring in Biology of Organisms and a Master’s degree in Bioinformatics. He has programming skills in different languages such as Java, Perl, Eiffel, C/C++ and Python. Pierre-Alain is currently working on the development of QFAB’s Systems Biology Platform to provide Australian researchers in R&D organisations and industry with direct, scalable access to the most internationally comprehensive, expert-curated and integrated genomic, proteomic and metabolic datasets available, and to industry-standard tools for data integration, analysis, visualisation and electronic collaboration.
Melissa Davis
Melissa is currently a Data Modeller with the Queensland Facility for Advanced Bioinformatics, where she is developing systems biology and bioinformatics research projects in pathway and network analysis of molecular interaction networks that are separately implicated in breast cancer and childhood obesity. This work is particularly interesting due to the challenges of integrating experimental results with biomolecular networks to add value to both bioinformatic and experimental analyses. Previously, Melissa held a post-doctoral research appointment in ARC Center of Excellence in Bioinformatics at the Institute for Molecular Bioscience, where she developed a number of projects both in ontological engineering and network analysis. Prior to her research appointments, Melissa worked as a knowledge management consultant for a Brisbane-based management company and as a consultant for a Canberra based systems engineering company where she provided specialist consulting services in the areas of knowledge management, ontological engineering, systems biology and biotechnology. Her research interests include, but are not limited to: Systems biology, specifically of the nuclear receptor super-family of transcription factors, and the application of bioinformatics to experimental and translational research. Melissa holds a PhD in Computational and Molecular Biology, and a BSc majoring in genetics, both from the University of Queensland.
Mhairi Marshall
Mhairi Marshall worked for five years as a bioinformatician at the Sanger Institute, Cambridge UK where she was the web and database administrator for the Pfam, Rfam & miRNA registry websites. Before that she worked for three years as a website administrator at the University of Newcastle-upon-Tyne Medical School. Mhairi has extensive programming experience in Perl, Java, JSP, PHP and has administered both MySQl and Oracle databases. Mhairi has an honours degree in Molecular Biology and a Masters degree in Information Technology from the University of Glasgow, UK.
Amanda Miotto
Amanda Miotto has recently graduated from the University of Southern Queensland with a Bachelor of Science majoring in Bioinformatics. She is currently situated at Griffith University working for the Research Computing Services and for the National Centre for Adult Stem Cell Research of the Eskitis Institute for Cell and Molecular Therapies. Amanda current focus is on managing the Griffith mirror of UCSC genome browser.
Nick Rhodes
Nick Rhodes has worked in the application of computer-based techniques to scientific problems for nearly thirty years. An Oracle-certified Database Administrator, he worked as DBA and SysAdmin to Bio-Layer Pty Ltd before joining QFAB. Prior to this he taught on the world’s first MSc in Chemoinformatics in the Department of Information Studies at the University of Sheffield, and as an Oracle DBA in the same department. Nick has extensive experience programming in a variety of languages (most recently SQL, C++ and Python) and a particular interest in data mining and data warehouses.
Cas Simons
Cas Simons has over six years experience in bioinformatics and molecular biology research. His current role in QFAB focuses on working with QFAB collaborators and clients to develop bioinformatic solutions to maximise the outcomes of their research. He has experience using a wide range of bioinformatic tools and techniques including extensive programming experience in Python and SQL. Cas also has molecular biology wet-lab experience working with a variety of model organisms including yeast, plants, cyanobacteria and zebrafish. Cas received his PhD in genomics and computational biology from the University of Queensland and has an honours degree in biochemistry from the University of Otago.
David Wood
David has over six years bioinformatic experience working for a variety of groups, including the Australian Genome Research Facility (AGRF) and the ARC Centre of Excellence in Bioinformatics (ACB). His current role in QFAB focuses on the development and management of high quality bioinformatic software systems. David has experience working in close collaboration with research and laboratory scientists, in both high throughput production environments and smaller research focused information and knowledge discovery and dissemination. At QFAB David also specialises in data integration techniques, including view integration using shared data models, deep integration using databases, middleware software services and biological discovery and analysis pipelines. He has a broad knowledge of and interest in molecular biology and bioinformatics techniques and couples this with robust industry best practice software engineering approaches. David has university undergraduate qualifications in computer science and genetics, and honours in computational biology from the Australian National University (ANU).