Chief Investigators

Chief Investigators

Dr Timothy L. Bailey, The University of Queensland
Dr Timothy Bailey has been active in bioinformatics and computational biology since the early 1990s, and since 2004 he has been a senior research fellow at the Institute for Molecular Bioscience. He is well-known as an expert in pattern recognition in biological sequences, and as the author of several important bioinformatics software programs, most notably MEME, one of the most heavily used tools in sequence analysis. The sequence analysis tools included in the MEME Suite are currently used by thousands of biologists each month. Tim's research applies state-of-the-art modeling approaches to understanding how the genome controls the development and functioning of cells and organsisms. His current focus is on deciphering how the cell controls the transcription of genes. To achieve this, he is developing detailed models of the interactions of transcription factors and chromatin marks (non-mutational chemical modifications of genes) to regulate gene transcription.

Professor Kevin Burrage
Professor Kevin Burrage founded Queensland Parallel Supercomputer Foundation (now Queensland Cyber Infrastructure Foundation), the Advanced Computational Modelling Centre, and the ViSAC visualisation laboratory at UQ. During 2004-2005 he was Oliver Smithies Fellow at Balliol College, Oxford, and in 2007 accepted a joint appointment as Professor of Computational Systems Biology at Oxford. He has co-authored 180 papers, two patents, and one monograph in systems biology, computational mathematics and mathematical modeling. His work has appeared in Nature Genetics, PNAS, Molecular and Cellular Biology, BMC Bioinformatics, Progress in Biophysics and Molecular Biology, Proteins, and Biophysical Journal. He co-authored the first modeling and simulation paper to appear in Molecular and Cellular Biology. In 2009 Kevin moved his primary affiliation from UQ to Queensland University of Technology, where he is Professor of Mathematics.

Professor Yi-Ping Phoebe Chen, La Trobe University
Professor Yi-Ping Phoebe Chen is Professor and Chair of Computer Science and Computer Engineering at La Trobe University, Melbourne. She has co-authored 150 papers in bioinformatics, multimedia, data mining and knowledge discovery. Her work has appeared in Nucleic Acids Research, BMC Genomics, BMC Bioinformatics, Current Drug Metabolism, Data Mining and Knowledge Discovery, IEEE Transactions on Knowledge and Data Engineering, Information Systems, IEEE Multimedia and ACM Transactions. Phoebe founded and continues to play an active role as steering committee chair of the annual Asia Pacific Bioinformatics Conference.

Professor Mike Fellows, The University of Newcastle
Professor Mike Fellows is internationally recognised for his foundational work on parameterised complexity, for which he and collaborator Prof. Rod Downey (Victoria University, New Zealand) were nominated for the Gödel Prize in 2005. They co-authored the foundational papers and the first comprehensive monograph for the field, now considered one of the main branches of theoretical computer science concerned with algorithms and complexity. For more than a decade, this area has had strong applications in bioinformatics and computational biology. Mike is also recognised for significant contributions to cryptography, algebraic graph theory, computational social choice and popular communication of the mathematical sciences. He was a recipient in 2006 of an Alexander von Humboldt Research Award, and in 2007 of an Inaugural Fellowship to the Durham University Institute for Advanced Studies, UK. He is an Associate Editor of Journal of Computer and System Sciences, and of ACM Transactions on Algorithms. In 2010 he will step down as a Chief Investigator in ACT to begin a five-year appointment as an ARC Professorial Fellow.

Dr Markus Hegland, The Australian National University
Dr Markus Hegland is a member of the Computational Mathematics Program at the ANU's Centre for Mathematics and Its Applications. He is known internationally for his work on ill-posed problems, parallel solution of linear systems of equations and fast Fourier transforms and, most recently, in high-dimensional approximation. He has pioneered the application of numerical techniques, in particular sparse grids in data mining applications. He has also developed chemical master equation solvers which have been shown to work for up to 100 different chemical species. He was co-initiator of the Australasian Data Mining Conference and of the High-Dimensional Approximation Workshop, which annually attract some of the most prominent researchers of the field world-wide to Australia.

Professor Geoffrey J. McLachlan, The University of Queensland
Professor Geoff McLachlan is internationally known for his research in statistics applied in the fields of classification, cluster and discriminant analysis, image analysis, intelligent systems, machine learning, neural networks, pattern recognition, and statistical inference. The focus in the latter has been on the theory and applications of finite mixture models, and on estimation via the EM (expectation-maximisation) algorithm. A common theme has been statistical computation, with particular attention to computational aspects of statistical methodology. This computational theme extends to the field of data mining. In 1994, he was awarded a Doctor of Science by the University of Queensland for his research contributions in these areas. More recently, Geoff has been actively involved in bioinformatics, focussing on the statistical analysis of microarray gene expression data. A joint Wiley monograph on the analysis of microarray data was published in 2004. In 2006 he was awarded a Professorial Research Fellowship for the period 2007-2011 by the Australian Research Council, and in 2007 was appointed to the ARC College of Experts. He is also a Fellow of the American Statistical Association, the Australian Mathematical Society, and the Royal Statistical Society, and is the current President (2010-2011) of the International Federation of Classification Societies. He is an associate editor of several journals in statistics and bioinformatics, including Biology Direct and BMC Bioinformatics.

Dr Brad J. Marsh, The University of Queensland
Research in Dr Brad Marsh's group at the Institute for Molecular Bioscience is centered on high-resolution 3D structure-function studies of mammalian cells, with a particular focus on the insulin-secreting beta cells of the pancreas. Brad is recognised internationally for his group's pioneering work developing novel approaches for 3D imaging and detailed computational analysis of large cellular volumes by electron tomography (ET) to map the spatial/structural organisation of beta cells at the nanometer scale in 3D. His work has been featured on the covers of Proceedings of the National Academy of Sciences USA, Proceedings of Microscopy & Microanalysis, Materials Today, Traffic, BBA Molecular Cell Research, Nucleic Acids Research and the Journal of Structural Biology, and has been highlighted in high-impact publications including La Recherche, Nature Reviews Molecular Cell Biology, Journal of Cell Biology, Current Opinion in Structural Biology, Current Opinion in Cell Biology, Molecular Cell Biology 5th Edition, Essential Cell Biology 2nd Edition, Genome Biology, Australian Life Scientist, Nature Chemical Biology and the 150th anniversary edition of Gray’s Anatomy. His inaugural PNAS article (2001) has been lauded as a landmark by seminal leaders across a range of disciplines including structural biology, microscopy, chemistry, molecular biology, cell biology, diabetes research, and systems biology. He recently played a major role drafting a 'position' paper on the current state of Golgi research [Emr et al. (2009) Journal of Cell Biology] and has just completed a book chapter for a new series in Systems Biology (to be published by Springer). Early this year, Dr Marsh was selected as an expert in 'Beta Cell Therapies & Bioimaging in Diabetes Research' and invited by the CEO of the Juvenile Diabetes Research Foundation (JDRF) to contribute to the development of a "National Type 1 Diabetes Agenda" policy document, which will serve as a framework for guiding future initiatives in Type 1 diabetes research in Australia for key government authorities and funding bodies (to be officially launched at a special sitting of the Australian Federal Parliament on March 18, 2010).

Professor John S. Mattick, The University of Queensland
Prof. John Mattick stepped down as Director of the Institute for Molecular Bioscience at the end of 2005 to take up an ARC Federation Fellowship, after serving as Foundation Co-Director (together with Prof. Peter Andrews) from 2000-2002, and as Director from 2003-2005. He was Foundation Director of the Centre for Molecular and Cellular Biology (previously the Centre for Molecular Biology and Biotechnology) from 1988-1999, Foundation Director of the Australian Genome Research Facility from 1996-2002, and Foundation Director of the ARC Special Research Centre for Functional and Applied Genomics from 2000-2002. His main research interest is the role of non-protein-coding RNA in the evolution and development of humans and other complex organisms. He has been awarded the Pharmacia-LKB Biotechnology Medal from the Australian Biochemical Society, an Honorary Fellowship of the Royal College of Pathologists of Australasia, the Centenary Medal by the Australian Government, the CSIRO Eureka Prize for Leadership in Science and the Julian Wells Medal of the Lorne Genome Society. He was appointed an Officer in the Order of Australia (AO) in 2001 for service to molecular biology and biotechnology, and elected as an Associate Member of the European Molecular Biology Organisation in 2007 and a Fellow of The Australian Academy of Science in 2008. Prof. Mattick serves on the advisory boards of several institutes in Australia and abroad, and on editorial boards of Bioessays, Genome Research, PLoS Computational Biology, Genomic Medicine, and RNA Biology.

Professor Pablo Moscato, The University of Newcastle
Professor Pablo Moscato is Co-Director and Founder of the Priority Research Centre for Bioinformatics, Biomarker Discovery and Information-based Medicine of The University of Newcastle, Australia. He also founded the Newcastle Bioinformatics Initiative in 2002. He is also one of the four members of the Strategic Research Advisory Panel of the Hunter Medical Research Institute. He is founding member of the Australian-New Zealand Multiple Sclerosis Genetic Consortium and the Pharmacogenomics Research for Individualised Medicine Consortium, and a Chief Investigator of the Australian Stroke Genetics Collaborative.

Pablo is a pioneer in the introduction of metaheuristic methods in high-performance computation and his applications. He introduced memetic algorithms in 1989 when he was a member of the Caltech Concurrent Computation Program, and has championed this field for two decades. He is a member of the editorial boards of Journal of Mathematical Modelling and Algorithms, Journal of Heuristics, and in 2008 Memetic Computing. He has shown how successful the application of these hybrid computing methodologies to large-scale problems in combinatorial optimization and bioinformatics can be. Pablo has served on program committees of numerous international conferences in bioinformatics, heuristics and optimisation and is currently leading research programs in data analysis from high-throughput technologies as applied to the study of samples from Alzheimer disease, multiple sclerosis, age-related macular degeneration, melanoma, and breast and prostate cancer.

Professor Mark Ragan (Director), The University of Queensland
Professor Mark Ragan joined IMB in 2000 after 28 years with National Research Council Canada, where he co-founded and developed programs in bioactive compounds, molecular biology, genomics and bioinformatics, including Canadian Bioinformatics Resource. With Prof. W. Ford Doolittle and Dr Robert Charlebois he received the largest single grant under the first Canadian genome program (CGAT) and sequenced Sulfolobus solfataricus. Since 2000, Mark has been actively involved in Australian bioinformatics including community-building, research, partnerships among institutions and across sectors, advanced training, awareness-raising with state and national government bodies, international partnerships and national infrastructure. He has served as Chair of the Executive group of the Association of Asian Societies of Bioinformatics (2008), and is a member of the Committee on Global Collaborations, European Life Sciences Infrastructure for Biological Information (ELIXIR) and the Steering Committee of Australian National Data Service. Under the overall theme of comparative and computational genomics, research in his group includes projects on the inference, cellular localisation and analysis of biomolecular-interaction networks, and applications of advanced bioinformatic and semantic web technologies to large-scale biomolecular, chemical and structural data especially in complex disease. His 150-plus peer-reviewed publications have attracted more than 4000 citations.

Professor Shoba Ranganathan, Macquarie University
Professor Shoba Ranganathan holds the first Chair in Bioinformatics in Australia, at Macquarie University. She holds an Adjunct Professor position at the National University of Singapore (since 2004). Her research interests include genome annotation, transcriptome analysis, structural bioinformatics, immunoinformatics and genome-phenome analysis. Shoba’s achievements include the development of graph-theoretical methods for alternative splicing analysis, a rapid and accurate docking protocol for vaccine design, software tools for the analysis of protein sequence and for modelling protein structure, and the development of boutique databases. She pursues collaborations with research groups at the National University of Singapore and the Institute for Infocomm Research, Singapore. Shoba serves on the editorial boards of several bioinformatics journals including Briefings in Bioinformatics and BMC Bioinformatics, and contributes to the organisation and scientific program of several international bioinformatics conferences. She was re-elected as President of the Asia-Pacific Bioinformatics Network (2008-2011).

Dr Rohan D. Teasdale, The University of Queensland
Associate Professor Rohan Teasdale holds a Senior Research Fellowship A from the National Health & Medical Research Council. He leads a multidisciplinary research group at IMB that applies both cellular and computational techniques to investigate how subcellular compartments are generated and how proteins are trafficked within the mammalian cell. Rohan played a key role in the formation of Bioinformatics Australia and is a member of its steering committee. Rohan is author of 65 research publications, many in high-profile and leading bioinformatics and cell biology journals. These publications have focused on how individual proteins are compartmentalized within the cell and defining the protein trafficking machinery responsible for this process. In addition he has numerous publications outlining novel bioinformatics methodologies, database resources and collaborative projects.

Professor Xiaofang Zhou, The University of Queensland
Xiaofang Zhou, Professor of Computer Science at UQ, is Research Director of ARC Research Network in Enterprise Information Infrastructure, and an Investigator in the DART e-research middleware project funded by DEST. His research focuses on effective solutions to managing, integrating and analysing very large amounts of complex data. Professor Zhou’s research interests include scientific, spatial and multimedia databases, data mining, bioinformatics, high-performance query processing, information systems interoperability, Web information systems, and e-research. He has 100+ research papers, many in leading venues including ACM Transactions on Database Systems, IEEE Transactions on Data and Knowledge Engineering, VLDB Journal, SIGMOD, and ICDE.

Partner Investigators

Professor Michael A. Langston, The University of Tennessee
Professor Mike Langston's research interests include computational biology, graph theory, discrete optimization and high-performance computation. He is currently Professor of Electrical Engineering and Computer Science at the University of Tennessee, and Collaborating Scientist in the Biosciences Division at Oak Ridge National Laboratory. Mike is lead investigator on a variety of research projects focused on the design and synthesis of combinatorial algorithms used to process high-throughput biological data. His collaborations extend across the US and to research groups in Australia, Canada, Europe and the Middle East. He has worked closely for over twenty years with Professor Mike Fellows, and has authored over 200 refereed journal articles, conference papers, book chapters and other reports. Beginning in 2007, Mike led the development of the Bertinoro Systems Biology series of workshops. His work has been funded in the US by the National Science Foundation, the National Institutes of Health, the Department of Defence and the Department of Energy, and internationally by the Australian Research Council and the European Commission.

Dr Isidore Rigoutsos, IBM Thomas J. Watson Research Center
Dr Isidore Rigoutsos manages the Bioinformatics and Pattern Discovery group at IBM's Thomas J. Watson Research Center, and has been a visiting lecturer at MIT since 2000, where he teaches a Spring semester course and a Summer professional class in bioinformatics. Isidore is a Fulbright Scholar, and in 2003 was elected a Fellow of the American Institute for Medical and Biological Engineering. He serves on editorial boards of several journals in bioinformatics, and is a member of the Advisory Board for the Master's program in bioinformatics of Oxford University. He recently edited a two-volume book on Systems Biology (Oxford University Press, September 2006). His research activities currently focus on the computational study of RNA interference (RNAi) and its application to regenerative medicine and therapy, the study of cancer as a disruption of normal regulatory processes, the analysis of "junk" DNA in animal and plant genomes, and meta-phylogenomics. In early 2010 Isidore took up a Professorship in the Department of Pathology at Jefferson Medical College, Philadelphia, and in the university’s Kimmel Cancer Center.

Professor Allen Rodrigo The University of Auckland (Affiliation National Evolutionary Synthesis Center (NESCent), and Duke University, USA)
Professor Allen Rodrigo FRSNZ is the Director of the US National Evolutionary Synthesis Center and Professor of Biology at Duke University, and an Adjunct Professor at the University of Auckland. He is author of over 90 international publications on bioinformatics and computational biology, phylogenetics, and evolutionary genetics, and the molecular evolution of viruses. Allen was founding Director of Bioinformatics Institute New Zealand, and is an Associate Editor of Evolutionary Bioinformatics and on the Editorial Board of Mathematical Biosciences. He also sits on the Scientific Advisory Board of two bioinformatics companies, and is involved numerous international collaborative projects on genomics and bioinformatics. His major research contributions are in the area of virus evolutionary genetics, where he has spearheaded the development of new methods to analyse time-series genetic data from viral populations.