Biomolecular Frontiers Research Centre
People
Management committee
Professor Nicki Packer (Director)
BSc, PhD (Syd)
Formerly Executive Vice President of the biotechnology company Proteome Systems, Nicki was part of the team that set up the Australian Proteome Analysis Facility at Macquarie. She is a senior editor of Proteomics and holds several patents in glycobiology.
Research interests: The post-translational modification of proteins by sugars (glycomics). This encompasses the role of glycosylation in many systems including the innate immune system, cancer glycomics and improved techniques for analysis of glycoproteins.
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Professor Ian Paulsen (Deputy Director)
BSc (Hons), PhD (Monash)
An expert in genomics, Ian worked for several years as an investigator for the Institute for Genomic Research in the US, where he led the sequencing of many microbial genomes. He is an ISI Highly Cited Researcher and holds a NSW Life Science Research Award at Macquarie. Ian is currently using genome sequencing, metagenomics and functional genomics to understand how lateral gene transfer in bacteria enables them to adapt to different environmental niches Research interests: Understanding microbial physiology and evolution through global approaches such as genome sequencing, metagenomics, bioinformatics, transcriptomics and proteomics.
Research interests: Understanding microbial physiology and evolution through global approaches such as genome sequencing, metagenomics, bioinformatics, transcriptomics and proteomics.
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Professor Mark Baker
BSc (Hons), PhD (Macquarie)
Mark has many years' experience managing research programs in academic, industrial and clinical cancer discovery. At Macquarie his team focuses on molecular cell proteomics. An advocate for the commercialisation of Australian biotechnology, he is Chair of the HUPO Nominations Committee.
Research interests: Advanced proteomic technologies, cancer metastasis and how proteases (their receptors, partners and inhibitors) regulate biological processes.
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Emeritus Professor Peter Bergquist
MSc (Hons), PhD, DSc (Auckland)
Peter is regarded as an international authority on the cloning and high-level expression of genes coding for enzymes useful to industry. His pioneering work includes developing novel methods for enzyme evolution, and using them to modify thermophile enzymes for improved performance in biofuels research and oil and gas recovery.
He has published extensively on the diversity of culturable and unculturable thermophilic bacteria, and chairs the Ramaciotti Gene Function Analysis Management Committee.
Research interests: The high-level expression of industrially-useful enzymes in fungal hosts, and rapid methods for the field detection of environmental pathogens using isothermal nucleic acids amplification.
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Professor Bill Hancock
An expert in clinical proteomics, Bill has worked as a principal scientist at Hewlett Packard Laboratories, and is a former Vice President of Proteomics at ThermoFisher. He was President of the California Separation Science Society for 10 years and is Editor-in-Chief of the Journal of Proteomic Research.
His honours include the Martin Gold Medal in Separation Science (British Chromatographic Society) and the ACS Award in Chromatography.
Research interests: Disease mechanisms; the discovery of potential therapeutic agents by lectin enrichment and proteomic analysis of biological fluids and tissue samples.
Professor Paul Haynes
BAppScs (UTS), PhD (Macquarie)
Before joining Macquarie, Paul pursued a research career in the US, including working at the Rockefeller University in New York, and as Associate Professor at the University of Arizona. In 2006 he took up a New South Wales Government Biofirst Fellowship.
He has published 55 scientific papers, is a senior editor for Proteomics, and has four issued patents.
Research interests: Environmental proteomics; applying protein identification and characterisation by mass spectrometry to solve problems in plant biology. Recent projects include: molecular analysis of hot and cold temperature stress in rice plants; heavy metal stress on Sydney rock oysters and amphipods; geographical adaptation to environmental stresses in Pachycladon, an endemic New Zealand plant.
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A/Professor Mark Molloy
BSc (Hons), PhD (Biochemistry) (Macquarie)
Mark is a biochemist with 14 years' experience in proteomics. He completed his post-doctoral training at the University of Michigan Medical School. Later he worked in the proteomics R & D group at Pfizer, leading a team to identify biomarkers of new drug entities.
He is currently Director of the Australian Proteome Analysis Facility.
Research interests: Using proteomic technologies for cancer research. This research sits at the interface of biochemistry/cell biology/analytical chemistry/clinical chemistry. The group uses quantitative mass spectrometry and other bioanalytical techniques including electrophoresis and chromatography.
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Professor Helena Nevalainen
BSc (Genetics), MSc (Genetics), PhD (Genetics) (Helsinki)
Helena is an experienced research manager, and has worked in the biotechnology industry on strain and product development. She has also researched for multinational biotech companies in the US and Finland.
A member of the Academy of Finland as an expert in fungal biotechnology, she has published over 120 papers in refereed journals.
Research interests: Molecular biology and the enzymology of biotechnologically important filamentous fungi. This includes biological control mediated by fungi, fungal proteomics and molecular prospecting of the environment for novel bioactivities and valuable gene products.
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Members
Dr Sinan Ali
Research interests: Understanding the functioning of the pituitary-adrenal cortical axis.
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A/Professor Brian Atwell
Research interests: Cell responses to abiotic factors, using molecular and proteomic techniques to identify key changes when rice plants are chilled, heated or deprived of oxygen.
The effects of elevated CO2 on plant function. In particular, using classical plant physiology to define the experimental conditions under which stress is assessed at the gene level.
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Dr Louise Brown
BMedSci (Hons), PhD (Syd)
Research interests: Using biophysical spectroscopy techniques to determine the structure of proteins. Conformational changes that accompany the function of proteins. The main technique involves spectroscopic probes or labels that can report on the local environment of the protein.
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Professor Michael Gillings
BA, BSc (Hons), PhD (Macquarie)
Seven of his recent publications have been listed as 'must read' or 'recommended' on the Faculty of 1000 website.
Research interests: The exploration of genetic diversity in a range of organisms. Current projects investigate lateral gene transfer in bacteria, population structure in freshwater fish and sharks, and molecular prospecting as a means of recovering novel genes and gene products.
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Professor Ewa Goldys
Ewa's expertise spans the fields of biophotonics, optical characterisation, ultrasensitive detection of analytes, biosensing and bioimaging. She has also developed advanced methods of synthesis and characterisation of fluorescent nanoparticles for applications in fluorescence labelling. Her current research draws on her achievements in materials science and ultrasensitive optical characterisation.
Research interests: The interface of materials science, photonics and biotechnology; optical characterisation, ultrasensitive detection of analytes, biosensing, bioimaging; materials synthesis and characterisation and cathodoluminescence.
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A/Professor Ben Herbert
Protein separation technologies
Recipient of MQ Vice-Chancellor's Innovation Fellowship
Dr Fei Liu
BSc (John Carroll), PhD (Organic chemistry) (Yale)
Research interests: The development of catalytic and stereo-selective reactions for efficient generation of useful small molecules as synthetic building blocks or biological probes. This aids in the understanding of phenotypic variation for studying cancer or antibiotic resistance.
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A/Professor Bridget Mabbutt
BSc (Chemistry)(Hons), PhD (Chemistry) (Syd)
Research interests: Solving the three-dimensional structures of bio-molecules; the recombinant expression of these molecules, and their function and structure.
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Dr Sham Nair
Research Interests: Host-pathogen interactions in invertebrates from genomic and molecular perspectives.
Current projects: Investigating the generation of diversity in the 185/333 gene family in echinoderms; evolution of immune gene families in deuterostomes from a comparative genomics perspective; molecular basis of re-infection immunity in insects; and the effects of biotic and abiotic stressors on immune reactivity in marine invertebrate.
A/Professor James Rabeau
BSC (Hons) (Waterloo), PhD (Physics) (Heriot-Watt)
An Australian Research Council Future Fellow, James worked at DALSA, a CCD and CMOS image sensor and camera company, before completing his PhD. As a research fellow at the University of Melbourne, he developed a technique to grow diamonds on optical fibres. He has spoken at numerous international conferences and owns a number of patents.
Research interests: Using precision Atomic Force Microscopy (AFM) combined with single photon confocal microscopy and spectroscopy, to learn about nanoscale objects (e.g. nanodiamonds). We can now attach a nanodiamond to the tip of an AFM cantilever, to enable scanning magnetic field detection.
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A/Professor David Raftos
Research interests: Evolution of defence: Investigates the internal defence (immune) mechanisms of advanced invertebrtes (ascidians/tunicates) at the cell and molecular biological levels. The overall goals of this works are (i) to determine the ways in which invertebrate animals defence themselves from investion, and (ii) to study the ways in which immune mechanisms have evolved throughout the animal kingdom.
Effects of environmental pollutants on marine invertebrates. Studies the effects of environmental pollutants on the cell and molecular biological systems of common marine invertebrates (ascidians/tunicates). The aims of this research are (i) to identify the cellular systems that are affected by specific pollutants, and determine the ramifications of those cellular effects of the whole animal, and (ii) to develop rapid and reproducible cell or molecular biological assays for the biomonitoring of pollution.
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Professor Shoba Ranganathan
Shoba is one the few principal researchers in the world working in several key areas of bioinformatics, to understand biological systems using computational approaches. A former director of the International Society for Computational Biology (ISCB), she is highly acclaimed internationally for her numerous contributions to bioinformatics education.
Research interests: Computational structural biology and comparative genome sequence analysis.
Dr Tom Roberts
BScAgr, PhD (Plant biochemistry) (Syd)
Research interests: Serpin function and the control of proteolysis in plants and green algae including the eudicot Arabidopsis thaliana, the monocot Oryza sativa (rice) and the unicellular green alga Chlamydomonas reinhardtii, through quantitative analysis of gene expression, gene silencing, production and characterisation of recombinant serpins, and immunolocalisation; and the effects of climate change on abundance and allergenicity of food allergens using peanuts as a model system.
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A/Professor Rob Willows
Research interests: Chlorophyll biosynthesis and plant hormones; the biological processes in milling wheat to make flour (in association with the CRC for Innovative Grain Food Products).
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Adjuncts
Dr Belinda Ferrari
University of New South Wales
Dr Moreland Gibbs
Research Fellow
Applimex Systems
Dr Georgina Learmonth
Postdoctoral Fellow
Applimex Systems
Mr Josh Smith
Visiting Co-op
Northeastern University, Boston, United States
Dr Junior Te'o
Research Fellow
Applimex Systems
Dr Graham Vesey
CEO and Executive Director
Regeneus Animal Health
Associate members
Dr David Inglis
Australian Postdoctoral Fellow
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Dr Amanda Mackie
Research Assistant, Bioinformatics
Dr Anwar Sunna
Senior Research Fellow and Program Leader Manager
Dr Morten Thaysen-Andersen
Visiting Research Fellow
University of Southern Denmark, Odense M, Denmark
Dr Steve Van Sluyter
Research Fellow
Research interests: Grapevine genome annotation improvement using peptide mass spectrometry-proteogenomics; grape berry enzyme activity related to cell death and wine quality; and discovery of fungal enzymes for use in winemaking.
Postgraduates
Hana Faisal J Bali
Supervisor: Professor Helena Nevalainen
Thesis title: Modification of protease production in the filamentous fungus Trichoderma
Sinead Blaber
Supervisor: Professor Benjamin Herbert
Thesis title: Anti-inflammatory effects of adipose derived cells and secretions
Katy Breakwell
Supervisors: Professor Ian Paulsen and A/Professor Paul Haynes
Thesis title: Systems Biology Analysis of Secondary Metabolite Production in Biocontra Pseudomonas Species
Andrew Care
Supervisor: Professor Helena Nevalainen
Thesis title: Development of a Solid Matrix Capture System for Environmental Pathogens and Related Proteins
Elsa Chacko
Supervisors: Professor Shoba Ranganathan and Professor Helena Nevalainen
Thesis title: Transcript Diversity and Conservation of Alternative Splicing Events by Whole Genome Comparison
Clara Wai Yuen Cheah
Supervisors: Professor Nicki Packer and Professor Helena Nevalainen
Thesis title: Sugar-protein interactions: the first line of defence against pathogens
Jenny Chik
Supervisor: A/Professor Mark Molloy
Thesis title: Glyoprotein markers of toxicity to chemotherapy in colorectal cancer
Nicole Cordina
Supervisor: Dr Louise Brown
Thesis title: Pushing the Limits of Paramagnetic Relaxation Enhancement - The Structure of Troponin
Sibasish Dolai
Supervisor: A/Professor Mark Molloy
Thesis title: Quantitative proteomics using chemical probes
Joshua Edwards
Supervisor: A/Professor Brian Atwell
Thesis title: Energy metabolism of germinating rice - regulation of ATP turnover
Arun Vijay Everest Dass
Supervisor: Professor Nicki Packer
Thesis title: Body fluids: sweet protection against infection?
Renan Ali Ersoy
Supervisor: Dr Tom Roberts and A/Professor Brian Atwell
Thesis title: Functional expression analyses of serpin genes in Arabidopsis and rice
Phyllis Farmer
Supervisor: A/Professor Robert Willows
Thesis title: Application of an inplanta transcerit expression system for genetic and biochemical of the structure and function of magnesium chelatase
Daniel John Farrugia
Supervisors: Professor Ian Paulsen and A/Professor Bridget Mabbutt
Thesis title: Mechanisms of drug resistance in Acinetobacter
Sheila Francis
Supervisors: A/Professor Brian Atwell
Thesis title: Identification and expression of serpins in rice
Gagan Garg
Supervisor: Professor Shoba Ranganathan
Thesis title: Advanced Computational Methods for Mitochondrial DNA Analysis
Sophia Goodchild
Supervisor: Dr Louise Brown
Thesis title: Structural Studies of CLIC Ion Channels
Karthikeyan Gunasekaran
Supervisor: Professor Helena Nevalainen
Thesis title: Optimization and Stabilization of an Isothermal Application System
Andre Hallen
Supervisors: A/Professor Robert Willows and A/Professor Paul Haynes
Thesis title: Amino acid metabolism and mental illness
Cameron Hill
Supervisors: A/Professor Benjamin Herbert and A/Professor Paul Haynes
Thesis title: Proteomics of human adipose stem cells
Kathryn Louise Hughes
Supervisor: Professor Michael Gillings and Emeritus Professor Peter Bergquist
Thesis title: Exploring the bacterial diversity of the McMurdo dry valleys, Antarctica
Jeff Kelly
Supervisors: A/Professor Brian Atwell
Thesis title: Productivity and water use of Australian forests under climatic change
Ante Jerkovic
Supervisor: A/Professor Robert Willows and A/Professor Brian Atwell
Thesis title: Biochemical Studies on Wheat Grain to Improve Milling Performance
Javed Mohammed Khan
Supervisors: Professor Shoba Ranganathan and A/Professor Bridget Mabbutt
Thesis title: A bioformatics approach to structure-based T cell epitope prediction
Varun Khanna
Supervisor: Professor Shoba Ranganathan
Thesis title: Molecular similarity and diversity analysis of bioactive small molecules using chemoinformatics approaches
Rajeev Koundinya Nagarajan
Supervisor: Professor Helena Nevalainen
Thesis title: Noval Nitrilases from Filamentous Fungi
Christoph Krisp
Supervisors: A/Professor Mark Molloy and A/Professor Paul Haynes
Thesis title: Proteomic Analysis of Human Wounds Fluids
Gaurav Kumar
Supervisor: Professor Shoba Ranganathan
Thesis title: Bioinformatics Integration and Analysis of Omic Data
Ling Yen Lee
Supervisors: Professor Nicki Packer, Professor Bill Hancock and A/Professor Paul Haynes
Thesis title: Identification of novel biomarkers for breast cancer
Chee Lim
Supervisor: Professor Ian Paulsen
Thesis title: Lateral gene transfer and secondary metabolite biosynthesis in Pseudomonas spp
Michael Mariani
Supervisor: A/Professor Paul Haynes
Thesis title: Development of chip-based Mass Spectrometry Proteomics Techniques
Juan Martinez-Aguilar
Supervisor: A/Professor Mark Molloy and A/Professor Paul Haynes
Thesis title: Mass Spectrometry Investigation of Plasma Biomarkers for Colon Cancer
Michael Medynskyj
Supervisors: A/Professor Benjamin Herbert and A/Professor Paul Haynes
Thesis title: Proteomic analysis of adipose-denied stem cells
Ranjeet Menon
Supervisor: Professor Shoba Ranganathan
Thesis title: Computational Systems Biology of Host-Parasite Interactions
Mehdi Mirzei
Supervisors: A/Professor Paul Haynes and A/Professor Brian Atwell
Thesis title: Functional proteomics of drought response in rice
Suja Mohammed
Supervisor: Professor Helena Nevalainen
Thesis title: Prospecting for novel cold active enzymes and the genes from Antarctic microfungi; and isolation and characterisation of a lipase gene from Penicillium expansum
Jens Mark Moll
Supervisors: A/Professor Bridget Mabbutt and A/Professor Paul Haynes
Thesis title: Structural Organisation of Yeast LSM Complexes
Sridevi Muralidharan
Supervisor: A/Professor Paul Haynes
Thesis title: Proteomic analysis of water stress in grapes
Jerran Naidoo
Supervisor: Dr Benjamin Herbert
Thesis title: Proteomics of differentiated stem cells
Karlie Ann Neilson
Supervisor: A/Professor Paul Haynes
Thesis title: Analysis of protein complexes in plants
Robyn Ann Peterson
Supervisor: Professor Helena Nevalainen
Thesis title: Enzymes from fungi isolated from faeces of Australian herbivores
Sarah Alison Randall
Supervisor: A/Professor Mark Molloy
Thesis title: Plasma biomarkers in cancer
Andrew Scafaro
Supervisor: A/Professor Brian Atwell
Thesis title: Physiological and molecular mechanisms of heat stress tolerance in wild and domesticated rice
Bhumika Shripal Shah
Supervisor: A/Professor Bridget Mabbutt
Thesis title: Structural and functional genomics of acinetobacter baumannii
Prasanth Subramani
Supervisor: Professor Ian Paulsen
Thesis title: Geonomics of emerging nosocomial pathogens: Burkholderia and acine to bacter species
Juliet Suich
Supervisor: A/Professor Brian Atwell
Thesis title: Characterising the growth and development of Australian wild rices
Angela Yu-Hsin Sun
Supervisor: Professor Helena Nevalainen
Thesis title: Expression of obestatin in filamentous fungus Trichoderma reesei
Visaahini Sureshan
Supervisor: A/Professor Bridget Mabbutt
Thesis title: Protein structures selected from the environmental cassette metagenome
John Taylor
Supervisor: A/Professor Brian Atwell
Thesis title: Quantifying the architecture of Australian wild rice relatives
Vignesh Venkatakrishnan
Supervisor: Professor Nicki Packer
Thesis title: Interactions of microbial pathogens with sputum from cystic fibrosis patients.
Rebecca Webster
Supervisor: A/Professor Benjamin Herbert
Thesis title: The role of adipose stem cells in osteoarthritis
Katherine Wongtrakul-Kish
Supervisors: Professor Nicki Packer and A/Professor Ben Herbert
Thesis title: Carbohydrate-specific markers of breast cancer