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Bioinformatics and Integrative Genomics Group

About us

Research Focus

With the proliferation of biological data over the past decade, bioinformatics has become an indispensable tool in understanding biological processes.  The major focus of our research is to contribute to the understanding of the functional aspects of the human genome in health and disease through integrative analysis of the different levels of information encoded by the genome. Our research involves the application of methods in data mining and machine learning to a broad range of problems in genomics, proteomics and molecular evolution with particular focus on cancer biology. Our research group also extensively use mass spectrometry as a technique to study proteins and the proteome in relation of gene regulation and protein function.

Our research is in the following core areas:

  1. Discovering cis-regulatory mutations in cancer.
     
  2. Integrative analysis of epigenetics and transcriptomics next-generation sequencing datasets to study how epigenetic therapies work in cancer.
     
  3. Investigating the extent to which the human genome is translated into proteins.
     
  4. Control of gene regulation in haematopoiesis and leukaemia.
     
  5. Development of computational and proteomics techniques to study post-translational regulation of proteins including allosteric disulfide bonds.


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Team

Collaborators

Resources & Tools

Our research group have published a range of bioinformatics software tools and datasets. These can be access through the links below:

Grants & Funding

ARC Discovery

JW Wong; Exploring novel coding genomic features through integrative proteogenomic; 2014-2017; $705,585

KM Downard & JW Wong; Predicting the evolution of influenza virus on mass; 2012-2014; $275,000

NHMRC Project Grant

JE Pimanda, B Gottgens, O Igoshin, K McKenzie, JW Wong; Reconstructing Transcriptional Networks in Leukaemic Cells; 2013-2015; $733,000

JE Pimanda, P Campbell, P Gunaratne, K McKenzie, M Buckley, D Miranda-Saavedra, JW Wong; Epigenetic therapy in Myelodysplasia and Chronic Myelomonocytic Leukaemia; 2012-2014; $640,000

Cure Cancer Australia

JW Wong; Exploration of cis-regulatory mutations in acute myeloid leukaemia; 2014-2016; $172,298

Cancer Institute NSW

JW Wong, LB Hesson, JE Pimanda, J Thurbon; 'Big Data, Big Impact' Grant, Exploring the 'dark matter' of cancer genomes; 2013-2014; $60,000

JW Wong; Early Career Development Fellowship; A bioinformatics and mass spectrometry-based approach for identification of alternatively spliced and fusion proteins in cancer; 2011-2013; $417,000

JW Wong & JE Pimanda; Innovation Grant; Identifying transcriptional regulatory protein complexes in leukaemia; 2011; $50,000

JW Wong; Innovation Grant; Chlorotyosine proteomics in lung cancer; 2009; $50,000

University of New South Wales

JW Wong; Vice-Chancellors Post-doctoral research fellowship; High-performance data parallel algorithms for mass spectrometry-based proteomics; 2010-2012; $365,000

JW Wong; Early Career Grant; Computational mass spectrometry-based identification of alternatively spliced proteins in cancer cells; 2010; $30,000

grants

Opportunities

  • Identification of alternatively splice proteins in cancer through protein mass spectrometry

    PhD Opportunity / Masters by Research:
    It is estimated that as much as 74% of all multi-exon genes are alternatively spliced in humans, adding enormous diversity to the human proteome. While alternatively spliced proteins are involved in many natural biological processes, specific alterations in splicing patterns have been found in association with cancers. Despite the apparent importance of alternative splicing in human biology, the full extent of alternative splicing remains poorly characterised. The discovery of splice variants at a genomic level remains largely confounded by the lack of reliable methods for its identification. Using protein mass spectrometry, this research project will identify splice variants at both the protein and proteomics level. The ability to identification of specific functionally aberrant protein variants in cancer cells will provide insights into how alternative splicing results in altered function. Methods used in this project will include protein mass spectrometry and/or computational biology.

    Applicants should contact Dr Jason Wong jason.wong@unsw.edu.au or Dr John Pimanda j.pimanda@unsw.edu.au for more information and application forms.

    Contact: Dr Jason Wong

  • Screening of candidate binding proteins to functional DNA elements in leukaemic cell lines

    PhD Opportunity / Masters by Research:
    Traditionally, the interaction between DNA and its binding proteins has been queried by chromatin immunoprecipitation (ChIP). The limitation of ChIP is that it will only provide information on the DNA interaction of the protein chosen for precipitation. Recent advances in mass spectrometry and DNA technologies has enabled reversal of this process whereby a DNA probe is used to pull down all proteins associated with a targeted DNA locus. This project will investigate the use of “reverse ChIP” to identify protein binding targets to DNA elements of interest in different leukaemic cell lines. Identification of novel transcription factors and scaffold proteins is expected to reveal how mRNA expression is regulated in different types of leukaemia. Methods used in this project will include mass spectrometry, stable isotope labelling with amino acids in cell culture and PCR.

    Applicants should contact Dr Jason Wong jason.wong@unsw.edu.au or Dr John Pimanda j.pimanda@unsw.edu.au for more information and application forms.

    Contact: Dr Jason Wong

Group contacts