Associate Professor Jonathan Arthur

Associate Professor
Medicine, Children's Medical Research Institute

Telephone +61 2 88652977
Fax +61 2 98672120

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Research interests

Proteomic bioinformatics: Proteomics depends critically on the ability to be able to identify and then characterize the thousands of proteins whose expression makes up the proteome of a particular individual at a particular time. The vast quantity of data generated by typical proteomic projects requires appropriate bioinformatics algorithms to enable this. Jonathan is interested in developing novel algorithms for the robust, accurate, and efficient identification and characterization of proteins using mass spectrometry.

Multiple sclerosis: Multiple sclerosis is an inflammatory and demyelinating autoimmune disorder of the central nervous system. It is the most common chronic neurological disease affecting young adults and affects approximately 15,000 people throughout Australia. Jonathan is interested in applying proteomics and bioinformatics to address ongoing questions regarding the aetiology, diagnosis, prognosis, and molecular basis of this disease.

Selected grants

2014

  • Towards real time data sharing to support patient-centred care, quality health delivery, improvement programmes, performance management and research; Morris J, Roberts C, Simpson S, Kay J, Venkatesh S, Fazekas de St Groth B, Arthur J, Feng D, Holmes E, James D, Yang J, Engel A; NSW Ministry of Health, Office for Health and Medical Research/Bioinformatics Collaborative Grants Program.
  • Aberrant mesenchymal-epithelial transition: a pathogenic mechanism in tissue maintenance and differentiation; Tam P, Loebel D, Graham M, Arthur J; National Health and Medical Research Council (NHMRC)/Project Grants.

2013

  • Molecular function of the RNA binding protein, RBM47, in embryonic and mature endoderm cells; Tam P, Arthur J; Australian Research Council (ARC)/Discovery Projects (DP).

2010

  • Systems biology: New generation DNA sequencing to functional analysis; Trent R, Waterhouse P, Dawes I, Paulsen I, Henry, R, Crossley P, Bergguist P, Janitz M, Arthur J, Reichardt J, Packer N, Yu B, Scott R, Wade C; Australian Research Council (ARC)/Linkage Infrastructure, Equipment and Facilities (LIEF).

2009

  • Statistical and computational methods using a multiscale approach for protein identification and quantification; Yang J, Raimondo M, Stewart M, Arthur J; Australian Research Council (ARC)/Discovery Projects (DP).

2006

  • Molecular response to interferon beta treatment in multiple sclerosis; Arthur J, Stewart G, Heard R, Booth D, Sedger L, Booth D, Stewart G, Heard R; Australian Research Council (ARC)/Linkage Projects (LP).
  • Sequencing of transmissible Pseudomonas aeruginosa from patients with cystic fibrosis; Harbour C, Rose B, Manos J, Arthur J, Bye P; Australian Cystic Fibrosis Research Trust/Research Support.
  • Advanced Bioinformatics Teaching Facility; Arthur J, Triccas J, Jermiin L, Charleston M, Yang J, Britton W; DVC Research/Teaching Equipment Grant (Sesqui).

Selected publications

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Journals

  • Liao, W., Arthur, J. (2011). Predicting Peptide binding affinities to MHC molecules using a modified semi-empirical scoring function. PloS One, 6(9), e25055-1-e25055-8. [More Information]
  • Liao, W., Arthur, J. (2011). Predicting peptide binding to Major Histocompatibility Complex molecules. Autoimmunity reviews, 10(8), 469-473. [More Information]
  • Wang, P., Yang, P., Arthur, J., Yang, J. (2010). A dynamic wavelet-based algorithm for pre-processing tandem mass spectrometry data. Bioinformatics, 26(18), 2242-2249. [More Information]
  • Austin, C., Mailu, B., Maghzal, G., Sanchez-Perez, A., Rahlfs, S., Zocher, K., Yuasa, H., Arthur, J., Becker, K., Stocker, R., Hunt, N., Ball, H. (2010). Biochemical characteristics and inhibitor selectivity of mouse indoleamine 2,3-dioxygenase-2. Amino Acids, 39(2), 565-578. [More Information]
  • Lam, L., Tsoutsman, T., Arthur, J., Semsarian, C. (2010). Differential protein expression profiling of myocardial tissue in a mouse model of hypertrophic cardiomyopathy. Journal of Molecular and Cellular Cardiology, 48(5), 1014-1022. [More Information]
  • Fung, C., Naughton, S., Turnbull, L., Tingpej, P., Rose, B., Arthur, J., Hu, H., Harmer, C., Harbour, C., Hassett, D., Manos, J., et al (2010). Gene expression of Pseudomonas aeruginosa in a mucin-containing synthetic growth medium mimicking CF lung sputum. Journal of Medical Microbiology, 59(Pt9), 1089-1100. [More Information]
  • McHugh, L., Arthur, J. (2010). Harvest: an open-source tool for the validation and improvement of peptide identification metrics and fragmentation exploration. BMC Bioinformatics, 11(448), 1-14. [More Information]
  • Arthur, J., Reichardt, J. (2010). Modeling Single Nucleotide Polymorphisms in the Human AKR1C1 and AKR1C2 Genes: Implications for Functional and Genotyping Analyses. PloS One, 5(12), e15604-1-e15604-9. [More Information]
  • Gandhi, K., McKay, F., Diefenbach, E., Crossett, B., Schibeci, S., Heard, R., Stewart, G., Booth, D., Arthur, J. (2010). Novel approaches to detect serum biomarkers for clinical response to interferon-beta treatment in multiple sclerosis. PloS One, 5(5), e10484 - 1-e10484 - 9. [More Information]
  • Musumeci, L., Arthur, J., Cheung, F., Hoque, A., Lippman, S., Reichardt, J. (2010). Single Nucleotide Differences (SNDs) in the dbSNP Database May Lead to Errors in Genotyping and Haplotyping Studies. Human Mutation, 31(1), 67-73. [More Information]
  • Manos, J., Arthur, J., Rose, B., Bell, S., Tingpej, P., Hu, H., Webb, J., Kjelleberg, S., Gorrell, M., Bye, P., Harbour, C. (2009). Gene expression characteristics of a cystic fibrosis epidemic strain of Pseudomonas aeruginosa during biofilm and planktonic growth. FEMS Microbiology Letters, 292(1), 107-114. [More Information]
  • Gandhi, K., McKay, F., Schibeci, S., Arthur, J., Heard, R., Stewart, G., Booth, D. (2008). BAFF is a Biological Response Marker to IFN-beta Treatment in Multiple Sclerosis. Journal of Interferon and Cytokine Research, 28(9), 529-540. [More Information]
  • McHugh, L., Arthur, J. (2008). Computational methods for protein identification from mass spectrometry data. PLoS Computational Biology, 4(2), e12-e24. [More Information]
  • Arthur, J. (2008). Identification and characterization of microbial proteins using peptide mass fingerprinting strategies. Methods in molecular medicine, 141, 257-270. [More Information]
  • Wilkins, M., Arthur, J., Junius, F., Harrison, M., Traini, M., Bizannes, P., Doggett, P., McDonald, W. (2008). Information management for proteomics: a perspective. Expert Review of Proteomics, 5(5), 663-678. [More Information]
  • Manos, J., Arthur, J., Rose, B., Tingpej, P., Fung, C., Curtis, M., Webb, J., Hu, H., Kjelleberg, S., Gorrell, M., Bye, P., Harbour, C. (2008). Transcriptome analyses and biofilm-forming characteristics of a clonal Pseudomonas aeruginosa from the cystic fibrosis lung. Journal of Medical Microbiology, 57(12), 1454-1465. [More Information]
  • Cattley, S., Arthur, J. (2007). BioManager: The use of a bioinformatics web application as a teaching tool in undergraduate bioinformatics training. Briefings in Bioinformatics, 8(6), 457-465. [More Information]
  • Chiu, C., Tebo, M., Ingles, J., Yeates, L., Arthur, J., Lind, J., Semsarian, C. (2007). Genetic screening of calcium regulation genes in familial hypertrophic cardiomyopathy. Journal of Molecular and Cellular Cardiology, 43, 337-343. [More Information]
  • Lam, L., Arthur, J., Semsarian, C. (2007). Proteome map of the normal murine ventricular myocardium. Proteomics, 7(19), 3629-3633. [More Information]
  • Chiu, C., Lind, J., Ingles, J., Arthur, J., Semsarian, C. (2006). Leu39ter mutation identified in the phospholamban gene in a family with hypertrophic cardiomyopathy. 15(Supplement 1), S57 (abstract 141)-S58.
  • Arthur, J., Sanchez-Perez, A., Cook, D. (2006). Scoring of predicted GRK2 phosphorylation sites in Nedd4-2. Bioinformatics. [More Information]
  • Arthur, J., Wilkins, M. (2004). Using proteomics to mine genome sequences. Journal of Proteome Research, 3(3), 393-402.

Conferences

  • McHugh, L., Arthur, J. (2009). Using neural networks to identify more proteins in high-throughput proteomics. 2009 World Congress on Nature and Biologically Inspired Computing (NaBIC 2009), USA: (IEEE) Institute of Electrical and Electronics Engineers. [More Information]
  • Arthur, J., Ng, S. (2008). Genome Informatics 2008. GENOME INFORMATICS 2008, Australia: Imperial College Press.
  • Sutton, R., Lind, J., Maher, A., Arthur, J., Garcia, R. (2006). Modelling the impact of T-20 (enfuvirtide) resistance mutations on HIV envelope gp41 structure. Australian Health and Medical Research Congress, Melbourne: Australian Health and Medical Research Congress.

Other

  • Manos, J., Arthur, J., Rose, B., Harbour, C. (2006), Assessment of infectious bacteria.
  • Arthur, J., Traini, M., Wilkins, M. (2003), Annotation of genome sequences.

2011

  • Liao, W., Arthur, J. (2011). Predicting Peptide binding affinities to MHC molecules using a modified semi-empirical scoring function. PloS One, 6(9), e25055-1-e25055-8. [More Information]
  • Liao, W., Arthur, J. (2011). Predicting peptide binding to Major Histocompatibility Complex molecules. Autoimmunity reviews, 10(8), 469-473. [More Information]

2010

  • Wang, P., Yang, P., Arthur, J., Yang, J. (2010). A dynamic wavelet-based algorithm for pre-processing tandem mass spectrometry data. Bioinformatics, 26(18), 2242-2249. [More Information]
  • Austin, C., Mailu, B., Maghzal, G., Sanchez-Perez, A., Rahlfs, S., Zocher, K., Yuasa, H., Arthur, J., Becker, K., Stocker, R., Hunt, N., Ball, H. (2010). Biochemical characteristics and inhibitor selectivity of mouse indoleamine 2,3-dioxygenase-2. Amino Acids, 39(2), 565-578. [More Information]
  • Lam, L., Tsoutsman, T., Arthur, J., Semsarian, C. (2010). Differential protein expression profiling of myocardial tissue in a mouse model of hypertrophic cardiomyopathy. Journal of Molecular and Cellular Cardiology, 48(5), 1014-1022. [More Information]
  • Fung, C., Naughton, S., Turnbull, L., Tingpej, P., Rose, B., Arthur, J., Hu, H., Harmer, C., Harbour, C., Hassett, D., Manos, J., et al (2010). Gene expression of Pseudomonas aeruginosa in a mucin-containing synthetic growth medium mimicking CF lung sputum. Journal of Medical Microbiology, 59(Pt9), 1089-1100. [More Information]
  • McHugh, L., Arthur, J. (2010). Harvest: an open-source tool for the validation and improvement of peptide identification metrics and fragmentation exploration. BMC Bioinformatics, 11(448), 1-14. [More Information]
  • Arthur, J., Reichardt, J. (2010). Modeling Single Nucleotide Polymorphisms in the Human AKR1C1 and AKR1C2 Genes: Implications for Functional and Genotyping Analyses. PloS One, 5(12), e15604-1-e15604-9. [More Information]
  • Gandhi, K., McKay, F., Diefenbach, E., Crossett, B., Schibeci, S., Heard, R., Stewart, G., Booth, D., Arthur, J. (2010). Novel approaches to detect serum biomarkers for clinical response to interferon-beta treatment in multiple sclerosis. PloS One, 5(5), e10484 - 1-e10484 - 9. [More Information]
  • Musumeci, L., Arthur, J., Cheung, F., Hoque, A., Lippman, S., Reichardt, J. (2010). Single Nucleotide Differences (SNDs) in the dbSNP Database May Lead to Errors in Genotyping and Haplotyping Studies. Human Mutation, 31(1), 67-73. [More Information]

2009

  • Manos, J., Arthur, J., Rose, B., Bell, S., Tingpej, P., Hu, H., Webb, J., Kjelleberg, S., Gorrell, M., Bye, P., Harbour, C. (2009). Gene expression characteristics of a cystic fibrosis epidemic strain of Pseudomonas aeruginosa during biofilm and planktonic growth. FEMS Microbiology Letters, 292(1), 107-114. [More Information]
  • McHugh, L., Arthur, J. (2009). Using neural networks to identify more proteins in high-throughput proteomics. 2009 World Congress on Nature and Biologically Inspired Computing (NaBIC 2009), USA: (IEEE) Institute of Electrical and Electronics Engineers. [More Information]

2008

  • Gandhi, K., McKay, F., Schibeci, S., Arthur, J., Heard, R., Stewart, G., Booth, D. (2008). BAFF is a Biological Response Marker to IFN-beta Treatment in Multiple Sclerosis. Journal of Interferon and Cytokine Research, 28(9), 529-540. [More Information]
  • McHugh, L., Arthur, J. (2008). Computational methods for protein identification from mass spectrometry data. PLoS Computational Biology, 4(2), e12-e24. [More Information]
  • Arthur, J., Ng, S. (2008). Genome Informatics 2008. GENOME INFORMATICS 2008, Australia: Imperial College Press.
  • Arthur, J. (2008). Identification and characterization of microbial proteins using peptide mass fingerprinting strategies. Methods in molecular medicine, 141, 257-270. [More Information]
  • Wilkins, M., Arthur, J., Junius, F., Harrison, M., Traini, M., Bizannes, P., Doggett, P., McDonald, W. (2008). Information management for proteomics: a perspective. Expert Review of Proteomics, 5(5), 663-678. [More Information]
  • Manos, J., Arthur, J., Rose, B., Tingpej, P., Fung, C., Curtis, M., Webb, J., Hu, H., Kjelleberg, S., Gorrell, M., Bye, P., Harbour, C. (2008). Transcriptome analyses and biofilm-forming characteristics of a clonal Pseudomonas aeruginosa from the cystic fibrosis lung. Journal of Medical Microbiology, 57(12), 1454-1465. [More Information]

2007

  • Cattley, S., Arthur, J. (2007). BioManager: The use of a bioinformatics web application as a teaching tool in undergraduate bioinformatics training. Briefings in Bioinformatics, 8(6), 457-465. [More Information]
  • Chiu, C., Tebo, M., Ingles, J., Yeates, L., Arthur, J., Lind, J., Semsarian, C. (2007). Genetic screening of calcium regulation genes in familial hypertrophic cardiomyopathy. Journal of Molecular and Cellular Cardiology, 43, 337-343. [More Information]
  • Lam, L., Arthur, J., Semsarian, C. (2007). Proteome map of the normal murine ventricular myocardium. Proteomics, 7(19), 3629-3633. [More Information]

2006

  • Manos, J., Arthur, J., Rose, B., Harbour, C. (2006), Assessment of infectious bacteria.
  • Chiu, C., Lind, J., Ingles, J., Arthur, J., Semsarian, C. (2006). Leu39ter mutation identified in the phospholamban gene in a family with hypertrophic cardiomyopathy. 15(Supplement 1), S57 (abstract 141)-S58.
  • Sutton, R., Lind, J., Maher, A., Arthur, J., Garcia, R. (2006). Modelling the impact of T-20 (enfuvirtide) resistance mutations on HIV envelope gp41 structure. Australian Health and Medical Research Congress, Melbourne: Australian Health and Medical Research Congress.
  • Arthur, J., Sanchez-Perez, A., Cook, D. (2006). Scoring of predicted GRK2 phosphorylation sites in Nedd4-2. Bioinformatics. [More Information]

2004

  • Arthur, J., Wilkins, M. (2004). Using proteomics to mine genome sequences. Journal of Proteome Research, 3(3), 393-402.

2003

  • Arthur, J., Traini, M., Wilkins, M. (2003), Annotation of genome sequences.

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