Mark Watson  from Murdoch University in Perth Australia.

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    Associate Professor Mark Watson
    B.Sc. Hon Biochemistry, Ph.D.

    Director of Laboratory Services

    About me

    I was trained as a molecular biologist in the United Kingdom and conducted my first post doc with Prof Steven Holgate, Prof Newton Morten and Prof Patricia Jacobs in Southampton, UK,  performing genetic linkage analysis to atopy and allergic disease. In 1994, I took up a position as the Manager of the Centre for Cell and Molecular Biology at the University of Western Australia.

    In 1996 I was successful in obtaining NHMRC funding for a project looking at the molecular aspects of the Murine AIDS virus. I then moved to a research position within the WA Health Department at the Royal Perth Hospital Department of Microbiology and Infectious Diseases to study the Hepatitis C Virus which remains one my main research areas to date.

    In 2006 Dr Watson took up the position of Manager of the newly established Geomics Node of the Lotterywest Biomedical facility located within the Department of Immunology and Immunogenetics at Royal Perth Hospital.

    I have been highly active in organising conferences both local and national (CBSM and ASM) and has previously chaired CBSM (2002-2005)

    I have directly supervised PhD and  honours students and an Adjunct senior lecturer at the University of Western Australia.  I have  lectured to years 1, 2 and 3 science students as well as medical students. I have acted as a consultant to several successful molecular biotechnology companies.

    I have presented my work in oral and poster format at many local, national and international conferences and have published work from a diverse range of research projects. Since arriving in Australia I have been successful in attracting funding from many local and national funding bodies including the NHMRC and commercial funding sources. I have many local, interstate and international collaborators for my areas of research focus.

    I joined Murdoch University as the Laboratory Manager at the Institute for Immunology and Infectious Diseases  in December 2008. His most active area of current research is in the area of the Hepatitis C virus with particular focus on molecular immunology and antivirals.

    As a person that has been involved with service provision, research and diagnostic environments I bring the best of each of these roles to the positions I hold.  I am particulary interested in improving research and diagnostic efficiency reducing duplication, improving compliance and data integrity through the use of IT.  I am a closet programmer and have developed web based applications and database solutions for a large variety of research and diagnostic needs.

    I head a team of postdoctoral scientists and postgraduate laboratory staff dedicated our vision of improving clinical outcomes for patients with immunological and infectious disease ailments.  I also lead a team of computer scientists and hardware specialists to bring computing solutions to the diagnostic and research endeavors of the institute, develop agile analysis solutions for genomics research and improve sample and data integrity and workflow.  This has resulted in a 15 year project to develop an electronic laboratory system able to manage all aspects of laboratory projects including interfacing with lab automation systems.  Currently going through a major update this to our knowledge is the most comprehensive system of it’s type for managing laboratory projects.

    My core capabilities, experience and expertise lays in the following areas and I have direct access to the resources and equipment for research and industrial engagement in these areas.

    • Molecular biotechnology and genomics, particularly in the human bacterial and viral fields
    • Sanger sequencing
    • Second generation sequencing Illumina MiSeq
    • Third generation sequencing Oxford Nanopore MinIon
    • Liquid handling workstations for assay automation
    • NATA accreditation
    • ASHI accreditation
    • Real time PCR
    • Digital droplet PCR
    • High throughput PCR
    • LIMS systems development
    • Single cell genomics and transcriptomics
    • Data analysis software and data visualisation tools
    • Immunoassay design and execution
    • Flow cytometry
    • PC3 facility
    • HLA typing (accredited)
    • T cell receptor typing
    • Targeted Single nucleotide polymorphism analysis
    • ERAP typing
    • KIR typing
    • Microbiome analysis
    • Viral integration site analysis
    • Bacterial genome sequencing
    • Viral genome sequencing


    Teaching area

    I currently have no postgraduate students under my supervision though I am mentoring several PhD students and am the chair of the progress committee for one Ph.D. student. I give guest lectures to undergraduate students at several institutions and deliver the Safety in Research and Teaching Working Safely with Biological Material lectures at the beginning of each semester.

    Research areas

    My research interests are quite diverse but all have a common theme of Human Immunology and or Microbiology.  I have an affinity for virus based research and have published in the area of Rhinoviruses, HCV, and HIV.  I am particularly interested in how the human host influences organisms that encounter and how they in tern influence our immune systems.  More recently The role of the immune system and the HLA genes have become an area of interest and I am intimately involved in developing methodologies for interrogation of the human HLA system (HLA typing) and the MHC  (Major Histocompatibility Complex) region in general for both research and diagnostic purposes.

    Current projects

    I am involved with manyf research projects.  If you have an immunology / infectious disease based project then I am interested :-)  particularly those with a molecular biology bent and particularly difficult questions to answer.  Currently the following are active areas of research in our laboratories at IIID

    Human HLA
    Drug hypersensitivity
    Multiple sclerosis research
    Microbiome research
    Virome research
    Second and third generation sequencing technologies
    Digital PCR
    Bacterial and viral genome sequencing
    Single cell transcriptomics
    T-cell receptor sequencing bulk and single cell


    Awards and grants

    1991: Named research officer and writer for a successful UK MRC project grant, £101,000.

    1994: Successfully obtained a Lotteries Commission grant to better equip the Centre for Cell and Molecular Biology at UWA.  Grant applied for under the umbrella of the Centre. Total amount received = $200,000

    1995: Successfully applied as co-chief investigator with Dr Manfred Beilharz for an NHMRC grant to study Murine AIDS, $260,000 over 3 years.

    1995: Successfully applied for a UWA travel grant for research ties with Indonesia, $2500.

    1995: Successfully applied to the Dept. of Commerce and Trade (DOCAT) for a travel award to establish research ties withSurabaya,Indonesia, $2500.

    1998: Successfully applied as chief investigator with Dr Manfred Beilharz to the NH&MRC to study the molecular pathogenesis of the MAIDS virus.  $207,360 over three years.  Included a promotion to Senior Research Officer.

    1999: Successfully applied as co-chief investigator with Dr James Flexman to Royal Perth Hospital Medical Research Foundation to establish an in vitro culture system and in vivo small animal model of HCV, $10,750.

    2000: Successfully applied as co-chief investigator with Dr James Flexman and Dr Sasha Jaksic to Royal Perth Hospital Medical Research Foundation to study the correlation of the cellular immune response to Hepatitis C Virus (HCV) core antigen with the degree of fibrosis in HCV infected patients.  Outcome successful $7,203

    2002-2004: Successfully applied as co-chief investigator with Dr James Flexman and Dr Wenshuz Yeow to Royal Perth Hospital Medical Research Foundation to study Molecular Analyses of Viral Interference in Interferon-a Mediated Jak-STAT Signalling, $10,500 plus 0.9 FTE research assistant year 1; $7,800 plus 0.5 FTE research assistant year 2; 0.5 x FTE research assistant year 3.

    2002: Successfully applied co-chief investigator with Drs Jane Allan, George Yeo, Brett Dix, John Olnyk to WAIMR for Establishment Of Novel Systems To Analyse The Hepatic Response To Hepatitis C Virus Both in vivo And in vitro. $47,000.

    2005: Successfully applied to the Royal Perth Hospital Medical Research Foundation: to produce human monoclonal antibodies to the Hepatitis C Virus using new novel technologies. $12,000.

    2007: Successfully applied to the University of Western Australia Major equipment grants scheme to purchase a Roche LC480. $80,000.

    2008 Successfully applied to the faculty of Medicine and dentistry 50th Anniversary equipment fund for a Roche genome sequencer FLX.  $500,000

    2008. Successfully applied to the Royal Perth Hospital Medical Research Foundation for Infrastructure support for Massively parallel sequencing facility $127,893

    2009 Application to ACH2, Australia as CIF. Development of Novel Therapeutics for Treatment of Hepatitis C Infection. Outcome: successful, $130,000.

    Funding 2016-2018 Robinson, Craney, Lake Lesterhuis et al.  and Watson (CIE) Reactivities of CD8 T cells to mutated neo-antigens in lung malignancies. $661,979.00 NH&MRC (1107091)

    Funding 2017-2019. Robinson et al (Watson CIG) Compartmental analysis of T-cell responses in thoracic malignancies. NH&MRC $851,402.80:  To improve immune therapy for cancer we have to be able to determine how cancer patients ‘see’ mutated cancer proteins. Blood is the easiest & most useful source of immune ‘killer’ cells for that task, but the lymph node that drains the tumour and the fluid that bathes a tumour probably contain a much higher number of these killer cells than blood. If so, studying them would help us better track responses to therapy and enable us to choose the best mutated proteins for a vaccine

    Events and speaking engagements

    Invited Speaker: Development and Challenges of HLA Typing Using NGS in a Research and Clinical Setting. 6th NGS Asia Congress, 4th Single Cell Analysis Asia Congress and 3rd Microbiology Asia Congress, Concorde Hotel Singapore 11-12th October 2016

    Invited Speaker: Accurate Identification of HCV Sequence Variants Using Deep Sequencing With a Primer ID.  Don Cooper, Abha Chopra, John Blinco, Cassandra Jabara, Stan Lemon, Richard Barnard, Silvana Gaudieri, Mark Watson, Simon Mallal.  Australian Centre for HIV and Hepatitis Virology Research (ACH2) 9th Annual Scientific Workshop 5th -7th June 2013, Katoomba NSW

    Invited Speaker “Next generation Nucleic Acid Sequencing Wows and Woes”, Departmental Seminar Series, Department of Anatomy and Human Biology, University of Western Australia 15/5/12

    Invited Speaker: Translational Pharmacogenomics 45th ASCEPT Scientific Meeting in Perth, Western Australia.  Laboratory applications – “454″ and beyond, December 2011

    Invited Speaker, “Next Generation Sequencing” 21st Combined Biological Sciences Meeting, University Of Western Australia, 26th August 2011

    Invited speaker, “HCV Cross Genotype Neutralization: Identification and Cloning of Human Antibodies to HCV “. Australian Centre for HIV and Hepatitis Virology Research (ACH2), 7th Annual Workshop.  Sunshine Coast, Queensland, Australia.  June 2011

    Invited speaker, Department of Immunology and Biochemical Genetics, Royal Perth Hospital July 2005.  The Hepatitis C Virus

    Invited Speaker, Department of Gastroenterology Royal Perth Hospital.  Liver group meeting March 2003.  Molecular Aspects of the Hepatitis C Virus

    Invited speaker, Department of Microbiology, University of Western Australia.  `The Hepatitis C Virus’. October 2001

    Invited Speaker,  School of Biomedical Sciences, Curtin University, Perth WA.  Murine AIDS,  20th April 1999

    Invited speaker,  1997 annual meeting of the International Society for Interferon & Cytokine Research, San Diego, California, USA October 19-24 (1997).  Interferon and Murine AIDS

    Invited speaker,  University of Saskatchewan, Saskatoon Canada.  Honorarium presentation: The Molecular Pathology of the MAIDS Virus.  October 1997

    Invited Speaker at the 1996 Federation of Immunological Societies of Asia- Oceania Meeting Adelaide South Australia. Oral Administration of Interferon Alpha and The Mucosal Immune System

    Invited speaker, Eijkman Institute for Molecular Biology, Diponegoro 69, Jakarta 10430, Indonesia.  Genetic linkage to allergic disease and An Introduction to the Centre for Cell and Molecular Biology of the University of Western Australia. June 2nd 1995

    Professional and community service

    I was chair of the Murdoch University Institutional Biosafety Committee (IBC) resigned as chair 6/9/2017 but am still an active member of the Murdoch IBC and I sit on the Royal Perth Hospital IBC as well as being a current member of the Western Australian Biosafety Network (WABN)

    I have been an active member of the Australian Society for Microbiology 1998-2005 though these days I only help out with fundraising events like the quiz night.

    I was a member and organiser of the 1995-2005 annual Combined Biological Sciences meeting in Perth WA and chaired that committee with Dr Elizabeth Quail from 200-2005

    I am qualified in first aid and Hold a Bronze Medallion for Surf Life Saving Australia.

    I am a qualified Lacrosse Referee

    Doctoral and masters supervisions

    I have previously successfully supervised over 21  honours and 8 Ph.D. students.  



    • Noto, J., Chopra, A., Loh, J., Romero-Gallo, J., Piazuelo, B., Watson, M., Leary, S., Beckett, A., Wilson, K., Cover, T., Mallal, S., Israel, D., Peek, R., (2018), Pan-genomic analyses identify key Helicobacter pylori pathogenic loci modified by carcinogenic host microenvironments, Gut: an international journal of gastroenterology & hepatology, 67, 10, pages 1793 - 1804.
    • McGovern, A., Androga, G., Knight, D., Watson, M., Elliott, B., Foster, N., Chang, B., Riley, T., (2017), Prevalence of binary toxin positive Clostridiumdifficile in diarrhoeal humans in the absenceof epidemic ribotype 027, PLoS One, 12, 11, pages e0187658 -.
    • Almeida, C., van Miert, P., O'Driscoll, K., Zoet, Y., Chopra, A., Watson, M., de Santis, D., Witt, C., John, M., Claas, F., D'Orsogna, L., (2017), Stimulation of HIV-specific T cell clonotypes using allogeneic HLA, Cellular Immunology, 316, , pages 32 - 40.
    • Barnard, R., Chopra, A., James, I., Blinco, J., Watson, M., Jabara, C., Hazuda, D., Lemon, S., Mallal, S., Gaudieri, S., (2016), Primer ID ultra-deep sequencing reveals dynamics of drug resistance-associated variants in breakthrough hepatitis C viruses: relevance to treatment outcome and resistance screening, Antiviral Therapy, 21, 7, pages 567 - 577.
    • Creaney, J., Ma, S., Sneddon, S., Tourigny, M., Dick, I., Leon, J., Khong, A., Fisher, S., Lake, R., Lesterhuis, W., Nowak, A., Leary, S., Watson, M., Robinson, B., (2015), Strong spontaneous tumor neoantigen responses induced by a natural human carcinogen, OncoImmunology (Online), 4, 7, pages 1 - 7.
    • Hammond, T., Lee, S., Lee, S., Watson, M., Flexman, J., Cheng, W., Fernandez, S., Price, P., (2010), Toll-like receptor (TLR) expression on CD4+ and CD8+ T-cells in patients chronically infected with hepatitis C virus, Cellular Immunology, 264, 2, pages 150 - 155.
    • Lee, S., Watson, M., Flexman, J., Cheng, W., Hammond, T., Price, P., (2010), Increased proportion of the CD56bright NK cell subset in patients chronically infected with Hepatitis C Virus (HCV) receiving interferon- and ribavirin therapy, Journal of Medical Virology, 82, 4, pages 568 - 574.

    Coral-Ann Almeida, Paula van Miert, Kane O’Driscoll, Yvonne M. Zoet, Abha Chopra,Mark Watson, Dianne de Santis, Campbell Wittb,, Mina Johnb,, Frans H.J. Claas, Lloyd J. D’Orsogna. Stimulation of HIV-specific T cell clonotypes using allogeneic HLA. Cellular Immunology. In Press.

    Silvia Lee, Alfred Laiman, Martyn French, James Flexman, Mark Watson, Patricia Price. The dynamics of HCV-specific antibody responses in HIV/HCV patients on long-term antiretroviral therapy. Clinical Immunology 2017 In Press

    Allan, J; Felsberger, G; Silvia, L; Hayley, C; Flexman, J; Watson, M. Characterisation of the antibody response to hepatitis C virus by infected individuals. EUROPEAN JOURNAL OF IMMUNOLOGY. International Congress of Immunology. AUG 21-26, 2016

    Creaney J., Ma1, S., Sneddon, S., Tourigny, M.R., Dick, I.M., Leon, J.S., Khong, A., Fisher, S.A., Lake, R.A, Lesterhuis, W.J., Nowak, A.K., Leary, S., Watson, M.W. and Robinson, B.R. (2015) Strong spontaneous tumor neo-antigen responses to tumors induced by a natural human carcinogen. OncoImmunology 2015 May 11;4(7):e1011492

    Hammond, T., Lee, S., Watson, M. W., Flexman, J. P., Cheng, W. and Price, P. , (2011) Decreased IFNγ production correlates with diminished production of cytokines by dendritic cells in patients infected with hepatitis C virus and receiving therapy. Journal of Viral Hepatitis, 18: 482–492  no. doi: 10.1111/j.1365-2893.2010.01331.x

    Lee S, Watson MW, Flexman JP, Cheng W, Hammond T, Price P. (2010) Increased proportion of the CD56(bright) NK cell subset in patients chronically infected with hepatitis C virus (HCV) receiving interferon-alpha and ribavirin therapy. J Med Virol. 2010 Apr;82(4):568-574

    Hammond T, Lee S, Watson MW, Flexman JP, Cheng W, Fernandez S, Price P. (2010) Toll-like receptor (TLR) expression on CD4+ and CD8+ T-cells in patients chronically infected with hepatitis C virus. Cell Immunol.;264(2):150-155

    Lee, S., Hammond, T., Watson, M. W., Flexman, J. P., Cheng, W., Fernandez, S. and Price, P. (2010), Could a loss of memory T cells limit responses to hepatitis C virus (HCV) antigens in blood leucocytes from patients chronically infected with HCV before and during pegylated interferon-α and ribavirin therapy?. Clinical & Experimental Immunology, 161: 118–126. doi: 10.1111/j.1365-2249.2010.04141.x

    Silvia Lee, Julius Varano, James P. Flexman, Wendy Cheng, Mark W. Watson, Enrico Rossi, Leon A. Adams, Max Bulsara, Patricia Price, (2010) Decreased IP-10 and elevated TGFβ1 levels are associated with viral clearance following therapy in patients with hepatitis C virus. Disease Markers 28 (5): 273-280

    Li, M. S., N. Y. Chow, S. Sinha, D. Halliwell, M. Finney, A. R. Gorringe, M. W. Watson, J. S. Kroll, P. R. Langford and S. A. Webb (2009). “A Neisseria meningitidis NMB1966 mutant is impaired for invasion of respiratory epithelial cells, survival in human blood and for virulence in vivo.” Med Microbiol Immunol 198(1): 57-67

    Hughes, Q., M. Watson, V. Cole, M. Sayer, R. Baker and J. Staton (2007). “Upregulation of protein S by progestins.” J Thromb Haemost 5(11): 2243-9.

    Lee, S., M. W. Watson, B. Clark, J. P. Flexman, W. Cheng, M. A. French and P. Price (2006). “Hepatitis C virus genotype and HIV coinfection affect cytokine mRNA levels in unstimulated PBMC but do not shift the T1/T2 balance.” Immunol Cell Biol 84(4): 390-5

    Paun, A., K. Shaw, S. Fisher, L. M. Sammels, M. W. Watson and M. W. Beilharz (2005). “Quantitation of defective and ecotropic viruses during LP-BM5 infection by real time PCR and RT-PCR.” J Virol Methods 124(1-2): 57-63

    Beilharz, M. W., L. M. Sammels, A. Paun, K. Shaw, P. van Eeden, M. W. Watson and M. L. Ashdown (2004). “Timed ablation of regulatory CD4+ T cells can prevent murine AIDS progression.” J Immunol 172(8): 4917-25

    Watson MW, Beasley R, Holgate ST, Bardin PG.(2003) .Rhinovirus is not detectable in peripheral lung tissue after asthma death. Respirology. (2):234-8

    Watson, M. W., A. Jaksic, P. Price, W. Cheng, M. McInerney, M. A. French, S. Fisher, S. Lee and J. P. Flexman (2003). “Interferon-gamma response by peripheral blood mononuclear cells to hepatitis C virus core antigen is reduced in patients with liver fibrosis.” J Infect Dis 188(10): 1533-6

    Watson, M. W., R. Beasley, S. T. Holgate and P. G. Bardin (2003). “Rhinovirus is not detectable in peripheral lung tissue after asthma death.” Respirology 8(2): 234-8.

    Grando, D., L. J. Sullivan, J. P. Flexman, M. W. Watson and J. H. Andrew (1999). “Bartonella henselae associated with Parinaud’s oculoglandular syndrome.” Clin Infect Dis 28(5): 1156-8

    Gomes, I., A. Collins, C. Lonjou, N. S. Thomas, J. Wilkinson, M. Watson and N. Morton (1999). “Hardy-Weinberg quality control.” Ann Hum Genet 63(Pt 6): 535-538.

    Bosio, E., M. W. Beilharz, M. W. Watson and C. M. Lawson (1999). “Efficacy of low-dose oral use of type I interferon in cytomegalovirus infections in vivo.” J Interferon Cytokine Res 19(8): 869-76

    Beilharz, M. W., W. McDonald, M. W. Watson, J. Heng, J. McGeachie and C. M. Lawson (1997). “Low-dose oral type I interferons reduce early virus replication of murine cytomegalovirus in vivo.” J Interferon Cytokine Res 17(10): 625-30

    Townsend, K. M., H. J. Dawkins, B. J. Zeng, M. W. Watson and J. M. Papadimitriou (1996). “Cloning of a unique sequence specific to isolates of type B:2 Pasteurella multocida.” Res Vet Sci 61(3): 199-205

    Rakoczy, P. E., M. C. Lai, M. Watson, U. Seydel and I. Constable (1996). “Targeted delivery of an antisense oligonucleotide in the retina: uptake, distribution, stability, and effect.” Antisense Nucleic Acid Drug Dev 6(3): 207-13

    Doull, I. J., S. Lawrence, M. Watson, T. Begishvili, R. W. Beasley, F. Lampe, T. Holgate and N. E. Morton (1996). “Allelic association of gene markers on chromosomes 5q and 11q with atopy and bronchial hyperresponsiveness.” Am J Respir Crit Care Med 153(4 Pt 1): 1280-4

    Watson, M. W., I. N. Clarke, J. S. Everson and P. R. Lambden (1995). “The CrP operon of Chlamydia psittaci and Chlamydia pneumoniae.” Microbiology 141 ( Pt 10): 2489-97

    Watson, M., S. Lawrence, A. Collins, R. Beasley, I. Doull, B. Begishvili, F. Lampe, S. T. Holgate and N. E. Morton (1995). “Exclusion from proximal 11q of a common gene with megaphenic effect on atopy.” Ann Hum Genet 59(Pt 4): 403-11.

    Flexman, J. P., N. J. Lavis, I. D. Kay, M. Watson, C. Metcalf and J. W. Pearman (1995). “Bartonella henselae is a causative agent of cat scratch disease in Australia.” J Infect 31(3): 241-5

    Watson, M. W., P. R. Lambden, J. S. Everson and I. N. Clarke (1994). “Immunoreactivity of the 60 kDa cysteine-rich proteins of Chlamydia trachomatis, Chlamydia psittaci and Chlamydia pneumoniae expressed in Escherichia coli.” Microbiology 140 ( Pt 8) : 2003-11

    Watson, M. W., P. R. Lambden and I. N. Clarke (1991). “Genetic diversity and identification of human infection by amplification of the chlamydial 60-kilodalton cysteine-rich outer membrane protein gene.” J Clin Microbiol 29(6): 1188-93

    Watson, M. W., P. R. Lambden and I. N. Clarke (1990). “The nucleotide sequence of the 60 kDa cysteine rich outer membrane protein of Chlamydia psittaci strain EAE/A22/M.” Nucleic Acids Res 18(17): 5300

    Watson, M. W., S. al-Mahdawi, P. R. Lamden and I. N. Clarke (1990). “The nucleotide sequence of the 60 kDa cysteine rich outer membrane protein of Chlamydia pneumoniae strain IOL-207.” Nucleic Acids Res 18(17): 5299

    Watson, M. W., P. R. Lambden, M. E. Ward and I. N. Clarke (1989). “Chlamydia trachomatis 60 kDa cysteine rich outer membrane protein: sequence homology between trachoma and LGV biovars.” FEMS Microbiol Lett 53(3): 293-7