Professor Alan Baxter is a medical graduate who completed a PhD in immunogenetics at the Walter and Eliza Hall Institute under the supervision of Tom Mandel. He has worked as a Research Fellow at Harvard Medical School and at Cambridge University, where he was a Supervisor in Pathology for Trinity College. He was president of the Australasian Society for Immunology from 2006-2008, a member of the Council of the Federation of Immunological Societies of Asia-Oceania 2012-2015, the Council of the International Union of Immunological Societies 2013-2017, and the MSRA Research Management Council since 2013. He established the Autoimmunity Research Group at the Centenary Institute, where he worked for nine years before taking up his current appointment as Professor of Biochemistry and Molecular Cell Biology and Director of the Comparative Genomics Centre of James Cook University. His work is funded by James Cook University,  the MSRA, Townsville Hospital and Health Service and the Queensland Department of Health.


He is known internationally for his contributions to the genetics of autoimmune disease and has published on the genetics of gastritis, lupus, type 1 diabetes, multiple sclerosis and the role of NKT cells in autoimmunity, and made major contributions to our understanding of gene/environment interactions in autoimmune disease.


  • Immunogenetics of autoimmune disease
  • Innate immunity
  • Genetics of immune regulation
  • Multiple sclerosis
  • Type 1 diabetes
  • Systemic lupus erythematosus
  • Autoimmune gastritis
Research Disciplines
Socio-Economic Objectives
  • 2011 to 2015 - NHMRC Senior Research Fellowship (B)
  • 2006 to 2010 - NHMRC Senior Research Fellowship (B)
  • 2001 to 2005 - NHMRC Senior Research Fellowship (A)
  • 1997 to 2000 - NHMRC RD Wright Fellowship
  • 1992 to 1995 - NHMRC CJ Martin Fellowship
  • 2013 - Elected member of the Council for the International Union of Immunological Societies.
  • 2012 - Elected member of the Council for the Federation of Immunological Societies for Asia/Oceania.
  • 2012 - Senior Editorial Board, American J Clinical and Experimental Immunology
  • 2010 - Multiple Sclerosis Research Australia Research Management Council
  • 2006 - Board of the Australian Institute of Tropical Medicine
  • 2004 to 2007 - Professional Review Panel, Juvenile Diabetes Research Foundation
  • 1999 to 2003 - Professional Advisory Panel, Juvenile Diabetes Research Foundation Australia
  • 1997 to 2002 - Editorial Board, Autoimmunity
  • 2007 - Associate Editor, Immunology and Cell Biology
  • 2004 - Associate Editor, The Review of Diabetic Studies
  • 2006 to 2008 - President, Australasian Society for Immunology
  • 2004 to 2008 - Associate Editor, Journal of Immunology
  • 2005 to 2006 - Vice-President, Australasian Society for Immunology

These are the most recent publications associated with this author. To see a detailed profile of all publications stored at JCU, visit ResearchOnline@JCU. Hover over Altmetrics badges to see social impact.

Journal Articles
  • Dinh X, Stanley D, Smith L, Moreau M, Berzins S, Gemiarto A, Baxter A and Jordan M (2021) Modulation of TCR signalling components occurs prior to positive selection and lineage commitment in iNKT cells. Scientific Reports, 11.
  • Gresle M, Jordan M, Stankovich J, Spelman T, Johnson L, Laverick L, Hamlett A, Smith L, Jokubaitis V, Baker J, Haartsen J, Taylor B, Charlesworth J, Bahlo M, Speed T, Brown M, Field J, Baxter A and Butzkueven H (2020) Multiple Sclerosis risk variants regulate gene expression in innate and adaptive immune cells. Life Science Alliance, 3 (7).
  • Ng S, Rivera F, Yan J, Corvino D, Das I, Zhang P, Kuns R, Chauhan S, Hou J, Li X, Frame T, McEnroe B, Moore E, Na J, Engel J, Soon M, Singh B, Kueh A, Herold M, de Oca M, Singh S, Bunn P, Aguilera A, Casey M, Braun M, Ghazanfari N, Wani S, Wang Y, Amante F, Edwards C, Haque A, Dougall W, Singh O, Baxter A, Teng M, Loukas A, Daly N, Cloonan N, Degli-esposti M, Uzonna J, Heath W, Bald T, Tey S, Nakamura K, Hill G, Kumar R, Sundar S, Smyth M and Engwerda C (2020) The NK cell granule protein NKG7 regulates cytotoxic granule exocytosis and inflammation. Nature Immunology, 21. pp. 1205-1217
  • Patsopoulos N, Baranzini S, Santaniello A, Shoostari P, Cotsapas C, Wong G, Beecham A, James T, Replogle J, Vlachos I, McCabe C, Pers T, Brandes A, White C, Keenan B, Cimpean M, Winn P, Panteliadis I, Robbins A, Andlauer T, Zarzycki O, Dubois B, Goris A, Sondergaard H, Sellebjerg F, Sorensen P, Ullum H, Thorner L, Saarela J, Cournu-Rebeix I, Damotte V, Fontaine B, Guillot-Noel L, Lathrop M, Vukusic S, Berthele A, Pongratz V, Pongratz V, Gasperi C, Graetz C, Grummel V, Hemmer B, Hoshi M, Knier B, Korn T, Lill C, Luessi F, Muehlau M, Zipp F, Dardiotis E, Agliardi C, Amoroso A, Barizzone N, Benedetti M, Bernardinelli L, Cavalla P, Clarelli F, Comi G, Cusi D, Esposito F, Ferre L, Galimberti D, Guaschino C, Leone M, Martinelli V, Moiola L, Salvetti M, Sorosina M, Vecchio D, Zauli A, Santoro S, Mancini N, Zuccala M, Mescheriakova J, van Duijn C, Bos S, Celius E, Spurkland A, Comabella M, Montalban X, Alfredsson L, Bomfim I, Gomez-Cabrero D, Hillert J, Jagodic M, Linden M, Piehl F, Jelcic I, Martin R, Sospedra M, Baker A, Ban M, Hawkins C, Hysi P, Kalra S, Karpe F, Khadake J, Lachance G, Molyneux P, Neville M, Thorpe J, Bradshaw E, Caillier S, Calabresi P, Cree B, Cross A, Davis M, de Bakker P, Delgado S, Dembele M, Edwards K, Fitzgerald K, Frohlich I, Gourraud P, Haines J, Hakonarson H, Kimbrough D, Isobe N, Konidari I, Lathi E, Lee M, Li T, An D, Zimmer A, Madireddy L, Manrique C, Mitrovic M, Olah M, Patrick E, Pericak-Vance M, Piccio L, Schaefer C, Weiner H, Lage K, Scott R, Lechner-Scott J, Leal R, Moscato P, Booth D, Stewart G, Vucic S, Pame G, BamettO M, Mason D, GriffithS L, Broadley S, Tajouri L, Baxter A, Slee M, Taylor B, Charlesworth J, Kilpatrick T, Rubio J, Jokubaitis V, Wiley J, Butzkueven H, Leslie S, Motyer A, Stankovich J, Carroll W, Kermode A, Edrin M, Barclay M, Peyrin-Biroulet L, Chamaillard M, Colombe J, Cottone M, Croft A, D'Inca R, Halfvarson J, Hanigan K, Henderson P, Hugot J, Karban A, Kennedy N, Khan M, Lemann M, Levine A, Massey D, Milla M, Motoey G, Ng S, Oikonomnou J, Peeters H, Proctor D, Rahier J, Roberts R, Rutgeerts P, Seibold F, Stronati L, Taylor K, Torkvist L, Ublick K, Van Limbergen J, Van Gossum A, Vatn M, Zhang H, Zhang W, Donnelly P, Barroso I, Blackwe J, Bramon E, Brown M, Casas J, Corvin A, Deloukas P, Duncanson A, Jankowski J, Markus H, Mathew C, Palmer C, Plomin R, Rautanen A, Sawcer S, Trembath R, Viswanathan A, Wood N, Spencer C, Band G, Bellenguez C, Freeman C, Hellenthal G, Giannoulatou E, Pirinen M, Pearson R, Strange A, Sul Z, Vukcevic D, Donnelly P, Langford C, Hunt S, Edkins S, Gwilliam R, Blackburn H, Bumpstead S, Dronov S, Gillman M, Gray E, Hammond N, Jayakumar A, McCann O, Liddle J, Potter S, Ravindrarajah R, Ricketts M, Waller M, Weston P, Widaa S, Whittaker P, Barroso I, Deloukas P, Mathew C, Blackwe J, , Corvin A, Spencer C, Compston A, Hafler D, Harbo H, Hauser S, D'Alfonso S, Hadjigeorgiou G, Barcellos L, Booth D, Hintzen R, Kockum I, Martinelli-Boneschi F, McCauley J, Oksenberg J, Oturai A, Ivinson A, Olsson T and De Jager P (2019) Multiple sclerosis genomic map implicates peripheral immune cells and microglia in susceptibility. Science, 365 (6460).
  • Too L, Yau B, Baxter A, McGregor I and Hunt N (2019) Double deficiency of toll-like receptors 2 and 4 alters long-term neurological sequelae in mice cured of pneumococcal meningitis. Scientific Reports, 9.
  • Wiede F, Brodnicki T, Goh P, Leong Y, Jones G, Yu D, Baxter A, Jones S, Kay T and Tiganis T (2019) T-Cell-specific PTPN2 deficiency in NOD mice accelerates the development of type 1 diabetes and autoimmune comorbidities. Diabetes, 68 (6). pp. 1251-1266
  • Kling J, Jordan M, Pitt L, Meiners J, Thanh-Tran T, Son Tran L, Nguyen T, Mittal D, Villani R, Steptoe R, Khosrotehrani K, Berzins S, Baxter A, Godfrey D, Blumenthal A and (2018) Temporal regulation of natural killer T cell interferon gamma responses by β-catenin-dependent and -independent Wnt signaling. Frontiers in Immunology, 9.
  • Schultz T, Wiesmueller K, Lucas M, Dobos K, Baxter A and Blumenthal A (2018) The N-terminal peptide moiety of the Mycobacterium tuberculosis 19 kDa lipoprotein harbors RP105-agonistic properties. Journal of Leukocyte Biology, 103 (2). pp. 311-319
  • Zeng B, Middelberg A, Gemiarto A, Macdonald K, Baxter A, Talekar M, Moi D, Tullett K, Caminschi I, Lahoud M, Mazzieri R, Dolcetti R and Thomas R (2018) Self-adjuvanting nanoemulsion targeting dendritic cell receptor Clec9A enables antigen-specific immunotherapy. Journal of Clinical Investigation, 128 (5). pp. 1971-1984
  • Field J, Fox A, Jordan M, Baxter A, Spelman T, Gresle M, Butzkueven H, Kilpatrick T and Rubio J (2017) Interleukin-2 receptor-alpha proximal promoter hypomethylation is associated with multiple sclerosis. Genes and Immunity, 18. pp. 59-66
  • Mariño E, Richards J, McLeod K, Stanley D, Yap Y, Knight J, Mckenzie C, Kranich J, Oliveira A, Rossello F, Krishnamurthy B, Nefzger C, Macia L, Thorburn A, Baxter A, Morohan G, Wong L, Polo J, Moore R, Lockett T, Clarke J, Topping D, Harrison L and Mackay C (2017) Gut microbial metabolites limit the frequency of autoimmune T cells and protect against type 1 diabetes. Nature Immunology, 18. pp. 552-562
Book Chapters

ResearchOnline@JCU stores 111+ research outputs authored by Prof Alan Baxter from 1989 onwards.

Current Funding

Current and recent Research Funding to JCU is shown by funding source and project.

Tropical Australian Academic Health Centre Limited - Contract Research

Genomics of lung cancer in Indigenous people of North Queensland

Indicative Funding
$50,000 over 1 year
Cancer genomic profiling is a major determinant of chemotherapy selection for non-small cell lung cancer and is widely used internationally. Indigenous genomes carry ~10X more uncharacterised DNA sequence variation than people of European heritage. THHS is currently trialling the use of whole exome sequencing, instead of the existing 4 gene panel, to base choice of targeted therapies in lung cancer. This creates an opportunity to study whether the cancer-associated variation currently being used to select therapies is adequate, and if not, these data will form the foundation for an NHMRC funding application to identify improved markers.
Alan Baxter, Sabe Sabesan, Martin Nakata, Margaret Jordan, Justin Lee and Letitia Smith in collaboration with Matt Brown and Trevor Prior (College of Public Health, Medical & Vet Sciences, Townsville Hospital and Health Services, Indigenous Education & Research Centre and Queensland University of Technology)
Cancer; Non-small cell lung cancer; Genomics; Whole exome sequencing; Indigenous health care; Closing The Gap

Queensland Health - Queensland Genomics Health Alliance Project Fund

Bringing Modern Genomics to the Management of Lung Cancer in Queensland

Indicative Funding
$221,388 over 1 year (administered by QUT)
Our project will overcome many of the issues slowing the implementation of cancer genomics and personalised medicine in the state, including (and where relevant, in partnership with the QGHA capability projects): ? We will develop models of care covering all aspects from consent, sample collection and handling, genomic profiling, data analysis and reporting of both somatic and heritable variants, to enable clinical uptake. ? We will develop education programs for health care workers and patients. ? We will establish protocols for cancer genomics in Indigenous populations in consensus with Indigenous communities. ? We will perform a comprehensive analysis of the performance of all aspects of the upgraded model of care and compare it with the current standard of care to identify areas for improvement, and to establish the case for its broader implementation. A system of performance analysis and systems improvement will be built into the care pathways developed, to ensure continuous service improvement beyond the life of this project.
Paul Leo, Ken O'Byrne, Fong Kwun, Ian Yang, Stephen Fox, Jayesh Desai, Alan Baxter, Emily Callander, Sabe Sabesan, Jacinta Elston and Nick Graves (Queensland University of Technology, Princess Alexandra Hospital, The Prince Charles Hospital, The University of Queensland, Peter MacCallum Cancer Institute, College of Public Health, Medical & Vet Sciences, Australian Institute of Tropical Health & Medicine, College of Medicine & Dentistry and Academy - THM)
Genomics; Lung Cancer; Clinical care

Multiple Sclerosis Research Australia - Project Grant

An immune transcriptional regulatory network approach to Multiple Sclerosis

Indicative Funding
$240,000 over 4 years
Multiple Sclerosis (MS) is an autoimmune disease resulting from a complex interaction between genetic and environmental factors. In an attempt to understand the integration of both sets of risk factors, we have compared mRNA transcripts between relapsing/remitting (RR) MS patients and healthy controls in 5 leukocyte subsets: CD4 and CD8 T cells, B cells, NK cells and monocytes. A gene co-expression network was generated based on correlation of expression levels across >700 gene expression microarrays, and a major co-ordinately regulated sub-network (module) of mRNA transcripts that is differentially expressed in the monocytes of RR-MS patients was identified. This project validates, characterizes and attempts to manipulate this transcriptional module in human cells ex-vivo and in the experimental autoimmune encephalomyelitis (EAE) model of central nervous system (CNS) autoimmunity. These results should provide greater explanatory power than the analyses of individual risk factors separately and may provide a multi-faceted target for intervention.
Alan Baxter, Margaret Jordan, Helmut Butzkueven and Louise Laverick in collaboration with Letitia Smith (College of Public Health, Medical & Vet Sciences and The University of Melbourne)
Autoimmunity; Cellular Immunology; Immunogenetics; Multiple Sclerosis; mouse models; humans

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These Higher Degree Research projects are either current or by students who have completed their studies within the past 5 years at JCU. Linked titles show theses available within ResearchOnline@JCU.


The map shows research collaborations by institution from the past 7 years.
Note: Map points are indicative of the countries or states that institutions are associated with.

  • 5+ collaborations
  • 4 collaborations
  • 3 collaborations
  • 2 collaborations
  • 1 collaboration
  • Indicates the Tropics (Torrid Zone)

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