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Associate Professor Jakob Begun
Associate Professor

Jakob Begun

Email: 

Overview

Background

Associate Professor Jakob Begun is the IBD Group leader in the Immunity, Infection, and Inflammation Program at Mater Research University of Queensalnd, and has a basic and translational laboratory at the Translational Research Institute in Brisbane. He is an Associate Professor in the University of Queensland Faculty of Medicine. After completing his Bachelor of Science at Cornell University Jakob attended Cambridge University where he completed an MPhil in Biochemistry. He then moved on to Harvard Medical School where he completed his MD and PhD in genetics studying the host pathogen interaction using C. elegans as a model system. He completed his clinical training in internal medicine at Brigham and Women’s hospital and went on to complete general gastroenterology training at Massachusetts General Hospital (MGH) as well as advanced training in the treatment of Inflammatory Bowel Disease (IBD).

Dr Begun first joined Mater Research - University of Queensland in 2014, and at the same time received a clinical staff appointment in Gastroenterology at the Mater Hospital Brisbane. His clinical activities are focussed on the treatment and mangement of patients with IBD. He is the director of the IBD unit at the Mater Hospital Brisbane and at the Mater Young Adult Health Centre Brisbane .In January 2015 he was awarded the University of Queensland Reginald Ferguson Fellowship in Gastroenterology to support his research activity. He leads a basic and translational laboratory at the Translational Research Institute investigating the interaction between the innate immune system and the gut microbiome, as well as genetic contributions to disease. He also performs clinical research examining predictors of response to therapy, minimising barriers of care for adolescents and young adults with IBD, improving outcomes in pregnancy and IBD, and the use of intestinal ultrasound in IBD. He is the chair of the Gastroenterology Society of Australia-IBD Faculty and of the president of the Gastroenterology Network of Intestinal Ultrasound (GENIUS).

Availability

Associate Professor Jakob Begun is:
Available for supervision
Media expert

Qualifications

  • Bachelor of Biology, Cornell University
  • Doctoral Diploma of Medicine, Harvard University
  • Doctor of Philosophy of Genetics, Harvard University
  • Member, Gastroenterological Society of Australia, Gastroenterological Society of Australia
  • Fellow, Royal Australasian College of Physicians, Royal Australasian College of Physicians

Research impacts

Inflammatory bowel disease(IBD) is a complex disease with genetic and environmental triggers. The microbiota is one of the biggest environmental contributors and interest in its impact on human health and disease is a growing. Studies in IBD have led the way in identifying disease associated microbial signals, but has not yet led to any new therapies.

As a clinician-scientist I am driven by my patients’ needs to address all aspects of their disease: including genetic and environmental risk factors, disease monitoring, and developing novel therapeutics. My tranlsational research program contributes to KNOWLEDGE IMPACT by discovering the function of IBD-susceptibility genes and anti-inflammatory bio-actives produced by the gut microbiota. My clinical research program advances HEALTH IMPACT by optimizing patient monitoring through evidence-based use of biochemical tests and imaging technology.

-Knowledge Impact. My research into the interaction between IBD susceptibility genes and bacterial handling has been highly cited, and led to an NHMRC collaborative project grant.

-Health Impact. My research program into advances in patient monitoring has led to the application for faecal calprotectin testing to be covered by the Medicare Benefit Scheme – which will have a direct impact on patient monitoring in the clinic. Additionally my monitoring research into the use of intestinal ultrasound has led to the formation of the Gastroenterology Network of Intestinal Ultrasound and the increase in ultrasound use in IBD patients in Australia.

Works

Search Professor Jakob Begun’s works on UQ eSpace

209 works between 1996 and 2025

161 - 180 of 209 works

2018

Journal Article

Gastrointestinal ultrasound in inflammatory bowel disease: an underused resource with potential paradigm-changing application

Bryant, Robert Venning, Friedman, Antony, Wright, Emily Kate, Taylor, Kirstin, Begun, Jakob, Maconi, Giovanni, Maaser, Christian, Novak, Kerri L., Kucharzik, Torsten, Atkinson, Nathan S. S., Asthana, Anil and Gibson, Peter R. (2018). Gastrointestinal ultrasound in inflammatory bowel disease: an underused resource with potential paradigm-changing application. Gut, 67 (5), 973-985. doi: 10.1136/gutjnl-2017-315655

Gastrointestinal ultrasound in inflammatory bowel disease: an underused resource with potential paradigm-changing application

2018

Journal Article

P328 Crohn’s colitis care (CCCare): development and testing of a bespoke cloud-based clinical management system for inflammatory bowel disease (IBD)

Krishnaprasad, K, Walsh, A, Begun, J, Bell, S, Carter, D, Grafton, R, Sechi, A, Sewell, K, McMahon, A, Connor, S, Radford-Smith, G, Andrews, J and Consortium, Crohn's Colitis Cure ANZIBD (2018). P328 Crohn’s colitis care (CCCare): development and testing of a bespoke cloud-based clinical management system for inflammatory bowel disease (IBD). Journal of Crohn's and Colitis, 12 (supplement_1). doi: 10.1093/ecco-jcc/jjx180.455

P328 Crohn’s colitis care (CCCare): development and testing of a bespoke cloud-based clinical management system for inflammatory bowel disease (IBD)

2018

Conference Publication

Positioning biologics-A case-based discussion: Ustekinumab

Begun, Jakob (2018). Positioning biologics-A case-based discussion: Ustekinumab. Personalizing Inflammatory Bowel Disease Treatment, Melbourne, Australia, 17-18 March 2018. Richmond, VIC, Australia: Wiley-Blackwell. doi: 10.1111/jgh.14423

Positioning biologics-A case-based discussion: Ustekinumab

2018

Conference Publication

Crohn's colitis care (CCCare): development and testing of a bespoke cloud-based clinical management system for inflammatory bowel disease (IBD)

Krishnaprasad, K., Walsh, A., Begun, J., Bell, S., Carter, D., Grafton, R., Sechi, A., Sewell, K., McMahon, A., Connor, S., Radford-Smith, G. and Andrews, J. (2018). Crohn's colitis care (CCCare): development and testing of a bespoke cloud-based clinical management system for inflammatory bowel disease (IBD). 13th Congress of ECCO, Vienna, Austria, 14-17 February 2018. Oxford, United Kingdom: Oxford University Press.

Crohn's colitis care (CCCare): development and testing of a bespoke cloud-based clinical management system for inflammatory bowel disease (IBD)

2018

Conference Publication

Selectively targeting the gut in inflammatory bowel disease: session four summary

Begun, Jakob (2018). Selectively targeting the gut in inflammatory bowel disease: session four summary. Personalizing Inflammatory Bowel Disease Treatment, Melbourne, Australia, 17-18 March 2018. Richmond, VIC, Australia: Wiley-Blackwell. doi: 10.1111/jgh.14430

Selectively targeting the gut in inflammatory bowel disease: session four summary

2017

Journal Article

Review article: consensus statements on therapeutic drug monitoring of anti-tumour necrosis factor therapy in inflammatory bowel diseases

Mitrev, N., Vande Casteele, N., Seow, C. H., Andrews, J. M., Connor, S. J., Moore, G. T., Barclay, M., Begun, J., Bryant, R., Chan, W., Corte, C., Ghaly, S., Lemberg, D. A., Kariyawasam, V., Lewindon, P., Martin, J., Mountifield, R., Radford-Smith, G., Slobodian, P., Sparrow, M., Toong, C., van Langenberg, D., Ward, M. G. and Leong, R. W. (2017). Review article: consensus statements on therapeutic drug monitoring of anti-tumour necrosis factor therapy in inflammatory bowel diseases. Alimentary Pharmacology & Therapeutics, 46 (11-12), 1037-1053. doi: 10.1111/apt.14368

Review article: consensus statements on therapeutic drug monitoring of anti-tumour necrosis factor therapy in inflammatory bowel diseases

2017

Journal Article

Colonic thioguanine pro-drug: investigation of microbiome and novel host metabolism

Florin, Timothy, Movva, Ramya, Begun, Jakob, Duley, John, Oancea, Iulia and O Cuiv, Paraic (2017). Colonic thioguanine pro-drug: investigation of microbiome and novel host metabolism. Gut Microbes, 9 (2), 1-4. doi: 10.1080/19490976.2017.1387343

Colonic thioguanine pro-drug: investigation of microbiome and novel host metabolism

2017

Journal Article

The gut bacterium and pathobiont Bacteroides vulgatus activates NF-κB in a human gut epithelial cell line in a strain and growth phase dependent manner

Cuív, Páraic Ó., de Wouters, Tomas, Giri, Rabina, Mondot, Stanislas, Smith, Wendy J., Blottière, Hervé M., Begun, Jakob and Morrison, Mark (2017). The gut bacterium and pathobiont Bacteroides vulgatus activates NF-κB in a human gut epithelial cell line in a strain and growth phase dependent manner. Anaerobe, 47, 209-217. doi: 10.1016/j.anaerobe.2017.06.002

The gut bacterium and pathobiont Bacteroides vulgatus activates NF-κB in a human gut epithelial cell line in a strain and growth phase dependent manner

2017

Journal Article

Cancer therapeutics with epigallocatechin-3-gallate encapsulated in biopolymeric nanoparticles

Tyagi, Nisha, De, Ranjit, Begun, Jakob and Popat, Amirali (2017). Cancer therapeutics with epigallocatechin-3-gallate encapsulated in biopolymeric nanoparticles. International Journal of Pharmaceutics, 518 (1-2), 220-227. doi: 10.1016/j.ijpharm.2016.12.030

Cancer therapeutics with epigallocatechin-3-gallate encapsulated in biopolymeric nanoparticles

2017

Conference Publication

A Randomized Controlled Trial of Mindfulness-Based Cognitive Therapy for Youth Living with Inflammatory Bowel Disease and Depression

Ewais, T., Begun, J., Barclay, J., Tefay, M. and Tremellen, A. (2017). A Randomized Controlled Trial of Mindfulness-Based Cognitive Therapy for Youth Living with Inflammatory Bowel Disease and Depression. American Psychiatric Association 2017 Annual Meeting, San Diego, 20-24 May 2017. London, United Kingdom: Sage Publications .

A Randomized Controlled Trial of Mindfulness-Based Cognitive Therapy for Youth Living with Inflammatory Bowel Disease and Depression

2017

Conference Publication

Endoscopic balloon dilatation has a high success rate and appears to reduce the need for surgery in patients with stricturing Crohn's disease

Lim, E., Thai, M., Hendy, P., Alchlaihawi, M., Leong, R. and Begun, J. (2017). Endoscopic balloon dilatation has a high success rate and appears to reduce the need for surgery in patients with stricturing Crohn's disease. Australian Gastroenterology Week: Precision Medicine in Gastroenterology, Gold Coast, Queensland, 20-22 August 2017. Richmond, VIC, Australia: Wiley-Blackwell.

Endoscopic balloon dilatation has a high success rate and appears to reduce the need for surgery in patients with stricturing Crohn's disease

2017

Conference Publication

Factors influencing the need for endoscopic intervention in esophageal meat bolus impaction: a retrospective, multicenter study

Cheng, D., Lee, R., Lee, A., Begun, J. and St John, A. (2017). Factors influencing the need for endoscopic intervention in esophageal meat bolus impaction: a retrospective, multicenter study. Australian Gastroenterology Week: Precision Medicine in Gastroenterology, Gold Coast, Queensland, 20-22 August 2017. Richmond, VIC, Australia: Wiley-Blackwell.

Factors influencing the need for endoscopic intervention in esophageal meat bolus impaction: a retrospective, multicenter study

2017

Conference Publication

Role of anti-inflammatory gut bioactives in the modulation of immune response in Crohn's disease

Giri, R., Cuiv, P. O. and Begun, J. (2017). Role of anti-inflammatory gut bioactives in the modulation of immune response in Crohn's disease. Gastroenterological Society of Australia Australian Gastroenterology Week Precision Medicine in Gastroenterology, Gold Coast, QLD Australia, 20–22 August 2017. Richmond, VIC Australia: Wiley.

Role of anti-inflammatory gut bioactives in the modulation of immune response in Crohn's disease

2017

Conference Publication

Subsets of innate lymphoid cells in acute liver injury

Alabbas, S. Y., Mowa, R., Purdon, A. S., Begun, J., Florin, T. H. and Oancea, I. (2017). Subsets of innate lymphoid cells in acute liver injury. Australian Gastroenterology Week: Precision Medicine in Gastroenterology, Gold Coast, Queensland, 20-22 August 2017. HOBOKEN: Wiley-Blackwell.

Subsets of innate lymphoid cells in acute liver injury

2017

Conference Publication

Targeting interleukin-23(p19) secretion from intestinal epithelial cells to improve intestinal barrier integrity in inflammatory bowel disease

Wang, R., Lourie, R., Tong, H., Giri, R., Schreiber, V., Begun, J., Florin, T., McGuckin, M. A. and Hasnain, S. Z. (2017). Targeting interleukin-23(p19) secretion from intestinal epithelial cells to improve intestinal barrier integrity in inflammatory bowel disease. Gastroenterological Society of Australia Australian Gastroenterology Week Precision Medicine in Gastroenterology, Gold Coast, QLD Australia, 20–22 August 2017. Richmond, VIC Australia: Wiley.

Targeting interleukin-23(p19) secretion from intestinal epithelial cells to improve intestinal barrier integrity in inflammatory bowel disease

2016

Journal Article

The role of barrier function, autophagy, and cytokines in maintaining intestinal homeostasis

Elshaer, Dana and Begun, Jakob (2016). The role of barrier function, autophagy, and cytokines in maintaining intestinal homeostasis. Seminars in Cell and Developmental Biology, 61, 51-59. doi: 10.1016/j.semcdb.2016.08.018

The role of barrier function, autophagy, and cytokines in maintaining intestinal homeostasis

2016

Journal Article

Colonic microbiota can promote rapid local improvement of murine colitis by thioguanine independently of T lymphocytes and host metabolism

Oancea, I., Movva, R., Das, I., Aguirre de Carcer, D., Schreiber, V., Yang, Y., Purdon, A., Harrington, B., Proctor, M., Wang, R., Sheng, Y., Lobb, M., Lourie, R., Cuiv, P.O., Duley, J.A., Begun, J. and Florin, T.H.J. (2016). Colonic microbiota can promote rapid local improvement of murine colitis by thioguanine independently of T lymphocytes and host metabolism. Gut, 66 (1), 59-69. doi: 10.1136/gutjnl-2015-310874

Colonic microbiota can promote rapid local improvement of murine colitis by thioguanine independently of T lymphocytes and host metabolism

2016

Journal Article

High fat diets induce colonic epithelial cell stress and inflammation that is reversed by IL-22

Gulhane, Max, Murray, Lydia, Lourie, Rohan, Tong, Hui, Sheng, Yong H., Wang, Ran, Kang, Alicia, Schreiber, Veronika, Wong, Kuan Yau, Magor, Graham, Denman, Stuart, Begun, Jakob, Florin, Timothy H., Perkins, Andrew, Cuiv, Paraic O., McGuckin, Michael A. and Hasnain, Sumaira Z. (2016). High fat diets induce colonic epithelial cell stress and inflammation that is reversed by IL-22. Scientific Reports, 6 (1) 28990, 28990. doi: 10.1038/srep28990

High fat diets induce colonic epithelial cell stress and inflammation that is reversed by IL-22

2016

Journal Article

Genetic coding variant in GPR65 alters lysosomal pH and links lysosomal dysfunction with colitis risk

Lassen, Kara G., McKenzie, Craig I., Mari, Muriel, Murano, Tatsuro, Begun, Jakob, Baxt, Leigh A., Goel, Gautam, Villablanca, Eduardo J., Kuo, Szu-Yu, Huang, Hailiang, Macia, Laurence, Bhan, Atul K., Batten, Marcel, Daly, Mark J., Reggiori, Fulvio, Mackay, Charles R. and Xavier, Ramnik J. (2016). Genetic coding variant in GPR65 alters lysosomal pH and links lysosomal dysfunction with colitis risk. Immunity, 44 (6), 1392-1405. doi: 10.1016/j.immuni.2016.05.007

Genetic coding variant in GPR65 alters lysosomal pH and links lysosomal dysfunction with colitis risk

2016

Conference Publication

Inflammatory bowel disease in the clinic: escalation and de-escalation of therapy: a longitudinal case-based discussion

Begun, Jakob (2016). Inflammatory bowel disease in the clinic: escalation and de-escalation of therapy: a longitudinal case-based discussion. The Takeda Symposium, Sydney, NSW Australia, 13-14 February 2016. Richmond, VIC, Australia: Wiley-Blackwell Publishing Asia. doi: 10.1111/jgh.13348

Inflammatory bowel disease in the clinic: escalation and de-escalation of therapy: a longitudinal case-based discussion

Funding

Current funding

  • 2024 - 2026
    Gut Health anti-inflammatory potential of Yumbah abalone and mussels
    Marine Bioproducts Cooperative Research Centre
    Open grant
  • 2024 - 2027
    Harnessing microbial immunomodulatory function to improve treatment of inflammatory bowel diseases
    NHMRC IDEAS Grants
    Open grant
  • 2023 - 2028
    Immunity, Infection and Inflammation Program at MRI-UQ
    Mater Foundation
    Open grant
  • 2023 - 2025
    Understanding the regulation and function of OTUD3, a novel ulcerative colitis gene
    The Gutsy Group Inflammatory Bowel Disease Research Grants
    Open grant

Past funding

  • 2023 - 2025
    Epithelial tissue mechanics: a new key to relapse in chronic inflammatory bowel disease
    United States Congressionally Directed Medical Research Programs - Peer Reviewed Medical Research Program
    Open grant
  • 2021 - 2024
    Drugs from Bugs: Developing New Inflammatory Bowel Disease Drugs from Gut Bacteria-Derived Bioactives
    United States Congressionally Directed Medical Research Programs - Peer Reviewed Medical Research Program
    Open grant
  • 2020 - 2021
    Functionally characterizing IBD dysbiosis and harnessing gut bioactives to suppress IL-23 driven inflammation
    The Global Grants for Gut Health
    Open grant
  • 2019
    Improving IBD treatment through harnessing the microbiome and improving outcomes in young adults with IBD
    Ferguson Foundation (Reginald Ferguson)
    Open grant
  • 2018 - 2020
    Mater Health Services IBD Biobank
    Research Donation Generic
    Open grant
  • 2018 - 2022
    The regulatory role of Clec12A in antigen presentation and inflammatory disease (NHMRC Project Grant led by Monash University)
    Monash University
    Open grant
  • 2017 - 2020
    Invention of a Genetic Toolkit for Immunomodulatory Gut Bacteria to Expedite the Development of New Crohn's Disease Therapeutics
    United States Congressionally Directed Medical Research Programs - Peer Reviewed Medical Research Program
    Open grant
  • 2017
    Identification of novel genetic causes of ulcerative colitis to inform individualised treatment
    Sylvia and Charles Viertel Charitable Foundation
    Open grant
  • 2015 - 2016
    Improving IBD treatment through an understanding of genetics and obstacles to adolescent care
    Ferguson Foundation (Reginald Ferguson)
    Open grant
  • 2014 - 2015
    Towards an oral IL-22 agonist for ulcerative colitis
    Ferring Research Institute
    Open grant

Supervision

Availability

Associate Professor Jakob Begun is:
Available for supervision

Before you email them, read our advice on how to contact a supervisor.

Supervision history

Current supervision

  • Doctor Philosophy

    Reducing post-operative Crohn's disease recurrence

    Principal Advisor

    Other advisors: Professor David Clark, Dr Rabina Giri

  • Doctor Philosophy

    Novel and real-world use of Janus Kinase inhibitors for the management of Inflammatory Bowel Disease

    Principal Advisor

  • Doctor Philosophy

    Microbial Regulation of Host Inflammatory Pathways in Inflammatory Bowel Disease

    Principal Advisor

    Other advisors: Professor Mark Morrison

  • Doctor Philosophy

    Study of TOfacitinib for the treatment of chronic Pouchitis

    Principal Advisor

    Other advisors: Professor Gerald Holtmann

  • Doctor Philosophy

    Study of TOfacitinib for the treatment of chronic Pouchitis

    Principal Advisor

    Other advisors: Professor Gerald Holtmann

  • Doctor Philosophy

    Bacteria x Archaea Interactions in Crohn's disease

    Associate Advisor

    Other advisors: Professor Mark Morrison

  • Doctor Philosophy

    Medicinal chemistry of new Nature-inspired treatments for Inflammatory Bowel Disease (IBD)

    Associate Advisor

    Other advisors: Dr Angela Salim, Dr Zeinab Khalil, Professor Rob Capon

  • Doctor Philosophy

    Designer Nanoparticles for Oral and Targeted Delivery of Protein Therapeutics

    Associate Advisor

    Other advisors: Dr Md Moniruzzaman, Professor Amirali Popat

  • Doctor Philosophy

    Designer Nanoparticles for Oral and Targeted Delivery of Protein Therapeutics

    Associate Advisor

    Other advisors: Dr Md Moniruzzaman, Professor Amirali Popat, Dr Rabina Giri

  • Doctor Philosophy

    Defining the Role of the Mucosa-Associated Microbiota in Digestive Health and Disease Using Novel ex-vivo Combinations of Microbe Culture with Metagenomics

    Associate Advisor

    Other advisors: Professor Mark Morrison

  • Doctor Philosophy

    Investigating immunomodulatory function of gut microbiome and FXR pathway in IBD

    Associate Advisor

    Other advisors: Dr Rabina Giri

Completed supervision

Media

Enquiries

Contact Associate Professor Jakob Begun directly for media enquiries about:

  • adolescent
  • autophagy
  • Crohn's disease
  • Inflammatory Bowel Disease
  • ulcerative colitis

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