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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

141 - 160 of 209 works

2019

Journal Article

Gastrointestinal ultrasound in inflammatory bowel disease care: patient perceptions and impact on disease‐related knowledge

Rajagopalan, Arvind, Sathananthan, Dharshan, An, Yoon‐Kyo, Van De Ven, Lucinda, Martin, Serena, Fon, James, Costello, Samuel P, Begun, Jakob and Bryant, Robert V (2019). Gastrointestinal ultrasound in inflammatory bowel disease care: patient perceptions and impact on disease‐related knowledge. JGH Open, 4 (2) jgh3.12268, 267-272. doi: 10.1002/jgh3.12268

Gastrointestinal ultrasound in inflammatory bowel disease care: patient perceptions and impact on disease‐related knowledge

2019

Journal Article

Distinct tissue-specific roles for the disease-associated autophagy genes ATG16L2 and ATG16L1

Khor, Bernard, Conway, Kara L., Omar, Abdifatah S., Biton, Moshe, Haber, Adam L., Rogel, Noga, Baxt, Leigh A., Begun, Jakob, Kuballa, Petric, Gagnon, John D., Lassen, Kara G., Regev, Aviv and Xavier, Ramnik J. (2019). Distinct tissue-specific roles for the disease-associated autophagy genes ATG16L2 and ATG16L1. The Journal of Immunology, 203 (7), ji1800419-1829. doi: 10.4049/jimmunol.1800419

Distinct tissue-specific roles for the disease-associated autophagy genes ATG16L2 and ATG16L1

2019

Journal Article

MUC13 promotes the development of colitis-associated colorectal tumors via β-catenin activity

Sheng, Yong Hua, Wong, Kuan Yau, Seim, Inge, Wang, Ran, He, Yaowu, Wu, Andy, Patrick, Maya, Lourie, Rohan, Schreiber, Veronika, Giri, Rabina, Ng, Choa Ping, Popat, Amirali, Hooper, John, Kijanka, Gregor, Florin, Timothy H., Begun, Jakob, Radford, Kristen J., Hasnain, Sumaira and McGuckin, Michael A. (2019). MUC13 promotes the development of colitis-associated colorectal tumors via β-catenin activity. Oncogene, 38 (48), 7294-7310. doi: 10.1038/s41388-019-0951-y

MUC13 promotes the development of colitis-associated colorectal tumors via β-catenin activity

2019

Journal Article

Mindfulness based cognitive therapy experiences in youth with inflammatory bowel disease and depression: protocol for a mixed methods qualitative study

Ewais, Tatjana, Begun, Jake, Kenny, Maura, Headey, Alan and Kisely, Steve (2019). Mindfulness based cognitive therapy experiences in youth with inflammatory bowel disease and depression: protocol for a mixed methods qualitative study. JMIR Research Protocols, 8 (7) e14432, e14432. doi: 10.2196/14432

Mindfulness based cognitive therapy experiences in youth with inflammatory bowel disease and depression: protocol for a mixed methods qualitative study

2019

Conference Publication

Immune responses to the microbiome tune MHC class II antigen presentation by the intestinal epithelium to control gut pathology

Koyama, Motoko, Mukhopadhyay, Pamela, Schuster, Iona S., Henden, Andrea S., Hülsdünker, Jan, Varelias, Antiopi, Vetizou, Marie, Kuns, Rachel D., Robb, Renee J., Zhang, Ping, Blazar, Bruce R., Thomas, Ranjeny, Begun, Jakob, Waddell, Nicola, Trinchieri, Giorgio, Zeiser, Robert, Clouston, Andrew D., Degli-Esposti, Mariapia A. and Hill, Geoffrey R. (2019). Immune responses to the microbiome tune MHC class II antigen presentation by the intestinal epithelium to control gut pathology. Immunology 2019™ Meeting, San Diego, CA United States, 9-13 May 2019. Rockville, MD United States: American Association of Immunologists. doi: 10.4049/jimmunol.202.supp.69.38

Immune responses to the microbiome tune MHC class II antigen presentation by the intestinal epithelium to control gut pathology

2019

Journal Article

Interleukin-22: friend or foe?

Hasnain, Sumaira Z. and Begun, Jakob (2019). Interleukin-22: friend or foe?. Immunology and Cell Biology, 97 (4), 355-357. doi: 10.1111/imcb.12249

Interleukin-22: friend or foe?

2019

Journal Article

Clinical decision support improves quality of care in patients with ulcerative colitis

Jackson, Belinda, Begun, Jake, Gray, Kathleen, Churilov, Leonid, Liew, Danny, Knowles, Simon and De Cruz, Peter (2019). Clinical decision support improves quality of care in patients with ulcerative colitis. Alimentary Pharmacology and Therapeutics, 49 (8), 1040-1051. doi: 10.1111/apt.15209

Clinical decision support improves quality of care in patients with ulcerative colitis

2019

Journal Article

Protocol for a pilot randomised controlled trial of mindfulness-based cognitive therapy in youth with inflammatory bowel disease and depression

Ewais, Tatjana, Begun, Jake, Kenny, Maura, Chuang, Kai-Hsiang, Barclay, Johanna, Hay, Karen and Kisely, Steve (2019). Protocol for a pilot randomised controlled trial of mindfulness-based cognitive therapy in youth with inflammatory bowel disease and depression. BMJ Open, 9 (4) e025568, e025568. doi: 10.1136/bmjopen-2018-025568

Protocol for a pilot randomised controlled trial of mindfulness-based cognitive therapy in youth with inflammatory bowel disease and depression

2019

Conference Publication

Endoscopic balloon dilatation is safe and has a high success rate in patients with stricturing Crohn's disease

Lim, E., Thai, M., Hendy, P., Alchlaihawi, M., Leong, R., Connor, S., Ng, W., Gu, B., van Langenberg, D., Thin, L., Schulberg, J., Kamm, M., Gilmore, R., Taylor, K., Sallis, O., Andrews, J., Daker, C., Barclay, M., Wark, G., Ghaly, S., Begun, M., Krishnaprasad, K. and Begun, J. (2019). Endoscopic balloon dilatation is safe and has a high success rate in patients with stricturing Crohn's disease. 14th Congress of ECCO, Copenhagen, Denmark, 6-9 March 2019. Oxford, United Kingdom: Oxford University Press. doi: 10.1093/ecco-jcc/jjy222.647

Endoscopic balloon dilatation is safe and has a high success rate in patients with stricturing Crohn's disease

2019

Conference Publication

Switching Australian patients with moderate to severe inflammatory bowel disease from originator infliximab to biosimilar Inflectra: Interim results from a multicenter parallel cohort study

Haifer, C., Srinivasan, A., Menon, S., An, Y., Picardo, S., Van Langenberg, D., Begun, J., Ghaly, S. and Thin, L. (2019). Switching Australian patients with moderate to severe inflammatory bowel disease from originator infliximab to biosimilar Inflectra: Interim results from a multicenter parallel cohort study. Gastroenterological Society of Australia (GESA) Australian Gastroenterology Week (AGW) “The Universe Within”, Adelaide, SA, Australia, 8–10 September 2019. Richmond, VIC, Australia: Wiley-Blackwell Publishing Asia. doi: 10.1111/jgh.14801

Switching Australian patients with moderate to severe inflammatory bowel disease from originator infliximab to biosimilar Inflectra: Interim results from a multicenter parallel cohort study

2019

Conference Publication

Investigating the role of bioactives produced by gut bacteria to modulate immune response in inflammatory bowel disease

Giri, R., Cuiv, P. O. and Begun, J. (2019). Investigating the role of bioactives produced by gut bacteria to modulate immune response in inflammatory bowel disease. Gastroenterological Society of Australia (GESA) Australian Gastroenterology Week (AGW) “The Universe Within”, Adelaide, Australia, 8-10 September 2019. Hoboken, NJ, United States: Wiley-Blackwell. doi: 10.1111/jgh.14800

Investigating the role of bioactives produced by gut bacteria to modulate immune response in inflammatory bowel disease

2019

Journal Article

A systematic review and meta-analysis of mindfulness based interventions and yoga in inflammatory bowel disease

Ewais, Tatjana, Begun, Jake, Kenny, Maura, Rickett, Kirsty, Hay, Karen, Ajilchi, Bita and Kisely, Steve (2019). A systematic review and meta-analysis of mindfulness based interventions and yoga in inflammatory bowel disease. Journal of Psychosomatic Research, 116, 44-53. doi: 10.1016/j.jpsychores.2018.11.010

A systematic review and meta-analysis of mindfulness based interventions and yoga in inflammatory bowel disease

2019

Conference Publication

Effectiveness of fecal calprotectin testing to identify patients with organic gastrointestinal diseases: a systematic review and diagnostic meta-analysis

An, Y., Prince, D., Gardiner, F., Linedale, E., Andrews, J., Connor, S. and Begun, J. (2019). Effectiveness of fecal calprotectin testing to identify patients with organic gastrointestinal diseases: a systematic review and diagnostic meta-analysis. Gastroenterological Society of Australia (GESA) Australian Gastroenterology Week (AGW) “The Universe Within”, Adelaide, South Australia, 8-10 September 2019. Richmond, VIC, Australia: Wiley-Blackwell Publishing Asia. doi: 10.1111/jgh.14803

Effectiveness of fecal calprotectin testing to identify patients with organic gastrointestinal diseases: a systematic review and diagnostic meta-analysis

2019

Conference Publication

On the role of inflammation in acute paracetamol injury

Alabbas, Saleh, Movva, Ramya, Begun, Jakob, Florin, Timothy and Oancea, Iulia (2019). On the role of inflammation in acute paracetamol injury. International Liver Congress, Vienna Austria, 10-14 April 2019. Amsterdam, Netherlands: Elsevier. doi: 10.1016/S0618-8278(19)30823-0

On the role of inflammation in acute paracetamol injury

2018

Journal Article

Letter: vedolizumab drug concentrations in neonates following intrauterine exposure

Flanagan, Emma, Gibson, Peter R., Begun, Jakob, Ghaly, Simon, Garg, Mayur, Andrews, Jane M., Rosella, Ourania, Rosella, Gennaro and Bell, Sally J. (2018). Letter: vedolizumab drug concentrations in neonates following intrauterine exposure. Alimentary Pharmacology and Therapeutics, 48 (11-12), 1328-1330. doi: 10.1111/apt.15027

Letter: vedolizumab drug concentrations in neonates following intrauterine exposure

2018

Conference Publication

Predictors in inflammatory bowel disease: Looking into the magic ball: session one summary

Begun, Jakob (2018). Predictors in inflammatory bowel disease: Looking into the magic ball: session one summary. The Takeda Symposium, Melbourne, VIC Australia, 17 – 18 March 2018. Richmond, VIC Australia: Wiley-Blackwell. doi: 10.1111/jgh.14415

Predictors in inflammatory bowel disease: Looking into the magic ball: session one summary

2018

Conference Publication

Enteric microbiota shape the inflammatory response in mice with a Muc2 misfolding mutation

Wang, R., Giri, R., Moniruzzaman, M., Tong, H., Wong, K. Y., Begun, J., McGuckin, M. A. and Hasnain, S. Z. (2018). Enteric microbiota shape the inflammatory response in mice with a Muc2 misfolding mutation. Gastroenterological Society of Australia (GESA) Australian Gastroenterology Week (AGW) “Gut Matters”, Brisbane, QLD, Australia, 8-10 September 2018. Richmond, VIC, Australia: John Wiley & Sons.

Enteric microbiota shape the inflammatory response in mice with a Muc2 misfolding mutation

2018

Journal Article

Personalizing inflammatory bowel disease treatment symposium: Foreward

Begun, Jakob (2018). Personalizing inflammatory bowel disease treatment symposium: Foreward. Journal of Gastroenterology and Hepatology, 33 (S3), 3-3. doi: 10.1111/jgh.14414

Personalizing inflammatory bowel disease treatment symposium: Foreward

2018

Journal Article

Enterococcus faecalis AHG0090 is a genetically tractable bacterium and produces a secreted peptidic bioactive that suppresses nuclear factor Kappa B activation in human gut epithelial cells

Ó Cuív, Páraic, Giri, Rabina, Hoedt, Emily C., McGuckin, Michael A., Begun, Jakob and Morrison, Mark (2018). Enterococcus faecalis AHG0090 is a genetically tractable bacterium and produces a secreted peptidic bioactive that suppresses nuclear factor Kappa B activation in human gut epithelial cells. Frontiers in Immunology, 9 (April) 790, 790. doi: 10.3389/fimmu.2018.00790

Enterococcus faecalis AHG0090 is a genetically tractable bacterium and produces a secreted peptidic bioactive that suppresses nuclear factor Kappa B activation in human gut epithelial cells

2018

Journal Article

The role of IL-22 in the resolution of sterile and nonsterile inflammation

Alabbas, Saleh Y, Begun, Jakob, Florin, Timothy H and Oancea, Iulia (2018). The role of IL-22 in the resolution of sterile and nonsterile inflammation. Clinical and Translational Immunology, 7 (4) e1017, e1017. doi: 10.1002/cti2.1017

The role of IL-22 in the resolution of sterile and nonsterile inflammation

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

    Study of TOfacitinib for the treatment of chronic Pouchitis

    Principal Advisor

    Other advisors: Professor Gerald Holtmann

  • 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

    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

  • Doctor Philosophy

    Bacteria x Archaea Interactions in Crohn's disease

    Associate Advisor

    Other advisors: Professor Mark Morrison

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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