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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

211 works between 1996 and 2025

61 - 80 of 211 works

2023

Conference Publication

Delayed flexible sigmoidoscopy remains a challenge in tertiary care of acute severe colitis

Rice, K., Fernandes, R., Hendy, P., Khoo, E., Walker, N., Howlett, M., An, Y-K and Begun, J. (2023). Delayed flexible sigmoidoscopy remains a challenge in tertiary care of acute severe colitis. Gastroenterological Society of Australia (GESA) Australian Gastroenterology Week (AGW) 2023, Brisbane, QLD Australia, 2-5 September 2023. Richmond, VIC Australia: John Wiley & Sons.

Delayed flexible sigmoidoscopy remains a challenge in tertiary care of acute severe colitis

2023

Conference Publication

From enemies to friends: Exploring the capacity of novel compounds secreted by "pathobiont" gut bacteria to attenuate inflammation in inflammatory bowel disease

Reed, H., Sehgal, A., Morrison, M. and Begun, J. (2023). From enemies to friends: Exploring the capacity of novel compounds secreted by "pathobiont" gut bacteria to attenuate inflammation in inflammatory bowel disease. Gastroenterological Society of Australia (GESA) Australian Gastroenterology Week (AGW) 2023, Brisbane, QLD Australia, 2—5 September 2023. Richmond, VIC Australia: John Wiley & Sons.

From enemies to friends: Exploring the capacity of novel compounds secreted by "pathobiont" gut bacteria to attenuate inflammation in inflammatory bowel disease

2023

Conference Publication

Cessation of corticosteroids after acute severe ulcerative colitis may be associated with increased colectomy risk: Results of the ANZ-ASUC study in collaboration with the ANZIBDC

Fernandes, R., Gilmore, R., Ruddick-Collins, L., Rice, K., Moore, G., Gazelakis, K., Vasudevan, A., Zhang, J., Wright, E., Schildkraut, T., Clark, N., Schultz, M., Brownson, A., Haifer, C., Bracken, L. M. L., Mahy, G., Swe, E., Judge, C., Ngoi, B., Lynch, K., Begun, J. and An, Y-K (2023). Cessation of corticosteroids after acute severe ulcerative colitis may be associated with increased colectomy risk: Results of the ANZ-ASUC study in collaboration with the ANZIBDC. Gastroenterological Society of Australia (GESA) Australian Gastroenterology Week (AGW) 2023, Brisbane, QLD Australia, 2—5 September 2023. Richmond, VIC Australia: John Wiley & Sons.

Cessation of corticosteroids after acute severe ulcerative colitis may be associated with increased colectomy risk: Results of the ANZ-ASUC study in collaboration with the ANZIBDC

2023

Conference Publication

Impact of point-of-care intestinal ultrasound in patients with inflammatory bowel disease

Tan, W. L., Barr, E., Pham, H., Fernandes, R., Khoo, E., An, Y-K and Begun, J. (2023). Impact of point-of-care intestinal ultrasound in patients with inflammatory bowel disease. Gastroenterological Society of Australia (GESA) Australian Gastroenterology Week (AGW) 2023, Brisbane, QLD Australia, 2-5 September 2023. Richmond, VIC Australia: John Wiley & Sons.

Impact of point-of-care intestinal ultrasound in patients with inflammatory bowel disease

2023

Conference Publication

Upadacitinib and vedolizumab combination therapy for recalcitrant, steroid-refractory Crohn's disease: A case report

Etchegaray, A., Gilmore, R., An, Y-K and Begun, J. (2023). Upadacitinib and vedolizumab combination therapy for recalcitrant, steroid-refractory Crohn's disease: A case report. Gastroenterological Society of Australia (GESA) Australian Gastroenterology Week (AGW) 2023, Brisbane, QLD Australia, 2—5 September 2023. Richmond, VIC Australia: John Wiley & Sons.

Upadacitinib and vedolizumab combination therapy for recalcitrant, steroid-refractory Crohn's disease: A case report

2023

Conference Publication

Patients from East Asia with acute severe ulcerative colitis have worse endoscopic severity but are more responsive to intravenous steroids than patients from Australasia: Preliminary results of the APAC-ASUC study in collaboration with the ANZIBDC and AOCC

Fernandes, R., Gilmore, R., Ruddick-Collins, L., Rice, K., Gazelakis, K., Moore, G., Vasudevan, A., Zhang, J., Wright, E., Schildkraut, T., Clark, N., Schultz, M., Brownson, A., Haifer, C., Bracken, L. M. L., Mahy, G., Swe, E., Lynch, K., Ngoi, B., Judge, C., Kim, D. H., Kim, H. S., Lee, H. S., Kim, K. O., Lee, Y. J., Kim, S-J, Lee, J., Song, E. M., Park, S. H. ... An, Y-K (2023). Patients from East Asia with acute severe ulcerative colitis have worse endoscopic severity but are more responsive to intravenous steroids than patients from Australasia: Preliminary results of the APAC-ASUC study in collaboration with the ANZIBDC and AOCC. Gastroenterological Society of Australia (GESA) Australian Gastroenterology Week (AGW) 2023, Brisbane, QLD Australia, 2-5 September 2023. Richmond, VIC Australia: John Wiley & Sons.

Patients from East Asia with acute severe ulcerative colitis have worse endoscopic severity but are more responsive to intravenous steroids than patients from Australasia: Preliminary results of the APAC-ASUC study in collaboration with the ANZIBDC and AOCC

2023

Conference Publication

Upadacitinib improves endoscopic outcomes in patients with moderate to severely active Crohn's disease irrespective of previous failure to respond to biologics or conventional therapies

Begun, J., Feagan, B., Horst, S., Dryden, G., Lindsay, J., Ferrante, M., Dubcenco, E., Lacerda, A., Ford, S., Anyanwu, S., Zhou, Q., Liu, J., Chen, M. and Schreiber, S. (2023). Upadacitinib improves endoscopic outcomes in patients with moderate to severely active Crohn's disease irrespective of previous failure to respond to biologics or conventional therapies. HOBOKEN: WILEY.

Upadacitinib improves endoscopic outcomes in patients with moderate to severely active Crohn's disease irrespective of previous failure to respond to biologics or conventional therapies

2023

Conference Publication

Australian multicenter real-world experience of upadacitinib induction therapy for moderate to severe ulcerative colitis

Gilmore, R., Fernandes, R., Hartley, I., Arzivian, A., Leong, R., Andrew, B., Vasudevan, A., Greeve, T., Moore, G., Kim, S., Lightowler, D., Singh, A., Mahy, G., Mithanthaya, A., Venugopal, K., Han, S., Bryant, R., Corte, C., Ding, J. N., An, Y-K and Begun, J. (2023). Australian multicenter real-world experience of upadacitinib induction therapy for moderate to severe ulcerative colitis. Gastroenterological Society of Australia (GESA) Australian Gastroenterology Week (AGW) 2023, Brisbane, QLD Australia, 2—5 September 2023. Richmond, VIC Australia: John Wiley & Sons.

Australian multicenter real-world experience of upadacitinib induction therapy for moderate to severe ulcerative colitis

2023

Conference Publication

Fistulizing Crohn's disease in a large real-world cohort: Crohn's Colitis Cure data insights program

Mcnamara, J., Wilson, W., Pipicella, J., Ghaly, S., Gearry, R., Forbes, A., Begun, J., Ng, W., Lynch, K., Lawrence, I., Schultz, M., Walker, G., Radford-Smith, G., Britt, L., Verdon, C., Andrews, J. and Connor, S. (2023). Fistulizing Crohn's disease in a large real-world cohort: Crohn's Colitis Cure data insights program. HOBOKEN: WILEY.

Fistulizing Crohn's disease in a large real-world cohort: Crohn's Colitis Cure data insights program

2023

Conference Publication

Real-world study finds similar effectiveness of biologics but higher durability of ustekinumab in patients with Crohn's disease: Preliminary results from the COMPARE-IT Crohn's disease study

Etchegaray, A., Fernandes, R., Anandan, A. Shanmuga, Selvanathan, P., Malloy, R., Gilmore, R., Pham, H., Begun, J. and An, Y-K (2023). Real-world study finds similar effectiveness of biologics but higher durability of ustekinumab in patients with Crohn's disease: Preliminary results from the COMPARE-IT Crohn's disease study. Gastroenterological Society of Australia (GESA) Australian Gastroenterology Week (AGW) 2023, Brisbane, QLD Australia, 2—5 September 2023. Richmond, VIC Australia: John Wiley & Sons.

Real-world study finds similar effectiveness of biologics but higher durability of ustekinumab in patients with Crohn's disease: Preliminary results from the COMPARE-IT Crohn's disease study

2023

Conference Publication

Reducing hospital resource utilization and improving patient satisfaction with an innovative inflammatory bowel disease nurse-led clinical care pathway with rapid-access intestinal ultrasound

Fernandes, R., Harris, H., Khoo, E., Gilmore, R., Howlett, M., Walker, N., Hendy, P., Begun, J. and An, Y-K (2023). Reducing hospital resource utilization and improving patient satisfaction with an innovative inflammatory bowel disease nurse-led clinical care pathway with rapid-access intestinal ultrasound. Gastroenterological Society of Australia (GESA) Australian Gastroenterology Week (AGW) 2023, Brisbane, QLD Australia, 2—5 September 2023. Richmond, VIC Australia: John Wiley & Sons.

Reducing hospital resource utilization and improving patient satisfaction with an innovative inflammatory bowel disease nurse-led clinical care pathway with rapid-access intestinal ultrasound

2023

Conference Publication

Vedolizumab has longer persistence than infliximab for ulcerative colitis in a real-world cohort study: Preliminary results from the COMPARE-IT study

Anandan, A. Shanmuga, Fernandes, R., Etchegaray, A., Malloy, R., Selvanathan, P., Gilmore, R., Pham, H., Begun, J. and An, Y-K (2023). Vedolizumab has longer persistence than infliximab for ulcerative colitis in a real-world cohort study: Preliminary results from the COMPARE-IT study. Gastroenterological Society of Australia (GESA) Australian Gastroenterology Week (AGW) 2023, Brisbane, QLD Australia, 2-5 September 2023. Richmond, VIC Australia: John Wiley & Sons.

Vedolizumab has longer persistence than infliximab for ulcerative colitis in a real-world cohort study: Preliminary results from the COMPARE-IT study

2023

Conference Publication

Australian consensus on ustekinumab in Crohn's disease

Begun, J., An, Y-K, Bryant, R., Christensen, B., Leong, R., Studd, C. and Thin, L. (2023). Australian consensus on ustekinumab in Crohn's disease. HOBOKEN: WILEY.

Australian consensus on ustekinumab in Crohn's disease

2023

Conference Publication

Withdrawal vs continuation of thiopurine in vedolizumab-treated patients with ulcerative colitis (VIEWS): A multicenter randomized controlled trial

Pudipeddi, A., Paramsothy, S., Kariyawasam, V., Paramsothy, R., Ghaly, S., Haifer, C., An, Y-K, Begun, J., Connor, S., Corte, C., Ward, M., De Cruz, P., Fung, C., Redmond, D., Chan, W., Mourad, F. and Leong, R. (2023). Withdrawal vs continuation of thiopurine in vedolizumab-treated patients with ulcerative colitis (VIEWS): A multicenter randomized controlled trial. HOBOKEN: WILEY.

Withdrawal vs continuation of thiopurine in vedolizumab-treated patients with ulcerative colitis (VIEWS): A multicenter randomized controlled trial

2023

Journal Article

Protocol for a single-arm feasibility study of photobiomodulation for fatigue, depression, and pain in inflammatory bowel disease

Ewais, Tatjana, Begun, Jakob and Laakso, E-Liisa (2023). Protocol for a single-arm feasibility study of photobiomodulation for fatigue, depression, and pain in inflammatory bowel disease. Biomedicines, 11 (8) 2179, 1-11. doi: 10.3390/biomedicines11082179

Protocol for a single-arm feasibility study of photobiomodulation for fatigue, depression, and pain in inflammatory bowel disease

2023

Journal Article

Upadacitinib salvage therapy for infliximab experienced patients with acute severe ulcerative colitis

Gilmore, Robert, Tan, Lian, Fernandes, Richard, An, Yoon-Kyo and Begun, Jakob (2023). Upadacitinib salvage therapy for infliximab experienced patients with acute severe ulcerative colitis. Journal of Crohn's and Colitis, 17 (12), 2033-2036. doi: 10.1093/ecco-jcc/jjad115

Upadacitinib salvage therapy for infliximab experienced patients with acute severe ulcerative colitis

2023

Conference Publication

Goblet cell specific anti-apoptotic role of interleukin-24 in spondyloarthritis-associated ileitis

Cameron, A., Giri, R., Begun, J., Wells, T., Bergot, A. S. and Thomas, R. (2023). Goblet cell specific anti-apoptotic role of interleukin-24 in spondyloarthritis-associated ileitis. EULAR 2023 European Congress of Rheumatology, Milan, Italy, 31 May-3 June 2023. London, United Kingdom: BMJ Group. doi: 10.1136/annrheumdis-2023-eular.1346

Goblet cell specific anti-apoptotic role of interleukin-24 in spondyloarthritis-associated ileitis

2023

Journal Article

Upadacitinib induction and maintenance therapy for Crohn's disease

Loftus, Edward V., Panés, Julian, Lacerda, Ana P., Peyrin-Biroulet, Laurent, D'Haens, Geert, Panaccione, Remo, Reinisch, Walter, Louis, Edouard, Chen, Minhu, Nakase, Hiroshi, Begun, Jakob, Boland, Brigid S., Phillips, Charles, Mohamed, Mohamed-Eslam F, Liu, Jianzhong, Geng, Ziqian, Feng, Tian, Dubcenco, Elena and Colombel, Jean-Frederic (2023). Upadacitinib induction and maintenance therapy for Crohn's disease. The New England journal of medicine, 388 (21), 1966-1980. doi: 10.1056/NEJMoa2212728

Upadacitinib induction and maintenance therapy for Crohn's disease

2023

Conference Publication

Post-ustekinumab induction IL-12, IL-23, and ustekinumab levels are associated with clinical response in a multicentre prospective cohort study of Crohn's disease patients: results from the Aurora Study

An, Yoon-Kyo, Lindsay, Niamh, Allan, Natalie, Khoo, Emi, Fernandes, Richard, Amiss, Anna, Pham, Hai, Wong, Kam Fai, Ooi, Soong-Yuan, Thin, Lena, Lightowler, Daniel, Connor, Susan J., Williams, Astrid-Jane, De Cruz, Peter, Suen, Christopher Li Wai, Kariyawasam, Viraj C., Mitrev, Nikola, Ghaly, Simon, Andrews, Jane M., Christensen, Britt, Sparrow, Miles, White, Lauren S., Bryant, Robert V., Ding, Nik S., Leong, Rupert, Van Langenberg, Daniel R., Seltenreich, Hansjoerg, Subramaniam, Kavitha, Radford-Smith, Graham L. and Begun, Jakob (2023). Post-ustekinumab induction IL-12, IL-23, and ustekinumab levels are associated with clinical response in a multicentre prospective cohort study of Crohn's disease patients: results from the Aurora Study. Digestive Disease Week (DDW), Chicago, IL United States, 6-9 May 2023. Philadelphia, PA United States: Elsevier.

Post-ustekinumab induction IL-12, IL-23, and ustekinumab levels are associated with clinical response in a multicentre prospective cohort study of Crohn's disease patients: results from the Aurora Study

2023

Conference Publication

WITHDRAWAL VERSUS CONTINUATION OF THIOPURINE IN VEDOLIZUMAB-TREATED PATIENTS WITH ULCERATIVE COLITIS (VIEWS): A MULTI-CENTRE RANDOMISED CONTROLLED TRIAL

Pudipeddi, Aviv, Paramsothy, Sudarshan, Kariyawasam, Viraj C., Paramsothy, Ramesh, Ghaly, Dr Simon, Haifer, Craig, An, Yoon-Kyo, Begun, Jakob, Connor, Susan J., Corte, Crispin, Ward, Mark, De Cruz, Peter, Fung, Caroline, Chan, Pak Wo, Mourad, Fadi H., Redmond, Diane and Leong, Rupert (2023). WITHDRAWAL VERSUS CONTINUATION OF THIOPURINE IN VEDOLIZUMAB-TREATED PATIENTS WITH ULCERATIVE COLITIS (VIEWS): A MULTI-CENTRE RANDOMISED CONTROLLED TRIAL. Digestive Disease Week (DDW), Chicago Il, May 06-09, 2023. PHILADELPHIA: W B SAUNDERS CO-ELSEVIER INC.

WITHDRAWAL VERSUS CONTINUATION OF THIOPURINE IN VEDOLIZUMAB-TREATED PATIENTS WITH ULCERATIVE COLITIS (VIEWS): A MULTI-CENTRE RANDOMISED CONTROLLED TRIAL

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
  • 2021 - 2025
    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

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
  • 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

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Supervision history

Current supervision

  • Doctor Philosophy

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

    Principal Advisor

  • Doctor Philosophy

    Reducing post-operative Crohn's disease recurrence

    Principal Advisor

    Other advisors: Professor David Clark, Dr Rabina Giri

  • Doctor Philosophy

    Study of TOfacitinib for the treatment of chronic Pouchitis

    Principal Advisor

    Other advisors: Professor Gerald Holtmann

  • 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

    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

    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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