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Associate Professor Jakob Begun
Associate Professor

Jakob Begun

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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

184 works between 1996 and 2024

161 - 180 of 184 works

2016

Conference Publication

The burden of illness among adolescents and young adults with inflammatory bowel disease

Duffy, K. and Begun, J. (2016). The burden of illness among adolescents and young adults with inflammatory bowel disease. Gastroenterological Society of Australia, Australian Gastroenterology Week 2016, Adelaide, South Australia, Australia, 10–12 October 2016. HOBOKEN: WILEY-BLACKWELL. doi: 10.1111/jgh.13522

The burden of illness among adolescents and young adults with inflammatory bowel disease

2016

Conference Publication

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

Gulhane, M., Lourie, R., Tong, H., Kang, A., Schreiber, V., Magor, G., Denman, S., Begun, J., Florin, T., Perkins, A., O Cuiv, P., Mcguckin, M. and Hasnain, S. Z. (2016). High fat diets induce colonic epithelial cell stress and inflammation that is reversed by IL-22. ICI 2016 International Congress of Immunology, Melbourne, Australia, 21–26 August 2016. Weinheim, Germany: Wiley. doi: 10.1002/eji.201670200

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

2016

Conference Publication

Alleviation of Acute Drug-Induced Liver Injury Following Acetaminophen Overdose by Therapeutic Blockade of E-Selectin in Preclinical Mouse Model

Oancea, Iulia, Barbier, Valerie, Chee, David, Lourie, Rohan, Movva, Ramya, Proctor, Martina A., Begun, Jakob, Magnani, John L., Florin, Timothy H. and Winkler, Ingrid (2016). Alleviation of Acute Drug-Induced Liver Injury Following Acetaminophen Overdose by Therapeutic Blockade of E-Selectin in Preclinical Mouse Model. 57th Annual Meeting and Residents Fellow Conference of the Society for Surgery of the Alimentary Tract (SSAT) / 52nd Annual Meeting on Digestive Disease Week (DDW) / Meeting of the American-Gastroenterological-Association (AGA), San Diego, CA United States, 21-24 May 2016. Philadelphia, PA United States: Elsevier. doi: 10.1016/s0016-5085(16)33483-7

Alleviation of Acute Drug-Induced Liver Injury Following Acetaminophen Overdose by Therapeutic Blockade of E-Selectin in Preclinical Mouse Model

2016

Conference Publication

The incidence of 30-day adverse events after colonoscopy in an IBD population

An, Y. K., Wong, J., You, I. S., Mortimore, M., Hewett, D. G., Appleyard, M. N. and Begun, J. (2016). The incidence of 30-day adverse events after colonoscopy in an IBD population. Gastroenterological Society of Australia, Australian Gastroenterology Week 2016, Adelaide, South Australia, Australia, 10–12 October 2016. HOBOKEN: WILEY-BLACKWELL. doi: 10.1111/jgh.13522

The incidence of 30-day adverse events after colonoscopy in an IBD population

2016

Conference Publication

Thiopurine Mediated Chemoprevention of Colitis-Associated Colorectal Dysplasia

Jose, Beulah, Lourie, Rohan, Schreiber, Veronika, Florin, Timothy H., Oancea, Iulia and Begun, Jakob (2016). Thiopurine Mediated Chemoprevention of Colitis-Associated Colorectal Dysplasia. 57th Annual Meeting and Residents Fellow Conference of the Society for Surgery of the Alimentary Tract (SSAT) / 52nd Annual Meeting on Digestive Disease Week (DDW) / Meeting of the American Gastroenterological Association (AGA57th Annual Meeting and Residents Fellow Conference of the Society for Surgery of the Alimentary Tract (SSAT) / 52nd Annual Meeting on Digestive Disease Week (DDW) / Meeting of the American-Gastroenterological-Association (AGA), San Diego, CA United States, 21-24 May 2016. Philadelphia, PA United States: Elsevier. doi: 10.1016/s0016-5085(16)33291-7

Thiopurine Mediated Chemoprevention of Colitis-Associated Colorectal Dysplasia

2015

Conference Publication

Malnutrition and quality of life among inflammatory bowel disease outpatients

Pulley, J., Todd, A., Flatley, C. and Begun, J. (2015). Malnutrition and quality of life among inflammatory bowel disease outpatients. Gastro 2015 GESA‐AGW and WGO International Congress, Gastroenterological Society of Australia Australian Gastroenterology Week 2015, Brisbane, QLD Australia, 28 September‐2 October 2015. Richmond, VIC Australia: John Wiley and Sons. doi: 10.1111/jgh.13096

Malnutrition and quality of life among inflammatory bowel disease outpatients

2015

Journal Article

Integrated genomics of crohn's disease risk variant identifies a role for CLEC12A in antibacterial autophagy

Begun, Jakob, Lassen, Kara G., Jijon, Humberto B., Baxt, Leigh A., Goel, Gautam, Heath, Robert J., Ng, Aylwin, Tam, Jenny M., Kuo, Szu-Yu, Villablanca, Eduardo J., Fagbami, Lola, Oosting, Marije, Kumar, Vinod, Schenone, Monica, Carr, Steven A., Joosten, Leo A. B., Vyas, Jatin M., Daly, Mark J., Netea, Mihai G., Brown, Gordon D., Wijmenga, Cisca and Xavier, Ramnik J. (2015). Integrated genomics of crohn's disease risk variant identifies a role for CLEC12A in antibacterial autophagy. Cell Reports, 11 (12), 1905-1918. doi: 10.1016/j.celrep.2015.05.045

Integrated genomics of crohn's disease risk variant identifies a role for CLEC12A in antibacterial autophagy

2015

Journal Article

Enteroliths in a Kock continent ileostomy: case report and review of the literature

Moattar, Hadi, Begun, Jakob and Florin, Timothy (2015). Enteroliths in a Kock continent ileostomy: case report and review of the literature. Endoscopy, 47 (S 01), E200-E201. doi: 10.1055/s-0034-1391302

Enteroliths in a Kock continent ileostomy: case report and review of the literature

2014

Journal Article

IL-1 receptor blockade restores autophagy and reduces inflammation in chronic granulomatous disease in mice and in humans

de Luca, Antonella, Smeekens, Sanne P., Casagrande, Andrea, Iannitti, Rossana, Conway, Kara L., Gresnigt, Mark. S., Begun, Jakob, Plantinga, Theo S., Joosten, Leo A. B., van der Meer, Jos W. M., Chamilos, Georgios, Netea, Mihai G., Xavier, Ramnik J., Dinarello, Charles A., Romani, Luigina and van de Veerdonk, Frank L. (2014). IL-1 receptor blockade restores autophagy and reduces inflammation in chronic granulomatous disease in mice and in humans. Proceedings of the National Academy of Sciences of the United States of America, 111 (9), 3526-3531. doi: 10.1073/pnas.1322831111

IL-1 receptor blockade restores autophagy and reduces inflammation in chronic granulomatous disease in mice and in humans

2013

Journal Article

Autophagy at the crossroads of metabolism and cellular defense

Begun, Jakob and Xavier, Ramnik J. (2013). Autophagy at the crossroads of metabolism and cellular defense. Current Opinion in Gastroenterology, 29 (6), 588-596. doi: 10.1097/MOG.0b013e328365d34d

Autophagy at the crossroads of metabolism and cellular defense

2013

Journal Article

Deep resequencing of GWAS loci identifies rare variants in CARD9, IL23R and RNF186 that are associated with ulcerative colitis

Beaudoin, Melissa, Goyette, Philippe, Boucher, Gabrielle, Lo, Ken Sin, Rivas, Manuel A., Stevens, Christine, Alikashani, Azadeh, Ladouceur, Martin, Ellinghaus, David, Torkvist, Leif, Goel, Gautam, Lagace, Caroline, Annese, Vito, Bitton, Alain, Begun, Jakob, Brant, Steve R., Bresso, Francesca, Cho, Judy H., Duerr, Richard H., Halfvarson, Jonas, McGovern, Dermot P. B., Radford-Smith, Graham, Schreiber, Stefan, Schumm, Philip L., Sharma, Yashoda, Silverberg, Mark S., Weersma, Rinse K., D'Amato, Mauro, Vermeire, Severine ... Rioux, John D. (2013). Deep resequencing of GWAS loci identifies rare variants in CARD9, IL23R and RNF186 that are associated with ulcerative colitis. PLoS Genetics, 9 (9) e1003723, e1003723.1-e1003723.11. doi: 10.1371/journal.pgen.1003723

Deep resequencing of GWAS loci identifies rare variants in CARD9, IL23R and RNF186 that are associated with ulcerative colitis

2012

Journal Article

The LRR and RING domain protein LRSAM1 is an E3 ligase crucial for ubiquitin-dependent autophagy of intracellular salmonella typhimurium

Huett, Alan, Heath, Robert J., Begun, Jakob, Sassi, Slim O., Baxt, Leigh A., Vyas, Jatin M., Goldberg, Marcia B. and Xavier, Ramnik J. (2012). The LRR and RING domain protein LRSAM1 is an E3 ligase crucial for ubiquitin-dependent autophagy of intracellular salmonella typhimurium. Cell Host and Microbe, 12 (6), 778-790. doi: 10.1016/j.chom.2012.10.019

The LRR and RING domain protein LRSAM1 is an E3 ligase crucial for ubiquitin-dependent autophagy of intracellular salmonella typhimurium

2012

Journal Article

ATG16L1 T300A dependent differential gene expression identifies genes required for anti-bacterial autophagy : P-227 YI

Begun, Jakob, Ng, Aylwin and Xavier, Ramnik (2012). ATG16L1 T300A dependent differential gene expression identifies genes required for anti-bacterial autophagy : P-227 YI. Inflammatory Bowel Diseases, 18, S103. doi: 10.1097/00054725-201212001-00260

ATG16L1 T300A dependent differential gene expression identifies genes required for anti-bacterial autophagy : P-227 YI

2008

Journal Article

DAF-16-dependent suppression of immunity during reproduction in Caenorhabditis elegans

Miyata, Sachiko, Begun, Jakob, Troemel, Emily R. and Ausubel, Frederick M. (2008). DAF-16-dependent suppression of immunity during reproduction in Caenorhabditis elegans. Genetics, 178 (2), 903-918. doi: 10.1534/genetics.107.083923

DAF-16-dependent suppression of immunity during reproduction in Caenorhabditis elegans

2007

Journal Article

Staphylococcal biofilm exopolysaccharide protects against Caenorhabditis elegans immune defenses

Begun, Jakob, Gaiani, Jessica M., Rohde, Holger, Mack, Dietrich, Calderwood, Stephen B., Ausubel, Frederick M. and Sifri, Costi D. (2007). Staphylococcal biofilm exopolysaccharide protects against Caenorhabditis elegans immune defenses. PLoS Pathogens, 3 (4), 526-540. doi: 10.1371/journal.ppat.0030057

Staphylococcal biofilm exopolysaccharide protects against Caenorhabditis elegans immune defenses

2005

Journal Article

Staphylococcus aureus virulence factors identified by using a high-throughput Caenorhabditis elegans-killing model

Begun, Jakob, Sifri, Costi D., Goldman, Samuel, Calderwood, Stephen B. and Ausubel, Frederick M. (2005). Staphylococcus aureus virulence factors identified by using a high-throughput Caenorhabditis elegans-killing model. Infection and Immunity, 73 (2), 872-877. doi: 10.1128/IAI.73.2.872-877.2005

Staphylococcus aureus virulence factors identified by using a high-throughput Caenorhabditis elegans-killing model

2005

Journal Article

The worm has turned - Microbial virulence modeled in Caenorhabditis elegans

Sifri, CD, Begun, J and Ausubel, FM (2005). The worm has turned - Microbial virulence modeled in Caenorhabditis elegans. Trends in Microbiology, 13 (3), 119-127. doi: 10.1016/j.tim.2005.01.003

The worm has turned - Microbial virulence modeled in Caenorhabditis elegans

2004

Journal Article

Bacterial Resistance of daf-2 Mutants [2] (multiple letters)

Bolm, Maike, Chhatwal, Gursharan S., Jansen, Wouter T. M., Ausubel, Frederick M., Begun, Jakob, Kim, Dennis H., Moy, Terence, Ruvkun, Gary, Calderwood, Stephen B., Sifri, Costi D. and Garsin, Danielle A. (2004). Bacterial Resistance of daf-2 Mutants [2] (multiple letters). Science, 303 (5666)

Bacterial Resistance of daf-2 Mutants [2] (multiple letters)

2003

Journal Article

Long-lived C. elegans daf-2 Mutants are resistant to bacterial pathogens

Garsin, DA, Villanueva, JM, Begun, J, Kim, DH, Sifri, CD, Calderwood, SB, Ruvkun, G and Ausubel, FM (2003). Long-lived C. elegans daf-2 Mutants are resistant to bacterial pathogens. Science, 300 (5627), 1921-1921. doi: 10.1126/science.1080147

Long-lived C. elegans daf-2 Mutants are resistant to bacterial pathogens

2003

Journal Article

Caenorhabditis elegans as a model host for Staphylococcus aureus pathogenesis

Sifri, Costi D., Begun, Jakob, Ausubel, Frederick M. and Calderwood, Stephen B. (2003). Caenorhabditis elegans as a model host for Staphylococcus aureus pathogenesis. Infection and Immunity, 71 (4), 2208-2217. doi: 10.1128/IAI.71.4.2208-2217.2003

Caenorhabditis elegans as a model host for Staphylococcus aureus pathogenesis

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
    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
  • 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 - 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

Past funding

  • 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

    Microbial Regulation of Host Inflammatory Pathways in Inflammatory Bowel Disease

    Principal Advisor

    Other advisors: Professor Mark Morrison, Dr Anuj Sehgal

  • 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

  • Doctor Philosophy

    A randomised, open-label, non-inferiority study of upadacitinib compared with oral prednisolone

    Principal Advisor

  • Doctor Philosophy

    Designer Nanoparticles for Oral and Targeted Delivery of Protein Therapeutics

    Associate Advisor

    Other advisors: Dr Md Moniruzzaman, Associate Professor Amirali Popat

  • 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

    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

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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