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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

182 works between 1996 and 2024

81 - 100 of 182 works

2021

Journal Article

Ustekinumab levels in pregnant women with inflammatory bowel disease and infants exposed in utero

Flanagan, Emma, Prentice, Ralley, Wright, Emily K., Gibson, Peter R., Ross, Alyson L., Begun, Jakob, Sparrow, Miles P., Goldberg, Rimma, Rosella, Ourania, Burns, Megan, Kiburg, Katerina V. and Bell, Sally J. (2021). Ustekinumab levels in pregnant women with inflammatory bowel disease and infants exposed in utero. Alimentary Pharmacology and Therapeutics, 55 (6), 700-704. doi: 10.1111/apt.16739

Ustekinumab levels in pregnant women with inflammatory bowel disease and infants exposed in utero

2021

Journal Article

The psychosocial burden of inflammatory bowel disease in adolescents and young adults

Halloran, Jessica, McDermott, Brett, Ewais, Tatjana, Begun, Jakob, Karatela, Shamshad, D'Emden, Helen, Corias, Christian and Denny, Simon (2021). The psychosocial burden of inflammatory bowel disease in adolescents and young adults. Internal Medicine Journal, 51 (12) imj.15034, 2027-2033. doi: 10.1111/imj.15034

The psychosocial burden of inflammatory bowel disease in adolescents and young adults

2021

Journal Article

Facile synthesis of dendrimer like mesoporous silica nanoparticles to enhance targeted delivery of interleukin-22

Elshaer, Dana, Moniruzzaman, Md., Ong, Yi Theng, Qu, Zhi, Schreiber, Veronika, Begun, Jakob and Popat, Amirali (2021). Facile synthesis of dendrimer like mesoporous silica nanoparticles to enhance targeted delivery of interleukin-22. Biomaterials Science, 9 (22), 7402-7411. doi: 10.1039/d1bm01352a

Facile synthesis of dendrimer like mesoporous silica nanoparticles to enhance targeted delivery of interleukin-22

2021

Journal Article

Defining transabdominal intestinal ultrasound treatment response and remission in inflammatory bowel disease: systematic review and expert consensus statement

Ilvemark, Johan F. K. F., Hansen, Tawnya, Goodsall, Thomas M., Seidelin, Jakob B., Al-Farhan, Heba, Allocca, Mariangela, Begun, Jakob, Bryant, Robert V., Carter, Dan, Christensen, Britt, Dubinsky, Marla C., Gecse, Krisztina B., Kucharzik, Torsten, Lu, Cathy, Maaser, Christian, Maconi, Giovanni, Nylund, Kim, Palmela, Carolina, Wilson, Stephanie R., Novak, Kerri and Wilkens, Rune (2021). Defining transabdominal intestinal ultrasound treatment response and remission in inflammatory bowel disease: systematic review and expert consensus statement. Journal of Crohn's and Colitis, 16 (4), 554-580. doi: 10.1093/ecco-jcc/jjab173

Defining transabdominal intestinal ultrasound treatment response and remission in inflammatory bowel disease: systematic review and expert consensus statement

2021

Journal Article

Mindfulness based cognitive therapy for youth with inflammatory bowel disease and depression - Findings from a pilot randomised controlled trial

Ewais, T., Begun, J., Kenny, M., Hay, K., Houldin, Evan, Chuang, Kai-Hisang, Tefay, M. and Kisely, S. (2021). Mindfulness based cognitive therapy for youth with inflammatory bowel disease and depression - Findings from a pilot randomised controlled trial. Journal of Psychosomatic Research, 149 110594, 110594. doi: 10.1016/j.jpsychores.2021.110594

Mindfulness based cognitive therapy for youth with inflammatory bowel disease and depression - Findings from a pilot randomised controlled trial

2021

Journal Article

Expression of CD49f defines subsets of human regulatory T cells with divergent transcriptional landscape and function that correlate with ulcerative colitis disease activity

Weerakoon, Harshi, Straube, Jasmin, Lineburg, Katie, Cooper, Leanne, Lane, Steven, Smith, Corey, Alabbas, Saleh, Begun, Jakob, Miles, John J., Hill, Michelle M. and Lepletier, Ailin (2021). Expression of CD49f defines subsets of human regulatory T cells with divergent transcriptional landscape and function that correlate with ulcerative colitis disease activity. Clinical and Translational Immunology, 10 (9) e1334, e1334. doi: 10.1002/cti2.1334

Expression of CD49f defines subsets of human regulatory T cells with divergent transcriptional landscape and function that correlate with ulcerative colitis disease activity

2021

Journal Article

Higher anti-tumor necrosis factor-α levels correlate with improved radiological outcomes in Crohn's perianal fistulas

De Gregorio, Michael, Lee, Tanya, Krishnaprasad, Krupa, Amos, Gregory, An, Yoon-Kyo, Bastian-Jordan, Matthew, Begun, Jakob, Borok, Nira, Brown, Dougal J. M., Cheung, Wa, Connor, Susan J., Gerstenmaier, Jan, Gilbert, Lauren E., Gilmore, Robert, Gu, Bonita, Kutaiba, Numan, Lee, Allan, Mahy, Gillian, Srinivasan, Ashish, Thin, Lena, Thompson, Alexander J., Welman, Christopher J., Yong, Eric X. Z., De Cruz, Peter, van Langenberg, Daniel, Sparrow, Miles P. and Ding, Nik S. (2021). Higher anti-tumor necrosis factor-α levels correlate with improved radiological outcomes in Crohn's perianal fistulas. Clinical Gastroenterology and Hepatology, 20 (6), 1306-1314. doi: 10.1016/j.cgh.2021.07.053

Higher anti-tumor necrosis factor-α levels correlate with improved radiological outcomes in Crohn's perianal fistulas

2021

Journal Article

SARS‐CoV‐2 vaccination in patients with inflammatory bowel disease

Prentice, Ralley E., Rentsch, Clarissa, Al‐Ani, Aysha H., Zhang, Eva, Johnson, Douglas, Halliday, John, Bryant, Robert, Begun, Jacob, Ward, Mark G., Lewindon, Peter J., Connor, Susan J., Ghaly, Simon and Christensen, Britt (2021). SARS‐CoV‐2 vaccination in patients with inflammatory bowel disease. GastroHep, 3 (4), 212-228. doi: 10.1002/ygh2.473

SARS‐CoV‐2 vaccination in patients with inflammatory bowel disease

2021

Journal Article

Prospective randomised controlled trial of adults with perianal fistulising Crohn's disease and optimised therapeutic infliximab levels: PROACTIVE trial study protocol

Gu, Bonita, De Gregorio, Michael, Pipicella, Joseph Louis, Vande Casteele, Niels, Andrews, Jane M., Begun, Jakob, Connell, William, D'Souza, Basil, Gholamrezaei, Ali, Hart, Ailsa, Liew, Danny, Radford-Smith, Graham, Rimola, Jordi, Sutherland, Tom, Toong, Catherine, Woods, Rodney, Wu, Yang, Xuan, Wei, Williams, Astrid-Jane, Ng, Watson, Ding, Nik Sheng and Connor, Susan (2021). Prospective randomised controlled trial of adults with perianal fistulising Crohn's disease and optimised therapeutic infliximab levels: PROACTIVE trial study protocol. BMJ open, 11 (7) 043921. doi: 10.1136/bmjopen-2020-043921

Prospective randomised controlled trial of adults with perianal fistulising Crohn's disease and optimised therapeutic infliximab levels: PROACTIVE trial study protocol

2021

Journal Article

IFN-λ therapy prevents severe gastrointestinal graft-versus-host disease

Henden, Andrea S., Koyama, Motoko, Robb, Renee J., Forero, Adriana, Kuns, Rachel D., Chang, Karshing, Ensbey, Kathleen S., Varelias, Antiopi, Kazakoff, Stephen H., Waddell, Nicole, Clouston, Andrew D., Giri, Rabina, Begun, Jakob, Blazar, Bruce R., Degli-Esposti, Mariapia A., Kotenko, Sergei V., Lane, Steven W., Bowerman, Kate L., Savan, Ram, Hugenholtz, Philip, Gartlan, Kate H. and Hill, Geoffrey R. (2021). IFN-λ therapy prevents severe gastrointestinal graft-versus-host disease. Blood, 138 (8), 722-737. doi: 10.1182/blood.2020006375

IFN-λ therapy prevents severe gastrointestinal graft-versus-host disease

2021

Journal Article

pH – responsive colloidal carriers assembled from β-lactoglobulin and epsilon poly-l-lysine for oral drug delivery

Pujara, Naisarg, Giri, Rabina, Yau Wong, Kuan, Qu, Zhi, Rewatkar, Prarthana, Moniruzzaman, Md., Begun, Jakob, Ross, Benjamin P., McGuckin, Michael and Popat, Amirali (2021). pH – responsive colloidal carriers assembled from β-lactoglobulin and epsilon poly-l-lysine for oral drug delivery. Journal of Colloid and Interface Science, 589, 45-55. doi: 10.1016/j.jcis.2020.12.054

pH – responsive colloidal carriers assembled from β-lactoglobulin and epsilon poly-l-lysine for oral drug delivery

2021

Conference Publication

So many therapies—So little data: How to choose? Session two summary

Begun, Jakob (2021). So many therapies—So little data: How to choose? Session two summary. Takeda IBD Symposium IBD 2020: Right Therapy, Right Patient, Right Time#Choosing Wisely, Online, 5 September 2020. Richmond, VIC Australia: Wiley-Blackwell. doi: 10.1111/jgh.15450

So many therapies—So little data: How to choose? Session two summary

2021

Journal Article

Standardisation of intestinal ultrasound scoring in clinical trials for luminal Crohn’s disease

Goodsall, Thomas M., Jairath, Vipul, Feagan, Brian G., Parker, Claire E., Nguyen, Tran M., Guizzetti, Leonardo, Asthana, Anil K., Begun, Jakob, Christensen, Britt, Friedman, Antony B., Kucharzik, Torsten, Lee, Andrew, Lewindon, Peter J., Maaser, Christian, Novak, Kerri L., Rimola, Jordi, Taylor, Kirstin M., Taylor, Stuart A., White, Lauren S., Wilkens, Rune, Wilson, Stephanie R., Wright, Emily K., Bryant, Robert V. and Ma, Christopher (2021). Standardisation of intestinal ultrasound scoring in clinical trials for luminal Crohn’s disease. Alimentary Pharmacology and Therapeutics, 53 (8), 873-886. doi: 10.1111/apt.16288

Standardisation of intestinal ultrasound scoring in clinical trials for luminal Crohn’s disease

2021

Journal Article

Adhesion to E-selectin primes macrophages for activation through AKT and mTOR

Davies, Julie M., Radford, Kristen J., Begun, Jakob, Levesque, Jean-Pierre and Winkler, Ingrid G. (2021). Adhesion to E-selectin primes macrophages for activation through AKT and mTOR. Immunology and Cell Biology, 99 (6) imcb.12447, 622-639. doi: 10.1111/imcb.12447

Adhesion to E-selectin primes macrophages for activation through AKT and mTOR

2021

Journal Article

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)

Klionsky, Daniel J., Abdel-Aziz, Amal Kamal, Abdelfatah, Sara, Abdellatif, Mahmoud, Abdoli, Asghar, Abel, Steffen, Abeliovich, Hagai, Abildgaard, Marie H., Abudu, Yakubu Princely, Acevedo-Arozena, Abraham, Adamopoulos, Iannis E., Adeli, Khosrow, Adolph, Timon E., Adornetto, Annagrazia, Aflaki, Elma, Agam, Galila, Agarwal, Anupam, Aggarwal, Bharat B., Agnello, Maria, Agostinis, Patrizia, Agrewala, Javed N., Agrotis, Alexander, Aguilar, Patricia V., Ahmad, S. Tariq, Ahmed, Zubair M., Ahumada-Castro, Ulises, Aits, Sonja, Aizawa, Shu, Akkoc, Yunus ... Tong, Chun-Kit (2021). Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition). Autophagy, 17 (1), 1-382. doi: 10.1080/15548627.2020.1797280

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)

2021

Journal Article

IgM and IgA augmented autoantibody signatures improve early‐stage detection of colorectal cancer prior to nodal and distant spread

Roney, Md Saiful Islam, Lanagan, Catharine, Sheng, Yong Hua, Lawler, Karen, Schmidt, Christopher, Nguyen, Nam‐Trung, Begun, Jakob and Kijanka, Gregor Stefan (2021). IgM and IgA augmented autoantibody signatures improve early‐stage detection of colorectal cancer prior to nodal and distant spread. Clinical and Translational Immunology, 10 (9) e1330, e1330. doi: 10.1002/cti2.1330

IgM and IgA augmented autoantibody signatures improve early‐stage detection of colorectal cancer prior to nodal and distant spread

2021

Journal Article

A nucleotide analog prevents colitis associated cancer via Β-catenin independently of inflammation and autophagy

Sheng, Yong Hua, Giri, Rabina, Davies, Julie, Schreiber, Veronika, Alabbas, Saleh, Movva, Ramya, He, Yaowu, Wu, Andy, Hooper, John, McWhinney, Brett, Oancea, Iulia, Kijanka, Gregor, Hasnain, Sumaira, Lucke, Andrew J., Fairlie, David P., McGuckin, Michael A., Florin, Timothy H. and Begun, Jakob (2021). A nucleotide analog prevents colitis associated cancer via Β-catenin independently of inflammation and autophagy. Cellular and Molecular Gastroenterology and Hepatology, 11 (1), 33-53. doi: 10.1016/j.jcmgh.2020.05.012

A nucleotide analog prevents colitis associated cancer via Β-catenin independently of inflammation and autophagy

2021

Journal Article

Gut microbiota shape the inflammatory response in mice with an epithelial defect

Wang, Ran, Moniruzzaman, Md, Wong, Kuan Yau, Wiid, Percival, Harding, Alexa, Giri, Rabina, Tong, Wendy Hui, Creagh, Jackie, Begun, Jakob, McGuckin, Michael A. and Hasnain, Sumaira Z. (2021). Gut microbiota shape the inflammatory response in mice with an epithelial defect. Gut microbes, 13 (1), 1-18. doi: 10.1080/19490976.2021.1887720

Gut microbiota shape the inflammatory response in mice with an epithelial defect

2020

Journal Article

Crohn’s Colitis Care (CCCare): bespoke cloud-based clinical management software for inflammatory bowel disease

Krishnaprasad, Krupa, Walsh, Alissa, Begun, Jakob, Bell, Sally, Carter, David, Grafton, Rachel, Sechi, Alexandra, Sewell, Karen, McMahon, Anna, Connor, Susan, Radford-Smith, Graham and Andrews, Jane M. (2020). Crohn’s Colitis Care (CCCare): bespoke cloud-based clinical management software for inflammatory bowel disease. Scandinavian Journal of Gastroenterology, 55 (12), 1419-1426. doi: 10.1080/00365521.2020.1839960

Crohn’s Colitis Care (CCCare): bespoke cloud-based clinical management software for inflammatory bowel disease

2020

Journal Article

Mindfulness-based cognitive therapy experiences in youth with inflammatory bowel disease and depression: findings from a mixed methods qualitative study

Ewais, Tatjana, Begun, Jake, Kenny, Maura, Headey, Alan, Tefay, Merilyn and Kisely, Steve (2020). Mindfulness-based cognitive therapy experiences in youth with inflammatory bowel disease and depression: findings from a mixed methods qualitative study. BMJ Open, 10 (11) e041140, e041140. doi: 10.1136/bmjopen-2020-041140

Mindfulness-based cognitive therapy experiences in youth with inflammatory bowel disease and depression: findings from a mixed methods qualitative study

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

    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

    Other advisors: Dr Paul Clark

  • 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

    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, 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

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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