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Gut Immunogenomics Lab

The Gut Immunogenomics Lab aims to understand how intestinal cells and microbiota contribute to IBD and colitis-associated colorectal cancer.

Kylie James

Lab Leader

Inflammatory Bowel Disease (IBD) affects more than 100,000 Australians, and these numbers are on the rise. The most common IBD subtypes are ulcerative colitis and Crohn’s disease. The recurrent flares of intestinal inflammation experienced in IBD are, at best, managed rather than cured, placing a significant burden on the patients and healthcare system. Of considerable concern, people with IBD are at least twice as likely to be diagnosed with colorectal cancer than the general public, yet non-invasive methods for surveillance do not exist and surgical resection is the only treatment option.

A major burden to our progress in discovering effective treatment strategies for IBD is the complexity of the underlying disease mechanisms - resulting from the interplay of genetics, exacerbated immune responses, microbial dysbiosis and environmental factors.

Our group aims to understand how intestinal cells and microbiota contribute to IBD and colitis-associated colorectal cancer. To achieve this, we apply single-cell genomics and computational approaches to reconstruct cellular microenvironments, developmental hierarchies and interactions.

Research team

Selected publications

See all publications
  • 2023
    Nature Reviews. Gastroenterology & Hepatology10.1038/s41575-023-00784-1

    A Roadmap for the Human Gut Cell Atlas.

    Matthias Zilbauer, Kylie R James, Mandeep Kaur, Sebastian Pott, Zhixin Li, Albert Burger, Jay R Thiagarajah, Joseph Burclaff, Frode L Jahnsen, Francesca Perrone, Alexander D Ross, Gianluca Matteoli, Nathalie Stakenborg, Tomohisa Sujino, Andreas Moor, Raquel Bartolome-Casado, Espen S Bækkevold, Ran Zhou, Bingqing Xie, Ken S Lau, Shahida Din, Scott T Magness, Qiuming Yao, Semir Beyaz, Mark Arends, Alexandre Denadai-Souza, Lori A Coburn, Jellert T Gaublomme, Richard Baldock, Irene Papatheodorou, Jose Ordovas-Montanes, Guy Boeckxstaens, Anna Hupalowska, Sarah A Teichmann, Aviv Regev, Ramnik J Xavier, Alison Simmons, Michael P Snyder, Keith T Wilson, ,
  • 2021
    Nature10.1038/s41586-021-03852-1

    Cells of the human intestinal tract mapped across space and time.

    Rasa Elmentaite, Natsuhiko Kumasaka, Kenny Roberts, Aaron Fleming, Emma Dann, Hamish W King, Vitalii Kleshchevnikov, Monika Dabrowska, Sophie Pritchard, Liam Bolt, Sara F Vieira, Lira Mamanova, Ni Huang, Francesca Perrone, Issac Goh Kai'En, Steven N Lisgo, Matilda Katan, Steven Leonard, Thomas R W Oliver, C Elizabeth Hook, Komal Nayak, Lia S Campos, Cecilia Domínguez Conde, Emily Stephenson, Justin Engelbert, Rachel A Botting, Krzysztof Polanski, Stijn van Dongen, Minal Patel, Michael D Morgan, John C Marioni, Omer Ali Bayraktar, Kerstin B Meyer, Xiaoling He, Roger A Barker, Holm H Uhlig, Krishnaa T Mahbubani, Kourosh Saeb-Parsy, Matthias Zilbauer, Menna R Clatworthy, Muzlifah Haniffa, Kylie R James, Sarah A Teichmann
  • 2021
    Mucosal Immunology10.1038/s41385-021-00470-y

    Redefining intestinal immunity with single-cell transcriptomics.

    Kylie Renee James, Rasa Elmentaite, Sarah Amalia Teichmann, Georgina Louise Hold