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Kylie James

Dr Kylie James

Laboratory Head
Computational Genomics Lab

Dr Kylie James is Group Leader of the Gut Immunogenomics Group. She completed her PhD at University of Queensland working with Dr Ashraful Haque at QIMR Berghofer Medical Research Institute. In this role, she determined the response kinetics of T helper cells during blood-stage malaria. Kylie then continued to pursue her interest in the immune system as a postdoctoral researcher with Dr Sarah Teichmann at the Wellcome Sanger Institute and Junior Research Fellow at Christ’s College, University of Cambridge, UK. Her work redefined our understanding of the balance of immune and microbial cells across the healthy human colon. In 2021, Kylie returned to Australia to start her own team as Spinak Fellow and supported by an NHMRC Investigator Grant.

The Gut Immunogenomics Group investigates how environmental factors shape gut immune cell and microbial landscapes in health and disease. To achieve this goal, the team apply single-cell genomics and computational approaches to reconstruct cellular microenvironments, developmental hierarchies and interactions.


  • 2021Spinak Fellowship
  • 2020NHMCR Investigator Grant
  • 2018Christ’s College Junior Research Fellowship - University of Cambridge


  • 2011Bachelor of Science (Bachelor of Science (B.S)), ImmunologyUniversity of Queensland, Australia
  • 2017Doctor of Philosophy (Doctor of Philosophy (Ph.D)), ImmunologyUniversity of Queensland, Australia

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

    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