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Dr Kylie James

Dr Kylie James

Conjoint Senior Lecturer

PhD (Immunology), University of Queensland, 2016
BSc (Hons), University of Queensland, 2011

Medicine & Health
School of Biomedical Sciences

 

Dr Kylie James is head of the Gut Immunogenomics Laboratory. She completed a PhD in T cell immunity to malaria in 2017, with Dr Ashraful Haque at QIMR Berghofer. She then undertook postdoctoral training at the Wellcome Sanger Institute in the laboratory of Dr Sarah Teichmann, and a junior research fellowship at Christ’s College, University of Cambridge. Here, she spearheaded the cell atlas of the human intestinal tract across anatomical space and developmental time and showed the influence of the neighbouring microbiota in shaping the intestinal immune cell landscape. In 2021, Kylie returned to Australia to start her team as Spinak Fellow and NHMRC Investigator Fellow.

 

The Gut Immunogenomics Laboratory uses single-cell and spatially-resolved gene expression technologies to investigate cellular and microbial contributions to intestinal disease.
E-mail
k.james@garvan.org.au
Location
The Kinghorn Cancer Centre, The Garvan Institute of Medical Research, 370 Victoria St, Darlinghurst NSW 2010
  • Books | 2020
    Efremova M; Vento-Tormo R; Park JE; Teichmann SA; James KR, 2020, Immunology in the Era of Single-Cell Technologies, http://dx.doi.org/10.1146/annurev-immunol-090419-020340
  • Journal articles | 2025
    Levinger R; Tussia-Cohen D; Friedman S; Lender Y; Nissan Y; Fraimovitch E; Gavriel Y; Tearle JLE; Kolodziejczyk AA; Moon KM; Gomes T; Kunowska N; Weinberg M; Donati G; Foster LJ; James KR; Yovel Y; Hagai T, 2025, 'Single-cell and Spatial Transcriptomics Illuminate Bat Immunity and Barrier Tissue Evolution', Molecular Biology and Evolution, 42, http://dx.doi.org/10.1093/molbev/msaf017
    Journal articles | 2025
    Tearle J; Zhang F; Jackson K; Malhotra P; Tavakoli P; Koentgen S; Warren J; Williams C; Haque A; Arzivian A; Tedla N; Kim A; King H; Hold G; Ghaly S; James K, 2025, 'P0161 The primary sclerosing cholangitis and ulcerative colitis colonic mucosa defined through paired microbial and single-cell RNA sequencing', Journal of Crohn's and Colitis, 19, pp. i557 - i557, http://dx.doi.org/10.1093/ecco-jcc/jjae190.0335
    Journal articles | 2024
    James KR, 2024, 'Transcriptional diversity along the intestinal crypt–villi axis', Nature Reviews Genetics, 25, pp. 235, http://dx.doi.org/10.1038/s41576-024-00700-6
    Journal articles | 2024
    Oliver AJ; Huang N; Bartolome-Casado R; Li R; Koplev S; Nilsen HR; Moy M; Cakir B; Polanski K; Gudiño V; Melón-Ardanaz E; Sumanaweera D; Dimitrov D; Milchsack LM; FitzPatrick MEB; Provine NM; Boccacino JM; Dann E; Predeus AV; To K; Prete M; Chapman JA; Masi AC; Stephenson E; Engelbert J; Lobentanzer S; Perera S; Richardson L; Kapuge R; Wilbrey-Clark A; Semprich CI; Ellams S; Tudor C; Joseph P; Garrido-Trigo A; Corraliza AM; Oliver TRW; Hook CE; James KR; Mahbubani KT; Saeb-Parsy K; Zilbauer M; Saez-Rodriguez J; Høivik ML; Bækkevold ES; Stewart CJ; Berrington JE; Meyer KB; Klenerman P; Salas A; Haniffa M; Jahnsen FL; Elmentaite R; Teichmann SA, 2024, 'Single-cell integration reveals metaplasia in inflammatory gut diseases', Nature, 635, pp. 699 - 707, http://dx.doi.org/10.1038/s41586-024-07571-1
    Journal articles | 2024
    Tearle JLE; Tang A; Vasanthakumar A; James KR, 2024, 'Role reversals: non-canonical roles for immune and non-immune cells in the gut', Mucosal Immunology, 17, pp. 137 - 146, http://dx.doi.org/10.1016/j.mucimm.2023.11.004
    Journal articles | 2023
    Stewart BJ; Fergie M; Young MD; Jones C; Sachdeva A; Blain A; Bacon CM; Rand V; Ferdinand JR; James KR; Mahbubani KT; Hook L; Jonas N; Coleman N; Saeb-Parsy K; Collin M; Clatworthy MR; Behjati S; Carey CD, 2023, 'Spatial and molecular profiling of the mononuclear phagocyte network in classic Hodgkin lymphoma', Blood, 141, pp. 2343 - 2358, http://dx.doi.org/10.1182/blood.2022015575
    Journal articles | 2023
    Zilbauer M; James KR; Kaur M; Pott S; Li Z; Burger A; Thiagarajah JR; Burclaff J; Jahnsen FL; Perrone F; Ross AD; Matteoli G; Stakenborg N; Sujino T; Moor A; Bartolome-Casado R; Bækkevold ES; Zhou R; Xie B; Lau KS; Din S; Magness ST; Yao Q; Beyaz S; Arends M; Denadai-Souza A; Coburn LA; Gaublomme JT; Baldock R; Papatheodorou I; Ordovas-Montanes J; Boeckxstaens G; Hupalowska A; Teichmann SA; Regev A; Xavier RJ; Simmons A; Snyder MP; Wilson KT, 2023, 'A Roadmap for the Human Gut Cell Atlas', Nature Reviews Gastroenterology and Hepatology, 20, pp. 597 - 614, http://dx.doi.org/10.1038/s41575-023-00784-1
    Journal articles | 2022
    Bolton C; Smillie CS; Pandey S; Elmentaite R; Wei G; Argmann C; Aschenbrenner D; James KR; McGovern DPB; Macchi M; Cho J; Shouval DS; Kammermeier J; Koletzko S; Bagalopal K; Capitani M; Cavounidis A; Pires E; Weidinger C; McCullagh J; Arkwright PD; Haller W; Siegmund B; Peters L; Jostins L; Travis SPL; Anderson CA; Snapper S; Klein C; Schadt E; Zilbauer M; Xavier R; Teichmann S; Muise AM; Regev A; Uhlig HH, 2022, 'An Integrated Taxonomy for Monogenic Inflammatory Bowel Disease', Gastroenterology, 162, pp. 859 - 876, http://dx.doi.org/10.1053/j.gastro.2021.11.014
    Journal articles | 2022
    James KR; Elmentaite R; Teichmann SA; Hold GL, 2022, 'Correction to: Redefining intestinal immunity with single-cell transcriptomics (Mucosal Immunology, (2021), 10.1038/s41385-021-00470-y)', Mucosal Immunology, 15, pp. 526 - 526, http://dx.doi.org/10.1038/s41385-022-00483-1
    Journal articles | 2022
    James KR; Elmentaite R; Teichmann SA; Hold GL, 2022, 'Redefining intestinal immunity with single-cell transcriptomics', Mucosal Immunology, 15, pp. 531 - 541, http://dx.doi.org/10.1038/s41385-021-00470-y
    Journal articles | 2021
    Elmentaite R; Kumasaka N; Roberts K; Fleming A; Dann E; King HW; Kleshchevnikov V; Dabrowska M; Pritchard S; Bolt L; Vieira SF; Mamanova L; Huang N; Perrone F; Goh Kai’En I; Lisgo SN; Katan M; Leonard S; Oliver TRW; Hook CE; Nayak K; Campos LS; Domínguez Conde C; Stephenson E; Engelbert J; Botting RA; Polanski K; van Dongen S; Patel M; Morgan MD; Marioni JC; Bayraktar OA; Meyer KB; He X; Barker RA; Uhlig HH; Mahbubani KT; Saeb-Parsy K; Zilbauer M; Clatworthy MR; Haniffa M; James KR; Teichmann SA, 2021, 'Cells of the human intestinal tract mapped across space and time', Nature, 597, pp. 250 - 255, http://dx.doi.org/10.1038/s41586-021-03852-1
    Journal articles | 2021
    Haniffa M; Taylor D; Linnarsson S; Aronow BJ; Bader GD; Barker RA; Camara PG; Camp JG; Chédotal A; Copp A; Etchevers HC; Giacobini P; Göttgens B; Guo G; Hupalowska A; James KR; Kirby E; Kriegstein A; Lundeberg J; Marioni JC; Meyer KB; Niakan KK; Nilsson M; Olabi B; Pe’er D; Regev A; Rood J; Rozenblatt-Rosen O; Satija R; Teichmann SA; Treutlein B; Vento-Tormo R; Webb S; Barbry P; Bayraktar O; Behjati S; Bosio A; Canque B; Chalmel F; Gitton Y; Henderson D; Jorgensen A; Lisgo S; Liu J; Lundberg E; Maitre JL; Mazaud-Guittot S; Robertson E; Rolland A; Scharfmann R; Souyri M; Sundström E; Zaffran S; Zilbauer M, 2021, 'A roadmap for the Human Developmental Cell Atlas', Nature, 597, pp. 196 - 205, http://dx.doi.org/10.1038/s41586-021-03620-1
    Journal articles | 2020
    Beumer J; Puschhof J; Bauzá -Martinez J; Martínez-Silgado A; Elmentaite R; James KR; Ross A; Hendriks D; Artegiani B; Busslinger GA; Ponsioen B; Andersson-Rolf A; Saftien A; Boot C; Kretzschmar K; Geurts MH; Bar-Ephraim YE; Pleguezuelos-Manzano C; Post Y; Begthel H; van der Linden F; Lopez-Iglesias C; van de Wetering WJ; van der Linden R; Peters PJ; Heck AJR; Goedhart J; Snippert H; Zilbauer M; Teichmann SA; Wu W; Clevers H, 2020, 'Erratum: High-Resolution mRNA and Secretome Atlas of Human Enteroendocrine Cells (Cell (2020) 181(6) (1291–1306.e19), (S0092867420305018), (10.1016/j.cell.2020.04.036))', Cell, 182, pp. 1062 - 1064, http://dx.doi.org/10.1016/j.cell.2020.08.005
    Journal articles | 2020
    Beumer J; Puschhof J; Bauzá-Martinez J; Martínez-Silgado A; Elmentaite R; James KR; Ross A; Hendriks D; Artegiani B; Busslinger GA; Ponsioen B; Andersson-Rolf A; Saftien A; Boot C; Kretzschmar K; Geurts MH; Bar-Ephraim YE; Pleguezuelos-Manzano C; Post Y; Begthel H; van der Linden F; Lopez-Iglesias C; van de Wetering WJ; van der Linden R; Peters PJ; Heck AJR; Goedhart J; Snippert H; Zilbauer M; Teichmann SA; Wu W; Clevers H, 2020, 'High-Resolution mRNA and Secretome Atlas of Human Enteroendocrine Cells', Cell, 181, pp. 1291 - 1306.e19, http://dx.doi.org/10.1016/j.cell.2020.04.036
    Journal articles | 2020
    Elmentaite R; Ross ADB; Roberts K; James KR; Ortmann D; Gomes T; Nayak K; Tuck L; Pritchard S; Bayraktar OA; Heuschkel R; Vallier L; Teichmann SA; Zilbauer M, 2020, 'Single-Cell Sequencing of Developing Human Gut Reveals Transcriptional Links to Childhood Crohn's Disease', Developmental Cell, 55, pp. 771 - 783.e5, http://dx.doi.org/10.1016/j.devcel.2020.11.010
    Journal articles | 2020
    Hewitson JP; West KA; James KR; Rani GF; Dey N; Romano A; Brown N; Teichmann SA; Kaye PM; Lagos D, 2020, 'MALAT1 suppresses immunity to infection through promoting expression of Maf and IL-10 in Th cells', Journal of Immunology, 204, pp. 2949 - 2960, http://dx.doi.org/10.4049/jimmunol.1900940
    Journal articles | 2020
    James KR; Gomes T; Elmentaite R; Kumar N; Gulliver EL; King HW; Stares MD; Bareham BR; Ferdinand JR; Petrova VN; Polański K; Forster SC; Jarvis LB; Suchanek O; Howlett S; James LK; Jones JL; Meyer KB; Clatworthy MR; Saeb-Parsy K; Lawley TD; Teichmann SA, 2020, 'Distinct microbial and immune niches of the human colon', Nature Immunology, 21, pp. 343 - 353, http://dx.doi.org/10.1038/s41590-020-0602-z
    Journal articles | 2020
    James KR; King HW, 2020, 'Germs and germlines: how “public” B-cell clones evolve in the gut', Immunology and Cell Biology, 98, pp. 428 - 430, http://dx.doi.org/10.1111/imcb.12340
    Journal articles | 2020
    Soon MSF; Lee HJ; Engel JA; Straube J; Thomas BS; Pernold CPS; Clarke LS; Laohamonthonkul P; Haldar RN; Williams CG; Lansink LIM; Moreira ML; Bramhall M; Koufariotis LT; Wood S; Chen X; James KR; Lönnberg T; Lane SW; Belz GT; Engwerda CR; Khoury DS; Davenport MP; Svensson V; Teichmann SA; Haque A, 2020, 'Transcriptome dynamics of CD4+ T cells during malaria maps gradual transit from effector to memory', Nature Immunology, 21, pp. 1597 - 1610, http://dx.doi.org/10.1038/s41590-020-0800-8
    Journal articles | 2019
    Akter J; Khoury DS; Aogo R; Lansink LIM; SheelaNair A; Thomas BS; Laohamonthonkul P; Pernold CPS; Dixon MWA; Soon MSF; Fogg LG; Engel JA; Elliott T; Sebina I; James KR; Cromer D; Davenport MP; Haque A, 2019, 'Plasmodium-specific antibodies block in vivo parasite growth without clearing infected red blood cells', PLoS Pathogens, 15, pp. e1007599, http://dx.doi.org/10.1371/journal.ppat.1007599
    Journal articles | 2019
    Soon SFM; Engel J; Lee J; James K; Lonnberg T; Svensson V; Teichmann S; Haque A, 2019, 'Using single-cell RNA-seq to lineage trace effector to memory transitions in CD4+ T cells during malaria', The Journal of Immunology, 202, pp. 186.1 - 186.1, http://dx.doi.org/10.4049/jimmunol.202.supp.186.1
    Journal articles | 2018
    James KR; Soon MSF; Sebina I; Fernandez-Ruiz D; Davey G; Liligeto UN; Nair AS; Fogg LG; Edwards CL; Best SE; Lansink LIM; Schroder K; Wilson JAC; Austin R; Suhrbier A; Lane SW; Hill GR; Engwerda CR; Heath WR; Haque A, 2018, 'IFN regulatory factor 3 balances Th1 and t follicular helper immunity during nonlethal blood-Stage plasmodium infection', Journal of Immunology, 200, pp. 1443 - 1456, http://dx.doi.org/10.4049/jimmunol.1700782
    Journal articles | 2018
    Kunz DJ; Gomes T; James KR, 2018, 'Immune cell dynamics unfolded by single-cell technologies', Frontiers in Immunology, 9, http://dx.doi.org/10.3389/fimmu.2018.01435
    Journal articles | 2017
    Fernandez-Ruiz D; Lau LS; Ghazanfari N; Jones CM; Ng WY; Davey GM; Berthold D; Holz L; Kato Y; Enders MH; Bayarsaikhan G; Hendriks SH; Lansink LIM; Engel JA; Soon MSF; James KR; Cozijnsen A; Mollard V; Uboldi AD; Tonkin CJ; De Koning-Ward TF; Gilson PR; Kaisho T; Haque A; Crabb BS; Carbone FR; McFadden GI; Heath WR, 2017, 'Development of a novel CD4+ TCR transgenic line that reveals a dominant role for CD8+ dendritic cells and CD40 signaling in the generation of helper and CTL responses to blood-stage malaria', Journal of Immunology, 199, pp. 4165 - 4179, http://dx.doi.org/10.4049/jimmunol.1700186
    Journal articles | 2017
    Khoury DS; Cromer D; Akter J; Sebina I; Elliott T; Thomas BS; Soon MSF; James KR; Best SE; Haque A; Davenport MP, 2017, 'Host-mediated impairment of parasite maturation during blood-stage Plasmodium infection', Proceedings of the National Academy of Sciences of the United States of America, 114, pp. 7701 - 7706, http://dx.doi.org/10.1073/pnas.1618939114
    Journal articles | 2017
    Khoury DS; Cromer D; Elliott T; Soon MSF; Thomas BS; James KR; Best SE; Aogo RA; Engel JA; Gartlan KH; Akter J; Sebina I; Haque A; Davenport MP, 2017, 'Characterising the effect of antimalarial drugs on the maturation and clearance of murine blood-stage Plasmodium parasites in vivo', International Journal for Parasitology, 47, pp. 913 - 922, http://dx.doi.org/10.1016/j.ijpara.2017.05.009
    Journal articles | 2017
    Lönnberg T; Svensson V; James KR; Fernandez-Ruiz D; Sebina I; Montandon R; Soon MSF; Fogg LG; Nair AS; Liligeto UN; Stubbington MJT; Ly LH; Bagger FO; Zwiessele M; Lawrence ND; Souza-Fonseca-Guimaraes F; Bunn PT; Engwerda CR; Heath WR; Billker O; Stegle O; Haque A; Teichmann SA, 2017, 'Single-cell RNA-seq and computational analysis using temporal mixture modeling resolves TH1/TFH fate bifurcation in malaria', Science Immunology, 2, http://dx.doi.org/10.1126/sciimmunol.aal2192
    Journal articles | 2017
    Sebina I; Fogg LG; James KR; Soon MSF; Akter J; Thomas BS; Hill GR; Engwerda CR; Haque A, 2017, 'IL-6 promotes CD4+ T-cell and B-cell activation during Plasmodium infection', Parasite Immunology, 39, http://dx.doi.org/10.1111/pim.12455
    Journal articles | 2016
    Proserpio V; Piccolo A; Haim-Vilmovsky L; Kar G; Lönnberg T; Svensson V; Pramanik J; Natarajan KN; Zhai W; Zhang X; Donati G; Kayikci M; Kotar J; McKenzie ANJ; Montandon R; James KR; Fernandez-Ruiz D; Heath WR; Haque A; Billker O; Woodhouse S; Cicuta P; Nicodemi M; Teichmann SA; Fernandez Ruiz D, 2016, 'Erratum to: Single cell analysis of CD4+ T cell differentiation reveals three major cell states and progressive acceleration of proliferation [Genome Biol. 17 (2016) 103]', Genome Biology, 17, http://dx.doi.org/10.1186/s13059-016-0998-9
    Journal articles | 2016
    Sebina I; James KR; Soon MSF; Fogg LG; Best SE; Labastida Rivera FD; Montes de Oca M; Amante FH; Thomas BS; Beattie L; Souza-Fonseca-Guimaraes F; Smyth MJ; Hertzog PJ; Hill GR; Hutloff A; Engwerda CR; Haque A, 2016, 'IFNAR1-Signalling Obstructs ICOS-mediated Humoral Immunity during Non-lethal Blood-Stage Plasmodium Infection', PLoS Pathogens, 12, http://dx.doi.org/10.1371/journal.ppat.1005999
    Journal articles | 2015
    Edwards CL; Best SE; Gun SY; Claser C; James KR; de Oca MM; Sebina I; Rivera FDL; Amante FH; Hertzog PJ; Engwerda CR; Renia L; Haque A, 2015, 'Spatiotemporal requirements for IRF7 in mediating type I IFN-dependent susceptibility to blood-stage Plasmodium infection', European Journal of Immunology, 45, pp. 130 - 141, http://dx.doi.org/10.1002/eji.201444824
    Journal articles | 2015
    Edwards CL; Zhang V; Werder RB; Best SE; Sebina I; James KR; Faleiro RJ; De Labastida Rivera F; Amante FH; Engwerda CR; Phipps S; Haque A, 2015, 'Coinfection with blood-stage Plasmodium promotes systemic type I interferon production during pneumovirus infection but impairs inflammation and viral control in the lung', Clinical and Vaccine Immunology, 22, pp. 477 - 483, http://dx.doi.org/10.1128/CVI.00051-15
    Journal articles | 2015
    Khoury DS; Cromer D; Best SE; James KR; Sebina I; Haque A; Davenport MP, 2015, 'Reduced erythrocyte susceptibility and increased host clearance of young parasites slows Plasmodium growth in a murine model of severe malaria', Scientific Reports, 5, pp. 9412, http://dx.doi.org/10.1038/srep09412
    Journal articles | 2014
    Bunn PT; Stanley AC; De Labastida Rivera F; Mulherin A; Sheel M; Alexander CE; Faleiro RJ; Amante FH; De Oca MM; Best SE; James KR; Kaye PM; Haque A; Engwerda CR, 2014, 'Tissue requirements for establishing long-term CD4+ T cell-mediated immunity following Leishmania donovani infection', Journal of Immunology, 192, pp. 3709 - 3718, http://dx.doi.org/10.4049/jimmunol.1300768
    Journal articles | 2014
    Haque A; Best SE; De Oca MM; James KR; Ammerdorffer A; Edwards CL; De Labastida Rivera F; Amante FH; Bunn PT; Sheel M; Sebina I; Koyama M; Varelias A; Hertzog PJ; Kalinke U; Gun SY; Rénia L; Ruedl C; MacDonald KPA; Hill GR; Engwerda CR, 2014, 'Type I IFN signaling in CD8-DCs impairs Th1-dependent malaria immunity', Journal of Clinical Investigation, 124, pp. 2483 - 2496, http://dx.doi.org/10.1172/JCI70698
    Journal articles | 2013
    Anthony BJ; James KR; Gobert GN; Ramm GA; McManus DP, 2013, 'Schistosoma japonicum Eggs Induce a Proinflammatory, Anti-Fibrogenic Phenotype in Hepatic Stellate Cells', PLoS ONE, 8, http://dx.doi.org/10.1371/journal.pone.0068479
    Journal articles | 2013
    Khoury DS; Cromer D; Best SE; James KR; Kim PS; Engwerda CR; Haque A; Davenport MP, 2013, 'Effect of mature, blood-stage Plasmodium parasite sequestration on pathogen biomass in mathematical and in vivo models of malaria.', Infection and Immunity, 82, pp. 212 - 220, http://dx.doi.org/10.1128/IAI.00705-13
  • Preprints | 2024
    Gwynne M; West KA; van Dongen S; Kourtzelis I; Coverley D; Teichmann SA; James KR; Hewitson JP; Lagos D, 2024, Malat1regulates female Th2 cell cytokine expression through controlling early differentiation and response to IL2, http://dx.doi.org/10.1101/2024.10.23.619648
    Preprints | 2024
    Oliver AJ; Huang N; Li R; Bartolome-Casado R; Nilsen HR; Gudino V; Melon-Ardanaz CDIBE; Fitzpatrick MEB; Provine NM; Polanski K; Koplev S; Milchsack LM; Dann E; Predeus AV; Cakir B; To K; Prete M; Chapman JA; Masi AC; Stephenson E; Engelbert J; Lobentanzer S; Perera S; Richardson L; Kapuge R; Wilbrey-Clark A; Semprich CI; Moy M; Ellams S; Tudor CL; Joseph P; Garrido-Trigo A; Corraliza CDIBE; Oliver TRW; Hook CE; Saez-Rodriguez J; James KR; Meyer KB; Mahbubani KT; Saeb-Parsy K; Zilbauer M; Hoivik ML; Baekkevold ES; Salas CDIBE; Stewart CJ; Berrington JE; Klenerman P; Haniffa M; Jahnsen FL; Elmentaite R; Teichmann SA, 2024, Single Cell Integration Characterises Metaplasia in Inflammatory Intestinal Diseases, http://dx.doi.org/10.1101/2024.10.11.614415
    Preprints | 2024
    Tearle JLE; Zhang F; Jackson KJL; Malhotra P; Tavakoli P; Koentgen S; Warren J; Williams C; Haque A; Arzivian A; Tedla N; Kim A; King HW; Hold GL; Ghaly S; James KR, 2024, The primary sclerosing cholangitis and ulcerative colitis colonic mucosa defined through paired microbial and single-cell RNA sequencing, http://dx.doi.org/10.1101/2024.08.12.607536
    Preprints | 2023
    Krzak M; Alegbe T; Taylor DL; Jones G-R; Ghouraba M; Strickland M; Harris BT; Satti R; Arestang K; Ramirez-Navarro L; Nishad N; Cheam KAX; Tutert M; Ozols M; Noell G; Leonard S; Przybilla MJ; Petrova V; Jones CP; Wana N; Hu MX; Skelton J; Ostermayer J; Gu Y; Garri W; Brezina B; Caballes CQ; Corridoni D; Parkes M; Iyer V; Cotobal Martin C; McIntyre RE; Raine T; Anderson CA, 2023, Single-Cell RNA Sequencing of Terminal Ileal Biopsies Identifies Signatures of Crohn’s Disease Pathogenesis, http://dx.doi.org/10.1101/2023.09.06.23295056
    Preprints | 2023
    Levinger R; Tussia-Cohen D; Friedman S; Lender Y; Nissan Y; Fraimovitch E; Gavriel Y; Tearle J; Kolodziejczyk AA; Gomes T; Kunowska N; Weinberg M; Donati G; James KR; Yovel Y; Hagai T, 2023, Spatial and single-cell transcriptomics illuminate bat immunity and barrier tissue evolution, http://dx.doi.org/10.1101/2023.10.30.564705
    Preprints | 2022
    Stewart B; Fergie M; Young M; Jones C; Sachdeva A; Blain A; Bacon C; Rand V; Ferdinand J; James K; Mahbubani K; Hook L; Jonas N; Coleman N; Saeb-Parsy K; Collin M; Clatworthy M; Behjati S; Carey C, 2022, Spatial and molecular profiling of classic Hodgkin lymphoma reveals an immunosuppressive mononuclear phagocyte network, http://dx.doi.org/10.21203/rs.3.rs-1233380/v2
    Preprints | 2022
    Stewart B; Fergie M; Young M; Jones C; Sachdeva A; Blain A; Bacon C; Rand V; Ferdinand J; James K; Mahbubani K; Hook L; Jonas N; Coleman N; Saeb-Parsy K; Collin M; Clatworthy M; Behjati S; Carey C, 2022, Spatial and molecular profiling of the classic Hodgkin lymphoma microenvironment reveals an immunosuppressive mononuclear phagocyte network, http://dx.doi.org/10.21203/rs.3.rs-1233380/v1
    Preprints | 2022
    Stewart B; Fergie M; Young M; Jones C; Sachdeva A; Blain A; Bacon C; Rand V; Ferdinand J; James K; Mahbubani K; Hook L; Jonas N; Coleman N; Saeb-Parsy K; Collin M; Clatworthy M; Behjati S; Carey C, 2022, Spatial and molecular profiling reveals an immunosuppressive mononuclear phagocyte network in Classic Hodgkin lymphoma, http://dx.doi.org/10.21203/rs.3.rs-1233380/v3
    Preprints | 2021
    Elmentaite R; Kumasaka N; King HW; Roberts K; Dabrowska M; Pritchard S; Bolt L; Vieira SF; Mamanova L; Huang N; Goh Kai’En I; Stephenson E; Engelbert J; Botting RA; Fleming A; Dann E; Lisgo SN; Katan M; Leonard S; Oliver TRW; Hook CE; Nayak K; Perrone F; Campos LS; Dominguez-Conde C; Polanski K; Van Dongen S; Patel M; Morgan MD; Marioni JC; Bayraktar OA; Meyer KB; Zilbauer M; Uhlig H; Clatworthy MR; Mahbubani KT; Saeb Parsy K; Haniffa M; James KR; Teichmann SA, 2021, Cells of the human intestinal tract mapped across space and time, http://dx.doi.org/10.1101/2021.04.07.438755
    Preprints | 2020
    Elmentaite R; Ross A; James K; Ortmann D; Gomes T; Roberts K; Nayak K; Tuck L; Bayraktar OA; Heuschkel R; Vallier L; Teichmann S; Zilbauer M, 2020, Single-cell sequencing of developing human gut reveals transcriptional links to childhood Crohn’s disease, http://dx.doi.org/10.1101/2020.02.06.937110
    Preprints | 2019
    James KR; Gomes T; Elmentaite R; Kumar N; Gulliver EL; King HW; Stares MD; Bareham BR; Ferdinand JR; Petrova VN; Polanski K; Forster SC; Jarvis LB; Suchanek O; Howlett S; James LK; Jones JL; Meyer KB; Clatworthy MR; Saeb-Parsy K; Lawley TD; Teichmann SA, 2019, Distinct microbial and immune niches of the human colon, http://dx.doi.org/10.1101/2019.12.12.871657
    Preprints | 2019
    Soon M; Lee HJ; Engel J; Straube J; Thomas B; Clarke L; Laohamonthonkul P; Pernold C; Haldar R; Williams C; Lansink L; Koufariotis R; Lakis V; Wood S; Chen X; James K; Lönnberg T; Lane S; Davenport M; Khoury D; Svensson V; Teichmann S; Haque A, 2019, Transcriptome Dynamics Reveals Progressive Transition from Effector to Memory in CD4+T cells, http://dx.doi.org/10.1101/675967
    Preprints | 2018
    James K, 2018, Gut_All Cells_Human v1, http://dx.doi.org/10.17504/protocols.io.q3xdypn
    Preprints | 2018
    James K, 2018, Human colon tissue dissociation for immune cells v1, http://dx.doi.org/10.17504/protocols.io.tbfeijn
    Preprints | 2017
    Fernandez-Ruiz D; Lau LS; Ghazanfari N; Jones C; Ng WY; Davey G; Berthold D; Holz L; Kato Y; Bayarsaikhan G; Hendriks S; James K; Cozijnsen A; Mollard V; de Koning-Ward T; Gilson P; Kaisho T; Haque A; Crabb B; Carbone F; McFadden G; Heath W, 2017, Development of a Novel CD4+TCR Transgenic Line that Reveals a Dominant Role for CD8+DC and CD40-Signaling in the Generation of Helper and CTL Responses to Blood Stage Malaria, http://dx.doi.org/10.1101/113837
    Preprints | 2016
    Lönnberg T; Svensson V; James KR; Fernandez-Ruiz D; Sebina I; Montandon R; Soon MSF; Fogg LG; Stubbington MJT; Otzen Bagger F; Zwiessele M; Lawrence N; Souza-Fonseca-Guimaraes F; Heath WR; Billker O; Stegle O; Haque A; Teichmann SA, 2016, Temporal mixture modelling of single-cell RNA-seq data resolves a CD4+T cell fate bifurcation, http://dx.doi.org/10.1101/074971

NHMRC Investigator Grant (2021-2026)

Spinak Fellowship (2021-2024)

Ramaciotti Health Investment (2021-2024)

Perpetual IMPACT (2021)

Christ’s College Junior Research Fellowship (2018-2020)

My Research Supervision

PhD and intern students