By Dr Kylie Renee James

Books

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Preprints

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

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

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

Krzak M; Alegbe T; Taylor DL; Ghouraba M; Strickland M; Satti R; Thompson T; Arestang K; Przybilla MJ; Ramirez-Navarro L; Harris BT; Cheam KAX; Noell G; Leonard S; Petrova V; Jones-Bell C; James KR; Wana N; Hu MX; Skelton J; Ostermayer J; Gu Y; Dawson C; Corridoni D; Martin CC; Parkes M; Iyer V; Jones G-R; McIntyre RE; Raine T; Anderson CA, 2023, Single-cell RNA sequencing reveals dysregulated cellular programmes in the inflamed epithelium of Crohn’s disease patients, http://dx.doi.org/10.1101/2023.09.06.23295056

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

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

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

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

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

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

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

James K, 2018, Human colon tissue dissociation for immune cells v1, http://dx.doi.org/10.17504/protocols.io.tbfeijn

James K, 2018, Gut_All Cells_Human v1, http://dx.doi.org/10.17504/protocols.io.q3xdypn

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

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

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