Rik G.H. Lindeboom - Publications, H-index & Citations

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Rik G.H. Lindeboom

wellcome genome campus

26H-index

81Paper Count

4.9KCitation Count

Published Papers 33

Publication Date

Pre-existing and early cellular immune factors correlate with functionally complete protection against primary controlled human SARS-CoV-2 infection

Nature Communications

IF15.7

2025-12-07

OAAI

Helen R. Wagstaffe; Ryan S. Thwaites; Jasmin K. Sidhu; Rik G. H. Lindeboom; Lorenz Kretschmer; Kaylee B. Worlock; Lisa M. Dratva; Ao Huang; Stephanie Ascough; Loukas Papargyris; Richard McKendry; Ashley M. Collins; Jiayun Xu; Nana-Marie Lemm; Ben Killingley; Mariya Kalinova; Alex Mann; Andrew Catchpole; Leo Swadling; John S. Tsang; Mala K. Maini; Mahdad Noursadeghi; Marko Z. Nikolić; Sarah A. Teichmann; Peter J. M. Openshaw; Christopher Chiu

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Temporal multi-omics analysis of COVID-19 in end-stage kidney disease

Cell Genomics

IF9

2025-06-17

OAAI

Emily Stephenson; Erin Macdonald-Dunlop; Lisa M. Dratva; Rik G.H. Lindeboom; Zewen Kelvin Tuong; Win Min Tun; Lorenz Kretschmer; Norzawani B. Buang; Stephane Ballereau; Mia Cabantaus; Ana Peñalver; Elena Prigmore; John R. Ferdinand; Benjamin J. Stewart; Jack Gisby; Talat H. Malik; Candice L. Clarke; Nicholas Medjeral-Thomas; Maria Prendecki; Stephen McAdoo; Anais Portet; Michelle Willicombe; Eleanor Sandhu; Matthew C. Pickering; Marina Botto; Sarah A. Teichmann; Muzlifah Haniffa; Menna R. Clatworthy; David C. Thomas; James E. Peters

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SARS-CoV-2 human challenge reveals biomarkers that discriminate early and late phases of respiratory viral infections

NATURE COMMUNICATIONS

IF15.7

2024-11-30

OAAI

Rosenheim, Joshua; Gupta, Rishi K.; Thakker, Clare; Mann, Tiffeney; Bell, Lucy C. K.; Broderick, Claire M.; Madon, Kieran; Papargyris, Loukas; Dayananda, Pete; Kwok, Andrew J.; Greenan-Barrett, James; Wagstaffe, Helen R.; Conibear, Emily; Fenn, Joe; Hakki, Seran; Lindeboom, Rik G. H.; Dratva, Lisa M.; Lemetais, Briac; Weight, Caroline M.; Venturini, Cristina; Kaforou, Myrsini; Levin, Michael; Kalinova, Mariya; Mann, Alex J.; Catchpole, Andrew; Knight, Julian C.; Nikolic, Marko Z.; Teichmann, Sarah A.; Killingley, Ben; Barclay, Wendy; Chain, Benjamin M.; Lalvani, Ajit; Heyderman, Robert S.; Chiu, Christopher; Noursadeghi, Mahdad

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Early human lung immune cell development and its role in epithelial cell fate

EUROPEAN RESPIRATORY JOURNAL

IF21

2024-10-30

OAAI

Barnes, Josephine; Yoshida, Masahiro; He, Peng; Worlock, Kaylee; Lindeboom, Rik; Suo, Chenqu; Pett, J. Patrick; Wilbrey-Clark, Anna; Dann, Emma; Mamanova, Lira; Richardson, Laura; Polanski, Krzysztof; Pennycuick, Adam; Allen-Hytinnen, Jessica; Herczeg, Ivan; Arzili, Romina; Hynds, Robert; Teixeira, Vitor; Haniffa, Muzlifah; Lim, Kyungtae; Sun, Dawei; Rawlins, Emma; Oliver, Amanda; Lyons, Paul; Marioni, John; Ruhrberg, Christiana; Tuong, Zewen; Clatworthy, Menna; Reading, James; Janes, Sam; Teichmann, Sarah; Meyer, Kerstin; Nikolic, Marko

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Human SARS-CoV-2 challenge uncovers differences in local and systemic cellular responses associated with protection from infection and distinct infection states

EUROPEAN RESPIRATORY JOURNAL

IF21

2024-10-30

PREAI

Worlock, Kaylee; Lindeboom, Rik G. H.; Dratva, Lisa; Yoshida, Masahiro; Scobie, David; Wagstaffe, Helen; Richardson, Laura; Wilbrey-Clark, Anna; Barnes, Josephine; Mehta, Puja; Kretschmer, Lorenz; Polanski, Krzysztof; Allen-Hyttinen, Jessica; Sumanaweera, Dinithi; Boccacino, Jacqueline M.; Sungnak, Waradon; Elmentaite, Rasa; Huang, Ni; Mamanova, Lira; Kapuge, Rakeshlal; Bolt, Liam; Prigmore, Elena; Kilingley, Ben; Kalinova, Mariya; Mayer, Maria; Boyers, Alison; Mann, Alex; Swadling, Leo; Woodall, Maximillian; Ellis, Samuel; Smith, Claire M.; Teixeira, Vitor; Janes, Sam M.; Chambers, Rachel C.; Haniffa, Muzlifah; Catchpole, Andrew; Heyderman, Rob; Noursadeghi, Mahdad; Chain, Benny; Mayer, Andreas; Meyer, Kerstin B.; Chiu, Christopher; Teichmann, Sarah A.; Nikolic, Marko Z.

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Quantifying genome-wide transcription factor binding affinities for chromatin using BANC-seq

NATURE PROTOCOLS

IF16

2024-07-30

PREAI

Wester, Roelof A.; Neikes, Hannah K.; Lindeboom, Rik G. H.; Vermeulen, Michiel

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Multi-modal generative modeling for joint analysis of single-cell T cell receptor and gene expression data

NATURE COMMUNICATIONS

IF15.7

2024-07-03

OAAI

Drost, Felix; An, Yang; Bonafonte-Pardas, Irene; Dratva, Lisa M.; Lindeboom, Rik G. H.; Haniffa, Muzlifah; Teichmann, Sarah A.; Theis, Fabian; Lotfollahi, Mohammad; Schubert, Benjamin

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Early human lung immune cell development and its role in epithelial cell fate

SCIENCE IMMUNOLOGY

IF16.3

2023-12-22

OAAI

Barnes, Josephine L.; Yoshida, Masahiro; He, Peng; Worlock, Kaylee B.; Lindeboom, Rik G. H.; Suo, Chenqu; Pett, J. Patrick; Wilbrey-Clark, Anna; Dann, Emma; Mamanova, Lira; Richardson, Laura; Polanski, Krzysztof; Pennycuick, Adam; Allen-Hyttinen, Jessica; Herczeg, Ivan T.; Arzili, Romina; Hynds, Robert E.; Teixeira, Vitor H.; Haniffa, Muzlifah; Lim, Kyungtae; Sun, Dawei; Rawlins, Emma L.; Oliver, Amanda J.; Lyons, Paul A.; Marioni, John C.; Ruhrberg, Christiana; Tuong, Zewen Kelvin; Clatworthy, Menna R.; Reading, James L.; Janes, Sam M.; Teichmann, Sarah A.; Meyer, Kerstin B.; Nikolic, Marko Z.

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The 2023 generation

NATURE CANCER

IF28.5

2023-12-15

PREAI

Achinger-Kawecka, Joanna; Correa, Santiago; Hu, Jing; Li, Gaopeng; Lindeboom, Rik G. H.; Misale, Sandra; Monkkonen, Teresa; Nirmal, Ajit J.; Prekovic, Stefan; Sinha, Sanju; Trigos, Anna S.; Watson, Caroline J.

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Acid ceramidase regulates innate immune memory

CELL REPORTS

IF6.9

2023-12-01

OAAI

Rother, Nils; Yanginlar, Cansu; Prevot, Geoffrey; Jonkman, Inge; Jacobs, Maaike; van Leent, Mandy M. T.; van Heck, Julia; Matzaraki, Vasiliki; Azzun, Anthony; Morla-Folch, Judit; Ranzenigo, Anna; Wang, William; van der Meel, Roy; Fayad, Zahi A.; Riksen, Niels P.; Hilbrands, Luuk B.; Lindeboom, Rik G. H.; Martens, Joost H. A.; Vermeulen, Michiel; Joosten, Leo A. B.; Netea, Mihai G.; Mulder, Willem J. M.; van der Vlag, Johan; Teunissen, Abraham J. P.; Duivenvoorden, Raphael

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Dandelion uses the single-cell adaptive immune receptor repertoire to explore lymphocyte developmental origins

NATURE BIOTECHNOLOGY

IF41.7

2023-04-13

OAAI

Suo, Chenqu; Polanski, Krzysztof; Dann, Emma; Lindeboom, Rik G. H.; Vilarrasa-Blasi, Roser; Vento-Tormo, Roser; Haniffa, Muzlifah; Meyer, Kerstin B.; Dratva, Lisa M.; Tuong, Zewen Kelvin; Clatworthy, Menna R.; Teichmann, Sarah A.

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Quantification of absolute transcription factor binding affinities in the native chromatin context using BANC-seq

NATURE BIOTECHNOLOGY

IF41.7

2023-03-27

PREAI

Neikes, Hannah K.; Kliza, Katarzyna W.; Grawe, Cathrin; Wester, Roelof A.; Jansen, Pascal W. T. C.; Lamers, Lieke A.; Baltissen, Marijke P.; van Heeringen, Simon J.; Logie, Colin; Teichmann, Sarah A.; Lindeboom, Rik G. H.; Vermeulen, Michiel

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Obesity Is Associated with Attenuated Tissue Immunity in COVID-19

AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

IF19.4

2023-03-01

OAAI

Guo, Shuang A.; Bowyer, Georgina S.; Ferdinand, John R.; Maes, Mailis; Tuong, Zewen K.; Gillman, Eleanor; Liao, Mingfeng; Lindeboom, Rik G. H.; Yoshida, Masahiro; Worlock, Kaylee; Gopee, Hudaa; Stephenson, Emily; Gao, Catherine A.; Lyons, Paul A.; Smith, Kenneth G. C.; Haniffa, Muzlifah; Meyer, Kerstin B.; Nikolic, Marko Z.; Zhang, Zheng; Wunderink, Richard G.; Misharin, Alexander, V; Dougan, Gordon; Navapurkar, Vilas; Teichmann, Sarah A.; Morris, Andrew Conway; Clatworthy, Menna R.

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A spatially resolved atlas of the human lung characterizes a gland-associated immune niche

NATURE GENETICS

IF31.8

2022-12-21

OAAI

Madissoon, Elo; Oliver, Amanda J.; Kleshchevnikov, Vitalii; Wilbrey-Clark, Anna; Polanski, Krzysztof; Richoz, Nathan; Orsi, Ana Ribeiro; Mamanova, Lira; Bolt, Liam; Elmentaite, Rasa; Pett, J. Patrick; Huang, Ni; Xu, Chuan; He, Peng; Dabrowska, Monika; Pritchard, Sophie; Tuck, Liz; Prigmore, Elena; Perera, Shani; Knights, Andrew; Oszlanczi, Agnes; Hunter, Adam; Vieira, Sara F.; Patel, Minal; Lindeboom, Rik G. H.; Campos, Lia S.; Matsuo, Kazuhiko; Nakayama, Takashi; Yoshida, Masahiro; Worlock, Kaylee B.; Nikolic, Marko Z.; Georgakopoulos, Nikitas; Mahbubani, Krishnaa T.; Saeb-Parsy, Kourosh; Bayraktar, Omer Ali; Clatworthy, Menna R.; Stegle, Oliver; Kumasaka, Natsuhiko; Teichmann, Sarah A.; Meyer, Kerstin B.

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Liver Colonization by Colorectal Cancer Metastases Requires YAP-Controlled Plasticity at the Micrometastatic Stage

CANCER RESEARCH

IF16.6

2022-02-22

OAAI

Heinz, Maria C.; Peters, Niek A.; Oost, Koen C.; Lindeboom, Rik G. H.; van Voorthuijsen, Lisa; Fumagalli, Arianna; van der Net, Mirjam C.; de Medeiros, Gustavo; Hageman, Joris H.; Verlaan-Klink, Ingrid; Rinkes, Inne H. M. Borel; Liberali, Prisca; Gloerich, Martijn; van Rheenen, Jacco; Vermeulen, Michiel; Kranenburg, Onno; Snippert, Hugo J. G.

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To NMD or Not To NMD: Nonsense-Mediated mRNA Decay in Cancer and Other Genetic Diseases

TRENDS IN GENETICS

IF16.3

2021-07-01

141

OAAI

Supek, Fran; Lehner, Ben; Lindeboom, Rik G. H.

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Towards a Human Cell Atlas: Taking Notes from the Past

TRENDS IN GENETICS

IF16.3

2021-07-01

OAAI

Lindeboom, Rik G. H.; Regev, Aviv; Teichmann, Sarah A.

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Single-cell multi-omics analysis of the immune response in COVID-19

NATURE MEDICINE

IF50

2021-04-20

389

OAAI

Stephenson, Emily; Reynolds, Gary; Botting, Rachel A.; Calero-Nieto, Fernando J.; Morgan, Michael D.; Tuong, Zewen Kelvin; Bach, Karsten; Sungnak, Waradon; Worlock, Kaylee B.; Yoshida, Masahiro; Kumasaka, Natsuhiko; Kania, Katarzyna; Engelbert, Justin; Olabi, Bayan; Spegarova, Jarmila Stremenova; Wilson, Nicola K.; Mende, Nicole; Jardine, Laura; Gardner, Louis C. S.; Goh, Issac; Horsfall, Dave; McGrath, Jim; Webb, Simone; Mather, Michael W.; Lindeboom, Rik G. H.; Dann, Emma; Huang, Ni; Polanski, Krzysztof; Prigmore, Elena; Gothe, Florian; Scott, Jonathan; Payne, Rebecca P.; Baker, Kenneth F.; Hanrath, Aidan T.; van der Loeff, Ina C. D. Schim; Barr, Andrew S.; Sanchez-Gonzalez, Amada; Bergamaschi, Laura; Mescia, Federica; Barnes, Josephine L.; Kilich, Eliz; de Wilton, Angus; Saigal, Anita; Saleh, Aarash; Janes, Sam M.; Smith, Claire M.; Gopee, Nusayhah; Wilson, Caroline; Coupland, Paul; Coxhead, Jonathan M.; Kiselev, Vladimir Yu; van Dongen, Stijn; Bacardit, Jaume; King, Hamish W.; Rostron, Anthony J.; Simpson, A. John; Hambleton, Sophie; Laurenti, Elisa; Lyons, Paul A.; Meyer, Kerstin B.; Nikolic, Marko Z.; Duncan, Christopher J. A.; Smith, Kenneth G. C.; Teichmann, Sarah A.; Clatworthy, Menna R.; Marioni, John C.; Gottgens, Berthold; Haniffa, Muzlifah

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Hydroxychloroquine Inhibits the Trained Innate Immune Response to Interferons

CELL REPORTS MEDICINE

IF10.6

2020-12-01

OAAI

Rother, Nils; Yanginlar, Cansu; Lindeboom, Rik G. H.; Bekkering, Siroon; van Leent, Mandy M. T.; Buijsers, Baranca; Jonkman, Inge; de Graaf, Mark; Baltissen, Marijke; Lamers, Lieke A.; Riksen, Niels P.; Fayad, Zahi A.; Mulder, Willem J. M.; Hilbrands, Luuk B.; Joosten, Leo A. B.; Netea, Mihai G.; Vermeulen, Michiel; van der Vlag, Johan; Duivenvoorden, Raphael

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RNF43 truncations trap CK1 to drive niche-independent self-renewal in cancer

EMBO JOURNAL

IF8.3

2020-08-10

OAAI

Spit, Maureen; Fenderico, Nicola; Jordens, Ingrid; Radaszkiewicz, Tomasz; Lindeboom, Rik G. H.; Bugter, Jeroen M.; Cristobal, Alba; Ootes, Lars; van Osch, Max; Janssen, Eline; Boonekamp, Kim E.; Hanakova, Katerina; Potesil, David; Zdrahal, Zbynek; Boj, Sylvia F.; Medema, Jan Paul; Bryja, Vitezslav; Koo, Bon-Kyoung; Vermeulen, Michiel; Maurice, Madelon M.

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Research Directions