Cross-omics integration to identify modulators for improving vaccine efficacy

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Publications

Cell-type eQTL deconvolution of bronchial epithelium through integration of single-cell and bulk RNA-seq.

Author(s): Qi, C., Berg, M., Chu, X., Timens, W., Kole, T., van den Berge, M., Xu, C.-J., Koppelman, G. H., Nawijn, M. C. & Li, Y.
Published in: Allergy, 2022, ISSN 1398-9995
Publisher: Wiley

Long-term DNA methylation changes mediate heterologous cytokine responses after BCG vaccination.

Author(s): "Qi, C., Liu, Z., Kilic, G., Sarlea, A. S., Debisarun, P. A., Liu, X., Mekonnen, Y. A., Li, W., Grasshoff, M., Alaswad, A., Petkoglou, A., Koeken, V. A. C. M., Moorlag, S. J. C. F. M., de Bree, L. C. J., Mourits, V. P., Joosten, L. A. B., Li, Y.#, Netea, M. G. # & Xu, C.-J. #"
Published in: Genome Biology, 2025, ISSN 1474-760X
Publisher: Springer Nature

Nasal DNA methylation at three CpG sites predicts childhood allergic disease.

Author(s): van Breugel, M., Qi, C., Xu, Z., Pedersen, C.-E. T., Petoukhov, I., Vonk, J. M., Gehring, U., Berg, M., Bügel, M., Carpaij, O. A., Forno, E., Morin, A., Eliasen, A. U., Jiang, Y., van den Berge, M., Nawijn, M. C., Li, Y., Chen, W., Bont, L. J., Bønnelykke, K., Celedón, J. C., Koppelman, G. H. & Xu, C.-J.
Published in: Nat Commun, 2022, ISSN 2041-1723
Publisher: Nature Publishing Group

Multi‐Omics Analysis Reveals Sex‐Specific Signatures for BCG Vaccine Efficacy

Author(s): "Zhan, Q., Zhou, L., Fu, J., Jiang, X., Liu, X., Li, W., Moorlag, S. J. C. F. M., Koeken, V. A. C. M., de Bree, L. C. J., Mourits, V. P., Joosten, L. A. B., Li, Y. #, Netea, M. G.# & Xu, C#."
Published in: Eur J Immunol, 2026, ISSN 0014-2980
Publisher: John Wiley & Sons Ltd.

Immune memory in individuals with COVID-19

Author(s): Netea M.G., Li Y.
Published in: Nature Cell Biology, 2021, ISSN 1465-7392
Publisher: Nature Publishing Group
DOI: 10.1038/s41556-021-00689-8

Tan, I. L., Coutinho de Almeida, R., Modderman, R., Stachurska, A., Dekens, J., Barisani, D., Meijer, C. R., Roca, M., Martinez-Ojinaga, E., Shamir, R., Auricchio, R., Korponay-Szabó, I. R., Castillejo, G., Szajewska, H., Koletzko, S., Zhernakova, A., Kumar, V., Li, Y., Visschedijk, M. C., Weersma, R. K., Withoff, S.

Author(s): Circulating miRNAs as Potential Biomarkers for Celiac Disease Development.
Published in: Frontiers in immunology, 2021, ISSN 1664-3224
Publisher: Frontiers Media S.A.
DOI: 10.3389/fimmu.2021.734763

Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell Compartment

Author(s): Schulte-Schrepping J, Reusch N, Paclik D, Baßler K, Schlickeiser S, Zhang B, Krämer B, Krammer T, Brumhard S, Bonaguro L, De Domenico E, Wendisch D, Grasshoff M, Kapellos TS, Beckstette M, Pecht T, Saglam A, Dietrich O, Mei HE, Schulz AR, Conrad C, Kunkel D, Vafadarnejad E, Xu CJ, Horne A, Herbert M, Drews A, Thibeault C, Pfeiffer M, Hippenstiel S, Hocke A, Müller-Redetzky H, Heim KM, Machleidt
Published in: Cell, 2020, ISSN 0092-8674
Publisher: Cell Press
DOI: 10.1016/j.cell.2020.08.001

Identifying platelet-derived factors as amplifiers of B. burgdorferi-induced cytokine production.

Author(s): Kerstholt, M., van de Schoor, F. R., Oosting, M., Moorlag, S. J. C. F. M., Li, Y., Jaeger, M., van der Heijden, W. A., Tunjungputri, R. N., dos Santos, J. C., Kischkel, B., Vrijmoeth, H. D., Baarsma, M. E., Kullberg, B.-J., Lupse, M., Hovius, J. W., van den Wijngaard, C. C., Netea, M. G., de Mast, Q. & Joosten, L. A. B.
Published in: Clinical and Experimental Immunology, 2022, ISSN 0009-9104
Publisher: Blackwell Publishing Inc.

Single-cell profiles reveal distinctive immune response in atopic dermatitis in contrast to psoriasis.

Author(s): Zhang, B., Roesner, L. M., Traidl, S., Koeken, V. A. C. M., Xu, C.-J., Werfel, T. & Li, Y.
Published in: Allergy, 2023, ISSN 1398-9995
Publisher: Wiley

A comprehensive genetic map of cytokine responses in Lyme borreliosis.

Author(s): Botey-Bataller, J., Vrijmoeth, H. D., Ursinus, J., Kullberg, B.-J., van den Wijngaard, C. C., ter Hofstede, H., Alaswad, A., Gupta, M. K., Roesner, L. M., Huehn, J., Werfel, T., Schulz, T. F., Xu, C.-J., Netea, M. G., Hovius, J. W., Joosten, L. A. B. & Li, Y.
Published in: Nat Commun, 2024, ISSN 2041-1723
Publisher: Nature Publishing Group

Identification of Novel Population-Specific Cell Subsets in Chinese Ulcerative Colitis Patients Using Single-Cell RNA Sequencing.

Author(s): Li, G., Zhang, B., Hao, J., Chu, X., Wiestler, M., Cornberg, M., Xu, C.-J., Liu, X. & Li, Y.
Published in: Cell Mol Gastroenterol Hepatol, 2021, ISSN 2352-345X
Publisher: Elsevier Inc.

Integrative analysis reveals the multilateral inflammatory mechanisms of CD14 monocytes in gout.

Author(s): "Alaswad, A., Cabău, G., Crişan, T. O., Zhou, L., Zoodsma, M., Botey-Bataller, J., Li, W., Pamfil, C., Netea, M. G., Merriman, T., Xu, C.-J., Li, Y. # & Joosten, L. A. B. #"
Published in: Annals of the Rheumatic Diseases, 2025, ISSN 0003-4967
Publisher: BMJ Publishing Group

A distinct monocyte transcriptional state links systemic immune dysregulation to pulmonary impairment in long COVID.

Author(s): Kumar, S., Li, C., Zhou, L., Zhan, Q., Alaswad, A., Volland, S., Costa, B., Krooss, S. A., Klefenz, I., Schmaus, H., Zeuzem, A., von Witzendorff, D., Lickei, H., Pueschel, L., Kraft, A. R. M., Cornberg, M., Koczulla, A. R., Pink, I., Hoeper, M. M., Xu, C.-J., Häussler, S., Wiestler, M., Netea, M. G., Illig, T., Sun, J. & Li, Y.
Published in: Nat Immunol, 2026, ISSN 1529-2916
Publisher: Nature Publishing Group

Genome-wide analyses in Lyme borreliosis: identification of a genetic variant associated with disease susceptibility and its immunological implications.

Author(s): "Vrijmoeth, H. D., Ursinus, J., Botey-Bataller, J., Kuijpers, Y., Chu, X., van de Schoor, F. R., Scicluna, B. P., Xu, C.-J., Netea, M. G., Kullberg, B. J., van den Wijngaard, C. C., Li, Y., # Hovius, J. W. #& Joosten, L. A. B. #"
Published in: BMC Infectious Diseases, 2024, ISSN 1471-2334
Publisher: BioMed Central

DNA methylation landscapes of HIV controllers: an epigenome-wide association study.

Author(s): Gupta, M. K., Santos, J. C. dos, Vazquez, V. R., Ruijten, S. D. E., Navas, A., Jiang, X., Liu, Z., Zhang, Z., Botey-Bataller, J., Singh, O., Vadaq, N., Groenendijk, A. L., Vos, W. A. J. W., Blaauw, M. J. T., Eekeren, L. E. van, Li, Y., Joosten, L. A. B., Rokx, C., Verbon, A., Matzaraki, V., Netea, M. G., Ven, A. J. A. M. van der & Xu, C.-J.
Published in: eBioMedicine, 2025, ISSN 2352-3964
Publisher: Elsevier BV

Multi-Omics Integration Reveals Only Minor Long-Term Molecular and Functional Sequelae in Immune Cells of Individuals Recovered From COVID-19

Author(s): Liu, Z., Kilic, G., Li, W., Bulut, O., Gupta, M.K., Zhang, B., Qi, C., Peng, H., Tsay, H.-C., Soon, C. F., Mekonnen, Y.A., van der Made, C. I., van Cranenbroek, B., Koenen, H. J. P. M., Simonetti, E., Diavatopoulos, D., de Jonge, M. I., Müller, L., Schaal, H., Ostermann, P. N., Cornberg, M., Eiz-Vesper, B., van de Veerdonk, F., van Crevel, R., Joosten, L A. B., Domínguez-Andrés, J., Xu, C.-J.,
Published in: Frontiers in Immunology, 2022, ISSN 1664-3224
Publisher: Frontiers Media S.A.
DOI: 10.3389/fimmu.2022.838132

A single-cell view on host immune transcriptional response to in vivo BCG-induced trained immunity

Author(s): Li, W., Moorlag, S., Koeken, V.C.A.M., Röring, R.J., L de Bree, C., Mourits, V.P., Gupta, M.K., Zhang, B., Fu, J., Zhang, Z., Grondman, I., van Meijgaarden, K.E., Zhou, L., Alaswad, A., Joosten, L.A.B., van Crevel, R., Xu, C.-J., Netea, M.G., Li, Y.
Published in: Cell reports, 2023, ISSN 2211-1247
Publisher: Cell Press
DOI: 10.1016/j.celrep.2023.112487

Unveiling genetic signatures of immune response in immune-related diseases through single-cell eQTL analysis across diverse conditions.

Author(s): Zhang, Z., Li, W., Zhan, Q., Aillaud, M., Botey-Bataller, J., Zoodsma, M., ter Horst, R., Joosten, L. A. B., Bock, C., Schulte, L. N., Xu, C.-J., Netea, M. G., Bonder, M. J. & Li, Y.
Published in: Nat Commun, 2025, ISSN 2041-1723
Publisher: Nature Publishing Group

Distinct immunological and molecular signatures underpinning influenza vaccine responsiveness in the elderly.

Author(s): Riese, P., Trittel, S., Akmatov, M. K., May, M., Prokein, J., Illig, T., Schindler, C., Sawitzki, B., Elfaki, Y., Floess, S., Huehn, J., Błażejewski, A. J., Strowig, T., Hernandez-Vargas, E. A., Geffers, R., Zhang, B., Li, Y., Pessler, F. & Guzmán, C. A.
Published in: Nat Commun, 2022, ISSN 2041-1723
Publisher: Nature Publishing Group

A genome-wide association study identifies new loci associated with response to SARS-CoV-2 mRNA-1273 vaccine in a cohort of healthy healthcare workers

Author(s): Cabrera-Serrano, A. J., Ruiz-Durán, L., Gutiérrez-Bautista, J. F., Carretero-Fernández, M., ter Horst, R., Li, Y., Reyes-Zurita, F. J., García-Verdejo, F. J., Netea, M. G., Sánchez-Rovira, P., López-Nevot, M. Á., Sampedro, A. & Sainz, J.
Published in: Front. Immunol., 2025, ISSN 1664-3224
Publisher: Frontiers

BCG vaccination induces innate immune memory in γδ T cells in humans.

Author(s): Suen, T. K., Moorlag, S. J. C. F. M., Li, W., de Bree, L. C. J., Koeken, V. A. C. M., Mourits, V. P., Dijkstra, H., Lemmers, H., Bhat, J., Xu, C.-J., Joosten, L. A. B., Schultze, J. L., Li, Y., Placek, K. & Netea, M. G.
Published in: Journal of Leukocyte Biology, 2024, ISSN 1938-3673
Publisher: Oxford University Press

Integration of metabolomics, genomics, and immune phenotypes reveals the causal roles of metabolites in disease

Author(s): Xiaojing Chu; Xiaojing Chu; Martin Jaeger; Joep Beumer; Olivier B. Bakker; Raul Aguirre-Gamboa; Marije Oosting; Sanne P. Smeekens; Simone J.C.F.M. Moorlag; Vera P. Mourits; Valerie A. C. M. Koeken; Valerie A. C. M. Koeken; Charlotte de Bree; Trees Jansen; Ian T. Mathews; Ian T. Mathews; Khoi Dao; Mahan Najhawan; Jeramie D. Watrous; Irma Joosten; Sonia Sharma; Hans J. P. M. Koenen; Sebo Withoff; Ir
Published in: Genome Biology, Issue 3, 2021, ISSN 1474-760X
Publisher: BioMed Central
DOI: 10.1186/s13059-021-02413-z

The long-term effect of metabolic bariatric surgery on innate immune cell phenotype and function

Author(s): van Tuijl, J., Vreeken, D., Broeders, W., Cossins, B., van Emst, L., Seidel, F., Stienstra, R., Li, Y., Joosten, L. A. B., Netea, M. G., Hazebroek, E. J., Kleemann, R., Kiliaan, A. J., Bekkering, S. & Riksen, N. P.
Published in: Int J Obes, 2025, ISSN 1476-5497
Publisher: Nature Publishing Group

Single-cell immune aging clocks reveal inter-individual heterogeneity during infection and vaccination.

Author(s): Li, W., Zhang, Z., Kumar, S., Botey-Bataller, J., Zoodsma, M., Ehsani, A., Zhan, Q., Alaswad, A., Zhou, L., Grondman, I., Koeken, V., Yang, J., Wang, G., Volland, S., Crişan, T. O., Joosten, L. A. B., Illig, T., Xu, C.-J., Netea, M. G. & Li, Y.
Published in: Nat Aging, 2025, ISSN 2662-8465
Publisher: Nature Publishing Group

Differences in Immune Responses in Individuals of Indian and European Origin: Relevance for the COVID-19 Pandemic

Author(s): Geckin, B., Zoodsma, M., Kilic, G., Debisarun, P.A., Rakshit, S., Adiga, V., Ahmed, A., Parthiban, C., Chetan Kumar, N., D’Souza, G., Baltissen, M.P., Martens, J.H.A., Domínguez-Andrés, J., Li, Y., Vyakarnam, A., Netea, M.G
Published in: Microbiology Spectrum, 2023, ISSN 2165-0497
Publisher: American Society for Microbiology
DOI: 10.1128/spectrum.00231-23

IRF7 and RNH1 are modifying factors of HIV-1 reservoirs: a genome-wide association analysis.

Author(s): Zhenhua Zhang; Wim Trypsteen; Marc Blaauw; Xiaojing Chu; Xiaojing Chu; Sofie Rutsaert; Linos Vandekerckhove; Wouter A. van der Heijden; Jéssica Cristina dos Santos; Cheng-Jian Xu; Morris A. Swertz; André J. A. M. van der Ven; Yang Li
Published in: BMC Medicine, Issue 3, 2021, ISSN 1741-7015
Publisher: BioMed Central
DOI: 10.1186/s12916-021-02156-5

Multi-Omics Approaches in Immunological Research

Author(s): Chu, X., Zhang, B., Koeken, V., Gupta, M.K., Li, Y.
Published in: Frontiers in immunology, 2022, ISSN 1664-3224
Publisher: Frontiers Media S.A.
DOI: 10.3389/fimmu.2021.668045

Systemic dysregulation and molecular insights into poor influenza vaccine response in the aging population.

Author(s): Kumar, S., Zoodsma, M., Nguyen, N., Pedroso, R., Trittel, S., Riese, P., Botey-Bataller, J., Zhou, L., Alaswad, A., Arshad, H., Netea, M. G., Xu, C.-J., Pessler, F., Guzmán, C. A., Graca, L. & Li, Y.
Published in: Science Advances, 2024, ISSN 2375-2548
Publisher: American Association for the Advancement of Science

Different dynamics of soluble inflammatory mediators after clearance of respiratory SARS-CoV-2 versus blood-borne hepatitis C virus infections.

Author(s): Zeuzem, A., Kumar, S. D., Oltmanns, C., Witte, M., Mischke, J., Drick, N., Fuge, J., Pink, I., Tauwaldt, J., Debarry, J., Illig, T., Wedemeyer, H., Maasoumy, B., Li, Y., Kraft, A. R. M. & Cornberg, M.
Published in: Sci Rep, 2024, ISSN 2045-2322
Publisher: Nature Publishing Group

BCG vaccination-induced acquired control of mycobacterial growth differs from growth control preexisting to BCG vaccination.

Author(s): van Meijgaarden, K. E., Li, W., Moorlag, S. J. C. F. M., Koeken, V. A. C. M., Koenen, H. J. P. M., Joosten, L. A. B., Vyakarnam, A., Ahmed, A., Rakshit, S., Adiga, V., Ottenhoff, T. H. M., Li, Y., Netea, M. G. & Joosten, S. A.
Published in: Nat Commun, 2024, ISSN 2041-1723
Publisher: Nature Publishing Group

Targeted proteomics identifies circulating biomarkers associated with active COVID-19 and post-COVID-19.

Author(s): Zoodsma, M., de Nooijer, A. H., Grondman, I., Gupta, M. K., Bonifacius, A., Koeken, V. A. C. M., Kooistra, E., Kilic, G., Bulut, O., Gödecke, N., Janssen, N., Kox, M., Domínguez-Andrés, J., van Gammeren, A. J., Ermens, A. A. M., van der Ven, A. J. A. M., Pickkers, P., Blasczyk, R., Behrens, G. M. N., van de Veerdonk, F. L., Joosten, L. A. B., Xu, C.-J., Eiz-Vesper, B., Netea, M. G. & Li, Y.
Published in: Frontiers in Immunology, 2022, ISSN 1664-3224
Publisher: Frontiers

Evolutionary Trajectories of Complex Traits in European Populations of Modern Humans

Author(s): Yunus Kuijpers; Jorge Domínguez-Andrés; Olivier B. Bakker; Manoj Kumar Gupta; Martin Grasshoff; Cheng-Jian Xu; Leo A.B. Joosten; Jaume Bertranpetit; Mihai G. Netea; Yang Li
Published in: Frontiers in Genetics, Issue 3, 2022, ISSN 1664-8021
Publisher: Frontiers Media
DOI: 10.3389/fgene.2022.833190

Plasma metabolome predicts trained immunity responses after antituberculosis BCG vaccination

Author(s): Koeken, V.A.C.M., Qi, C., Mourits, V.P., de Bree, L.C.J., Moorlag, S.J.C.F.M., Sonawane, V., Heidi Lemmers, Dijkstra, H., Joosten, L.A.B., van Laarhoven, A., Xu, C.-J., van Crevel, R., Netea, M.G., Li, Y
Published in: PLoS Biology, 2022, ISSN 1544-9173
Publisher: Public Library of Science
DOI: 10.1371/journal.pbio.3001765

The role of DNA methylation in personalized medicine for immune-related diseases

Author(s): Gupta, M.K., Peng, H., Li, Y., Xu, C.-J.
Published in: Pharmacology & Therapeutics, 2023, ISSN 0163-7258
Publisher: Pergamon Press
DOI: 10.1016/j.pharmthera.2023.108508

The Genetic Risk for COVID-19 Severity Is Associated With Defective Immune Responses

Author(s): Kuijpers, Y., Chu, X., Jaeger, M., Moorlag, S.J.C.F.M., Koeken, V.A.C.M., Zhang, B., de Nooijer, A., Grondman, I., Gupta, M.K., Janssen, N., Mourits, V.P., de Bree, L.C.J., de Mast, Q., van de Veerdonk, F.L., Joosten, L.A.B., L,i Y., Netea, M.G., Xu, C.J.
Published in: Frontiers in Immunology, 2022, ISSN 1664-3224
Publisher: Frontiers Media S.A.
DOI: 10.3389/fimmu.2022.859387

Long-term histone lactylation connects metabolic and epigenetic rewiring in innate immune memory

Author(s): Ziogas, A., Novakovic, B., Ventriglia, L., Galang, N., Tran, K. A., Li, W., Matzaraki, V., Unen, N. van, Schlüter, T., Ferreira, A. V., Moorlag, S. J. C. F. M., Koeken, V. A. C. M., Moyo, M., Li, X., Baltissen, M. P. A., Martens, J. H. A., Li, Y., Divangahi, M., Joosten, L. A. B., Mhlanga, M. M. & Netea, M. G.
Published in: Cell, 2026, ISSN 0092-8674
Publisher: Cell Press

Evolution of cytokine production capacity in ancient and modern European populations

Author(s): Jorge Domínguez-Andrés; Yunus Kuijpers; Olivier B. Bakker; Martin Jaeger; Cheng-Jian Xu; Cheng-Jian Xu; Jos W. M. van der Meer; Mattias Jakobsson; Mattias Jakobsson; Jaume Bertranpetit; Leo A. B. Joosten; Yang Li; Mihai G. Netea; Mihai G. Netea
Published in: eLife, Issue 4, 2021, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.1101/2021.01.14.426690

Impact of COVID-19, lockdowns and vaccination on immune responses in a HIV cohort in the Netherlands.

Author(s): "Otten, T., Jiang, X., Gupta, M. K., Vadaq, N., Cleophas-Jacobs, M., dos Santos, J. C., Groenendijk, A., Vos, W., van Eekeren, L. E., Blaauw, M. J. T., Meeder, E. M. G., Richel, O., Matzaraki, V., van Lunzen, J., Joosten, L. A. B., Li, Y. #, Xu, C.-J. #, van der Ven, A. # & Netea, M. G. #"
Published in: Front. Immunol., 2024, ISSN 1664-3224
Publisher: Frontiers

MMR vaccination induces trained immunity via functional and metabolic reprogramming of γδ T cells.

Author(s): Röring, R. J., Debisarun, P. A., Botey-Bataller, J., Suen, T. K., Bulut, O., Kilic, G., Koeken, V. A. C. M., Sarlea, A., Bahrar, H., Dijkstra, H., Lemmers, H., Gössling, K. L., Rüchel, N., Ostermann, P. N., Müller, L., Schaal, H., Adams, O., Borkhardt, A., Ariyurek, Y., Meijer, E. J. de, Kloet, S. L., Oever, J. ten, Placek, K., Li, Y. & Netea, M. G.
Published in: J Clin Invest, 2024, ISSN 0021-9738
Publisher: American Society for Clinical Investigation

Resolving trained immunity with systems biology

Author(s): Valerie A. C. M. Koeken; Valerie A. C. M. Koeken; Reinout van Crevel; Mihai G. Netea; Mihai G. Netea; Yang Li; Yang Li
Published in: European Journal of Immunology, Issue 3, 2021, ISSN 0014-2980
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/eji.202048882

Sex-specific DNA methylation associations with circulating urate levels and BCG-induced urate changes.

Author(s): Liu, Z., Crișan, T. O., Qi, C., Gupta, M. K., Liu, X., Moorlag, S. J. C. F. M., Koeken, V. A. C. M., Jiang, X., Ballan, M., de Bree, L. C. J., Mourits, V. P., Gao, X., Baccarelli, A., Schwartz, J., Pessler, F., Guzmán, C. A., Li, Y., Netea, M. G., Joosten, L. A. B. & Xu, C.-J.
Published in: Commun Med, 2025, ISSN 2730-664X
Publisher: Nature Publishing Group

A genome-wide functional genomics approach uncovers genetic determinants of immune phenotypes in type 1 diabetes

Author(s): "Chu, X., Janssen, A.W.M., Koenen, H., Chang, L., He, X., Joosten, I., Stienstra, R., Kuijpers, Y., Wijmenga, C., Xu, C.- J., Netea, M.G, Tack, C.J., Li, Y.#"
Published in: eLife, 2022, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/elife.73709

Single-cell RNA sequencing reveals induction of distinct trained immunity programs in human monocytes.

Author(s): "Zhang, B., Moorlag, S., Domínguez-Andrés, J., Bulut, Ö., Kilic, G., Liu, Z., van Crevel, R., Xu,C.-J., Joosten, L.A.B., Netea, M.G.#, Li, Y.#"
Published in: Journal of Clinical investigation, 2022, ISSN 0021-9738
Publisher: American Society for Clinical Investigation
DOI: 10.1172/jci147719

Single-Cell RNA Sequencing of Peripheral Blood Mononuclear Cells From Pediatric Coeliac Disease Patients Suggests Potential Pre-Seroconversion Markers

Author(s): Aarón D. Ramírez-Sánchez; Xiaojing Chu; Rutger Modderman; Yvonne Kooy-Winkelaar; Sibylle Koletzko; Ilma R. Korponay-Szabó; Riccardo Troncone; Cisca Wijmenga; Luisa Mearin; Sebo Withoff; Iris H. Jonkers; Yang Li
Published in: Frontiers in Immunology, Issue 2, 2022, ISSN 1664-3224
Publisher: Frontiers Media S.A.
DOI: 10.3389/fimmu.2022.843086

Induction of trained immunity by influenza vaccination - impact on COVID-19.

Author(s): Priya A. Debisarun; Katharina L. Gössling; Ozlem Bulut; Gizem Kilic; Martijn Zoodsma; Zhaoli Liu; Marina Oldenburg; Nadine Rüchel; Bowen Zhang; Cheng-Jian Xu; Cheng-Jian Xu; Patrick Struycken; Valerie A. C. M. Koeken; Valerie A. C. M. Koeken; Jorge Domínguez-Andrés; Simone J.C.F.M. Moorlag; Esther Taks; Philipp Niklas Ostermann; Lisa Müller; Heiner Schaal; Ortwin Adams; Arndt Borkhardt; Jaap
Published in: Plos Pathogens, Issue 3, 2021, ISSN 1553-7366
Publisher: Public Library of Science
DOI: 10.1371/journal.ppat.1009928

Molecular signatures discriminating different types of rejection in human liver transplants.

Author(s): "Engel, B., Alaswad, A., Campos-Murguia, A., Zoodsma, M., Klingbeil, A., Ruiz, P., Crespo, G., Chihab, K., Bosselmann, E. A., Heinrich, S., Hartleben, B., Jonigk, D. D., Diaz, A., Verboom, M., Hallensleben, M., Geffers, R., Falk, C. S., Ruff, S., Lauber, C., Skovgaard, E. T., Karsdal, M., Leeming, D. J., Wedemeyer, H., Xu, C.-J., Colmenero, J., Jaeckel, E., Li, Y. # & Taubert, R. #"
Published in: Journal of Hepatology, 2025, ISSN 0168-8278
Publisher: Elsevier BV

11-deoxycortisol positively correlates with T cell immune traits in physiological conditions.

Author(s): Peng, C., Jiang, X., Jaeger, M., Houten, P. van, Herwaarden, A. E. van, Koeken, V. A. C. M., Moorlag, S. J. C. F. M., Mourits, V. P., Lemmers, H., Dijkstra, H., Koenen, H. J. P. M., Joosten, I., Cranenbroek, B. van, Li, Y., Joosten, L. A. B., Netea, M. G., Netea-Maier, R. T. & Xu, C.-J.
Published in: eBioMedicine, 2024, ISSN 2352-3964
Publisher: Elsevier BV

Deciphering cross-cohort metabolic signatures of immune responses and their implications for disease pathogenesis.

Author(s): Fu, J., Unen, N. van, Sarlea, A., Nguyen, N., Jaeger, M., Bataller, J. B., Koeken, V. A. C. M., Bree, L. C. de, Mourits, V. P., Moorlag, S. J. C. F. M., Temba, G., Kullaya, V. I., de Mast, Q., Joosten, L. A. B., Xu, C.-J., Netea, M. G. & Li, Y.
Published in: Mol Syst Biol, 2025, ISSN 1744-4292
Publisher: Nature Publishing Group

Genetic and molecular landscape of comorbidities in people living with HIV.

Author(s): Botey-Bataller, J., van Unen, N., Blaauw, M., Vos, W. A. J. W., van Eekeren, L., Vadaq, N., Matzaraki, V., Verbon, A., Groenendijk, A. L., dos Santos, J. C., Cleophas, M. C. P., Stalenhoef, J. E., Berrevoets, M. A. H., Jiang, X., Gupta, M. K., Nguyen, N., Xu, C.-J., Joosten, L. A. B., Netea, M. G., van der Ven, A. J. A. M. & Li, Y.
Published in: Nat Med, 2025, ISSN 1546-170X
Publisher: Nature Publisher

Altered and allele-specific open chromatin landscape reveals epigenetic and genetic regulators of innate immunity in COVID-19

Author(s): Zhang, B., Zhang, Z., Koeken, V.A.C.M., Kumar, S., Aillaud, M., Tsay, H.-C., Liu, Z., Kraft, A.R.M., Soon, C.F., Odak, I., Bošnjak, B., Vlot, A., Deutsche COVID-19 OMICS Initiative (DeCOI), Swertz, M.A., Ohler, U., Geffers, R., Illig, T., Huehn, J., Saliba, A.E., Sander, L.E., Förster, R., Xu, C.-J., Cornberg, M., Schulte, L.N., Li, Y
Published in: Cell Genomics, 2023, ISSN 2666-979X
Publisher: Elsevier
DOI: 10.1016/j.xgen.2022.100232

Metabolomics meets systems immunology

Author(s): Fu, J., Zhu, F., Xu, C.-J., Li, Y
Published in: EMBO Reports, 2023, ISSN 1469-221X
Publisher: Nature Publishing Group
DOI: 10.15252/embr.202255747

Reprogramming of myeloid cells and their progenitors in patients with non-medullary thyroid carcinoma.

Author(s): Rabold, K., Zoodsma, M., Grondman, I., Kuijpers, Y., Bremmers, M., Jaeger, M., Zhang, B., Hobo, W., Bonenkamp, H. J., de Wilt, J. H. W., Janssen, M. J. R., Cornelissen, L. A. M., van Engen-van Grunsven, I. C. H., Mulder, W. J. M., Smit, J. W. A., Adema, G. J., Netea, M. G., Li, Y., Xu, C.-J. & Netea-Maier, R. T.
Published in: Nat Commun, 2022, ISSN 2041-1723
Publisher: Nature Publishing Group

SegDecon bridges histology and transcriptomics through AI-based nuclei segmentation and image-informed spatial deconvolution.

Author(s): Xi, Y., Jiang, X., Schupp, J. C., Xu, C.-J. & Li, Y.
Published in: Computational and Structural Biotechnology Journal, 2025, ISSN 2001-0370
Publisher: elsevier

Single-cell RNA sequencing uncovers the nuclear decoy lincRNA PIRAT as a regulator of systemic monocyte immunity during COVID-19.

Author(s): Aznaourova, M., Schmerer, N., Janga, H., Zhang, Z., Pauck, K., Bushe, J., Volkers, S. M., Wendisch, D., Georg, P., Ntini, E., Aillaud, M., Gündisch, M., Mack, E., Skevaki, C., Keller, C., Bauer, C., Bertrams, W., Marsico, A., Nist, A., Stiewe, T., Gruber, A. D., Ruppert, C., Li, Y., Garn, H., Sander, L. E., Schmeck, B. & Schulte, L. N.
Published in: Proceedings of the National Academy of Sciences, 2022, ISSN 1091-6490
Publisher: National Academy of Sciences

The impact of BNT162b2 mRNA vaccine on adaptive and innate immune responses.

Author(s): Föhse, K., Geckin, B., Zoodsma, M., Kilic, G., Liu, Z., Röring, R. J., Overheul, G. J., van de Maat, J., Bulut, O., Hoogerwerf, J. J., ten Oever, J., Simonetti, E., Schaal, H., Adams, O., Müller, L., Ostermann, P. N., van de Veerdonk, F. L., Joosten, L. A. B., Haagmans, B. L., van Crevel, R., van Rij, R. P., GeurtsvanKessel, C., de Jonge, M. I., Li, Y., Domínguez-Andrés, J. & Netea, M. G.
Published in: Clinical Immunology, 2023, ISSN 1521-6616
Publisher: Academic Press

Immune memory in individuals with COVID-19.

Author(s): Netea, M. G. & Li, Y.
Published in: Nat Cell Biol, 2021, ISSN 1476-4679
Publisher: Nature Publisher

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