Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing

Publications - AUDACIS

Publications

Note: only publications that have been accepted are shown.


Related to TCR data modeling

  1. M. Boeren*, N. de Vrij*, M. Ha*, S. Valkiers*, A. Souquette, S. Gielis, M. Kuznetsova, J. Schippers, E. Bartholomeus, J. Van den Bergh, N. Michels, O. Aerts, J. Leysen, A. Bervoets, J. Lambert, E. Leuridan, J. Wens, K. Peeters, MP Emonds, G. Elias, N. Vandamme, H. Jansens, W. Adriaensen, A. Suls, S. Vanhee, N. Hens, E. Smits, P. Van Damme, PG. Thomas, Ph. Beutels, P. Ponsaerts, V. Van Tendeloo, P. Delputte, K. Laukens*, P. Meysman* & B. Ogunjimi*. Lack of functional TCR-epitope interaction is associated with herpes zoster through reduced downstream T cell activation. Cell Reports, 2024, 3(4):114062. *equal contribution
  2. K.A. Mullan, N. de Vrij, S. Valkiers, P. Meysman. Current annotation strategies for T cell phenotyping of single-cell RNA-seq data. Frontiers in Immunology, 2023.
  3. C. Dens, K. Laukens, W. Bittrimieux, P. Meysman. The pitfalls of negative data bias for the T-cell epitope specificity challenge. Nature Machine Intelligence, 2023.
  4. A. Vujkovic, M. Ha,T. de Block,L. van Petersen,I. Brosius,C. Theunissen,S. H. van Ierssel,E. Bartholomeus,W. Adriaensen,G. Vanham, G. Elias,P. Van Damme,V. Van Tendeloo, P. Beutels, M. van Frankenhuijsen, E. Vlieghe, B. Ogunjimi, K. Laukens, P. Meysman*, and K. Vercauteren*. Diagnosing Viral Infections Through T-Cell Receptor Sequencing of Activated CD8+ T Cells. The Journal of Infectious Diseases, 2023. *equal contribution
  5. P. Meysman, J. Barton, B. Bravi, L. Cohen-Lavi, V. Karnaukhov, E. Lilleskov, A. Montemurro, M. Nielsen, T. Mora, P. Pereira, A. Postovskaya, M. Rodríguez Martínez, J. Fernandez-de-Cossio-Diaz, A. Vujkovic, A. M. Walczak, A. Weber, R. Yin, A. Eugster, and V. Sharma. Benchmarking solutions to the T-cell receptor epitope prediction problem: IMMREP22 workshop report, Immunoinformatics, Volume 9, 2023, 100024.
  6. D. Bui-Thi, P. Meysman and K. Laukens. MoMAC: Multi-objective optimization to combine multiple association rules into an interpretable classification. Appl Intell, 52, 3090–3102, 2022.
  7. S. Valkiers, N. de Vrij, S. Gielis, S. Verbandt, B. Ogunjimi, K. Laukens and P. Meysman. Recent advances in T-cell receptor repertoire analysis: bridging the gap with multimodal single-cell RNA sequencing. Immunoinformatics, 2022, 100009.
  8. G. Elias*, Meysman P.*, E. Bartholomeus*, N. De Neuter, N. Keersmaekers, A. Suls, H . Jansens, A. Souquette, H. De Reu, MP Emonds, E. Smits, E. Lion, PG Thomas, G. Mortier, P. Van Damme, Ph. Beutels, K. Laukens*, V. Van Tendeloo* and B. Ogunjimi*. Preexisting memory CD4 T cells in naïve individuals confer robust immunity upon hepatitis B vaccination. eLife, 2022 Jan 25;11:e68388. *equal contribution
  9. S. Valkiers, M. Van Houcke, K. Laukens, P. Meysman. ClusTCR: a Python interface for rapid clustering of large sets of CDR3 sequences with unknown antigen specificity. Bioinformatics. 2021 Jun 16. JCR2020
  10. P. Moris, J. De Pauw, A. Postovskaya, S. Gielis, N. De Neuter, W. Bittremieux, B. Ogunjimi, K. Laukens and P. Meysman. Current challenges for unseen-epitope TCR interaction prediction and a new perspective derived from image classification. Briefings in Bioinformatics, 2021 Jul;22(4):bbaa318..
  11. S. Gielis, P. Moris, W. Bittremieux, N. De Neuter, B. Ogunjimi, K. Laukens and P. Meysman. Identification of Epitope-Specific T Cells in T-Cell Receptor Repertoires. Methods Mol Biol, 2020; 2120:183-195.
  12. S. Gielis, P. Moris, W. Bittremieux, N. De Neuter, B. Ogunjimi, K. Laukens and P. Meysman. Detection of Enriched T Cell Epitope Specificity in Full T Cell Receptor Sequence Repertoires. Frontiers in Immunology, 2019, 10:2820.
  13. P. Meysman, N. De Neuter, S. Gielis, D. Bui Thi, B. Ogunjimi and K. Laukens. On the viability of unsupervised T-cell receptor sequence clustering for epitope preference. Bioinformatics, 2019, May 1;35(9):1461-1468.
  14. N. De Neuter, E. Bartholomeus, G. Elias, N. Keersmaekers, A. Suls, H. Jansens, E. Smits, N. Hens, P. Beutels, P. Van Damme, G. Mortier, V. Van Tendeloo, K. Laukens, P. Meysman* and B. Ogunjimi*. Memory CD4+ T cell receptor repertoire data mining as a tool for identifying cytomegalovirus serostatus. Genes and Immunity, 2019, 20(3):255-260. *equal contribution
  15. N. De Neuter, C. Beirnaert, W. Bittremieux, B. Cuypers, A. Ligata, P. Moris, A. Suls, V. Van Tendeloo, B. Ogunjimi, K. Laukens* and P. Meysman*. *equal contribution. On the feasibility of mining CD8+ T-cell receptor patterns underlying immunogenic peptide recognition. Immunogenetics, 2018, 70(3):159-168.
  16. B. Ogunjimi, J. Van den Bergh*, P. Meysman*, S. Heynderickx , K. Bergs , H. Jansens , E. Leuridan , A. Vorsters , H. Goossens , K. Laukens , N. Cools , V. Van Tendeloo , N. Hens , P. Van Damme , E. Smits**  and P. Beutels**. *equal contribution, **equal contribution. Multidisciplinary study of the secondary immune response in grandparents re-exposed to chickenpox. Scientific Reports, 2017, Apr 24;7(1):1077.


Related to MHC data modeling

  1. R. Vandoren*, M. Boeren*, J. Schippers, E. Bartholomeus, K. Mullan, N. Michels, O. Aerts, J. Leysen, A. Bervoets, J. Lambert, E. Leuridan, J. Wens, K. Peeters, MP. Emonds, H. Jansens, JL. Casanova, P. Bastard, A. Suls, V. Van Tendeloo, P. Ponsaerts, P. Delputte, B. Ogunjimi*, K. Laukens*, P. Meysman*; Unravelling the immune signature of herpes zoster: Insights into pathophysiology and the HLA risk profile. The Journal of Infectious Diseases, 2024 Jan 9:jiad609. *equal contribution
  2. M. Boeren, P. Meysman, K. Laukens, P. Ponsaerts, B. Ogunjimi & P. Delputte. T cell immunity in HSV-1- and VZV-infected neural ganglia. Trends in Microbiology, 2022, S0966-842X(22)00190-1.
  3. N. de Vrij, P. Meysman, S. Gielis, W. Adriaensen, K. Laukens, B. Cuypers. HLA-DRB1 Alleles Associated with Lower Leishmaniasis Susceptibility Share Common Amino Acid Polymorphisms and Epitope Binding Repertoires. Vaccines. 2021 Mar;9(3):270. JCR2020
  4. N. De Neuter, E. Bartholomeus, G. Elias, N. Keersmaekers, A. Suls, H. Jansens, E. Smits, N. Hens, P. Beutels, P. Van Damme, G. Mortier, V. Van Tendeloo, K. Laukens, P. Meysman* and B. Ogunjimi*. Memory CD4+ T cell receptor repertoire data mining as a tool for identifying cytomegalovirus serostatus. Genes and Immunity, 2019, 20(3):255-260. *equal contribution
  5. P. Meysman, N. De Neuter, E. Bartholomeus, G. Elias, J. Van den Bergh, M.P. Emonds, G.W. Haasnoot, S. Heynderickx, J. Wens, N.R. Michels, J. Lambert, E. Lion, F.H.J. Claas, H. Goossens, E. Smits, P. Van Damme, V. Van Tendeloo, P. Beutels, A. Suls, G. Mortier, K. Laukens* and B. Ogunjimi*. *equal contribution. Increased herpes zoster risk associated with poor HLA-A Immediate Early 62 Protein (IE62) affinity. Immunogenetics, 2018, 70(6):363-372.
  6. P. Meysman, D. Federov, V. Van Tendeloo, B. Ogunjimi and K. Laukens. Immunological evasion of immediate-early varicella zoster virus proteins. Immunogenetics, 2016, Jul;68(6-7):483-6.
  7. P. Meysman, B. Ogunjimi, S. Naulaerts, P. Beutels, V. Van Tendeloo and K. Laukens. Varicella-zoster virus-derived MHC class I-restricted peptide affinity is a determining factor for HLA risk profile to develop PHN. Journal of Virology, 2015, 15;89(2):962-9. 

 

Related to whole blood RNA sequencing

  1. R. Vandoren*, M. Boeren*, J. Schippers, E. Bartholomeus, K. Mullan, N. Michels, O. Aerts, J. Leysen, A. Bervoets, J. Lambert, E. Leuridan, J. Wens, K. Peeters, MP. Emonds, H. Jansens, JL. Casanova, P. Bastard, A. Suls, V. Van Tendeloo, P. Ponsaerts, P. Delputte, B. Ogunjimi*, K. Laukens*, P. Meysman*; Unravelling the immune signature of herpes zoster: Insights into pathophysiology and the HLA risk profile; The Journal of Infectious Diseases, 2024 Jan 9:jiad609. *equal contribution
  2. M. Ha, E. Bartholomeus, L. Van Os, J. Dandelooy, J. Leysen, O. Aerts, V. Siozopoulou, E. De Smet, J. Gielen, K. Guerti, M. De Maeseneer, N. Herregods, B. Lechkar, R. Wittoek, E. Geens, L. Claes, M. Zaqout, W. Dewals, A. Lemay, D. Tuerlinckx, D. Weynants, K. Vanlede, G. van Berlaer, M. Raes, H. Verhelst, T. Boiy, P. Van Damme, A. C. Jansen, M. Meuwissen, V. Sabato, G. Van Camp, A. Suls, J. Van der Werff ten Bosch, J. Dehoorne, R. Joos, K. Laukens, P. Meysman & B. Ogunjimi. Blood Transcriptomics to Facilitate Diagnosis and Stratification in Pediatric Rheumatic Diseases - A Proof of Concept Study. Pediatric Rheumatology, accepted
  3. E. Bartholomeus, N. De Neuter, A. Suls, G. Elias, S. van der Heijden, N. Keersmaekers, H. Jansens, V. Van Tendeloo, P. Beutels, K. Laukens, B. Ogunjimi, G. Mortier, P. Meysman & P. Van Damme. Transcriptomic Profiling of Different Responder Types in Adults After a Priorix® Vaccination.Vaccine, 2020 Apr 3;38(16):3218-3226.
  4. E. Bartholomeus, N. De Neuter, P. Meysman, A. Suls, N. Keersmaekers, G. Elias, H. Jansens, N. Hens, E. Smits, V. Van Tendeloo, P. Beutels, P. Van Damme, B. Ogunjimi*, K. Laukens* and G. Mortier*. Transcriptome profiling in blood before and after hepatitis B vaccination shows significant differences in gene expression between responders and non-responders. Vaccine, 2018, 36(42):6282-6289. *equal contribution


Related to longitudinal mathematical modeling

  1. H. Besbassi, I. Garcia-Fogeda, M. Quinlivan, J. Breuer, S. Abrams, N. Hens*, B. Ogunjimi* & Ph. Beutels*. Modeling antibody dynamics following herpes zoster indicates that higher varicella-zoster virus (VZV) viremia generates more VZV-specific antibodies. Frontiers in Immunology, 2023, 14:1104605. IF (2021): 8.786 *equal contribution
  2. I. Garcia-Fogeda, H. Besbassi, Y. Lariviere, B. Ogunjimi, S. Abrams & N. Hens. Within-host modeling to measure dynamics of antibody responses after natural infection or vaccination: A systematic review. Vaccine, 2023. 41(25):3701-3709.


Related to other applications

  1. E. Van Breedam, T. Buyle-Huybrecht, J. Govaerts, P. Meysman, A. Bours, M. Boeren, J. Di Stefano, T. Caers, H. De Reu, L. Dirikx, J. Schippers, E. Bartholomeus, M. Lebrun, C. Sadzot-Delvaux, P. Rybakowska, M.E. Alarcon-Riquelme, C. Maranon, K. Laukens, P. Delputte*, B. Ogunjimi* & P. Ponsaerts*. Lack of strong innate immune reactivity renders macrophages alone unable to control productive Varicella-Zoster Virus infection in an isogenic human iPSC-derived neuronal co-culture model. Frontiers in Immunology, 2023, 14:1177245. *equal contribution
  2. S. van der Heijden, D. Flumens, M. Versteven, S. Peeters, D. Campillo-Davo, Y. Willemen, B. Ogunjimi, V. Van Tendeloo, Z.N. Berneman, S. Anguille, E. Smits & E. Lion. In vitro expansion of Wilms’ tumor protein 1 epitope-specific primary T cells from healthy human peripheral blood mononuclear cells. Star Protocols, 2023, 4(1):102053. IF(2021): 1.340
  3. M. Van Delen, I. Janssens, A. Dams, L. Roosens, B. Ogunjimi, Z.N. Berneman, J. Derdelinckx & N. Cools. Tolerogenic dendritic cells induce apoptosis-independent T cell hyporesponsiveness of SARS-CoV-2-specific T cells in an antigen-specific manner. International Journal of Molecular Sciences, 2022, Dec 2;23(23):15201. IF(2021): 6.208.
  4. M. Boeren, E. Van Breedam, T. Buyle-Huybrecht, M. Lebrun, P. Meysman, C. Sadzot-Delvaux, V.F.I. Van Tendeloo, G. Mortier, K. Laukens, B. Ogunjimi*, P. Ponsaerts* & P. Delputte*. Activation of interferon-stimulated genes following varicella-zoster virus infection in a human iPSC-derived neuronal model depends on exogenous interferon-α. Viruses, 2022, 14(11):2517. *equal contribution
  5. Arnaout RA, Prak ET, Schwab N, Meysman P*, Rubelt F. The future of blood testing is the immunome. Frontiers in immunology. 2021
  6. Van Hees S, Cuypers B, Bourgeois S, Groothuismink ZM, Meysman P, Van der Vlies P, de Knegt R, Vonghia L, Michielsen P, Francque S, Laukens K, Boonstra A, Vanwolleghem T. Sorted B cell transcriptomes point towards actively regulated B cell responses during ongoing chronic hepatitis B infections. Cellular Immunology. 2021 Apr 1;362:104283
  7. N. Keersmaekers, B. Ogunjimi, P. Van Damme, P. Beutels and N. Hens. An ODE-based mixed modelling approach for B- and T-cell dynamics induced by Varicella-Zoster Virus vaccines in adults shows higher T-cell proliferation with Shingrix than with Varilrix. Vaccine, 2019 May 1;37(19):2537-2553.
  8. G. Elias, B. Ogunjimi and V. Van Tendeloo. Tracking Dye-Independent Approach to Identify and Isolate In Vitro Expanded T Cells. Cytometry A. 2019, 95(10):1096-1107.
  9. G. Elias, A. Souquette, S. Heynderickx, I. De Meester, H. Jansens, P. Beutels, P. Van Damme, E. Smits, P. Thomas, V. Van Tendeloo and B. Ogunjimi. Altered CD4+ T-Cell Immunity in Nurses Occupationally Exposed to Viral Pathogens.Clinical and Experimental Immunology, 2018, 194(2):192-204.
  10. B. Ogunjimi*, S. Y . Zhang*, K. Sorenson*, K. Skipper , M. Carter - Timofte, G. K erner , S. Lucke, T . Prabakaran, Y . Cai, J. Meester , E. Bartholomeus, N. Ajit Bolar , G. V andeweyer , C. Claes, Y . Sillis, L. Lorenzo, R. Fiorenza, S. Boucherit, C. Dielman, Steven Heynderickx, G. Elias, A. Kurotova, A. Vander Auwera, L. Verstraete, L. Lagae, H. Verhelst, A. Jansen, J. Ramet, A. Suls, E. Smits, B. Ceulemans, L. Van Laer , G. Plat Wilson, J. Kreth, C. Picard, H. V on Bernuth, J. Fluss, S. Chabrier , L. Abel, G. Mortier, S. Fribourg, J. Giehm Mikkelsen, J.L. Casanova, S.R Paludan and T.H. Mogensen. *equal contribution. Inborn errors in RNA polymerase III underlie severe varicella zoster virus infections. Journal of Clinical Investigation, 2017, Aug 7.

 

Editorials or commentaries on publications

  1. P. Meysman. Simulations that capture antigen–antibody complexity. Nature Comput Sci, 2, 781–782. 2022.
  2. About Ogunjimi et al, Journal of Clinical Investigation, 2017: J. Miner. Deterring zoster. Science Translational Medicine, 2017, 30 Aug.