COSMIC Publications (click on the title to see the article)

• Chrysi Galigalidou, Laura Zaragoza-Infante, Anastasia Iatrou, Anastasia Chatzidimitriou, Kostas Stamatopoulos and Andreas Agathangelidis. Understanding Monoclonal B Cell Lymphocytosis: An Interplay of Genetic and Microenvironmental Factors. Front. Oncol., 11 November 2021 | https://doi.org/10.3389/fonc.2021.769612
• Laura Zaragoza-Infante, Andreas Agathangelidis, Valentin Junet, Nikos Pechlivanis, Triantafylia Koletsa, Alessio Bruscaggin, Zadie Davis, Sotiria Markantonatou, Valeria Spina, Aurelie Verney, Anastasia Iatrou, Fotis Psomopoulos, David Oscier, Alexandra Traverse-Glehen, Maria Papaioannou, Davide Rossi, Anastasia Chatzidimitriou, Kostas Stamatopoulos. Distinct Modes of Ongoing Antigen Interactions Shape Intraclonal Dynamics in Splenic Marginal Zone Lymphoma. Blood (2021) 138 (Supplement 1): 1330.
• Dornatien C Anang, Giulia Balzaretti, Antoine van Kampen, Niek de Vries, Paul L Klarenbeek. The Germinal Center Milieu in Rheumatoid Arthritis: The Immunological Drummer or Dancer? Int J Mol Sci 2021 Sep 29;22(19):10514. doi: 10.3390/ijms221910514.
• Theinmozhi Arulraj, Sebastian C Binder, Michael Meyer-Hermann. In Silico Analysis of the Longevity and Timeline of Individual Germinal Center Reactions in a Primary Immune Response. Cells 2021 Jul 9;10(7):1736. doi: 10.3390/cells10071736.
• Arulraj, T., Binder, S. C., Robert, P. A., & Meyer-Hermann, M. (2021). Germinal Centre Shutdown. Frontiers in Immunology, 12, 2730.
• Junet V and Daura X (2021). CNN-PepPred: An open-source tool to create convolutional NN models for the discovery of patterns in peptide sets. Application to peptide-MHC class II binding prediction. Bioinformatics, btab687.

• Gutiérrez-Casares JR, Quintero J, Jorba G, Junet V, Martínez V, Pozo-Rubio T, Oliva B, Daura X, Mas JM and Montoto C (2021). Methods to Develop an in silico Clinical Trial: Computational Head-to-Head Comparison of Lisdexamfetamine and Methylphenidate. Front. Psychiatry, 2021, 12:741170

• Elena Merino Tejero, Danial Lashgari, Rodrigo García-Valiente, Jiaojiao He, Philippe A. Robert, Michael Meyer-Hermann, Jeroen E. J. Guikema, Huub Hoefsloot and Antoine H. C. van Kampen. Coupled Antigen and BLIMP1 Asymmetric Division With a Large Segregation Between Daughter Cells Recapitulates the Temporal Transition From Memory B Cells to Plasma Cells and a DZ-to-LZ Ratio in the Germinal Center. Front. Immunol., 17 August 2021 

• Philippe A. Robert, Theinmozhi Arulraj and Michael Meyer-Hermann. Ymir: A 3D structural affinity model for multi-epitope vaccine simulations.iScience. 2021 Sep 24; 24(9): 102979. Published online 2021 Aug 14. 

• Juhee Pae, Jonatan Ersching, Tiago B.R. Castro, Marta Schips, Luka Mesin, Samuel J. Allon, Jose Ordovas-Montanes, Coraline Mlynarczyk, Ari Melnick, Alejo Efeyan, Alex K. Shalek, Michael Meyer-Hermann, Gabriel D. Victora. Cyclin D3 drives inertial cell cycling in dark zone germinal center B cells. J Exp Med. 2021 Apr 5;218(4):e20201699.
• Arulraj, T., Binder, S. C., & Meyer-Hermann, M. (2021). Rate of Immune Complex Cycling in Follicular Dendritic Cells Determines the Extent of Protecting Antigen Integrity and Availability to Germinal Center B Cells. The Journal of Immunology, 206(7), 1436-1442. 
• Sahamoddin Khailaie, Tanmay Mitra, Arnab Bandyopadhyay, Marta Schips, Pietro Mascheroni, Patrizio Vanella, Berit Lange, Sebastian C. Binder, Michael Meyer-Hermann. Development of the reproduction number from coronavirus SARS-CoV-2 case data in Germany and implications for political measures. BMC Med19, 32 (2021). 
• Valentin Junet, Judith Farrés, José M Mas, Xavier Daura, CuBlock: a cross-platform normalization method for gene-expression microarrays. Bioinformatics, 2021; btab105   
• Rinako Nakagawa, Amparo Toboso-Navasa, Marta Schips, George Young, Leena Bhaw-Rosun, Miriam Llorian-Sopena, Probir Chakravarty, Abdul Karim Sesay, George Kassiotis, Michael Meyer-Hermann, Dinis Pedro Calado. Permissive selection followed by affinity-based proliferation of GC light zone B cells dictates cell fate and ensures clonal breadth. PNAS January 12, 2021 118 (2) e2016425118; 
• Laura Zaragoza-Infante, Andreas Agathangelidis, Maria Papaioannou, Anastasia Chatzidimitriou, Kostas Stamatopoulos. The B cell receptor in marginal zone lymphoma ontogeny and evolution. Ann Lymphoma 2020;4:10. 

• Jorba, Guillem; Aguirre-Plans, Joaquim; Junet, Valentin; Segú-Vergés, Cristina; Ruiz, José Luis; Pujol, Albert; Fernandez-Fuentes, Narcis; Mas, José Manuel; Oliva, Baldo. In-silico simulated prototype-patients using TPMS technology to study a potential adverse effect of sacubitril and valsartan. PLOS ONE. Published online February 13, 2020.

• Aurélien Pélissier, Youcef Akrout, Katharina Jahn, Jack Kuipers, Ulf Klein, Niko Beerenwinkel and María Rodríguez Martínez. Computational Model Reveals a Stochastic Mechanism behind Germinal Center Clonal Bursts. Cells 2020, 9(6), 1448;
• Katerina Gemenetzi, Andreas Agathangelidis, Laura Zaragoza-Infante, Electra Sofou, Maria Papaioannou, Anastasia Chatzidimitriou, Kostas Stamatopoulos. B Cell Receptor Immunogenetics in B Cell Lymphomas: Immunoglobulin Genes as Key to Ontogeny and Clinical Decision Making. Front. Oncol., 31 January 2020  
• Mahnoush Bahjat, Maria Stratigopoulou, Bas Pilzecker, Tijmen P. van Dam, Simon Mobach, Richard J. Bende, Carel J.M. van Noesel, Heinz Jacobs, Jeroen E.J. Guikema. DNA polymerase β prevents AID-instigated mutagenic non-canonical mismatch DNA repair bioRxiv 2020.01.30.926964; 
• Guillem Jorba, Joaquim Aguirre-Plans, Valentin Junet, Cristina Segú-Vergés, José Luis Ruiz, Albert Pujol, Narcis Fernandez-Fuentes, José Manuel Mas and Baldo Oliva.
  TPMS technology to infer biomarkers of macular degeneration prognosis in in silico simulated prototype-patients under the study of heart failure treatment with sacubitril and valsartan. PLOS ONE doi: 10.1371/journal.pone.0228926
• Arulraj T, Binder SC, Robert PA and Meyer-Hermann M (2019) Synchronous Germinal Center Onset Impacts the Efficiency of Antibody Responses. Front. Immunol. 10:2116.