COmbatting disorders of adaptive immunity with Systems MedICine

Deliverables

Publications and Open Source software regarding mechanistic B/T cell-based models of GCR in BCN/RA. (M24 and M42) Publication and Open Source software regarding mechanistic molecular network GCR models (M24, M42)

PhD theses and training certificates

PhD theses for 13 ESRsThe Redoxis ESR will not engage in a PhD programmeESR training certificates

1. Dissemination reports

Dissemination reports (M24,38,48) This will include information about: -Science Cafes, patient seminars -Education secondary school completed -8 COSMIC Newsletters -Data, software, education material available -(White) paper best practices systems medicine

(White) paper systems medicine training

Based on experiences with systems medicine training in COSMIC the consortium will write a white paper systems medicine training discussion directions for the future

3. Dissemination reports

Dissemination reports M243857This will include information aboutScience Cafes patient seminarsEducation secondary school completed8 COSMIC NewslettersData software education material availableWhite paper best practices systems medicine

2. Dissemination reports

Dissemination reports M243848This will include information aboutScience Cafes patient seminarsEducation secondary school completed8 COSMIC NewslettersData software education material availableWhite paper best practices systems medicine

Collection and review of all ethical approvals

1. Quantitative/single cell/molecular data of the GCR

Publications and Open Access data regarding. Quantitative and temporal data of the normal GCR. (M24) Publications and Open Access data regarding (Single cell) molecular signatures (transcriptomics, ChipSeq, ATACseq). (M24, M42)

Vacancies, Recruitment, Declarations on conformity

Advertise positions; Recruit ESRs. Declarations on conformity.

Supervisory board of COSMIC

Supervisory Board of COSMIC installed

Publications

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

Author(s): Elena Merino Tejero, Danial Lashgari, Rodrigo García-Valiente, Jiaojiao He, Philippe A. Robert, Michael Meyer-Hermann, Jeroen E. J. Guikema, Huub Hoefsloot, Antoine H. C. van Kampen
Published in: Frontiers in Immunology, 12, 2021, ISSN 1664-3224
Publisher: Frontiers Media SA
DOI: 10.3389/fimmu.2021.716240

The immunological drummer or dancer?

Author(s): Dornatien C. Anang; Giulia Balzaretti; Antoine van Kampen; Niek de Vries; Paul L. Klarenbeek
Published in: International Journal of Molecular Sciences, 14220067, 2021, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms221910514

Investigating the Mechanism of Germinal Center Shutdown

Author(s): Theinmozhi Arulraj, Sebastian C. Binder and Michael Meyer-Hermann
Published in: Frontiers in Immunology, 2022, ISSN 1664-3224
Publisher: Lausanne: Frontiers Media S.A.
DOI: 10.3389/fimmu.2022.922318

Germinal Centre Shutdown

Author(s): Theinmozhi Arulraj; Sebastian C. Binder; Philippe A. Robert; Philippe A. Robert; Michael Meyer-Hermann; Michael Meyer-Hermann
Published in: Frontiers in Immunology, 4, 2021, ISSN 1664-3224
Publisher: Frontiers Media S.A.
DOI: 10.3389/fimmu.2021.705240

Permissive selection followed by affinity-based proliferation of GC light zone B cells dictates cell fate and ensures clonal breadth

Author(s): 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
Published in: Proceedings of the National Academy of Sciences, 118/2, 2021, Page(s) e2016425118, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.2016425118

Understanding Monoclonal B Cell Lymphocytosis: An Interplay of Genetic and Microenvironmental Factors

Author(s): Galigalidou C, Zaragoza-Infante L, Iatrou A, Chatzidimitriou A, Stamatopoulos K, Agathangelidis A.
Published in: Frontiers in Oncology, 11:769612, 2021, ISSN 2234-943X
Publisher: Frontiers Media S. A.
DOI: 10.3389/fonc.2021.769612

SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems

Author(s): Andreas Dräger; Tomáš Helikar; Matteo Barberis; Matteo Barberis; Marc R. Birtwistle; Laurence Calzone; Claudine Chaouiya; Claudine Chaouiya; Jan Hasenauer; Jonathan R. Karr; Anna Niarakis; Anna Niarakis; María Rodríguez Martínez; Julio Saez-Rodriguez; Juilee Thakar
Published in: Bioinformatics, 10, 2020, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btab229

Computational Model Reveals a Stochastic Mechanism behind Germinal Center Clonal Bursts

Author(s): Aurélien Pélissier, Youcef Akrout, Katharina Jahn , Jack Kuipers , Ulf Klein , Niko Beerenwinkel, María Rodríguez Martínez
Published in: Cells, 9/6, 2020, Page(s) 1448, ISSN 2073-4409
Publisher: MDPI
DOI: 10.3390/cells9061448

CuBlock: a cross-platform normalization method for gene-expression microarrays

Author(s): Valentin Junet, Judith Farrés, José M Mas, Xavier Daura
Published in: Bioinformatics, 2021, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btab105

B Cell Receptor Immunogenetics in B Cell Lymphomas: Immunoglobulin Genes as Key to Ontogeny and Clinical Decision Making

Author(s): Katerina Gemenetzi, Andreas Agathangelidis, Laura Zaragoza-Infante, Electra Sofou, Maria Papaioannou, Anastasia Chatzidimitriou, Kostas Stamatopoulos
Published in: Frontiers in Oncology, 10, 2020, ISSN 2234-943X
Publisher: Frontiers Media S. A.
DOI: 10.3389/fonc.2020.00067

Synchronous Germinal Center Onset Impacts the Efficiency of Antibody Responses

Author(s): Theinmozhi Arulraj, Sebastian C. Binder, Philippe A. Robert, Michael Meyer-Hermann
Published in: Frontiers in Immunology, 10, 2019, ISSN 1664-3224
Publisher: Frontiers Media SA
DOI: 10.3389/fimmu.2019.02116

In-silico simulated prototype-patients using TPMS technology to study a potential adverse effect of sacubitril and valsartan

Author(s): Guillem Jorba, Joaquim Aguirre-Plans, Valentin Junet, Cristina Segú-Vergés, José Luis Ruiz, Albert Pujol, Narcís Fernández-Fuentes, José Manuel Mas, Baldo Oliva
Published in: PLOS ONE, 15/2, 2020, Page(s) e0228926, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0228926

Multi-Scale Modeling Recapitulates the Effect of Genetic Alterations Associated With Diffuse Large B-Cell Lymphoma in the Germinal Center Dynamics

Author(s): Elena Merino Tejero, Qirong Mao, Danial Lashgari, Rodrigo García-Valiente, Philippe A. Robert, Michael Meyer-Hermann, María Rodríguez Martínez, Jeroen E. J. Guikema, Huub H. C. Hoefsloot and Antoine H. C. van Kampen
Published in: Frontiers in Systems Biology, 2, 2022, ISSN 2674-0702
Publisher: Frontiers SA
DOI: 10.3389/fsysb.2022.864690

Rate of Immune Complex Cycling in Follicular Dendritic Cells Determines the Extent of Protecting Antigen Integrity and Availability to Germinal Center B Cells

Author(s): Theinmozhi Arulraj, Sebastian C. Binder, Michael Meyer-Hermann
Published in: The Journal of Immunology, 206/7, 2021, Page(s) 1436-1442, ISSN 0022-1767
Publisher: American Association of Immunologists
DOI: 10.4049/jimmunol.2001355

Multiscale Modeling of Germinal Center Recapitulates the Temporal Transition From Memory B Cells to Plasma Cells Differentiation as Regulated by Antigen Affinity-Based Tfh Cell Help

Author(s): Merino Tejero, E., D. Lashgari, R. Garcia-Valiente, X. Gao, F. Crauste, P. A. Robert, M. Meyer-Hermann, M. R. Martinez, S. M. van Ham, J. E. J. Guikema, H. Hoefsloot, and A. H. C. van Kampen
Published in: Frontiers in Immunology, 11, 2022, Page(s) 620716., ISSN 1664-3224
Publisher: Frontiers Media SA
DOI: 10.3389/fimmu.2020.620716

The B cell receptor in marginal zone lymphoma ontogeny and evolution

Author(s): Laura Zaragoza-Infante, Andreas Agathangelidis, Maria Papaioannou, Anastasia Chatzidimitriou, Kostas Stamatopoulos
Published in: Annals of Lymphoma, 4, 2020, Page(s) 10-10, ISSN 2616-2695
Publisher: AME Publishing Company
DOI: 10.21037/aol-20-18

Methods to Develop an in silico Clinical Trial: Computational Head-to-Head Comparison of Lisdexamfetamine and Methylphenidate

Author(s): José Ramón Gutiérrez-Casares, Javier Quintero, Guillem Jorba, Valentin Junet, Vicente Martínez, Tamara Pozo-Rubio, Baldomero Oliva, Xavier Daura, José Manuel Mas, Carmen Montoto
Published in: Frontiers in Psychiatry, 12, 2021, ISSN 1664-0640
Publisher: Frontiers Research Foundation
DOI: 10.3389/fpsyt.2021.741170

Increased Frequency of CD4+ Follicular Helper T and CD8+ Follicular T Cells in Human Lymph Node Biopsies during the Earliest Stages of Rheumatoid Arthritis

Author(s): Anang DC, Ramwadhdoebe TH, Hähnlein JS, van Kuijk B, Smits N, van Lienden KP, Maas M, Gerlag DM, Tak PP, de Vries N, van Baarsen LGM.
Published in: Cells., 11(7), 2022, Page(s) 1104, ISSN 2073-4409
Publisher: MDPI
DOI: 10.3390/cells11071104

Cyclin D3 drives inertial cell cycling in dark zone germinal center B cells

Author(s): 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
Published in: Journal of Experimental Medicine, 218/4, 2021, ISSN 0022-1007
Publisher: Rockefeller University Press
DOI: 10.1084/jem.20201699

Ymir: A 3D structural affinity model for multi-epitope vaccine simulations

Author(s): Philippe A. Robert, Theinmozhi Arulraj, Michael Meyer-Hermann
Published in: iScience, 24/9, 2021, Page(s) 102979, ISSN 2589-0042
Publisher: Elsevier
DOI: 10.1016/j.isci.2021.102979

From affinity selection to kinetic selection in Germinal Centre modelling

Author(s): Danial Lashgari; Elena Merino Tejero; Michael Meyer-Hermann; Mathieu A. F. Claireaux; Marit J. van Gils; Huub C. J. Hoefsloot; Antoine H. C. van Kampen
Published in: PLoS computational biology, 18;6, 2022, Page(s) 5, ISSN 1553-734X
Publisher: Public Library of Science
DOI: 10.1371/journal.pcbi.1010168

IgIDivA: immunoglobulin intraclonal diversification analysis

Author(s): Laura Zaragoza-Infante, Valentin Junet, Nikos Pechlivanis, Styliani-Christina Fragkouli, Serovpe Amprachamian, Triantafyllia Koletsa, Anastasia Chatzidimitriou, Maria Papaioannou, Kostas Stamatopoulos, Andreas Agathangelidis, Fotis Psomopoulos
Published in: Briefings in Bioinformatics, bbac349,, 2022, ISSN 1467-5463
Publisher: Oxford University Press
DOI: 10.1093/bib/bbac349

In Silico Analysis of the Longevity and Timeline of Individual Germinal Center Reactions in a Primary Immune Response.

Author(s): Theinmozhi Arulraj, Sebastian C Binder, Michael Meyer-Hermann
Published in: Cells, 10(7):1736, 2021, ISSN 2073-4409
Publisher: MDPI
DOI: 10.3390/cells10071736

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

Author(s): Junet, Valentin; Daura, Xavier
Published in: Bioinformatics, 7, 2021, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btab687

Development of the reproduction number from coronavirus SARS-CoV-2 case data in Germany and implications for political measures

Author(s): Sahamoddin Khailaie, Tanmay Mitra, Arnab Bandyopadhyay, Marta Schips, Pietro Mascheroni, Patrizio Vanella, Berit Lange, Sebastian C. Binder, Michael Meyer-Hermann
Published in: BMC Medicine, 19/1, 2021, ISSN 1741-7015
Publisher: BioMed Central
DOI: 10.1186/s12916-020-01884-4

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

Author(s): Valentin Junet, Xavier Daura
Published in: Bioinformatics, 2021, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btab687

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

Author(s): Jorba, Guillem; Aguirre-Plans, Joaquim; Junet, Valentin; Segú-Vergés, Cristina; Ruiz, José Luis; Pujol, Albert; Fernandez-Fuentes, Narcis; Mas, José Manuel; Oliva, Baldo
Published in: bioRxiv, 1, 2019
Publisher: Cold Spring Harbor
DOI: 10.1101/625889

DNA polymerase β prevents AID-instigated mutagenic non-canonical mismatch DNA repair

Author(s): 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
Published in: bioXrive, 1, 2020
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2020.01.30.926964

Software

Germinal centre simulation software

Author(s): Meyer-Hermann, Michael; Binder, Sebastian C.; Theinmozhi Arulraj
DOI: 10.5281/zenodo.5012498; 10.5281/zenodo.5012497
Publisher: Zenodo

Germinal center intercommunication via soluble antibodies

Author(s): Theinmozhi Arulraj; Sebastian C. Binder; Michael Meyer-Hermann
DOI: oai:zenodo.org:6568368; 10.5281/zenodo.6568368
Publisher: Zenodo

CNN-PepPred

Author(s): Daura, Xavier
Publisher: bio.tools

Germinal center intercommunication via soluble antibodies

Author(s): Theinmozhi Arulraj; Binder, Sebastian C.; Meyer-Hermann, Michael
DOI: 10.5281/zenodo.6568368; 10.5281/zenodo.6568367
Publisher: Zenodo

Code for mechanisms of germinal center shutdown

Author(s): Theinmozhi Arulraj; Sebastian C. Binder; Michael Meyer-Hermann
DOI: 10.5281/zenodo.6395395; 10.5281/zenodo.6395396
Publisher: Zenodo

Deliverables

Publications

Software

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