COmbatting disorders of adaptive immunity with Systems MedICine

Livrables

Initial setup of external website, Facebook, Twitter, etc

Plan for dissemination strategy
1. Mechanistic models of GCR in BCN/RA

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)

COSMIC international conference
2. Network workshops, e-learning

The ESRs participate in COSMIC workshops elearning activities local training activities etc Training takes place from M9 to M36ESR can receive prizes from COSMIC for their work M31 M553 annual prizes best publication presentation collaboration 250 euro eachBest expose for layman

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

Auteurs: 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
Publié dans: Frontiers in Immunology, Numéro 12, 2021, ISSN 1664-3224
Éditeur: Frontiers Media SA
DOI: 10.3389/fimmu.2021.716240

The immunological drummer or dancer?

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

Investigating the Mechanism of Germinal Center Shutdown

Auteurs: Theinmozhi Arulraj, Sebastian C. Binder and Michael Meyer-Hermann
Publié dans: Frontiers in Immunology, 2022, ISSN 1664-3224
Éditeur: Lausanne: Frontiers Media S.A.
DOI: 10.3389/fimmu.2022.922318

Germinal Centre Shutdown

Auteurs: Theinmozhi Arulraj; Sebastian C. Binder; Philippe A. Robert; Philippe A. Robert; Michael Meyer-Hermann; Michael Meyer-Hermann
Publié dans: Frontiers in Immunology, Numéro 4, 2021, ISSN 1664-3224
Éditeur: 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

Auteurs: 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
Publié dans: Proceedings of the National Academy of Sciences, Numéro 118/2, 2021, Page(s) e2016425118, ISSN 0027-8424
Éditeur: National Academy of Sciences
DOI: 10.1073/pnas.2016425118

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

Auteurs: Galigalidou C, Zaragoza-Infante L, Iatrou A, Chatzidimitriou A, Stamatopoulos K, Agathangelidis A.
Publié dans: Frontiers in Oncology, Numéro 11:769612, 2021, ISSN 2234-943X
Éditeur: 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

Auteurs: 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
Publié dans: Bioinformatics, Numéro 10, 2020, ISSN 1367-4803
Éditeur: Oxford University Press
DOI: 10.1093/bioinformatics/btab229

Computational Model Reveals a Stochastic Mechanism behind Germinal Center Clonal Bursts

Auteurs: Aurélien Pélissier, Youcef Akrout, Katharina Jahn , Jack Kuipers , Ulf Klein , Niko Beerenwinkel, María Rodríguez Martínez
Publié dans: Cells, Numéro 9/6, 2020, Page(s) 1448, ISSN 2073-4409
Éditeur: MDPI
DOI: 10.3390/cells9061448

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

Auteurs: Valentin Junet, Judith Farrés, José M Mas, Xavier Daura
Publié dans: Bioinformatics, 2021, ISSN 1367-4803
Éditeur: 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

Auteurs: Katerina Gemenetzi, Andreas Agathangelidis, Laura Zaragoza-Infante, Electra Sofou, Maria Papaioannou, Anastasia Chatzidimitriou, Kostas Stamatopoulos
Publié dans: Frontiers in Oncology, Numéro 10, 2020, ISSN 2234-943X
Éditeur: Frontiers Media S. A.
DOI: 10.3389/fonc.2020.00067

Synchronous Germinal Center Onset Impacts the Efficiency of Antibody Responses

Auteurs: Theinmozhi Arulraj, Sebastian C. Binder, Philippe A. Robert, Michael Meyer-Hermann
Publié dans: Frontiers in Immunology, Numéro 10, 2019, ISSN 1664-3224
Éditeur: 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

Auteurs: Guillem Jorba, Joaquim Aguirre-Plans, Valentin Junet, Cristina Segú-Vergés, José Luis Ruiz, Albert Pujol, Narcís Fernández-Fuentes, José Manuel Mas, Baldo Oliva
Publié dans: PLOS ONE, Numéro 15/2, 2020, Page(s) e0228926, ISSN 1932-6203
Éditeur: 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

Auteurs: 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
Publié dans: Frontiers in Systems Biology, Numéro 2, 2022, ISSN 2674-0702
Éditeur: 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

Auteurs: Theinmozhi Arulraj, Sebastian C. Binder, Michael Meyer-Hermann
Publié dans: The Journal of Immunology, Numéro 206/7, 2021, Page(s) 1436-1442, ISSN 0022-1767
Éditeur: 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

Auteurs: 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
Publié dans: Frontiers in Immunology, Numéro 11, 2022, Page(s) 620716., ISSN 1664-3224
Éditeur: Frontiers Media SA
DOI: 10.3389/fimmu.2020.620716

The B cell receptor in marginal zone lymphoma ontogeny and evolution

Auteurs: Laura Zaragoza-Infante, Andreas Agathangelidis, Maria Papaioannou, Anastasia Chatzidimitriou, Kostas Stamatopoulos
Publié dans: Annals of Lymphoma, Numéro 4, 2020, Page(s) 10-10, ISSN 2616-2695
Éditeur: 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

Auteurs: José Ramón Gutiérrez-Casares, Javier Quintero, Guillem Jorba, Valentin Junet, Vicente Martínez, Tamara Pozo-Rubio, Baldomero Oliva, Xavier Daura, José Manuel Mas, Carmen Montoto
Publié dans: Frontiers in Psychiatry, Numéro 12, 2021, ISSN 1664-0640
Éditeur: 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

Auteurs: 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.
Publié dans: Cells., Numéro 11(7), 2022, Page(s) 1104, ISSN 2073-4409
Éditeur: MDPI
DOI: 10.3390/cells11071104

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

Auteurs: 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
Publié dans: Journal of Experimental Medicine, Numéro 218/4, 2021, ISSN 0022-1007
Éditeur: Rockefeller University Press
DOI: 10.1084/jem.20201699

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

Auteurs: Philippe A. Robert, Theinmozhi Arulraj, Michael Meyer-Hermann
Publié dans: iScience, Numéro 24/9, 2021, Page(s) 102979, ISSN 2589-0042
Éditeur: Elsevier
DOI: 10.1016/j.isci.2021.102979

From affinity selection to kinetic selection in Germinal Centre modelling

Auteurs: 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
Publié dans: PLoS computational biology, Numéro 18;6, 2022, Page(s) 5, ISSN 1553-734X
Éditeur: Public Library of Science
DOI: 10.1371/journal.pcbi.1010168

IgIDivA: immunoglobulin intraclonal diversification analysis

Auteurs: Laura Zaragoza-Infante, Valentin Junet, Nikos Pechlivanis, Styliani-Christina Fragkouli, Serovpe Amprachamian, Triantafyllia Koletsa, Anastasia Chatzidimitriou, Maria Papaioannou, Kostas Stamatopoulos, Andreas Agathangelidis, Fotis Psomopoulos
Publié dans: Briefings in Bioinformatics, bbac349,, 2022, ISSN 1467-5463
Éditeur: 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.

Auteurs: Theinmozhi Arulraj, Sebastian C Binder, Michael Meyer-Hermann
Publié dans: Cells, Numéro 10(7):1736, 2021, ISSN 2073-4409
Éditeur: 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

Auteurs: Junet, Valentin; Daura, Xavier
Publié dans: Bioinformatics, Numéro 7, 2021, ISSN 1367-4803
Éditeur: 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

Auteurs: Sahamoddin Khailaie, Tanmay Mitra, Arnab Bandyopadhyay, Marta Schips, Pietro Mascheroni, Patrizio Vanella, Berit Lange, Sebastian C. Binder, Michael Meyer-Hermann
Publié dans: BMC Medicine, Numéro 19/1, 2021, ISSN 1741-7015
Éditeur: BioMed Central
DOI: 10.1186/s12916-020-01884-4

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

Auteurs: Jorba, Guillem; Aguirre-Plans, Joaquim; Junet, Valentin; Segú-Vergés, Cristina; Ruiz, José Luis; Pujol, Albert; Fernandez-Fuentes, Narcis; Mas, José Manuel; Oliva, Baldo
Publié dans: bioRxiv, Numéro 1, 2019
Éditeur: Cold Spring Harbor
DOI: 10.1101/625889

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

Auteurs: 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
Publié dans: bioXrive, Numéro 1, 2020
Éditeur: Cold Spring Harbor Laboratory
DOI: 10.1101/2020.01.30.926964

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