COSMIC has 14 research positions available.

Below you will find a short description of each (PhD) research project with a link to the full job description.

 

ESR1 (PhD student). 
Host: Prof. dr. Antoine van Kampen, AMC, Amsterdam.
Duration: 48 months
Development of multiscale mathematical models of the germinal center (GC) to study its role in B-cell lymphoma (BCL) and/or rheumatoid arthritis (RA).  
The PhD candidate will develop agent-based models of the germinal center and differential equation-based models of gene regulatory networks determine the behavior of immune cells in the GC. These cellular and molecular models will be integrated into multiscale models to study the role of the GC in BCL and/or RA. In addition, we will use these models to determine the effect of molecular perturbations on the cellular level. [Full job description].
 
ESR2 (PhD student). 
Host: Dr. Niek de Vries, AMC, Amsterdam
Duration: 48 months
Title
Description
 
ESR3 (PhD student). 
Host: Dr. Jeroen Guikema, AMC, Amsterdam
Duration: 48 months
Characterising the regulation of DNA repair activities and consequences of B-cell neoplasia associated oncogene expression in the germinal center.
The PhD candidate will study the GC B-cell specific regulation of DNA repair fidelity and the effects of GC B-cell specific oncogene overexpression on GC resolution using genetically engineered human and mouse cell lines, transgenic mouse models, and 'multi-OMICS' approaches.[Full job description]

 
ESR4 (PhD student). 
Host: Dr. Olivier Gandrillon / Dr. Fabien Crauste, INRIA, Lyon
Duration: 36 months
Infering gene regulatory networks from single-cell data. 

The PhD candidate will investigate gene regulatory network inference from single-cell transcriptomics data, using probabilistic models (piecewise deterministic Markov processes). These networks aim at being plugged into computational multiscale models of the germinal center that will help focusing on specific diseases and in particular on the molecular perturbations that could affect cellular dynamics [Full job description]. 

 
ESR5 (PhD student). 
Host: Prof. dr. Rikard Holmdahl, Karolinska Institute, Stockholm
Duration: 36 months
Title
Description
 
ESR6 (PhD student). 
Host: Dr. Martin Turner, Babraham Institute, Cambridge
Duration: 36 months
Molecular mechanisms of selection in the germinal center
The student will develop and apply state of the art next generation based sequencing technologies to study how selection germinal center B cells takes place.  The student will learn to sort positively selected B cells by FACS, prepare avariety of library types for probing the transcriptome and epigenetic status of the cells.  Bioinformatics analysis and data integration will be conducted and learnt in collaboration with COSMIC partners [Full job description].
 
ESR7 (PhD student). 
Host: Dr. Stefano Casola, IFOM, Milan
Duration: 36 months
Title
Description
  
ESR8 (PhD student). 
Host: Dr. Judith Farres, Anaxomics, Barcelona
Duration: 36 months
Graph theory and machine learning approaches for immunological diseases research and clinical diagnostic applications.
The candidate will design, develop and validate new algorithms in network-based machine learning and graph theory for immunological diseases research and clinical diagnostic applications. The candidate will develop novel approaches to incorporate different spatiotemporal scales using machine learning techniques and implementing GPU-based graph processing [Full job description].
  
ESR9 (Industrial Researcher). 
Host: Dr. Malin Hultqvist-Hopkinks, Redoxis, Lund
Duration: 36 months
Molecular characterisation of autoimmune response in preclinical models of arthritis for identification of biomarkers and drug efficacy validation
The candidate will characterise and validate currently used animal models for RA in respect to B cell function and pathogenic and regulatory antibodies. Based on findings the project will involve development new protocols (in vivo, ex vivo and in vitro) for mechanism and efficacy evaluation. We will validate new and classical drugs and biomarkers using the new protocols as a tool for the pharmaceutical industry preclinical efficacy evaluation [Full job description].
 
ESR10 (PhD student). 
Host: Prof. dr. Michael Meyer-Hermann, HZI, Braunschweig
Duration: 36 months

Agent-based modelling of affinity maturation and germinal centre shutdown

The student will develop and evaluate mathematical models of the germinal centre (GC) reaction with a focus on clinical applications in the context of vaccination, B cell lymphoma and rheumatoid arthritis. We aim at elucidating the role of GC for disease development and identifying key determinants of pathological GC states by extending and developing an agent-based model.[Full project description]

  
ESR11 (PhD student). 
Host: Prof. dr. Michael Meyer-Hermann, HZI, Braunschweig
Duration: 36 months

Modelling the initialization of the germinal centre reaction with ordinary differential equations

The student will develop and evaluate mathematical models of the germinal centre (GC) reaction with a focus on clinical applications in the context of vaccination, B cell lymphoma and rheumatoid arthritis. This part of our project is focused on elucidating the role of the initiation of a GC reaction for vaccination success and the development of pathological GC states using an ordinary differential equation model. [Full project description]

  
ESR12 (PhD student). 
Host: Prof. dr. Rikard Holmdahl, Karolinska Institute, Stockholm
Duration: 36 months
Title
Description
  
ESR13 (PhD student). 
Host: Dr. Maria Martinez, IBM, Zurich
Duration: 36 months
 

Development of multiscale mathematical models of the germinal center to elucidate its role in B-cell lymphoma and/or rheumatoid arthritis. 

COSMIC will focus on B-cell neoplasia and rheumatoid arthritis, prototypical diseases originating from abnormal functioning of immune cells, often resulting in similar antigen specificities. The successful candidate will develop new algorithms to understand the molecular mechanisms of these diseases, and to identify strategies for optimal personalized patient treatment. [Full job description]

ESR14 (PhD student)
Host: Dr. Kostas Stamatopoulos, CERTH, Thessaloniki
Duration: 36 months
Functional implications of affinity maturation for the ontogeny and evolution of B cell lymphomas through combined NGS immunogenetics and 3D analysis

The PhD candidate will explore the implications of affinity maturation processes occurring within the context of the germinal center reaction for the ontogeny and evolution of B cell lymphomas (BCL). This will be achieved though high throughput analysis of the immunoglobulin (IG) variable gene repertoire combined with structural analysis of the clonotypic IG receptors from selected cases. [Full job description]

 

 

 

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