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Prof. Olli Kallioniemi, MD, PhD,
Principal Investigator
Dr. Johan Lundin, MD, PhD,
Co-Principal Investigator
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Spatial Systems Molecular Pathology of cancer model systems and human tumors
This research project aims to develop new technologies for spatial systems molecular pathology with the aim of deeper understanding of the expression patterns and context of therapeutic targets across the spectrum of clinical tumour types and cancer model systems developed in the PREDECT consortium. The project will also develop an integrated molecular pathology image resource and spatial systems biological modelling of data from cancer model systems that will be widely useful for drug target validation and for predicting the success of the drug development process in the personalized medicine era.
Objectives
- Develop new methods for multi-parametric immunostaining of therapeutic targets and the tumour microenvironment, both in the human tumours and the mouse and cell line models.
- Develop multispectral imaging and quantitative image analysis methods to score for the presence of therapeutic targets in individual cells and their contextual relationships and heterogeneity along with cell phenotypes and cell signalling
- Develop web microscopic databases of the multiparametric profiling of cancer model systems, and integrate these with molecular pathology information of human tumours
- Develop spatial systems pathology based quantitative and mathematical models of targets and their contextual relationships within and between cells and cell types, tissue compartments and the tumour microenvironment across the PREDECT model systems and clinical tumours.
Research Site
Institute for Molecular Medicine Finland (FIMM)
Nordic EMBL Partnership in Molecular Medicine
University of Helsinki
Finland
olli.kallioniemi@helsinki.fi
Vacancy: currently no open position
Lab website
http://www.fimm.fi/en/research
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Outi Monni, PhD,
Principal Investigator
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Project Description
This project focuses on molecular characterisation and cross-comparison of the cancer model systems developed in PREDECT consortium. Dynamic reciprocity of
in vivo and
in vitro models and clinical tumours will be explored using transcriptome profiling, exome sequencing, arrayCGH and molecular pathology. This project also aims to establish novel preclinical 3D and tissue slice culture models together with other PREDECT partners. These models will be employed for drug target validation, pathway perturbations and testing drug efficacy.
Objectives
- Provide platforms for characterisation of in vitro, in vivo cancer model systems and clinical tumours
- Cross-compare mouse models to clinical tumour samples using molecular pathology, genomic (exome sequencing, aCGH) and transcriptomic profiling (mRNA-Seq, exon arrays)
- Develop preclinical 3D platforms and tissue slice systems for drug efficacy testing and drug target validation
Research Site
Biomedicum Genomics Ltd.
Biomedicum Helsinki
Haartmaninkatu 8
00290 Helsinki, FINLAND
Vacancy: currently no open position
Lab website
http://www.biomedicumgenomics.fi
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Jaak Vilo, PhD,
Principal Investigator
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Project Description
This research project aims to develop analysis resources and methods to support target validation through comparative analysis and systems biology approaches.
Objectives
- Develop new methods for comparative pathway analysis in different model systems
- Manage biomolecular data and analysis tools for the PREDECT consortium
- Integrate BIIT tools (g:Profiler, MEM, etc) and other public analysis software for the PREDECT
- Assist participating labs to perform necessary analysis tasks and identify promising areas for bioinformatics methods development
Research Site
Institute of Computer Science
University of Tartu
Estonia
Vacancy: currently no open position
Lab website
http://biit.cs.ut.ee/
