EpiPredict>Research>Projects>Development of a knowledge base and integrative bioinformatics analysis of epigenetic regulation in endocrine resistance

Development of a knowledge base and integrative bioinformatics analysis of epigenetic regulation in endocrine resistance

Maryam Soleimani Dodaran

Stage Researcher 2
Name: Maryam Soleimani Dodaran
Gender: Female
Country of Birth: Iran
MSc in: Bioinformatics (University of Leicester, UK)

Marie Skłodowska Curie PhD Fellowship in Bioinformatics/Biosystems data analysis, at the University of Amsterdam (UvA), the Netherlands, Swammerdam Institute for Life Sciences (SILS), in the research group of Prof. Van Kampen.

Project title: “Development of a knowledge base and integrative bioinformatics analysis of epigenetic regulation in endocrine resistance”

Supervisors: PI: Prof. Antoine van Kampen, Prof. Age Smilde (Swammerdam Institute for Life Sciences / Academic Medical Center, University of Amsterdam, the Netherlands), co-supervisor: Dr Perry Moerland (Academic Medical Center, the Netherlands), Dr Pernette Verschure (SILS, UvA); EpiPredict co-PI: Dr Alex Michie (ClinicaGeno, UK)

PhD programme: Swammerdam Inst. for Life Sciences SILS, UvA (www.sils.uva.nl); Netherlands Bioinformatics and Systems Biology Research School (www.biosb.nl)

Key Objectives & Expected Results

Objectives

To build a Tamoxifen-Resistance knowledge base (TRkb) from literature/expert knowledge as input for downstream computational approaches
To develop bioinformatics tools that use prior knowledge from TRkb in bioinformatics analysis to refine/elucidate Tamoxifen resistance pathways
To determine disease signatures (multivariate biomarkers) to subclassify patient’s resistance outcome
To analyse and/or reconstruct resistance pathways

Expected Results

Tamoxifen-Resistance knowledge base (TRkb)
Bioinformatics methods that incorporate prior knowledge from TRkb in bioinformatics analyses
Bioinformatics methods for pathway reconstruction/analysis
Predictive disease signatures (multivariate biomarkers)

Host training: Integrative bioinformatics, (multivariate) statistical analyses (multivariate)

Planned secondment(s): CGO: co-development TR-KB/signature determination (M29-30), ICL: Epigenetic profiles/patient diagnosis (M9), DKFZ: RPPA profiling (M10-11).