Research Project 7

Interactome predictions from long-read transcriptome sequencing data

About the Project

Max Planck Institute for Molecular Genetics 

Berlin, Germany

Ralf Herwig

Main Supervisor

Freie Universitaet Berlin

PhD enrolment

Yearly salary

36.898,99 € (Gross)

Research Objectives

LRS improves our annotation of protein isoforms expressed in a specific biological context and allows the construction of isoform-aware protein-protein interaction networks (IsoPPIs). These IsoPPIs can be used as a scaffold to integrate multi-omics data and to analyze expression effects at the network level. Our objectives are:

  • Catalogue LRS-based isoform expression on a large number of publicly available and proprietary data.
  • Develop an analysis pipeline to predict IsoPPIs from these data and additional PPI and domain information.
  • Apply and validate these IsoPPIs in the context of drug toxicity prediction and cancer drug resistance mechanisms.
  • Implement methods in the IsoTools software.

Envisioned Secondments

  • EI: Method application to cancer datasets.
  • Biobam: Development of isoform network visualization options.

About the Main Supervisor and Host Group

Ralf Herwig

Max Plank Institute,

The group has developed computational methods for RNA-seq and MeDIP-seq and works on the integrative analysis of these data in order to elucidate the interplay of methylation, gene expression and genome structure that are operative in human (disease) processes related to cancer, diabetes and drug toxicity.

Research covers i) the development of computational methods for the analysis of molecular data often in collaborative research projects with the focus on human diseases and ii) the integration and interpretation of these data in the context of biological networks.