Biomedical Data Science
(formerly: Algorithmic Bioinformatics)

PhD theses

  • Dr. Yupeng Cun, Network-Based Biomarker Discovery: Development of Prognostic Biomarkers for Personalized Medicine by Integrating Data and Prior Knowledge, University of Bonn, 2014
  • Dr. Paurush Praveen, Reverse engineering of biological signaling networks via integration of data and knowledge using probabilistic graphical models, University of Bonn, 2014
  • Dr. Khalid Abnaof, Finding Common Patterns in Heterogeneous Perturbation Data, University of Bonn, 2016
  • Dr. Satya Samal, Analysis of Biochemical Reaction Networks using Tropical and Polyhedral Geometry Methods, University of Bonn, 2016 (joint supervision with Prof. Andreas Weber and Prof. Ovidiu Radulescu)
  • Dr. Benjamin Engelhardt, Mathematical Analysis and Modeling of Signaling Networks, University of Bonn, 2017
  • Dr. Ashar Ahmad, Dissecting patient heterogeneity via statistical modeling based on multi-modal omics data, University of Bonn, 2019

Masters theses

  • Amit Kawalia, Network Based Comparison of Gene Signatures, 2011
  • Stephan Andonov, Ontology Tester, 2011
  • Afhsin Sadeghi, Empirical Comparison of Steiner Tree Methods on Protein Interaction Networks, 2012
  • Sohil Anand, Networks in TGF-beta Stimulated Multipotant Progenitor & Dendritic Progenitor Cells, 2012
  • Nikhil Vinod Mallela, Analysis of Cell Type Specific Response of Gene Expression to TGF-beta Treatment, 2013
  • Richard Schaefer, Reconstruction of gene interaction networks from combined SNP and mRNA expression data, 2013
  • Tabea Madeline Diekmann, Inference of nested effects models from combinatorial perturbation data with application to reconstructing the yeast kinome network, 2013
  • Mohsen Ahmadi Fahandar, Predicting Potent Compounds via Model-Based Global Optimization, 2014
  • Muhammad Ahmer Jamil, Developing a tool for fast analysis of LINE-1 Next-Generation Sequencing Methylation data, 2014
  • Deena Gergis,Modeling Hedgehog pahway in medulloblastoma using Dynamic Bayesian networks with systems biology approach, 2014
  • Nikolas Kleanthous, Biomarker Signature Discovery from Multiple Omics and Clinical Data, 2015
  • Shashank Khanna, Early AD Onset Prediction Integrating Heterogeneous Data Sources and Model Interpretation via Bayesian Networks, 2017
  • Sabyasachi Patjoshi, Towards Mechanism Based Biomarkers in Personalized Medicine, 2017
  • Vladimir Stashkov, Automated Translation of Signaling Pathway Into Reaction Graphs  and Subsequent Analysis, 2017
  • Aybuge Altay, BNenrich: A Novel Method for Estimation of Pathway Enrichment Scores by Integrating Partially Overlapping Multi-Omics Data via Bayesian networks, 2018
  • Akrishta Sahay, Development of longitudinal Bayesian Network Model for Parkinson's disease and simulation of virtual cohort using multi-modal data, 2018
  • Özlem Muslu, GuiltyTargets: Target Prioritization with Network Representation Learning, 2018
  • Camilla Duitama, External validation and characterisation of cancer subtypes using SBC, 2019

Interested in a thesis project?

Come with your own ideas or get inspired by some of these ideas. Please send us your CV and transcripts in advance.

Opportunity of an external student internship with possibility to extend into a Master thesis project.