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.