| Name | Thesis | submitted |
| Wasinee Rungsarityotin | Algorithms to Identify Protein Complexes from High-Throughput Data | Jun 2007 |
| Philipp Messer | Tandem Duplications in the Human Genome | Feb 2008 |
| Zhike Zi | Mathematical Modeling and Kinetic Analysis of Cellular Signaling Pathways | Apr 2008 |
| Markus Bauer | A Combinatorial Approach to RNA Sequence-Structure Alignments | Apr 2008 |
| Utz J. Pape | Statistics for Transcription Factor Binding Sites | Jul 2008 |
| Ole Schulz-Trieglaff | Computational Methods for Quantitative Peptide Mass Spectrometry | Oct 2008 |
| Evelyn Dittmer | Hidden Markov Models with Time-Continuous Output Behavior | Nov 2008 |
| Andrea Weiße | Global Sensitivity Analysis of Ordinary Differential Equations | Apr 2009 |
| Tobias Rausch | Dissecting Multiple Sequence Alignment Methods | Sep 2009 |
| Federico Squartini | Stationarity and Reversibility in the Nucleotide Evolutionary Process | Mar 2010 |
| Ben-Fillippo Krippendorff | Integrating Cell-level Kinetic Modeling into the Optimization of Cancer Therapeutics | Apr 2010 |
| Paz Polak | Discovering Mutational Patterns in Mammals Using Comparative Genomics | Jun 2010 |
| Marcel Schulz | Data Structures and Algorithms for Analysis of Alternative Splicing with RNA-seq Data | Jul 2010 |
| Ewa Szczurek | Modelling Signal Transduction Pathways and Their Transcriptional Response | Oct 2010 |
| Sayed-Amir Marashi | Constraint-based Analysis of Substructures of Metabolic Networks | Apr 2011 |
| Atanas Kamburov | More Accurate Interactomes for Elucidating the Mechanisms of Complex Diseases | Aug 2011 |
| Henning Stehr | Graph-based Approaches to Protein Structure- and Function Prediction | May 2011 |
| Akdes Serin | Biclustering Analysis for Large Scale Data | Sep 2011 |
| Rosa Karlić | Influence of Histone Modifications on mRNA Abundance and Structure | Sep 2011 |
| Martin Held | Novel Concepts to Study Conformation and Association Dynamics of Biomolecules | Jan 2012 |
| Jonathan Göke | Analysis of Long-Distance Gene Regulatory Elements | May 2012 |
| Martina Fröhlich | Computational and Experimental Investigation of the Mechanisms Involved in Cellular Water Transport and (Cat)ion Homeostasis | May 2012 |
| Chris Bielow | Quantication and Simulation of Liquid Chromatography-Mass Spectrometry Data | Jun 2012 |
| Yves Clément | The Evolution of Base Composition in Mammalian Genomes | Aug 2012 |
| Christian Diener | Localized Signaling and Communication during Yeast Mating | Sep 2012 |
| Marvin Schulz | Identification of Potential Drug Targets in Kinetic Networks Described by Ordinary Differential Equations | Sep 2012 |
| Anne-Katrin Emde | Next-Generation Sequencing Algorithms: From Read Mapping to Variant Detection | Nov 2012 |
| Michael Love | Statistical Analysis of High-Throughput Sequencing Count Data | Jun 2013 |
| Stephan Aiche | Inferring Proteolytic Processes from Mass Spectrometry Time Series Data | May 2013 |
| Birte Kehr | Contributions to Computing and Modeling Multiple Whole-Genome Alignments | Nov 2013 |
| Arne Reimers | Metabolic Networks, Thermodynamic Constraints, and Matroid Theory | Jun 2014 |
| Johannes Schöneberg | Reaction-Diffusion Dynamics in Biological Systems | Jul 2014 |
| Sharon Hüffner | Modularity in Biological Networks | Apr 2014 |
| Sandro Andreotti | Linear Programming and Integer Linear Programming in Bioinformatics | Sep 2014 |
| Alena van Bömmel | Prediction of transcription factor co-occurrence using rank based statistics | Jul 2014 |
| Enrico Siragusa | Approximate string matching for high-throughput sequencing | May 2015 |
| Juliane Perner | Bioinformatic Approaches for Understanding Chromatin Regulation | Jun 2015 |
| Han Cheng Lie | On a strongly convex approximation of a stochastic optimal control problem for importance sampling of metastable diffusions | Sep 2015 |
| Alessandro Mammana | Patterns and algorithms in high-throughput sequencing count data | Sep 2015 |
| Xintian You | Tailored Analysis in Studying Transcriptome Landscape | Sep 2015 |
| Iliusi Vega del Valle | Reconstruction and analysis of the state space for the identification of dynamical states in real-world time series | Jan 2016 |
| Wolfgang Kopp | Statistical methods for motif hit enrichment in DNA sequences | Oct 2016 |
| Johannes Helmuth | Robust normalization of next generation sequencing data | Feb 2017 |
| Kirsten Thobe | Logical modeling of uncertainty in signaling pathways of cancer systems | Mar 2017 |
| Matthias Lienhard | Computational analysis of genome-wide methylation enrichment experiments | Mar 2017 |
| Alexandra Reimers | Understanding metabolic regulation and cellular resource allocation through optimization | Aug 2017 |
| Matthew Huska | Using machine learning to predict and better understand DNA methylation and genomic enhancers | Aug 2017 |
| Sven-Leon Kuchenbecker | Analysis of Antigen Receptor Repertoires Captured by High Throughput Sequencing | Jan 2018 |
| Christoph Gorgulla | Free Energy Methods Involving Quantum Physics, Path Integrals, and Virtual Screenings: Development, Implementation and Application in Drug Discovery | Apr 2018 |
| Evgenia Youett | Adaptive Multilevel Monte Carlo Methods for Random Elliptic Problems | Jun 2018 |
| Mohammadhossein Moeinzadeh | De novo and haplotype assembly of polyploid genomes | Aug 2018 |
| Christopher M. Pockrandt | Approximate String Matching - Improving Data Structures and Algorithms | Feb 2019 |
| Temesgen Hailemariam Dadi | Whole Genome Shotgun Sequencing Based Taxonomic Profiling Methods for Comparative Study of Microbial Communities | Jan 2019 |
| Anna Ramisch | Enhancer Prediction Based on Epigenomic Data | Feb 2019 |
| Sabrina Krakau | Statistical models to capture protein-RNA interaction footprints from truncation-based CLIP-seq data | Jan 2019 |
| Luigi Sbailò | Efficient multi-scale sampling methods in statistical physics | Sep 2019 |
| Hongqing Han | Towards accurate and efficient live cell imaging data analysis | Dec 2019 |
| Stefan Budach | Explainable Deep Learning Models for Biological Sequence Classification | Dec 2019 |
| Lisa Barros de Andrade e Sousa | Using interpretable machine learning to understand gene silencing dynamics during X-chromosome inactivation | Jan 2020 |
| Tobias Zehnder | Computational approaches for the prediction of gene regulatory elements and the analysis of their evolutionary conservation | Sep 2020 |
| David Heller | Structural variant calling using third-generation sequencing data | Sep 2020 |
| Gal Barel | Network propagation with node core for genotype-phenotype associations and module identification | Sep 2020 |
| Melissa Bothe | Investigating the genomic effects of glucocorticoid receptor activation - an analysis of transcriptional memory and mechanisms that direct divergent genomic occupancy of related transcription factors | Mar 2021 |
| Roman Schulte-Sasse | Integration of multi-omics data with graph convolutional networks to identify cancer-associated genes | Dec 2020 |