PhD Theses
Completed PhD theses
If you are interested in pursuing a Ph.D. with us, please consider applying to our Internationational Max Planck Research School Biology And Computation (IMPRS-BAC).
2025
Modeling the impact of double X-dosage on pluripotency maintenance in mouse embryonic stem cells. Dissertation (2025)
Unveiling the Epigenetic Role of Arabidopsis PWO1: Linking Linear Chromatin Features to 3D Genome Architecture. Dissertation (2025)
Exploring Alzheimer's Disease Pathology Using Gene Co-Expression Networks: Insights into lncRNA and Protein-coding Genes Dysregulation. Dissertation (2025)
2024
ZEB2 and its regulatory impact on human brain evolution. Dissertation (2024)
Functional investigation of the regulatory landscape around the Xist locus. Dissertation (2024)
Development of a method to tune endogenous gene expression and its application to study dose-sensitivity in transcriptional regulation and random X-chromosome inactivation. Dissertation (2024)
Correspondence analysis based biclustering and joint visualization of cells and genes for single cell transcriptomic data. Dissertation (2024)
Machine Learning for Cancer Survival Prediction. Dissertation (2024)
Allosteric small-molecule probes to study splicing switches via conformational control of a spliceosomal RNA helicase. Dissertation (2024)
Copy number variation characterization using nanopore sequencing. Dissertation (2024)
Hybrid algorithm for efficient simulation of spreading processes on adaptive networks. Dissertation (2024)
The dispersion of aromatic residues in TF IDRs controls a molecular trade-off between activity and specificity. Dissertation (2024)
Exploring feature identification and machine learning in predicting protein-protein interactions of disordered proteins. Dissertation (2024)
Role of the putative cohesin cofactors PDS5A and PDS5C in nuclear organization and gene regulation. Dissertation (2024)
2023
Utilizing alignment-free methods to enable quantitative gene expression analysis of large collections of sequencing data. Dissertation (2023)
Transcriptome regulation during the X chromosome inactivation process. Dissertation (2023)
The molecular landscape of developmental pausing in mammals. Dissertation (2023)
Single cell sequencing as a phenotyping strategy to decipher the molecular mechanisms of developmental disorder. Dissertation (2023)
Algorithms for finding RNA sequence-structure motifs. Dissertation, XIII, 137 pp. (2023)
Design and multi-criteria optimization of cell classifier circuits in cancer therapy. Dissertation, xvii, 139 pp. (2023)
Body temperature-controlled antiviral response and SARS-CoV-2 replication. Dissertation, 93 pp. (2023)
Mechano-sensitivity of vascular BMP signaling - Insights into Fluid Shear Stress modulations from ligand to chromatin. Dissertation (2023)
Impact of hypoxia on embryonic and extraembryonic stem cells and during differentiation via gastruloid formation. Dissertation, 106 pp. (2023)
Genetic and chemical hydrophobic modification of transcription factor condensates in human disease. Dissertation (2023)
Roles of endogenous retroviruses in transcriptional condensates. Dissertation (2023)
Investigation of DNA methylation heterogeneity in cancer. Dissertation (2023)
Dissecting regional heterogeneity and modeling transcriptional cascades in brain organoids. Dissertation, vii, 129 pp. (2023)
Identification and Prioritization of Putative Pathogenic Structural Variants based on Functional Annotation. Dissertation (2023)
A Multi-Omics Analysis of Transcription Control by BRD4. Dissertation, ix, 205 pp. (2023)
Methods for control strategy identification in Boolean networks. Dissertation, 101 pp. (2023)
2022
Identification of Protogenin as a novel surface marker for early cortical neural stem cells. Dissertation (2022)
Deciphering cellular heterogeneity by single-cell transcriptome analysis. Dissertation, xiii, 131 pp. (2022)
Computational interpretation of disease-causing, structural, and non-coding human genetic variants. Dissertation, 118 pp. (2022)
Analysis of the determinants of Pol II pausing. Dissertation, vi, 125 pp. (2022)
Dynamical Aspects of the Evolution of Segmental Duplications in the Human Genome. Dissertation, xiii, 129 pp. (2022)
Association Plots visualize cluster-specific genes from high-dimensional transcriptomics data. Dissertation, vi, 108 pp. (2022)
Finding Reusable Modules Using Sparse Matrix Decompositions. Dissertation, vi, 103 pp. (2022)
The effect of a gain-of-function mutation in the Cl-/H+ exchanger ClC-7 in lysosomal and mitochondrial morphology and function. Dissertation (2022)
2021
Experimental and theoretical analysis of X-chromosome inactivation as a paradigm for epigenetic memory and molecular decision-making. Dissertation, 191 pp. (2021)
Integration of multi-omics data with graph convolutional networks to identify cancer-associated genes. Dissertation, ix, 190 pp. (2021)
Investigating the Genomic Effects of Glucocorticoid Receptor Activation: An Analysis of Transcriptional Memory and Mechanisms That Direct Divergent Genomic Occupancy of Related Transcription Factors. Dissertation, xxi, 93 pp. (2021)
Using interpretable machine learning to understand gene silencing dynamics during X-chromosome inactivation. Dissertation, vii, 159 pp. (2021)
Identification of X-chromosomal genes that drive global X-dosage effects in mammals. Dissertation (2021)
Genome-wide Determination Of Splicing Efficiency And Dynamics From RNA-Seq Data. Dissertation, ix, 100 pp. (2021)
Explainable deep learning models for biological sequence classification. Dissertation, vii, 119 pp. (2021)
Network Propagation with Node Core for Genotype-Phenotype Associations and Module Identification. Dissertation, xii, 161 pp. (2021)
Computational Approaches for the Prediction of Gene Regulatory Elements and the Analysis of their Evolutionary Conservation. Dissertation, vii, 155 pp. (2021)
Towards accurate and efficient live cell imaging data analysis. Dissertation, xii, 119 pp. (2021)
Structural variant calling using third-generation sequencing data. Dissertation, xiii, 139 pp. (2021)
2020
Efficient multi-scale sampling methods in statistical physics. Dissertation, xiv, 120 pp. (2020)
Statistical models to capture protein-RNA interaction footprints from truncation-based CLIP-seq data. Dissertation, viii, 167 S pp. (2020)
2019
Bioinformatic Reconstruction of Gene Regulatory Networks Controlling EMT and Mesoderm Formation. Dissertation (2019)
De novo and haplotype assembly of polyploid genomes. Dissertation, vii, 157 pp. (2019)
Dissecting the genetic basis of transcriptional and translational regulation in heart and liver. Dissertation, V, 108 pp. (2019)
Enhancer Prediction Based on Epigenomic Data. Dissertation, iv, 186 pp. (2019)
Whole Genome Shotgun Sequencing Based Taxonomic Profiling Methods for Comparative Study of Microbial Communities. Dissertation, viii, 145 pp. (2019)
Approximate String Matching: Improving Data Structures and Algorithms. Dissertation, 175 pp. (2019)
2018
Adaptive Multilevel Monte Carlo Methods for Random Elliptic Problems. Dissertation, viii, 109 pp. (2018)
Efficient Sparse-Group Bayesian Feature Selection for Gene Network Reconstruction. Dissertation, Freie Universität, Berlin (2018)
Analysis of Antigen Receptor Repertoires Captured by High Throughput Sequencing. Dissertation, vii, 164 pp. (2018)
Free Energy Methods Involving Quantum Physics, Path Integrals, and Virtual Screenings: Development, Implementation and Application in Drug Discovery. Dissertation, xxv, 258 pp. (2018)
Using machine learning to predict and better understand DNA methylation and genomic enhancers. Dissertation, viii, 143 pp., Freie Universität, Berlin (2018)
2017
Computational Analysis of Genome-wide Methylation Enrichment Experiments. Dissertation, xii, 125 pp. (2017)
Understanding metabolic regulation and cellular resource allocation through optimization. Dissertation, 248 pp. (2017)
Logical modeling of uncertainty in signaling pathways of cancer systems. Dissertation, v, 153 pp. (2017)
The structure of the social brain: Dissociating socio-affective networks through the study of individual differences, brain plasticity, and disease models. Dissertation, XVII, 193 pp., Humboldt University, Berlin, Germany (2017)
Robust Normalization of Next Generation Sequencing Data. Dissertation, xii, 145 pp. (2017)
Statistical methods for motif hit enrichment in DNA sequences. Dissertation, 216 pp. (2017)
Reconstruction and analysis of the state space for the identification of dynamical states in real-world time series. Dissertation, viii, 99 pp. (2017)
Conceptualization, assessment, and plasticity of attentional, socio-affective, and socio-cognitive capacities. Dissertation, University of Leipzig, Leipzig (2017)
Body awareness, voluntary physiological regulation, and their modulation by contemplative training. Dissertation, Humboldt University Berlin (2017)
On the endogenous generation of emotion. Dissertation, VIII, 314 pp., Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig (2017)
Aspects of Quality Control for Next Generation Sequencing Data in Medical Genetics. Dissertation, vi, 137, XXVII pp pp., Freie Universität, Berlin (2017)
The social behavioral, emotional, and cognitive mechanisms underlying narcissistic personality traits. Dissertation, FU Berlin (2017)
2016
The role of Osr1 in postnatal muscle development and muscle regeneration. Dissertation (2016)
Proteome and metabolome changes associated with mitochondrial diseases. Dissertation (2016)
Funktionelle Charakterisierung von krankheitsassoziierten BMP-Varianten und ihre potentiellenImplikationen für die regenerative Medizin. Dissertation (2016)
Patterns and Algorithms in High-Throughput Sequencing Count Data. Dissertation (2016)
Computational and Statistical Analysis of Sequence and Expression Features of MicroRNA and Long Noncoding RNA in Primate Brains. Dissertation (2016)
Association measures and prior information in the reconstruction of gene networks. Dissertation (2016)
CRISPR/Cas9 a Tool to Recapitulate Unresolved Human Cases in Mouse. Dissertation (2016)
2015
Nicht kodierende RNAs in der Knochenentwicklung. Dissertation, Medizinische Fakultät Charité - Universitätsmedizin Berlin (2015)
Deciphering human cytocplasmic tyrosine kinase phosphorylation specificity in yeast. Dissertation, Freie Universität Berlin (2015)
Bioinformatic approaches for understanding chromatin regulation. Dissertation (2015)
Discriminative Learning for Probabilistic Sequence Analysis. Dissertation (2015)
Prediction of transcription factor co-occurrence using rank based statistics. Dissertation (2015)
Bioinformatic Analysis of microRNA Genes in Free-Living and Parasitic Nematodes. Dissertation (2015)
Assembly and analysis of a comprehensive and unbiased phosphotyrosine-dependent protein-protein interaction network. Dissertation, 407 pp., Humboldt-Universität zu Berlin (2015)
Emotional egocentricity in development and psychopathology. Dissertation, Faculty of Life Sciences, Humboldt University, Berlin, Germany (2015)
Hochdurchsatz-Sequenz-Analyse zur Identifikation von prädisponierenden sowie somatischen Mutationen bei Patienten mit Nicht-kleinzelligem Bronchialkarzinom (NSCLC) zur Vorhersage von Chemotherapie-Resistenzen. Dissertation, 212 pp., Free University, Department of Biology, Chemistry and Pharmacy, Berlin (2015)
Transcriptional characterization and functional analysis of long non-coding RNA/protein-coding gene pairs encoded in the human genome. Dissertation, XX, 143 pp., Freie Universität Berlin (2015)
Diverse regulatory functions of lncRNAs. Dissertation, Freie Universität Berlin (2015)
2014
Statistical analysis of high-throughput sequencing count data. Dissertation (2014)
ChIP-seq Reveals Mutation-Specific Pathomechanismus of HOXD13 Missense Mutations. Dissertation, Humboldt University, FB Mathemathik, Berlin (2014)
Genome-wide analysis of LXR-alpha regulated transcriptional networks in human atherosclerotic foam cell development. Dissertation, Free University Berlin, Berlin (2014)
Investigating the Role of Brachyury (T) in the Control of Chromatin State in Early Mesodermal Cells. Dissertation, Free University Berlin, Faculty of Biology, Chemistry and Pharmacy, Berlin (2014)
Brachydaktylie Typ E und ZNF521. Dissertation, Charité Berlin, Berlin (2014)
Functional Analysis of Autism Genes in Zebrafish: Investigation of the Autism Related 16p11.2 Deletion. Dissertation, XI, 128 pp., Free University Berlin, Department of Biology, Chemistry and Pharmacy, Berlin (2014)
The role of the tumour suppressor Nf1 in growth and metabolism of skeletal muscle cells. Dissertation, TU Berlin, Fakultät III - Prozesswissenschaften, Berlin (2014)