IMPRS Alumni

March 27, 2024

Alumni from the IMPRS for Computational Biology and Scientific Computing and from the IMPRS for Biology and Computation


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
Roman Schulte-Sasse Integration of multi-omics data with graph convolutional networks to identify cancer-associated genes Dec 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
Vı́ctor Mireles Chávez Finding Reusable Modules Using Sparse Matrix Decompositions July 2021
Martyna Gajos Analysis of the determinants of Pol II pausing Feb 2022
Elzbieta Gralinska Association Plots visualize cluster-specific genes from high-dimensional transcriptomics data April 2022
Eldar Abdullaev Dynamical Aspects of the Evolution of Segmental Duplications in the Human Genome April 2022
Lam-Ha Ly Deciphering cellular heterogeneity by single-cell transcriptome analysis April 2022
Philip Kleinert Computational interpretation of disease-causing, structural, and non-coding human genetic variants June 2022
Annkatrin Bressin A Multi-Omics Analysis of Transcription Control by BRD4 May 2022
Shroddha Bose The effect of a gain-of-function mutation in the Cl-/H+ exchanger ClC-7 in lysosomal and mitochondrial morphology and function June 2022
Shaon Basu Genetic and chemical hydrophobic modification of transcription factor condensates in human disease September 2022
Jörg Winkler Algorithms for finding RNA sequence-structure motifs September 2022
Laura Cifuentes Fontanals Methods for control strategy identification in Boolean networks October 2022
Natalia López Anguita Impact of hypoxia on embryonic and extraembryonic stem cells and during differentiation via gastruloid formation November 2022
Amèlia Aragonés Hernández Identification of Protogenin as a novel surface marker for early cortical neural stem cells December 2022
Daniel Rosebrock

Dissecting regional heterogeneity and modeling transcriptional cascades in brain organoids

December 2022
Bruna Los Body temperature-controlled antiviral response and SARS-CoV-2 replication April 2023
Sara Hetzel Investigation of DNA methylation heterogeneity in cancer June 2023
Melania Nowicka Design and multi-criteria optimization of cell classifier circuits in cancer therapy June 2023
Vahid Asimi Roles of endogenous retroviruses in transcriptional condensates June 2023

Paul-Lennard Mendez

Mechano-sensitivity of vascular BMP signaling - Insights into Fluid Shear Stress modulations from ligand to chromatin July 2023
Mitra Darja Darvish Utilizing alignment-free methods to enable quantitative gene expression analysis of large collections of sequencing data August 2023
Gözde Kibar Exploring feature identification and machine learning in predicting protein-protein interactions of disordered proteins October 2023
Jana Henck Single cell sequencing as a phenotyping strategy to decipher the molecular mechanisms of developmental disorder October 2023
Dhanur Iyer The molecular landscape of developmental pausing in mammals November 2023
Guido Pacini Transcriptome regulation during the X chromosome inactivation process December 2023
Claire Jourdain Role of the putative cohesin cofactors PDS5A and PDS5C in nuclear organization and gene regulation February 2024
Anna Kristina Thedinga Machine Learning for Cancer Survival Prediction March 2024
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