IMPRS Alumni*ae

December 13, 2024

Alumni*ae from the IMPRS for Computational Biology and Scientific Computing (CBSC) and from the IMPRS for Biology and Computation (BAC)

 

Name Affiliation Thesis Submission date
1 Wasinee Rungsarityotin CBSC Algorithms to Identify Protein Complexes from High-Throughput Data Jun 2007
2 Philipp Messer CBSC Tandem Duplications in the Human Genome Feb 2008
3 Zhike Zi CBSC Mathematical Modeling and Kinetic Analysis of Cellular Signaling Pathways Apr 2008
4 Markus Bauer CBSC A Combinatorial Approach to RNA Sequence-Structure Alignments Apr 2008
5 Utz J. Pape CBSC Statistics for Transcription Factor Binding Sites Jul 2008
6 Ole Schulz-Trieglaff CBSC Computational Methods for Quantitative Peptide Mass Spectrometry Oct 2008
7 Evelyn Dittmer CBSC Hidden Markov Models with Time-Continuous Output Behavior Nov 2008
8 Andrea Weiße CBSC Global Sensitivity Analysis of Ordinary Differential Equations Apr 2009
9 Tobias Rausch CBSC Dissecting Multiple Sequence Alignment Methods Sep 2009
10 Federico Squartini CBSC Stationarity and Reversibility in the Nucleotide Evolutionary Process Mar 2010
11 Ben-Fillippo Krippendorff CBSC Integrating Cell-level Kinetic Modeling into the Optimization of Cancer Therapeutics Apr 2010
12 Paz Polak CBSC Discovering Mutational Patterns in Mammals Using Comparative Genomics Jun 2010
13 Marcel Schulz CBSC Data Structures and Algorithms for Analysis of Alternative Splicing with RNA-seq Data Jul 2010
14 Ewa Szczurek CBSC Modelling Signal Transduction Pathways and Their Transcriptional Response Oct 2010
15 Sayed-Amir Marashi CBSC Constraint-based Analysis of Substructures of Metabolic Networks Apr 2011
16 Atanas Kamburov CBSC More Accurate Interactomes for Elucidating the Mechanisms of Complex Diseases Aug 2011
17 Henning Stehr CBSC Graph-based Approaches to Protein Structure- and Function Prediction May 2011
18 Akdes Serin CBSC Biclustering Analysis for Large Scale Data Sep 2011
19 Rosa Karlić CBSC Influence of Histone Modifications on mRNA Abundance and Structure Sep 2011
20 Martin Held CBSC Novel Concepts to Study Conformation and Association Dynamics of Biomolecules Jan 2012
21 Jonathan Göke CBSC Analysis of Long-Distance Gene Regulatory Elements May 2012
22 Martina Fröhlich CBSC Computational and Experimental Investigation of the Mechanisms Involved in Cellular Water Transport and (Cat)ion Homeostasis May 2012
23 Chris Bielow CBSC Quantication and Simulation of Liquid Chromatography-Mass Spectrometry Data Jun 2012
24 Yves Clément CBSC The Evolution of Base Composition in Mammalian Genomes Aug 2012
25 Christian Diener CBSC Localized Signaling and Communication during Yeast Mating Sep 2012
26 Marvin Schulz CBSC Identification of Potential Drug Targets in Kinetic Networks Described by Ordinary Differential Equations Sep 2012
27 Anne-Katrin Emde CBSC Next-Generation Sequencing Algorithms: From Read Mapping to Variant Detection Nov 2012
28 Michael Love CBSC Statistical Analysis of High-Throughput Sequencing Count Data Jun 2013
29 Stephan Aiche CBSC Inferring Proteolytic Processes from Mass Spectrometry Time Series Data May 2013
30 Birte Kehr CBSC Contributions to Computing and Modeling Multiple Whole-Genome Alignments Nov 2013
31 Arne Reimers CBSC Metabolic Networks, Thermodynamic Constraints, and Matroid Theory Jun 2014
32 Johannes Schöneberg CBSC Reaction-Diffusion Dynamics in Biological Systems Jul 2014
33 Sharon Hüffner CBSC Modularity in Biological Networks Apr 2014
34 Sandro Andreotti CBSC Linear Programming and Integer Linear Programming in Bioinformatics Sep 2014
35 Alena van Bömmel CBSC Prediction of transcription factor co-occurrence using rank based statistics Jul 2014
36 Enrico Siragusa CBSC Approximate string matching for high-throughput sequencing May 2015
37 Juliane Perner CBSC Bioinformatic Approaches for Understanding Chromatin Regulation Jun 2015
38 Han Cheng Lie CBSC On a strongly convex approximation of a stochastic optimal control problem for importance sampling of metastable diffusions Sep 2015
39 Alessandro Mammana CBSC Patterns and algorithms in high-throughput sequencing count data Sep 2015
40 Xintian You CBSC Tailored Analysis in Studying Transcriptome Landscape Sep 2015
41 Iliusi Vega del Valle CBSC Reconstruction and analysis of the state space for the identification of dynamical states in real-world time series Jan 2016
42 Wolfgang Kopp CBSC Statistical methods for motif hit enrichment in DNA sequences Oct 2016
43 Johannes Helmuth CBSC Robust normalization of next generation sequencing data Feb 2017
44 Kirsten Thobe CBSC Logical modeling of uncertainty in signaling pathways of cancer systems Mar 2017
45 Matthias Lienhard CBSC Computational analysis of genome-wide methylation enrichment experiments Mar 2017
46 Alexandra Reimers CBSC Understanding metabolic regulation and cellular resource allocation through optimization Aug 2017
47 Matthew Huska CBSC Using machine learning to predict and better understand DNA methylation and genomic enhancers Aug 2017
48 Sven-Leon Kuchenbecker CBSC Analysis of Antigen Receptor Repertoires Captured by High Throughput Sequencing Jan 2018
49 Christoph Gorgulla CBSC Free Energy Methods Involving Quantum Physics, Path Integrals, and Virtual Screenings: Development, Implementation and Application in Drug Discovery Apr 2018
50 Evgenia Youett CBSC Adaptive Multilevel Monte Carlo Methods for Random Elliptic Problems Jun 2018
51 Mohammadhossein Moeinzadeh CBSC De novo and haplotype assembly of polyploid genomes Aug 2018
52 Christopher M. Pockrandt CBSC Approximate String Matching - Improving Data Structures and Algorithms Feb 2019
53 Temesgen Hailemariam Dadi CBSC Whole Genome Shotgun Sequencing Based Taxonomic Profiling Methods for Comparative Study of Microbial Communities Jan 2019
54 Anna Ramisch CBSC Enhancer Prediction Based on Epigenomic Data Feb 2019
55 Sabrina Krakau CBSC Statistical models to capture protein-RNA interaction footprints from truncation-based CLIP-seq data Jan 2019
56 Luigi Sbailò CBSC Efficient multi-scale sampling methods in statistical physics Sep 2019
57 Hongqing Han CBSC Towards accurate and efficient live cell imaging data analysis Dec 2019
58 Stefan Budach CBSC Explainable Deep Learning Models for Biological Sequence Classification Dec 2019
59 Lisa Barros de Andrade e Sousa CBSC Using interpretable machine learning to understand gene silencing dynamics during X-chromosome inactivation Jan 2020
60 Tobias Zehnder CBSC Computational approaches for the prediction of gene regulatory elements and the analysis of their evolutionary conservation Sep 2020
61 David Heller CBSC Structural variant calling using third-generation sequencing data Sep 2020
62 Gal Barel CBSC Network propagation with node core for genotype-phenotype associations and module identification Sep 2020
63 Roman Schulte-Sasse CBSC Integration of multi-omics data with graph convolutional networks to identify cancer-associated genes Dec 2020
64 Melissa Bothe CBSC 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
65 Vı́ctor Mireles Chávez CBSC Finding Reusable Modules Using Sparse Matrix Decompositions July 2021
66 Martyna Gajos CBSC Analysis of the determinants of Pol II pausing Feb 2022
67 Elzbieta Gralinska CBSC Association Plots visualize cluster-specific genes from high-dimensional transcriptomics data April 2022
68 Eldar Abdullaev CBSC Dynamical Aspects of the Evolution of Segmental Duplications in the Human Genome April 2022
69 Lam-Ha Ly CBSC Deciphering cellular heterogeneity by single-cell transcriptome analysis April 2022
70 Philip Kleinert CBSC Computational interpretation of disease-causing, structural, and non-coding human genetic variants June 2022
71 Annkatrin Bressin CBSC A Multi-Omics Analysis of Transcription Control by BRD4 May 2022
72 Shroddha Bose BAC The effect of a gain-of-function mutation in the Cl-/H+ exchanger ClC-7 in lysosomal and mitochondrial morphology and function June 2022
73 Shaon Basu BAC Genetic and chemical hydrophobic modification of transcription factor condensates in human disease September 2022
74 Jörg Winkler CBSC Algorithms for finding RNA sequence-structure motifs September 2022
75 Laura Cifuentes Fontanals CBSC Methods for control strategy identification in Boolean networks October 2022
76 Natalia López Anguita BAC Impact of hypoxia on embryonic and extraembryonic stem cells and during differentiation via gastruloid formation November 2022
77 Amèlia Aragonés Hernández BAC Identification of Protogenin as a novel surface marker for early cortical neural stem cells December 2022
78 Daniel Rosebrock CBSC

Dissecting regional heterogeneity and modeling transcriptional cascades in brain organoids

December 2022
79 Bruna Los BAC Body temperature-controlled antiviral response and SARS-CoV-2 replication April 2023
80 Sara Hetzel CBSC Investigation of DNA methylation heterogeneity in cancer June 2023
81 Melania Nowicka CBSC Design and multi-criteria optimization of cell classifier circuits in cancer therapy June 2023
82 Vahid Asimi BAC Roles of endogenous retroviruses in transcriptional condensates June 2023
83

Paul-Lennard Mendez

BAC Mechano-sensitivity of vascular BMP signaling - Insights into Fluid Shear Stress modulations from ligand to chromatin July 2023
84 Mitra Darja Darvish BAC Utilizing alignment-free methods to enable quantitative gene expression analysis of large collections of sequencing data August 2023
85 Gözde Kibar CBSC Exploring feature identification and machine learning in predicting protein-protein interactions of disordered proteins October 2023
86 Jana Henck BAC Single cell sequencing as a phenotyping strategy to decipher the molecular mechanisms of developmental disorder October 2023
87 Dhanur Iyer BAC The molecular landscape of developmental pausing in mammals November 2023
88 Guido Pacini CBSC Transcriptome regulation during the X chromosome inactivation process December 2023
89 Claire Jourdain BAC Role of the putative cohesin cofactors PDS5A and PDS5C in nuclear organization and gene regulation February 2024
 
90 Anna Kristina Thedinga BAC Machine Learning for Cancer Survival Prediction March 2024
91 Gaojianyong Wang BAC Copy number variation characterization using nanopore sequencing May 2024
92 Nadezhda Malysheva CBSC Hybrid algorithm for efficient  simulation of spreading processes on adaptive networks June 2024
93 Julian Naderi BAC The dispersion of aromatic residues in TF IDRs controls a molecular trade-off between activity and specificity June 2024
94 Gopika Sasikumar BAC Allosteric small-molecule probes to study splicing switches via conformational control of a spliceosomal RNA helicase July 2024
95 Jeong-Eun Lee BAC ZEB2 and its regulatory impact on human brain evolution December 2024
96 Fatemeh Zebardast BAC Exploring Alzheimer's Disease Pathology Using Gene Co-Expression Networks: Insights into lncRNA and Protein-coding Genes Dysregulation January 2025
97 Philine Guckelberger BAC January 2025
98 Biswajit Ghosh BAC

Unveiling the Epigenetic Role of Arabidopsis  PWO1: Linking Linear Chromatin Features to 3D Genome Architecture

January 2025
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