Theses
In progress
Workflow Toward a Consensus Metabolic Network Model of Klebsiella Species
Master thesis
Examinee: Carolin Brune
Mentors: Dr. Reihaneh Mostolizadeh and M.Sc. Nantia Leonidou
Reviewers: Jun.-Prof. Dr. Andreas Dräger and Prof. Dr. Till Strowig
Problem: PDF
Analyzing the metabolic phenotypes of Staphylococcus capitis using contraint-based modeling
Bachelor thesis
Examinee: Anna Lefarova
Mentor: M.Sc. Nantia Leonidou
Reviewer: Jun.-Prof. Dr. Andreas Dräger
Problem: PDF
Harnessing Protein Language Models to improve classic Local Pairwise Alignments for more sensitive and scalable Deep Homology Detection
Master thesis
Examinee: Céline Behr
Mentors: Dr. Hajk-Georg Drost and Benjamin Buchfink
Reviewers: Jun.-Prof. Dr. Andreas Dräger und Prof. Dr. Detlef Weigel
Problem: PDF
Intermediate lecture on May 19, 2023 at 9 am s.t. at the Max Planck Institute and Friedrich Miescher Laboratory in Tübingen (EBIO seminar room on the first floor).
Final lecture on July 21, 2023 at 10 am s.t.
Reconstruction of strain-specific metabolic models of Staphylococcus haemolyticus
Master thesis
Examinee: Gwendolyn O. Gusak
Mentors: Jun.-Prof. Dr. Andreas Dräger and Dr. Bernhard Krismer
Problem: PDF
Interactions of Corynebacterium striatum with its environment
Master thesis
Examinee: Famke Bäeuerle
Mentors: Jun.-Prof. Dr. Andreas Dräger and Dr. Simon Heilbronner
Problem: PDF
Completed theses
2022
Reconstruction of a genome-scale metabolic network of Staphylococcus lugdunensis N920143
Bachelor thesis
Examinee: Selin Sahin
Mentor: Nantia Leonidou, Jun.-Prof. Dr. Andreas Dräger
Problem: PDF
Defense: September 20th, 2022 at 10 a.m. via Zoom.
A genome-scale metabolic model of Klebsiella pneumoniae HS11286
Bachelor thesis
Examinee: Meike Lips
Mentor: Nantia Leonidou
Problem: PDF
Defense: August 22nd 2022, 12 a.m. in lecture hall A104
Genome-scale metabolic modelling of Acinetobacter baumannii ATCC 17978
Bachelor thesis
Examinee: Yufan Xia
Mentors: Nantia Leonidou, Jun.-Prof. Dr. Andreas Dräger
Problem: PDF
Defense: August 22nd 2022, 11:30 a.m. in lecture hall A104
Reconstruction of a metabolic model of Proteus vulgaris
Master thesis
Examinee: Manuel O. Harke
Mentor: Jun.-Prof. Dr. Andreas Dräger
Problem: PDF
Defense: June 14th 2022 at 1 p.m. s.t. in room C109
Investigation of Finegoldia magna ATCC 29328 in the nasal environment
Bachelor thesis
Examinee: Josua Carl
Mentor: Nantia Leonidou
Problem: PDF
Defense:
March 15th, 2022, at 11:15 a.m. in room C09 and hybrid via Zoom.
2021
Reconstruction of a metabolic model of Staphylococcus lugdunensis
Erasmus project
Examinee: Austėja Sungailaitė
Mentor: Jun.-Prof. Dr. Andreas Dräger
Completion: December 14th, 2021
Problem: PDF
Reconstruction of Corynebacterium simulans PES1
Bachelor thesis
Examinee: Jan-Philipp Leusch
Mentor: Dr. Reihaneh Mostolizadeh
Problem: PDF
Defense:
November 16th, 2021, at 11 a.m. c.t. in room A104
Automating the refinement of C. striatum
Research project
Examinee: Famke Bäuerle
Mentor: Jun.-Prof. Dr. Andreas Dräger
Problem: PDF
Defense:
May 18th 2021 at 11:15 a.m. via Zoom
A Bioinformatics Study on Protein Sequence Clustering with DIAMOND
Bachelor thesis
Examinee: Jasmin Katz
Mentor: Dr. Hajk-Georg Drost
Reviewer: Jun.-Prof. Dr. Andreas Dräger
Problem: PDF
Repository: https://github.com/Yeahsmin/diamond
Defense:
March 3rd 2021 at 10:15 a.m. via Zoom
Tissue-specific reconstruction of constraint-based metabolic models based on ReconX
Master thesis
Examinee: Nantia Leonidou
Mentors: Alina Renz and Dr. Reihaneh Mostolizadeh
Problem: PDF
Defense:
January 26th 2021 at 11:15 a.m. via Zoom
2020
Towards a Consensus Genome-scale Reconstruction of Corynebacterium glutamicum ATCC 13032
Master thesis
Examinee: Martina Feierabend
Mentors: Jun.-Prof. Dr. Andreas Dräger, Dr. Katharina Nöh, and Prof. Dr. Wolfgang Wiechert
Problem: PDF
Defense:
October 21st 2020 at 10 a.m. in room C109 and via Zoom
Automating the Assignment of SBO-Terms
Bachelor thesis
Examinee: Elisabeth Fritze
Mentor: Alina Renz
Problem: PDF
Defense:
October 7th 2020 at 12:30 a.m. in C109
Visual analysis of flux sampling simulations based on extracellular metabolomic measurements
Master thesis
Examinee: Constantin Holzapfel
Mentors: Jun.-Prof. Dr. Michael Krone, Prof. Dr. Cora Weigert,
and Jun.-Prof. Dr. Andreas Dräger
Problem: PDF
Defense:
September 15th 2020 at 12:15 a.m. per online conference
Reconstruction and Analysis of Staphylococcus epidermidis
Bachelor thesis
Examinee: Anastasiia Grekova
Mentor: Alina Renz
Problem: PDF
Defense:
June 16th 2020 at 1:30 p.m. per online conference
Reconstruction of Corynebacterium striatum
Lab rotation project
Examinee: Tanja Urz
Mentor: Alina Renz
Problem: PDF
Defense:
June 2nd 2020 at 2:00 p.m. per online conference
Optimized Layouting of Biological Networks for the Comparative Visual Analysis
Bachelor thesis
Examinee: Ebru Cobanoglu
Mentors: Jun.-Prof. Dr. Michael Krone and Jun.-Prof. Dr. Andreas Dräger
Problem: PDF
Defense:
June 2nd 2020 at 1:30 p.m. per online conference
Graphical editor for systems biology models
Research project
Examinee: Marietta Hamberger
Mentor: Jun.-Prof. Dr. Andreas Dräger
Problem: PDF
Defense:
May 5th 2020 at 2 p.m. per online conference
Derivation of gene-protein reaction rules
Bachelor thesis
Examinee: Manuel Dienert
Mentors: Jun.-Prof. Dr. Andreas Dräger
Problem: PDF
Defense:
May 5th 2020 at 1:30 p.m. per online conference
Reconstruction of Dolosigranulum pigrum
Lab rotation project
Examinee: Lina Widerspick
Mentor: Alina Renz
Problem: PDF
Defense:
March 16th 2020 at 11:15 a.m. per online conference
2019
Visual analysis of clinical multi-omics data in biological networks
Bachelor thesis
Examinee: Manuel O. Harke
Mentors: Jun.-Prof. Dr. Michael Krone,
Jun.-Prof. Dr. Andreas Dräger
Problem: PDF
Defense:
November 19th 2019 at 10:15 a.m. in C109
What makes a review helpful or funny?
Research project
Examinee: Mykola Zakharchuk
Mentors: Markus Viggiato, Prof. Dr. Cor-Paul Bezemer, Jun.-Prof. Dr. Andreas Dräger
Modelling and Visualization of specific resistance mechanisms in Pseudomonas aeruginosa
Bachelor thesis
Examinee: Eike Pertuch
Mentor: Alina Renz
Problem: PDF
Defense:
September 24th 2019 at 10:15 a.m. in A104
Reconstruction of Moraxella catarrhalis BBH18
Research project
Examinee: Pia Rautenstrauch
Mentors: Alina Renz, Jun.-Prof. Dr. Andreas Dräger
Problem: PDF
Defense:
September 10th 2019 at 10:45 a.m. in C118a
Expanded genome-scale model of Haemophilus influenzae
Bachelor thesis
Examinee: Niklas Henle
Mentor: Dr. Reihaneh Mostolizadeh
Problem: PDF
Defense:
September 10th 2019 at 10 a.m. c.t. in C118a
Development of a plugin for the Insilico framework for the visual analysis of simulations of biological systems
Bachelor thesis
Development of a graphical editor for creating systems biology models with SBML
Bachelor thesis
2018
Modeling of potentially virulence-associated metabolic pathways in Pseudomonas aeruginosa PA14 and experimental verification
Master thesis
Genome-scale metabolic network reconstruction of the pathogen Treponema pallidum ssp. pallidum
Master thesis
Development of an interactive graphical editor for systems biology models
Bachelor thesis
Representation of ME-models in SBML
Master thesis
2017
Dynamic visualization of metabolic networks
Bachelor thesis
Examinee: Lea F. Buchweitz
Defense:
September 28th 2017 at 2 p.m. c.t. in A104
Visualization of time-series data with Escher
Bachelor thesis
2012
Extension of the SBMLsimulator by a module for flux balance analysis
Bachelor thesis
Examinee: Maike Aichele
Problem: PDF
Visual simulation of biochemical networks
Bachelor thesis
Examinee: Fabian Schwarzkopf
Problem: PDF
Automatic biomodel documentation
Bachelor thesis
Examinee: Mirjam Gutekunst
Problem: PDF
2011
Implementation of a flux balance analysis method in Java
Bachelor thesis
Examinee: Simon Schäfer
Problem: PDF
Computational Modeling of Biochemical Networks
Dissertation
Examinee: Andreas Dräger
Defense:
January 14th 2011 at 2:15 p.m. in A301
Awarding of the doctorate:
March 31st 2011
Available as a book from publisher Dr. Hut.
2009
Dynamics of reconstructed gene regulation networks
Bachelor thesis
Examinee: Sandra Nitschmann
Problem: PDF
Implementation of a stability analysis for biochemical networks
Bachelor thesis
Examinee: Alexander Dörr
Problem: PDF
Automated mathematical modeling of biochemical networks
Diploma thesis
Examinee: Michael Ziller
Problem: PDF
2008
Comparative analysis of the models on Biomodels.net
Diploma thesis
Examinee: Dieudonné M. Wouamba
Problem: PDF
Simulation of gene regulatory networks with JCell2
Diploma thesis
Examinee: Hannes Borch
Problem: PDF
Integration, visualization, and analysis of SNP data
Diploma thesis
Examinee: Gabrielle Doan
Problem: PDF
Comparison of JavaEvA and BioJava with respect to metabolic networks
Study project
Examinee: Susanne Merz
2007
Metabolic control analysis
Study project
Examinee: Michael Ziller
Automatic generation of kinetic equations from stoichiometries
Diploma theis
Examinee: Nadine Hassis
Problem: PDF
2005
Automatic and comparative analysis of bacterial genomes with focus on Ralstonia/Cupriavidus species and related proteobacteria
Diploma thesis
Examinee: Andreas Dräger
Defense: December 2005