Theses
In progress
Unraveling metabolic insights of Staphylococcus warneri using systems biology
Bachelor thesis
Examinee: Sophia Krappen
Mentor: M.Sc. Nantia Leonidou
Reviewers: Jun.-Prof. Dr. Andreas Dräger
Problem: PDF
Intermediate lecture on December 14th, 1:15 p.m., 2023 in A104
Final lecture in March 2024
Reconstruction of a metabolic model of Streptococcus sanguinis
Master thesis
Examinee: Tobias Fehrenbach
Mentor: M.Sc. Gwendolyn O. Gusak
Reviewers: Jun.-Prof. Dr. Andreas Dräger and Prof. Dr. Lisa Maier
Problem: PDF
Intermediate lecture on December 14th, 2023 by 2 p.m. in A104
Final lecture in April 2024
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.
Completed theses
2023
Workflow Toward a Consensus Metabolic Network Model of Klebsiella Species
Master thesis
Examinee: Carolin Brune
Mentors: M.Sc. Nantia Leonidou and Dr. Reihaneh Mostolizadeh
Reviewers: Jun.-Prof. Dr. Andreas Dräger and Prof. Dr. Till Strowig
Problem: PDF
Defense: July 26, 2023 at 9 a.m. in A104 and hybrid via Zoom.
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
Defense: May 23rd, 2023 at 1 p.m. via Zoom
Interactions of Corynebacterium striatum with its environment
Master thesis
Examinee: Famke Bäeuerle
Mentors: Jun.-Prof. Dr. Andreas Dräger and Dr. Simon Heilbronner
Reviewers: Prof. Dr. Kay Nieselt and Jun.-Prof. Dr. Andreas Dräger
Problem: PDF
Defense: May 17th, 4 p.m., C109
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
Defense: May 16th, 2023, 11:15 a.m. in C109
2022
Reconstruction of a genome-scale metabolic network of Staphylococcus lugdunensis N920143
Bachelor thesis
Examinee: Selin Sahin
Mentor: M.Sc. Nantia Leonidou
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: M.Sc. 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: M.Sc. Nantia Leonidou
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: M.Sc. 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