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

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 RenzJun.-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

Examinee: Mykola Zakharchuk

Problem: PDF

Defense:
June 17th 2019 at 2 p.m. c.t. in C118a

Development of a graphical editor for creating systems biology models with SBML

Bachelor thesis

Examinee: Robert Deibel

Problem: PDF

Defense:
March 1st 2019 at 4 p.m. c.t. in C215

2018

Modeling of potentially virulence-associated metabolic pathways in Pseudomonas aeruginosa PA14 and experimental verification

Master thesis

Examinee: Alina Renz

Problem: PDF

Defense:
December 19th 2018 at 10 a.m. c.t. in C215

Genome-scale metabolic network reconstruction of the pathogen Treponema pallidum ssp. pallidum

Master thesis

Examinee: Silvia Morini

Problem: PDF

Defense:
October 30th 2018 at 11 a.m. s.t. in A302

Development of an interactive graphical editor for systems biology models

Bachelor thesis

Examinee: Roman Schulte

Problem: PDF

Defense:
August 23rd 2018 at 2 p.m. c.t. in A104

Representation of ME-models in SBML

Master thesis

Examinee: Marc Alexander Voigt

Problem: PDF

Defense:
June 26th 2018 at 12 a.m. c.t. in C118a

Validation and Simulation of Qualitative Models

Bachelor thesis

Examinee: Lisa Falk

Problem: PDF

Defense:
May 17th 2018 at 2 p.m. c.t. in C215

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

Examinee: Christoph Blessing

Problem: PDF

Defense:
September 28th 2017 at 2:45 p.m. in A104


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