Theses | University of Tübingen

Workflow for Predictive Dynamic Modelling in Systems Biology: A Case Study in the Pharmaceutical Industry

Bachelor thesis

Examinee: Catalina Schlotterer
Mentor: Dr. Franz Baumdicker

Reviewer: Prof. Dr. Andreas Dräger

Final lecture on December 2^nd, 2024, 11 a.m. in A104

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 14^th, 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 14^th, 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.

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 23^rd, 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 17^th, 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 16^th, 2023, 11:15 a.m. in C109

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 20^th, 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 22^nd 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 22^nd 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 14^th 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 15^th, 2022, at 11:15 a.m. in room C09 and hybrid via Zoom.

Reconstruction of a metabolic model of Staphylococcus lugdunensis

Erasmus project

Examinee: Austėja Sungailaitė

Mentor: Jun.-Prof. Dr. Andreas Dräger

Completion: December 14^th, 2021

Problem: PDF

Reconstruction of Corynebacterium simulans PES1

Bachelor thesis

Examinee: Jan-Philipp Leusch

Mentor: Dr. Reihaneh Mostolizadeh
Problem: PDF

Defense:
November 16^th, 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 18^th 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 3^rd 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 26^th 2021 at 11:15 a.m. via Zoom

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 21^st 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 7^th 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 15^th 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 16^th 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 2^nd 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 2^nd 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 5^th 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 5^th 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 16^th 2020 at 11:15 a.m. per online conference

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 19^th 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 24^th2019 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 10^th 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 10^th 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 17^th 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 1^st 2019 at 4 p.m. c.t. in C215

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

Master thesis

Examinee: Alina Renz

Problem: PDF

Defense:
December 19^th 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 30^th 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 23^rd 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 26^th 2018 at 12 a.m. c.t. in C118a

Validation and Simulation of Qualitative Models

Bachelor thesis

Examinee: Lisa Falk

Problem: PDF

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

Dynamic visualization of metabolic networks

Bachelor thesis

Examinee: Lea F. Buchweitz

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

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

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 14^th 2011 at 2:15 p.m. in A301

Awarding of the doctorate:
March 31^st 2011

Available as a book from publisher Dr. Hut.

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

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

Metabolic control analysis

Study project

Examinee: Michael Ziller

Automatic generation of kinetic equations from stoichiometries

Diploma theis

Examinee: Nadine Hassis

Problem: PDF

Automatic and comparative analysis of bacterial genomes with focus on Ralstonia/Cupriavidus species and related proteobacteria

Diploma thesis

Examinee: Andreas Dräger

Defense: December 2005