PhD theses


Ulrike Münzner From birth to birth. A cell cycle control network of S. cerevisiae
Max Schelker Predictive computational modeling for improved treatment strategies
Sebastian, Thieme Bridging network reconstruction and mathematical modelling - rxncon a framework to reconstruct, visualise and model signal-transduction networks
Katja Tummler Exploring flexibility and context dependency in the mycobacterial central carbon metabolism
Wolfgang Giese The choreography of yeast mating : modelling intercellular communication, cell polarity and morphogenesis
Timo Lubitz From Signal to metabolism: a journay through the regulatory layers of the cell
Friedemann Uschner Information processing in cellular signaling
Till Philipp Scharp Systems biology apporaches to somatic cell reprogramming reveal new insights into the order of events, transcriptional and epigenetic control of the process
Max Flöttmann Functional analysis of high-throughput data for dynamic modeling in eukaryotic systems
József Bruck On the regulation of central carbon metabolism in S. cerevisiae
Christian Diener Localized signaling and communication in budding yeast
Martina Fröhlich Computational and experimental investigation of the mechanisms involved in cellular water transport and (cat)ion homeostasis
Margit Heiske Modeling the respiratory chain and the oxidative phosphorylation
Marvin Schulz Systems biology methods in the identification of potential drug targets
Thomas Spiesser Exploring mechanisms of size control and genomic duplication in Saccharomyces cerevisiae – a computational systems biology study
Katarzyna Tyc A modeling perspective on Candida albicans interactions with ist human host
Judith Wodke Organization and integration of large-scale datasets for designing a metabolic model and re-annotating the genome of Mycoplasma pneumoniae
Susanne Gerber In silico modeling of cation homeostasis in Saccharomyces cerevisiae
Clemens Kühn Modeling and analysis of yeast osmoadaptation in cellular context
Marija Cvijovic Mathematical model of accumulation of damaged proteins and its impact on ageing
Hendrik Hache Computational analysis of gene regulatory networks
Jana Schütze Synchronisation und räumliche Ausbreitung von glykolytischen Oszillationen
Simon Borger Parametrising kinetic models of biological networks
Thomas Handorf The synthesizing capacity of metabolic networks
Jürgen Pahle Stochastic simulation and analysis of biochemical networks
Zhike Zi Mathematical modeling and kinetic analysis of cellular signaling pathways
Wolfram Liebermeister     Analysis of optimal differential gene expression


Master theses

Wiebke Schmidt Visualization of spindle assembly checkpoint activation in budding yeast using YFP-tagged Mad2
Laura Stumpf Mathematical modeling of TNF-a-induced signaling pathway
Jorin Diemer Decryption of the journey of sperm: a three dimensional agent based model
Stefan Forgó Räumliche Modellierung der Zellwandmechanik und Signalübertragung am Beispiel der Feromonantwort von Saccharomyces cerevisiae
Marie Hemmen
A quantitative description of the mating morphology of Saccharomyces cerevisiae
Vera Schützhold Mathematical modeling of the lipid metabolism in yeast
Rubén Vázquez Uribe Modeling of the TOR pathway in the stress response of Saccharomyces cerevisiae
Ali Saitov Biomass Backtracking - Testing and validation
Jens Hahn Implementation of a simulation environment for the successive integration of mathematical models for cellular processes exemplified for central carbon metabolism in yeast
Arturo Blázquez Navarro Drug target identification for potential diseases using mathematical models
Matthias Bock Mitophagy in yeast, an autophagic process of intracellular organelle quality control
Gady Goldsobel Computational modelling and analysis of the baker’s yeast multi-branch HOG pathway
Adriana Supady Mathematical modeling of synthetic logic gates in S. cerevisiae
Ábel Vértesy Mapping and modeling genetic and morphological pheromone response infission yeast
Timo Lubitz Parameter balancing in kinetic models
Jian Li Creation of an online phenological database of the 20th century in Germany for analysis and prediction of global change issues
Wai-Cheung Ng Mathematical modeling of the regulation of osmotic pressure in Saccharomyces cerevisiae
Jannis Uhlendorf Prediction of optimal enzymatic regulation architectures
Max Flöttmann Automated model generation for osmoregulation in Saccharomyces cerevisiae with ModelMaGe
Falko Krause semanticSBML a tool for creating, checking, annotating and merging of SBML documents
Thomas Spiesser Modeling DNA replication in Saccharomyces cerevisiae
Clemens Kühn Mathematical modeling of a sea urchin rene regulatory network
Judith Wodke Qualitative modelling of the human cell cycle
Sebastian Schmeier     Automated recognition and extraction of entities related to enzyme kinetics from text


Diploma theses

Gregor Milicic Zeitschrittverfahren für gekoppelte Reaktions-Diffusionsgleichungen mit Anwendungen in der Biophysik
André Dautcourt Modelling ROS production by respiratory chain complex I
Katja Tummler Dynamic modeling of the central carbon metabolism of Mycobacterium tuberculosis
Wolfgang Giese Numerische Behandlung einer linearen Reaktions-Diffusions-Gleichung mit einer Anwendung in der interzellulären Kommunikation bei Hefezellen
October 2011 - For his diploma thesis Wolfgang Giese was awarded the "Humboldt-Preis"
Till Scharp Mathematical modeling of stem cell reprogramming
Nadine Töpfer Optimisation of enzym profiles in metabolic pathways
Ludwig Weh Analysis of elementary networks and topological motifs in the cell cycle
Margit Heiske Modelling of the respiratory chainMoritz KrogA systems biology approach to mathematical modelling of the Snf1 glucose sensing pathway in Saccharomyces cerevisiae
Moritz Krog A systems biology approach to mathematical modelling of the Snf1 glucose sensing pathway in Saccharomyces cerevisiae
Anselm Helbig Modelling the Tor pathway in Saccharomyces cerevisiae
Bente Kofahl Mathematische Modellierung von Signaltransduktionswegen in Hefe Saccharomyces cerevisiae
Heike Aßmus An approach to network-based selectivity of anti-parasitic inhibitorsRoland KrügerModellierung der Signaltransduktion infolge von hyperosmotischem Stress in Hefezellen
Roland Krüger Modellierung der Signaltransduktion infolge von hyperosmotischem Stress in Hefezellen

Bachelor theses

Mathias Wajnberg Petri Net Modelling of Regulatory Network Data Using the rxncon Framework
Robin Helling Translation of CellDesigner SBML to the rxncon language: turning large network maps into executable models
Maxim Karnetzki Biofilms: modeling approach for growth and spatial-separation
Felix Fauer Territorial Pattern Formation of Wild Pike - Modellierungsansatz zur Entstehung von Territorien bei wilden Hechten
Jorin Diemer Competition between viral and human protein synthesis during Influenza A virus infection
Adrian Zachariae A mathematical model linking oscillatory gene expression in Mycobacterium tuberculosis with DNA supercoiling
Maria Dost A model of the Ras/Raf/Mek/Erk pathway in Rxncon
Mareike Simon Dynamic modeling of the central carbon metabolism of HEK293 cells using Parameter Balancing
Phillipp Schmidt SBLink - A web based tool for accessing scientific spreadsheet data
Stephan Adler Single Cell and Population Modeling of the G1 network to explore growth, division and structural aspects in diverse budding yeast cultures
Lydia Farack ON/OFF: Insights into epigenetic regulation of gene silencing during human cell differentiation
Jens Hahn Arsenate replacing phosphate in yeast glycolysis
Helena Steinocher Mathematische Modellierung der Replikationsinitiation in Mycobacterium TuberculosisMartin WeilandModellierung und Simulation der mitogen-aktivierten Protein-Kinasen-Kaskade zur Untersuchung des Feedbacks der Phosphatase der 3. Stufe auf die aktivierte Kinase der 1. Stufe der Kaskade
Martin Weiland Modellierung und Simulation der mitogen-aktivierten Protein-Kinasen-Kaskade zur Untersuchung des des Feedbacks der Phosphatase der 3. Stufe auf die aktivierte Kinase der 1. Stufe der Kaskade
Claudia Beck Stochasic modelling of the G1/S transition in the S. cerevisiae cell cycleFelix NoeskeModellierung der Ausbildung des OXPHOS SuperkomplexesSebastian UllrichModellierung des mitochondrialen Superoxidabbaus in Podospera anserinaChang YanAuswirkung von Konzentrationsänderungen bindender Proteine auf die Komplexbildung
Felix Noeske Modellierung der Ausbildung des OXPHOS Superkomplexes
Sebastian Ullrich Modellierung des mitochondrialen Superoxidabbaus in Podospera anserina
Chang Yan Auswirkung von Konzentrationsänderungen bindender Proteine auf die Komplexbildung
Anna Kosenko Combination of mathematical models of signaling pathways
Adriana Supady Theoretical and computational analysis of negative feedback mechanisms and the dose-response alignment in the pheromone signalling pathway of the yeast Saccharomyces cerevisiae
Kai Kruse Vergleich der Synthesekapazitätsanalyse von Fluss-Balance-Analyse und Network Expansion
Christian Diener Spatiotemporal simulations for the pheromone signaling pathway in MATa cells of Saccharomyces cerevisiae
Marvin Schulz Dimension reduction of biochemical network models: implementation and comparison of different algorithms
Jannis Uhlendorf Development of a mathematical model for the occupancy of mRNA with ribosomes in Saccharomyces cerevisiae
Christof Daniel Robert Dehme Exakte stochastische Simulation der Genexpression bei hyperosmotischen Schockzuständen in Saccharomyces cerevisiaeStephan MenzVergleich einer deterministischen und stochastischen Modellierung des Hog Signalweges von S. cerevisiae zur Simulation eines hyperosmotischen Schocks
Stephan Menz Vergleich einer deterministischen und stochastischen Modellierung des Hog Signalweges von S. cerevisiae zur Simulation eines hyperosmotischen Schocks
Susanne Gerber Theoretische Untersuchung zur Wirkung von Inhibitoren in Abhängigkeit von ihrem Angriffsort im metabolischen Netzwerk und ihrem Typ
Sebastian Schmeier    Klassifizierung von biochemischen Texten mittels statistischer Lernverfahren