Theses completed


2017 Ruzianisra Mohamed Protein interactions and regulations of STIM and ORAI genes
2016 Ruslan Akulenko PhD Thesis: Data mining techniques for improving and enriching cancer epigenetics
2015 Ahmad Barghash PhD Thesis: Identifying biological associations from high-throughput datasets
2015 Christian Spaniol PhD Thesis: Integrated analysis and application pipelines for complex disease data
2015 Mohamed Hamed
Ali Fahmy
PhD Thesis: “Integrative computational approaches for studying stem cell differentiation and complex diseases
2015 Özlem Ulucan PhD Thesis: Molecular Modeling of biomolecular associations and quantifying allosteric effects
2015 Siba Shanak PhD Thesis: Dynamics of epigenetic reader proteins and their interplay with expression in development
2014 Po-Hsien Lee PhD Thesis: Computational approaches to Investigate structural and functional properties of transmembrane proteins
2013 Nadine Schaadt PhD Thesis: Computational Systems Biology Methods for Functional Classification of Membrane Proteins and Modeling of Quorum Sensing in Pseudomonas aeruginosa
2012 Mazen Ahmad PhD Thesis: Mechanisms of Protein-Protein Association
2012 Peter Walter PhD Thesis: Storing and Analysing Biomolecular Contacts
2010 Siti Azma Jusoh PhD Thesis: Molecular Modeling of the Transmembrane Domain of Envelope Glycoproteins from Flaviviridae Viruses
2010 Sikander Hayat PhD Thesis: Sequence Based Methods for the Prediction and Analysis of the Structural Topology of Transmembrane Beta Barrel Proteins
2009 Barbara Hutter PhD Thesis: Bioinformatics Analyses of Genomic Imprinting
2009 Susanne Eyrisch PhD Thesis: Computational Design and Analysis of Binding Pockets at Protein-Protein Interaction Interfaces
2008 Wei Gu PhD Thesis: Computer Simulation of Biomolecular Solvation, Recognition and Proton Transfer Equilibria
2007 Yungki Park PhD Thesis: Development of Computational Methods for Predicting Structural Characteristics of Helical Membrane Proteins
2007 Sam Ansari PhD Thesis: Computational Analysis of Protein-Protein Interactions
2006 Tomaso Frigato PhD Thesis: Computational Study of Charged Species Solvation: Proton Transfer in Aqueous Systems and Microhydration of Neural and Anionic Thymine


Master / Diploma

2017 Hema Sekhar Reddy Rajula Master Thesis: Identification of differentially expressed genes from RNA-seq data and topology analysis of disease-specific network via understanding the interplay of epigenetic marks from protein complexes
2016 Christoph Kreutzer Master Thesis: Understanding the interplay of epigenetic marks from protein complexes
2016 Sepideh Sadegh Master Thesis: Motif finding in miRNA & TF synergistic regulatory networks
2016 Jacob Ambat Master Thesis: Properties of pore lining residues of transporter families in different Staphylococcus aureus strains
2016 Anshika Chowdhary Master Thesis: Prediction of resistance mutations in beta-Lactamase TEM-1
2016 Zhao Yuan Master Thesis: Benchmark of pocket detection tools
2016 Anshika Chowdhary Master Thesis: Prediction of Resistance mutations in beta-lactamase tem-1
2016 Alexander Zapp Master Thesis: Integrated analysis of somatic mutations, genetic and epigenetic data in the context of complex diseases
2015 Taner Arslan Master Thesis: Detecting outliers at the sample and gene levels in TCGA and GEO databases
2015 Daria Gaidar Master Thesis: Mining redescriptions in S. aureus data
2014 Markus Merl Master Thesis: Batch effect correction of DNA methylation data
2014 Muhammad Ali Master Thesis: Characterizing the nature of protein residues at overlapping p-p and p-l binding surfaces
2014 Hezha Hassan Master Thesis: Relations between imprinted genes and protein kinases as well as chromatin remodelers
2014 Franziska Müller Master Thesis: Genome region-based analysis of ChIP-Seq data
2014 Junfang Chen Master Thesis: AKSmood: Whole human colon methylone profiling using low-coverage bisulfite sequencing data
2014 Tanushree Jaitly Master Thesis: Properties of confined water between two hydrophilic surfaces
2014 Thorsten Klingen Master Thesis: Inference of genome-wide evolutionary networks for influenca A viruses
2014 Thorsten Will Master Thesis: Identifying transcription factor complexes and their roles
2014 Vu Ha Tran Master Thesis: Classifying substrates transported by membrane tranporter proteins using neighboring genes
2013 Christoph Thiel Master Thesis: A knowlwdge-driven approach for cross species extrapolation in pharmaceutical development
2013 Kerstin Reuter Master Thesis: Finding human genes with non-AUG translational start
2013 Anne Gamber Master Thesis: Detection of monoallelic expressiom and RNA editing events in neuronal childhood cancers
2013 Sundararajan Srinivasan Master Thesis: Towards predicting how E.coli develops antibacterial resistance via modulating the AcrB efflux pump
2012 Duy Nguyen Master Thesis: Characterizing and predicting pore lining residues of helical membrane transporters
2012 Changsu Liu Master Thesis: Towards classifying the substrates of mammalian transporters
2012 Mayank Kumar Master Thesis: LocusVu: Large scale automated analysis of genomic loci
2012 Johannes Trumm Master Thesis: Automated and dataset independant machinery for gene regulatory network topology reconstruction
2012 Matthias Bieg Master Thesis: Investigation of Allele-Specific Methylation Patterns in Diploid Genomes
2012 Xian Jin Master Thesis: Efficient Parameter Optimization for Stochastic Dynamics Simulations of Subcellular Systems
2011 Eva Kiszka Master Thesis: A Pre-Docking Filter Based on Image Recognition
2011 Zhipei Du Master Thesis: Prediction of Binding Affinity of Nucleotide Aptamers Against Protein Binding Domains Using a PWM-based Scoring Function
2011 Andreas Wagenmann Master Thesis: Coarse-Grained Simulations of Protein Backbone Dynamics
2010 Ahmad Barghash Master Thesis: Membrane Transporter Classification
2010 Naharajan Lakshmanaperumal Master Thesis: DNA Affinity - Prediction of Binding Affinity of Protein DNA Complexes
2010 Nitesh Kumar Singh Master Thesis: A Frequency-Profile based HMM Model for Prediction of Structural Topology of Beta-based Membrane Proteins and Exposure Status of Transmembrane Residues
2009 Jennifer Metzger Master Thesis: Classifying Membrane Exposure of Transmembrane Helices
2009 Nadine Schaadt Master Thesis: Substrate Prediction of Membrane Transporters in Arabidopsis Thaliana
2009 Uwe Winter Master Thesis: Characterization of Ligand Binding Sites on Protein Surfaces
2009 Siba Ismael Master Thesis: On the Origin of Genomic Imprintig
2009 Christian Spaniol Master Thesis: Mebitoo - A Membrane Bioinformatics Sequence Analysis Toolbox
2009 Jan Christoph Master Thesis: Analysis of Membrane Transporters formed on Amino Acid Transporters and their Pore Region by Threading and Similarity Search
2008 Markus Krier Master Thesis: Structure Similarity by SMILES Alignment
2008 Susanne Pfeifer Master Thesis: SCAMPI - Identification of Molecular Markers in the Arabidopsis Genome
2008 Florian Lauck Master Thesis: Investigation of Complex Formation by Combining Spatial Simulation with Graph Analysis "Top View"
2008 Abdelhak Bellamou Diplom: Small-Molecule Protein-Protein Interactions-Inhibitors SMPII Datenbank
2008 Nadine Schneider Master Thesis: Analysis of non interacting consecutive transmembrane helices and development of the visual tool "Top View"
2008 Oliver Frings Master Thesis: eDrugScan: Development of an online based screening tool for drug-like compounds
2007 Kerstin Demme-Kunz Master Thesis: Identification of possible Proton Transfer Pathways
2007 Barbara Hutter Master Thesis: MPSIM, a database for membrane protein structures, diseases, function, and interactions
2006 Christian Dammer Diploma: Identifizierung von CpG-Inseln in Mensch und Maus
2006 Yungki Park Master Thesis: A Novel Scoring Function for Modeling Structures of Homololigomers of Transmembrane α-helices
2006 Wei Gu Master Thesis: Solvation Free Energies and Transfer Free Energies for Amino Acids from Hydrophobic Solution to Water Solution from a Simple Residue Model
2006 Susanne
Master Thesis: Detecting Transient Pockets on Protein Surfaces for Ligand Docking
2006 Peter Walter Diploma: Protein-Interaktions-Datenbank
2005 Gautam
Master Thesis: Cellular Agent: A Tool for Automating and Optimizing the Intracellular Process by using Genetic Algorithm


Fopra / Bachelor

2017 Maximilian Greil Bachelor Thesis: „Creation of differently altered context-specific metabolic models of antibiotically treated Escherichia coli in-silico using the results of a high-throughput microarray dataset“
2016 Markus Hollander Bachelor Thesis: „Automated SNP analysis in Staphylococcus aureus“
2016 Andreas Denger Bachelor Thesis: „The effects of genetic mutations on protein interaction networks“
2015 Nina Speicher Bachelor Thesis: „A new approach for descriptor selection in linear regression analysis“
2015 Tobias Fehlmann Bachelor Thesis: „Conservation and relevance of pharmacophore point types“
2015 Lukas Tost Bachelor Thesis: „Epigenetic relations of miRNA-mediated regulation on mRNA in correlation to Alzheimer´s disease. A database-assisted R package“
2015 Andreas Firczynski Bachelor Thesis: „A pdb checking tool for subsequent docking“
2014 Yvonne Saara Gladbach Bachelor Thesis: Epigenetic characterization of chromosomal breakpoints
2014 Michael Scherer Bachelor Thesis: Extension of ABC2 database by DNA-protein interactions
2014 Jan Forster Bachelor Thesis: Combinated design of actual drug fragments
2014 Laurena Koch Bachelor Thesis: Analysis of 5' untranslated regions
2014 Adrian Mang Bachelor Thesis: Generation of 3D-Structures from SMILES
2013 Sebastian Keller Bachelor Thesis: Automatic generation of hierarchical SMARTS trees from a set of SMILES
2013 Mustafa Kahraman Bachelor Thesis: A modular GUI pipeline for large scale locus processing (HERV example)
2013 Marcel Meyerheim Bachelor Thesis: Substrate classification of helical membrane transporters on the basis of pore composition
2013 Sascha Herzinger Bachelor Thesis: Automatisierte Auswertung von Dockingergebnissen zur Klassifizierung von Substraten und Liganden von Cytochrom P450-Enzymen
2013 Iris Langenbahn Bachelor Thesis: A new approach to protein-ligand docking
2012 Markus Merl Bachelor Thesis: Suitable 2-dimensional structure depiction of SMILES
2012 Max Fischer Bachelor Thesis: Contact properties of consecutive transmembrane helices
2012 Thorsten Klingen Bachelor Thesis: Automated Recombination Analysis using Recco and Mebitoo
2011 Thorsten Will Bachelor Thesis: Finding Low Energy Conformations in a Haystack of Tautomers
2011 Ammar Abdulmughni Bachelor Thesis: Beeinflussung er Homologiemodellierung von Transmembrabproteinen durch Sequenzalignments
2011 Daniel Becker Bachelor Thesis: Analysing Peptide Segments in Protein-Protein Interfaces with Reference to their SCOP Classification
2011 Anne Gamber Bachelor Thesis: Effect of Noise in Quantitative Structure-Activity Predictions
2011 Sherif Farag Bachelor Thesis: New Descriptors for the Prediction of CNS Drugs Permeability using Decision Tree
2011 Franziska Müller Bachelor Thesis: A Robust Method for Generating Unique SMILES: Finding new Drugs by Bioisosteric Similarity
2010 Stefan Helfrich Bachelor Thesis: Perform Motifsearch on Mebitoo Datasets
2010 Christoph Thiel Bachelor Thesis: Prediction of Hot Spots at Protein-Protein Interfaces
2010 Arthur Gollmer Bachelor Thesis: Molekular-stochastische Simulation der Cytochrom c-Oxidase
2010 Maha Ahmed Baker Bachelor Thesis: Fast Calculation of Topological Molecular Polar Surface Area (TPSA) directly from SMILES
2010 Johannes Trumm Bachelor Thesis: Bioinformatics Analysis of Transmembrane Helix Insertion Cooperativity
2009 Miriam Mangels Bachelor Thesis: In Silico Models for the Prediction of Metabolism by Cytochrome P450 Enzymes
2008 Marc Thobae Bachelor Thesis: Assigning Force Field Atom Types in SMILES
2008 Nadine Schaadt Bachelor Thesis: Quantitative Analyse of Quorum Sensing of Vibrio fischeri
2008 Hanna Lorig Bachelor Thesis: Analysing Protein-Protein Interaction Sites Using Surface Patches
2008 Uwe Winter Bachelor Thesis: Brown´sche Dynamik jenseits des überdämpften Regimes
2007 Xavier Mol Bachelor Thesis: Automatisierte Parameterbestimmung und -optimierung von stochastischen Simulationen metabolischer Systeme
2007 Alexander Baldauf Bachelor Thesis: Constructing Binding Pockets on Protein Surfaces using the A*-Algorithm
2007 Min Ye  Bachelor Thesis: Formanalyse von transienten Protein-Bindungstaschen als Vorarbeit für dynamische Pharmakophor-Modellierung
2007 Angela
Bachelor Thesis: Modellierung der Bindetasche von CYP206
2006 Christine
Bachelor Thesis: Clustering of QSAR Structures and Selection of QSAR Descriptors

2006 Florian Lauck Bachelor Thesis: Stochastische Simulation eines photosynthetischen Vesikels
2006 Mathieu Papdo FoPra: Docking an ein Konsensusmodell der Lactamasen, the β-lactamase in action
2006 Christine Hedderich FoPra: Aufbau einer Substanzdatenbank mit HTML - Benutzerschnittstelle (Teil II)

2006 Melanie Zimmer FoPra: Brownsche Dynamik mit expliziten Ionen - Effekte für biologische Systeme
2005 Johannes Tran FoPra: Aufbau einer Substanzdatenbank mit HTML-Benutzerschnittstelle (Teil 1)
2005 Cosima Graf FoPra: Virtual Screening of Peptides Binding to Adapter Domains by Flexible Docking and Molecular Dynamics Simulations
2005 Kerstin Kunz FoPra: BDOCK - Effizienz von Scoring-Matrizen
2005 Sandra Fischer FoPra: Parametrization of a Residue Scale Solvent Implicit Model
2005 Claudia Andres FoPra: Vorhersage der CNS-Aktivität einer chemischen Verbindung mittels eines Entscheidungsbaumes
2005 Christian Dammer FoPra: Analysis of the Association Pathways and Association Free Energy by Brownian Dynamics Simulations
2004 Oliver Müller FoPra: Designing proline-rich peptides for GYF domains