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Theses completed

PhD:


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:
2016
Jacob Ambat
Master Thesis: Properties of pore lining residues of transporter families in different Staphylococcus aureus strains
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


2006


Christian Dammer

Barbara
Hutter

Master Thesis: MPSIM, a database for membrane protein structures, diseases, function, and interactions


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
Eyrisch
Master Thesis: Detecting Transient Pockets on Protein Surfaces for Ligand Docking



2006
Peter Walter Diploma: Protein-Interaktions-Datenbank
2005

Gautam
Chaurasia
Master Thesis: Cellular Agent: A Tool for Automating and Optimizing the Intracellular Process by using Genetic Algorithm

FoPra/Bachelor:
2016
Christian Michels Bachelor Thesis: „A de-novo design approach“
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
Kling
Bachelor Thesis: Modellierung der Bindetasche von CYP206
2006

Christine
Jäckels
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








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