Let there be light.

I am currently involved in the reading of several modules as outlined below. Lecture material can be found at OPAL (Bildungsportal Sachsen). Further below you find past supervised theses and general remarks for theses.

Scripts, slides and files for my course in Computational Biology can be found here.

Bachelor Biotechnologie

Bachelor Allgemeine und Digitale Forensik

Master Genomische Biotechnologie

Studieren mit Kind?

Die Hochschule Mittweida tut einiges, um jungen Eltern das Studium zu erleichtern. Es lohnt sich ein Blick auf die Campusbüro Webseite. Infolgendem Imagefilm des Landkreises Mittelsachsen erfahren Sie mehr.

Supervised Theses

Currently and finished supervised theses can be found here.

Click to UN|FOLD theses supervised before 2009

2009

Ökologische Stöchiometrie: Einfluss der Nährstoffverfügbarkeit auf die Genexpression von Paralogen
Katrin Lotz
Diploma Thesis, Martin-Luther-University of Halle-Wittenberg, January 2009
Supervised together with: Prof. Falk Schreiber

2007

GaloisExplorer: Software zur interaktiven dreidimensionalen Visualisierung von genbasierter Metadaten mit Hilfe von Methoden der formalen Konzept Analyse
Sebastian Breuers
Diploma Thesis, University of Cologne, October 2007

OrfMapper: A Web-Based Application for Querying and Visualizing Gene Metadata
Martin Vellguth
PhD Thesis, University of Cologne, July 2007

Regulatory elements on eukaryotic transcripts
Jan Martin Büllesbach
Research Project (6 month), University of Cologne/Germany, April 2007

A sequence & PDB module for OrfMapper
Song Guo
Research Project (6 month), University of Cologne/Germany, April 2007

Predicting the effect of secondary structure on (R|D)NA-DNA hybridization
Diladruz Juraeva
Research Project (6 month), University of Cologne/Germany, April 2007

Analysis of polycistronic transcripts and transcript processing based on DNA-microarray data
Christian Otuteye
Research Project (6 month), University of Cologne/Germany, April 2007

A DNA-microarray for Phycomyces blakesleeanus
Sridevi Balarman
Research Project (6 month), University of Cologne/Germany, April 2007

Effekt von RNA-Sekundärstrukturen auf RNA-DNA-Hybridisierungen
Mario Dejung
Semesterarbeit, FH Bingen, since August 2006

Stöchiometrie Homologer Proteine in Saccharomyces cerevisiae
Marcel Blindert
Semesterarbeit, FH Bingen, since August 2006

2006

Organismische Stoichiometrie aus der Sicht des Transkriptoms
Sebastian Gustmann
Diploma Thesis; Oktober 2006

Ecological Stoichiometry: Effects on the Transcriptome
Koh Li Meng
Research Project (6 month), University of Cologne/Germany, April 2006

A Computational Approach to Find Potential Thioredoxin Target Enzymes
Peristera Ourania
Research Project (6 month), University of Cologne/Germany, April 2006

2005

Evolution of Acaryochloris marina
Srinivasa Rao Pidugu
Research Project (6 month), University of Cologne/Germany, April 2005

Regulatory Elements in the Cyanobacterium Nostoc PCC 7120
Long Li
Research Project (6 month), University of Cologne/Germany, April 2005

Identification of Regulatory Elements in Cyanobacteria by Comparative Genome Analysis
Sha Li
Research Project (6 month), University of Cologne/Germany, April 2005

2004

Proteome Analysis with Respect to Atomic Composition
Claudia Acquisti
Research Project (6 month), University of Cologne/Germany, March 2004

Hydaba - An Extended Hydrogenase Database
Heike Eckes
Research Project (6 month), University of Cologne/Germany, March 2004

2003

Mathematische Modelle und Methoden zur Genexpressionsanalyse in der Bioinformatik
Frank Thierolf
Diploma Thesis, Technical University Darmstadt/Germany, July 2003
Supervised together with: Prof. G-W Weber, Dipl. Math. J Gebert

Distance between Strings and its Application to Amino Acid Sequences
Martin Lätsch
Diploma Thesis, Chemnitz University of Technology, Germany, April 2003
Supervised together with: Prof. B Luderer, Prof. G-W Weber, Dipl. Math. J Gebert 

A Distance-Based Approach to Assign and Visualize Relatedness between Sequence-Based Phylogentic Trees
José Augusto Amgarten Quitzau
Research Project (6 month), University of Cologne/Germany, March 2003
Supervised together with: Prof. U Faigle, Prof. G-W Weber, Dipl. Math. J Gebert

2002

Moderne Mathematische Methoden zur Lösung von Alignment- und Mustererkennungsproblemen in der Bioinformatik
Andreas Ettl
Diploma Thesis, Technical University of Darmstadt/Germany, November 2002
Supervised together with: Prof. G-W Weber

Expression of Hydrogenase Specific C-Terminal Endopeptidases in Three Different Cyanobacteria
Mehtap Batur
Bachelor Thesis, Uppsala University, Sweden, January 2002

2001

Transcription of Hydrogenases/Proteases in Cyanobacteria
Tomas Söderström
Exam Thesis, Uppsala University, Sweden, June 2001

Allgemeine Hinweise

Praxis- und Forschungsmodul & Bachelor- und Masterarbeit

Weitreichende Informationen finden Sie hier. Meine LaTeX-Volage können Sie hier runterladen.

Zitierungen -> meine Spielregeln

Computational Biology Workshop

Special module on computational biology for the //Fast-Track M/D Programme// and the //Graduate School for Biological Sciences// at the Institute for Genetics, Cologne University. The content is yearly updated.

Script

Slides

Files

Projects

Genomic Analysis of the Pathogenicity Factors from E. coli Strain O157:H7 and EHEC Strain O104:H4

This guided exercise will show you how to use BLAST to compare two genomes. The objective is to find open reading frames (ORFs) that are unique to one genome. This exercise uses a local installation of BLAST+, AWK, MySQL, and R.

Files:

Querying for Potential Redox-Regulated Enzymes

The scientific background of this example is biochemistry. The activity of some enzymes is regulated by formation or cleavage of disulfide bonds near the protein surface. This can be catalyzed by a group of proteins known as thioredoxin. Comparison of primary structures reveals that there is no consensus motif present in most of the thioredoxin-regulated target enzymes. In order to identify potential proteins that could be targets for thioredoxin, one can investigate protein structure data. We just need to search for cysteine sulfur atoms that are no further than 3 Å apart and close to the surface. But how? This exercise uses Jmol, Surface Racer, AWK, and shell programming.

Hints:

Files:

Virtual Sequencing of pUC18c

The objective of this exercise is to sequence the pUC18c cloning vector. It is divided into the following major parts: a) downloading the cloning vector, b) run a virtual sequencing program, and c) assembling the virtual sequences obtained from sequencing with the TIGR Assembler. The quality of a particular assembly is visualized with a dot plot. The ultimate goal is to understand the effect of sequence coverage and sequence fragment length on the assembly process. This exercise uses a virtual sequencer, the TIGR Assembler, Dotter, R, and shell programming.

Files:

Programs: