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

• Wissenschaftliches Präsentieren – 3015 – –/Se/Pr
• Biochemie – 3013 – Vo/Se/Pr
• Computational Biology – 3008 – Vo/–/Pr
• Genetik/Molekularbiologie – 3020 – Vo/Se/Pr
• Biotechnologie II – 3021 – Vo/Se/–
• Bioethik – 3050 – –/Se/–

Bachelor Allgemeine und Digitale Forensik

• Komplexpraktikum Forensische Methoden - 6721 - Vo/Se/Pr

Master Genomische Biotechnologie

• Biodaten-Prozessierung – 4702 – Vo/–/Pr
• Genomische Biotechnologie I – 4723 – Vo/Se/–
• Genomische Biotechnologie II – 4734 – Vo/Se/–
• Gentechnik und Recht – 4717 – Vo/Se/–
• Molekularbiologie – 4719 – Vo/–/Pr
• Synthetische Biologie – 4732 – Vo/Se/–
• Forschungsmodul – 4729 – –/Se/–

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

Current and finished supervised theses can be found here.

Allgemeine Hinweise

Praxis- und Forschungsmodul & Bachelor- und Masterarbeit

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

Zitierungen -> meine Spielregeln

• Literaturreferenzen
  • keine Zahlen: [1-3]
  • Ein oder zwei Autoren
    • Die DNA-Struktur wurde in den 1950iger Jahren aufgeklärt und publiziert [Watson & Crick, 1953].
    • Im Literaturverzeichnis: Watson & Crick (1953) Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature 171:737-738
  • Drei oder mehr Autoren
    • Eines der ersten ESR-Spektren der NiFe-Hydrogenase aus //Methanobacterium thermoautotrophicum// beweist die Präsenz von Nickel [Albracht et al., 1982].
    • Im Literaturverzeichnis: Albracht, Graf & Thauer (1982) The EPR properties of nickel in hydrogenase from //Methanobacterium//. FEBS Lett. 140:311-313
  • Mehrere Quellen werden durch Semikolons getrennt und chronologisch sortiert: Bla … bla [Watson & Crick, 1953; Albracht et al., 1982].
• Internetreferenzen
  • URLs durchnummerieren
    • Wasserstoff kann auch von Algen gebildet werden [URL-1].
    • Im Literaturverzeichnis: URL-1 (Zugriff: 01/03/2011) http://www.biowasserstoff.de

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

• Course Script: PDF (V3)
• Ubuntu Installation: see section 2.1 in the script / Ubuntu / VirtualBox

Slides

• Set 1 PDF / Set 2 PDF / Set 3 PDF / Set 4 PDF

Files

• expression.tab and annotation.tab: tarball

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:

• pathogenic strain I
• pathogenic strain II

• autoblast-2.sh / autoblast.sh / h7vsk12.txt

• E. coli K12
• E. coli O157:H7

• E. coli O104:H4

• Replacement for Terminal 20: blastdbcmd -db eck12 -entry "all" -outfmt "%t" / sed -e 's/|ref.*| /\t/' -e 's/\[.*/\tK12/' -e 's/#/\t/' > annotation-k12.tab

• results with correct GIs: h7vsk12.tar.gz

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:

• To download structure XXXX use: https://files.rcsb.org/download/XXX.pdb
• If SurfaceRacer throws an error: sudo apt-get install libstdc++5

Files:

• distance-batch-surface.awk / distance-batch.awk / distance.awk

• Surface Racer

• PDB Structures: ecolistructures.tar.gz

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:

• counter.sh / counter2.sh

Programs:

• Sequencer / TIGR Assembler / Dotter