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Topics for master theses

Here is a listing of possible topics for projects. Please come and see us to learn more about the topics. Further suggestions are welcome. 

2018

  • Analysis of twin study microbiome samples - Minyue Qi, co-advisor: Prof. Ruth Ley, MPI-DB, Tübingen
  • Analysis of microbiomes in bioreactors -AVAILABLE Co-advisor: Prof. Lars Angenent, Center for for Applied GeoSciences, Tübingen
  • In silico analysis of the evolution and function of ABC transporters in bacterial secondary metabolite gene clusters  - AVAILABLE - Co-advisor: Prof. Nadine Ziemert (Biology Tübingen)
  • Protein k-mer methods for microbiome analysis - Joachim Fritscher
  • Functional annotation of long reads and contigs - AVAILABLE
  • Performance of DIAMOND+MEGAN on CAMI data - Thorsten Rohling
  • Machine learning algorithms applied to protein sequences - Jona Kübler - Advisor: Dr. Vikram Alva (MPI DB)
  • Prediction of genes in genomes with frequent (~10%) translational frameshifting (i.e. Euplotes - https://www.nature.com/articles/srep21139#t1 - with a fragmented genome like Oxytricha) - AVAILABLE-  Co-advisor: Dr. Estienne Swart, MPI for Developmental Biology
  • 2. Prediction of genes in genomes with ambiguous genetic codes (where “stop” codons can be sense or stop, depending on the context): (https://www.sciencedirect.com/science/article/pii/S0092867416307887 - AVAILABLE-  Co-advisor: Dr. Estienne Swart, MPI for Developmental Biology
  • Database analysis of function - Sylvia Siegel - Co-advisor: Prof. Lars Angenent, Dept. of Biological and Environmental Engineering

2017

  • JavaFX implementation of haplotype networks  (SplitsTree5 - part II) - done
  • Evolution and horizontal gene transfer of regulatory elements in bacterial secondary metabolite gene clusters  - done
  • Exploring the use of TPR "Trough to Peak Ratio" analysis to determine which bacteria are growing and which are stagnant in the human gut during a course of antibiotics - done
  • Design and implementation of a full-featured Time Series Analysis tool - done

2016

  • JavaFX implementation of Phylogenetic network drawing and GUI (SplitsTree5 - part I) - done
  • Pathogen identification - done
  • Correspondence between KEGG and InterPro in metagenome analysis - done

2015

  • Assembly of ancient mtDNA genomes - done
  • Real-time monitoring of resistance evolution - done
  • SamSifter - A toolbox for metagenomic analysis - done
  • Fingerprinting of microbial genomes - done

2014

  • Haplotype profile sharing in Arabidopsis thaliana - done
  • Visualization of very large numbers metagenome samples - done

2013

  • Functional analysis of trinucleotide repeats in plants - done
  • Sequencing and assembly strategies for a new plant genome - done

2012

  • Annotation of bacterial genomes - done
  • Reference-guided protein assembly - done
  • Naive Bayesian classifier for metagenomics - done

2011

  • Pathway evaluation in (meta) transcriptomics - done
  • Analysis of 16S data - done
  • Finding confidence interval for multiple metagenome comparison networks - done
  • Assembly and annotation of the Guppy transcriptome- done
  • Correlating taxonomy and gene function with environmental parameters - done
  • Short-Read aligners in Metagenomics -- done

2010

  • Faster BLAST analysis of metagenomic data - done
  • New methods for the comparison of phylogenetic trees and networks- done
  • Hybridization networks - done
  • TE Discovery by Next Gen Sequencing - done

  • Simulation of 3rd generation sequencing technologies - done

  • Analysis of human gut data - done
  • Analysis of 16 S rRNA - done
  • Datenbankgestützte Analyse von Metagenomikdaten - done
  • Functional and pathway analysis of metagenomic data - done

  • Efficient data mining techniques for two-locus association mapping- done
  • Finding Patterns in Intervals - done

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