Algorithmen der Bioinformatik

Bachelor Theses

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

2024

  • Accelerating taxonomic analysis by performing LCA calculations in SQL
  • Comparison of 16S databases for microbiome analysis
  • Extending Sankoff's algorithm to rooted networks
  • Mapping phylogenetic networks to trees - done
  • Implementation of frame-work for autocatalytic networks in Python - done
  • Phylogenetics tool kit - implement a webpage providing phylogenetic outlines and similar - Mathilda Rudd

2023

  • Visualization of haplotype data on maps - done
  • Implementation and applications of split-newick format in Python - done
  • Building a web server for remote visualization of metagenome sequencing data - done

2022

  • Exploring improvement possibilities for reference based metagenome binning using sequence specific properties - done
  • A machine learning approach for survival prediction using transcriptome profiling data from lung cancer patients - done
  • BioSurfDB and use in MEGAN for fruit waste microbiome analysis - done
  • Visual analysis of large phylogenetic profiles using unrooted densi-trees - done
  • Unrooted densitrees - done
  • Using the BioSurfantDB classification in microbiome analysis using MEGAN - done
  • A machine learning approach for survival prediction using transcriptome profiling data from lung cancer patients - done
  • - Webserver for remote visualization of metagenome sequencing data - done

2021

  • Simulation amplicon sequencing for applciations in disease analysis - done
  • LCA analysis of metagenomic sequences in Python - done
  • Simulation study on the impact of reagent contamination in metagenomic analysis - done
  • Inter-study comparison in metagenomics - done
  • Implementation and improvement of MEGAN's taxonomic binning algorithms, in Python - done
  • Implementation of a MDA simulator with applications to COVID, in Python - done

2020

  • Contamination filtering in microbiome analysis - done
  • Inter-study comparison in metagenomics - done

2019

  • Analysis of metagenomic long-read sequences from a biorector - done
  • Durchschnitt von Fraktalen mit Hyperebenen - done
  • Darstellung der Kanten von periodischen Kachelungen in allen Geometrien - done
  • Using Mash, Dashing and other k-mer approaches to compute phylogenetic networks on bacteria - done

2018

  • Analyse unterschiedlicher Zellpopulationen von und nach Therapie - done
  • Improved taxonomic profiles based on simulated binning - done
  • Completeness, contamination and annotation of long read metagenome datasets - done

2017

  • Analysis of antimicrobial resistance in microbiome sequencing data - done
  • Application of MetaCyc in microbiome analysis - done
  • Classification of phages and visualization -  done
  • Comparison of different KEGG-based microbiome analysis approaches - done

2016

  • Development of a MobileApp/Website for advising proper antibiotics usage - done
  • Phage identification in metagenomics - done
  • Fast computation of consensus splits - done
  • Structural variants of Bacteroides vulgatus - done
  • Ecoli assembly - done
  • NanoChain: An Empirical Nanopore Read Simulator - done

2015

  • Design and implementation of a web portal for microbiome data - done
  • Analysis of microbiome data in the context of Adipositas - done
  • Analysis of publicly available 16S human gut microbiome data - done
  • Deploying bioinformatics tools in the cloud using Docker -done
  • Steered Molecular Dynamics of 2fdt structure - done
  • Influence of Processing on 16S Analysis Data - done

2014

  • Visualisierung taxonomischer Daten mit Voronoi Trees - done
  • Fast comparison of metagenomic samples - done
  • Functional analysis using BioCyce - done
  • Genes associated with diabetes in the microbiome -done

2013

  • Comparision of metagenomic DNA, done
  • Clouding computing in bioinformatics, done
  • Android app for phylogenetic trees - done
  • Hybrid approach to analysis of 16S rRNA data - done

2012

  • Transskriptomanalyse von Krebszellen, done

2011

  • Vergleich von existierenden Metagenomics Pipelines -done
  • Analysis of ancient DNA - done

2010

  • Plattform für Next-Gen Transkriptomanalyse- done

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