Algorithms in Bioinformatics

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.

2021

  • State-of-the-art k-mer methods and applications in phylogeny - Fabian Rosner
  • Adding non-circular splits to a phylogenetic outline - AVAILABLE
    • Phylogenetic outlines are a new type of phylogenetic networks, based on circular splits. The aim here is to extend the algorithm so as to incorporate additional non-circular splits
  • Implementation and evalulation of phylogenetic methods in Python- Available
    • The aim of this and similar projects is to reimplement many of the algorithms provided by SplitsTree4 in Python and to compare the implementations
  • Consensus trees and consensus outlines - Julian Wolff 
  • Using the BioSurfantDB classification in microbiome analysis using MEGAN - Niclas Fischer
  • Phylogenetic networks on SARS-CoV-2 genomes- Systematically investigate the application of phylogenetic tree and network methods - Yi Zhou
  • Determining plant-growth promoting genes in incomplete genomes  - AVAILABLE
  • Analysis of long read metagenomic samples - Comparison of methods published in Arumugam et al ‎2019 and EL Moss et al ‎2020 - AVAILABLE
    • The aim is to apply the methods described in the one paper to the data of the other paper, and vice versa, to compare the two approaches
  • Textmining for PGPT traits in publicly available literature and comparison to the novel PGPT-Ontology - AVAILABLE
    • The project aims at improving/updating the current collection of orthologous protein groups of plant growth-promoting traits (PGPTs) by developing an automatic approach, that mines publications (e.g. via WhatIzIt, iTextMine) for new-announced PGPTs. In more detail, it will report on their taxonomic and functional assignments, and their experimental proof.
  • Comparison of hybrid assemblers for short and long sequencing reads - AVAILABLE
    •  Long read sequencing methods are useful to generate genome assemblies from sequencing data as the long reads are able to assemble repeating sequences better than short reads, however, they usually have a high per base error rate. This led to the development of hybrid assembly approaches using both short and long read data as input. The goal of the thesis is to test different hybrid assembly approaches on real data and evaluate the assemblies with various metrics.
  • Implementation and improvement of MEGAN's taxonomic binning algorithms, in Python - Tobias Lass
  • Implementation of a MDA simulator with applications to COVID, in Python - Indira Echsler

2020

  • Contamination filtering in microbiome analysis - Carmen Gil Bredehoeft
  • Inter-study comparison in metagenomics - Patrik Schirm

2019

  • Analysis of metagenomic long-read sequences from a biorector - 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