Algorithmen der Bioinformatik

Master Theses

Here is a listing of possible topics for projects. Further suggestions are welcome.

2024

  • Simulation of ancient cave microbiome data - Available - co-advisor Prof. Cosimo Posth
  • Acceleration of phylogenetic context calculations by performing them directly in SQL - Available - co-adivsor Prof. Torsten Grust
  • Interactive exploration tool to analyze data hosted at MGnify - Available
  • Interaction exploration tool to analyze data hosted at MG-Rast - Available
  • Extending Sankoff's and Felsenstein's algorithms to rooted networks - Available
  • Application of protein language-models in microbiome analysis - Available
  • Comparison of read-based and contig-based analysis of metagenomic RNA sequencing data - Available
  • Analysis of Nano-sequencing data in the context of biotechnology - Available - co-advisor: Prof. Lars Angenent

2023

  • Comparative visualization of multiple metagenome datasets - done - co-advisor: Prof Kay Nieselt
  • Visualization of gene trees - done - co-advisor
  • Mobile app for viewing MeganServer data -done - co-advisor
  • Mobile app for viewing everything Newick - done - co-advisor
  • Adapting microbiome health index to 16S rRNA data - done

2022

  • Comparison of Whole Genome Shotgun and 16S Amplicon Metagenomic Sequencing - done
  • Taxonomic Segmentation - done
  • Machine learning based codon prediction for recombinant gene design - done
  • Benchmarking and Comparative Analysis of a Graph-based Tool for CRISPR Array Detection in Metagenomic Datasets - done
  • Generation and validation of pangenome graphs to explore genetic diversity in Cannabis sativa - done
  • Bioinformatic Discovery and Analysis of Fusion Enzymes in the Shikimate Pathway - done
  • Adapting the MEGAN long-read LCA algorithm to Kraken-style data - done
  • Using IsoSeq to reveal NLR-diversity in Arabidopsis thaliana - done

 Multiple other theses

2021

  • Sex biased gene expression in red algae - done
  • Evaluation & Comparison Of Metagenomic Plant Growth-Promoting Traits Annotation Strategies - done
  • Interoperability of Microbiome Analysis Tools - done
  • Investigating AnnoTree for its potential to improve the analysis of metagenomic sequencing data - done
  • Improved consistency of taxonomic binning of microbiomes based on assembly graph analysis - done
  • Prediction of Genes in Genomes with Frequent Ribosomal Frameshifting - done
  • RNAseq and Iso-seq data analysis - done
  • Prediction of genes in genomes with frequent (~10%) translational frameshifting - done

 

2020

  • Comparison of Machine Learning and Deep Learning Methods for Multi-environment Genomic Predition - done
  • Impact of Repeats, Conserved Genes, Strains Richness and Chimeric Contigs on Metagenomic Assembly - done
  • Visualization and Analysis of Autocatalytic Networks - done
  • Improved Metagenomic Contig Binning using Haplotagging Data - done
  • Genome Mining of the Natural Product Potential and Diversity within the bacterial kingdom - done
  • Targeted functional annotation of bacterial genomes using DIAMOND and MEGAN in a phylogenomics approach  - done
  • Use assembly graphs in contig binning - develop methods and implement in Java - done
  • Use of GTDB and AnnoTree for protein-alignment-based microbiome analysis - done
  • 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)  - done

2019

  • Visualization and analysis of autocatalytic networks (implementation using JavaFX) - done
  • Protein k-mer methods for microbiome analysis - done
  • Identifying the Role of ALPs in Methanobacteriaceae - done
  • Inclusion of Environmental Data in Machine Learning Models for Genomic Prediction in Rice - done
  • Database analysis of function - done
  • Computational analysis of metagenome data from caprylate producing bioreactors” -done
  • Interpretability of Machine Learning Models for Genomic Selection in Maize” - done
  • Effect of reference genome choice on variant calling”- done
  • Assessment of assembly strategies for bioreactor metagenomics” - done
  • Improved metagenomic contig binning using haplotagging data - done

2018

  • Analysis of twin study microbiome samples - done
  • Performance of DIAMOND+MEGAN on CAMI data - done
  • Machine learning algorithms applied to protein sequences - done

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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