Publications - PhD/MSc/BSc/Diploma theses

Please find below various PhD, MSc, BSc and Diploma theses produced by our group.
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PhD theses written at University of Leipzig

Annotation of Small Proteins

John Anders (University of Leipzig, 2023)

Differential evolution of non-coding DANN across eukaryotes and ist close relationship with complex multicellularity on Earth

Irma Lozada (University of Leipzig, 2022)

Advancing the analysis of bisulfite sequencing data in ist application to ecological plant epigenetics

Adam Nunn (University of Leipzig, 2022)

The Folding Kinetics of RNA

Felix Kühnl (University of Leipzig, 2022)

Exploration of Chemical Space

Wilmer Leal (University of Leipzig, 2022)

New Algorithms for Fast and Economic Assembly: Advances in Transcriptome and Genome Assembly

Thomas Gatter (University of Leipzig, 2022)

Temperature-Related Proteogenomics of Cold-Adapted Apphipods from the Lake Baikal Region

Polina Lipaeva (University of Leipzig, 2022)

Computational Characterization of Long Non-coding RNAs

Rituparno Sen (University of Leipzig, 2021)

Evolution of DNA methylation across Metazoa

Jan Engelhardt (University of Leipzig, 2021)

Unraveling the genetic secrets of ancient Baikal amphipods

Lorena Riverola-Duarte (University of Leipzig, 2021)

Segmentation of Heterogeneous Multivariate Genome Annotation Data

Halima Saker (University of Leipzig, 2021)

Gene Family Histories - Theory and Algorithms

David Schaller (University of Leipzig, 2021)

On the Study of Fitness Landscapes and the Max-Cut Problem

Angel Rodriguez Fernandez (University of Leipzig, 2021)

Studying Evoltunionary Change - Transdisciplinary Advances in Understanding and Measuring Evolution

Nancy Retzlaff (University of Leipzig, 2020)

Towards Dynamic programming on Generalized Data Structures and Applications of Dynamic Programming in Bioinformatics

Sarah Berkemer (University of Leipzig, 2020)

Comparative Genomics in Distant Taxa

Fabian Gärtner (University of Leipzig, 2020)

The marvelou World of tRNAs

Anne Hoffmann (University of Leipzig, 2020)

Improved Workflows for RNA Homology Search

Ali M. Yazbeck (University of Leipzig, 2019)

A Parametric Model for the Analysis and Quantification of Fovel Shapes

Patrick Scheibe (University of Leipzig, 2019)

Novel Methods for Constructiing, Combining and Comparing Co-Expression Networks

Deisy Morselli Gysi (University of Leipzig, 2019)

From Best Match Graphs to Gene Trees - A new persepective on graph-based orthology inference

Manuela Geiß (University of Leipzig, 2019)

Adaptive Evolution of Long Non-Coding RNAs

Maria Beatriz Walter Costa (University of Leipzig, 2018)

Sequences Signature and Genome Rearrangements in Mitogenomes

Marwa Al Arab (University of Leipzig, 2018)

High quality gene annotation for deep phylogenetic analysis

Henrike Indrischek (University of Leipzig, 2018)

Understanding divergent evolution through comparative genomics

Sree Rohit Rai Kolora (University of Leipzig, 2018)

Linguistic Diversity Through Data

Damian Blasi (University of Leipzig, 2017)

Sequences Signature and Genome Rearrangements in Mitogenomes

Marwa Al Arab (University of Leipzig, 2017)

Insights into the Evolution of small nucleolar RNAs

Sebastian Canzler (University of Leipzig, 2017)

Boolean Implivations in Transcriptomics

Mehmet Volkan Cakir (University of Leipzig, 2017)

Tracing the evolution of long non-coding RNAs - Principles of comparative transcriptomics for splice site conservation and biological applications

Anne Nitzsche (University of Leipzig, 2017)

Exploring the transiptome with high-throughput sequencing data

Gero Doose (University of Leipzig, 2017)

Tracing the evolution of long non-coding RNAs - Principles of comparative transcriptomics for splice site conservation and biological applications

Anne Nitsche (University of Leipzig, 2017)

Methods for DNA Methylation Sequencing Analysis and their Application on Cancer Data

Helene Kretzmer (University of Leipzig, 2016)

BOOLEAN FUNCTIONS AND DISCRETE DYNAMICS: Analytic and Biological Application

Haleh Ebadi (University of Leipzig, 2016)

Rhythms and Evolution: Effects of Timing on Survival

Bruno Pace (University of Leipzig, 2016)

Expanding the SnoRNA Interaction Network

Stephanie Kehr (University of Leipzig, 2016)

Gene regulatory factors in the evolutionary history of humans

Alvaro Perdomo-Sabogal (University of Leipzig, 2016)

Computational investigations into the evolution of mitochondrial genomes

Abdullah Sahyoun (University of Leipzig, 2015)

The mapping task and its various applications in next-generation sequencing

Christian Otto (University of Leipzig, 2015)

(Relaxed) Product Structures of Graphs and Hypergraphs

Lydia Ostermeier (University of Leipzig, 2015)

Transcription factor networks play a key role in human brain evolution and disorders

Stefano Berto (University of Leipzig, 2015)

Genome Informatics for High-Throughput Sequencing Data Analysis - Methods and Application

Steve Hoffmann (University of Leipzig, 2014)

The Dynamic Epigenome - Analysis of the Distribution of Histone Modifications

Lydia Steiner (University of Leipzig, 2013) [ Details ]

Relative Timing of Intron Gain and a New marker for Phylogenetic Analyses

Jörg Lehmann (University of Leipzig, 2013)

High-troughput sequencing and small non-codings RNAs

David Langenberger (University of Leipzig, 2013)

The Orthology Road

Maribel Hernandez Rosales (University of Leipzig, 2013)

Stochastic Tree Models for Macroevolution

Stephanie Keller-Schmidt (University of Leipzig, 2012)

Analysis of large-scale molecular biological data using self-organizing maps

Henry Wirth (University of Leipzig, 2012)

Evolutionary Analysis of the Protein Domain Distribution in Eukaryotes

Arli Aditya Parikesit (University of Leipzig, 2012) [ Details ]

Perturbations in Boolean Networks

Fakhteh Ghanbarnejad (University of Leipzig, 2012)

Computational Studies on the Evolution of Metabolism

Alexander Ullrich (University of Leipzig, 2011)

Molecular Morphology

Alexander Donath (University of Leipzig, 2011)

Transcriptional Regulatory Elements

Wolfgang Otto (University of Leipzig, 2011)

The long and the short of computational ncRNA prediction

Dominic Rose (University of Leipzig, 2010) [ Details ]

Local Prime Factor Decomposition of Approximate Strong Product Graphs

Marc Hellmuth (University of Leipzig, 2010) [ Details ]

Strategies for Homology-Based Identification of Eukaryotic Non-Coding RNA Genes

Manuela Marz (University of Leipzig, 2009) [ Details ]

Structured non-coding RNAs

Jana Hertel (University of Leipzig, 2009)

PhD theses prepared in Leipzig for other institutions

MSc theses written at University of Leipzig

On the alignment of error-prone sequences with a high InDel rate

Anna-Marie Grunwald (University of Leipzig, 2023)

Generation of metabolic networks through reaction atom maps

Nora Beier (University of Leipzig, 2023)

Reevaluating secondary structure prediction programm RNAz for the annotation of ncRNAs in Yeast

Antje Westendorf (University of Leipzig, 2023)

Sorting by Tandem Duplication Random Loss and Inverse Tandem Duplication Random Loss

Bruno Schmidt (University of Leipzig, 2022)

Evolution of Mammalian Adhesion GPCR Splicing Patterns

Robert Felbier (University of Leipzig, 2022)

Transcriptional states underlying acquired resistance to BRAF/MEK-inhibitors in malignant melanoma

Mortensen, Lena Sünke (University of Leipzig, 2022)

Untersuchung genteischer Merkmale mikrobieller Gemeinschaften mittels long-read DNA-Sequwenzdaten

Franziska Erber (University of Leipzig, 2021)

Speeding up laziness - On the different implemetation of a low-coverage hybrid assembler

Kevin Klein (University of Leipzig, 2021)

Extraxting Table Information from Medical Literature using Neurl Networks

Christian Stur (University of Leipzig, 2020)

Dynamische Simulation und Analyse mikrobieller Gemeinschaftsmodelle

Jia Fu (University of Leipzig, 2020)

A new Approach to de Novo Genome Assembly Combining Short and Long Sequencing Data

Sarah von Löhneysen (University of Leipzig, 2020)

A benchmark for the prediction of RHO-independent termination based on high-throughput data

Sarah Strobel (University of Leipzig, 2020)

A search for self-splicing introns in interrupted bacterial genes

Viola Braunmüller (University of Leipzig, 2020)

Visualization and characterization of cross-feeding networks of microbial communities

Jens-Tilman Rau (University of Leipzig, 2020)

Applying Macine Learning Methods dor Transcriptome based Risk Assessment of Prostate Canser

Maximilian Josef Joas (University of Leipzig, 2020)

Classification of non-coding RNAs based on read patterns in mapping data

Tobias Hagemann (University of Leipzig, 2020)

Support vector machine retraining for de novo detection of functional non-coding RNAs

Christopher Klapproth (University of Leipzig, 2020)

Modular Analysis of Differential Splicing and Trancript Isoform Quantification using RNA-Seq Data

Robin Goldmann (University of Leipzig, 2020)

RAP: Ribozeq Analysis Pipeline

Christiane Gärtner (University of Leipzig, 2020)

Charakterisierung von Dynamiken mikrobieller Gemeinschaften durhc kombiierte Analyse von Durchflusszytometrie- und Amplikon-Sequenzierungsdaten

Sebastian Luhnburg (University of Leipzig, 2019)

Partially Local Multi-Way Alignments

Falco Kirchner (University of Leipzig, 2019)

Constructing event-labeled rooted median graphs from generalized orthology relations

Carmen Bruckmann (University of Leipzig, 2019)

Inference of Best Matches from Evolutionary Distance Data

David Schaller (University of Leipzig, 2019)

Automatic Dialect Classification in Spoken German

Johanna Dobbriner (University of Leipzig, 2019)

Evaluation of Knowledge Base Population via Natutal Language Processing on Biomedical Documents

Albert Gass (University of Leipzig, 2019)

Inference of gene regulatory networks from time series

Paul Michaelis (University of Leipzig, 2019)

Evaluating Clustering Methods for Transcriptomic Fingerprints

Nora Grieb (University of Leipzig, 2019)

Analyses of an Unknown Endosymbiont Found in Placozoa sp H23

Sofia Haller (University of Leipzig, 2019)

The Ecotoxicogenomic Self-Organizing Map of Fathead Minnow

Stefan Krämer (University of Leipzig, 2018)

Evaluation of different muscle models through neuroevolution of human locomotion

Elias Müller (University of Leipzig, 2018)

Computational analysis of neandertal contribution to modern human developmental phenotypes

Sophie Wolf (University of Leipzig, 2018)

CCA-like enzymes in the order clostridiales: distribution and horizontal gene transfer

Franziska Reinhardt (University of Leipzig, 2018)

Development of a universal methylation-based cancer classifier

Anastasia Wolschewski (University of Leipzig, 2018)

Detection of rearrangements in cancer genome with ChIP-seq data

Jeremias Schebera (University of Leipzig, 2018)

Visualization of synteny-based orthology data

Yuan Peng (University of Leipzig, 2018)

Screening of Prostate Cancer Tissue - Samples for Gene Fusions in a Custom Assembly

Carolin Schimmelpfennig (University of Leipzig, 2017)

Partition function algorithm applied to prediction of paralog evolution

Gabor Balogh (University of Leipzig, 2017)

SOM portrayal of the blood transcriptome

Maria Schmidt (University of Leipzig, 2017)

Host prediction in RNA viruses

Adrian Viehweger (University of Leipzig, 2017)

Planares Zeichnen von RNA-Sekundärstrulturen

Daniel Alexander (University of Leipzig, 2017)

NGS Data Analysis within the Scope of Molecular Diagnostics

Alexander Scholz (University of Leipzig, 2017)

Automatischer Workflog für die Analyse von agonistischen und antagonistischen Effekten mittels Schild-Analyse

(University of Leipzig, 2017)

Automatischer Workflog für die Analyse von agonistischen und antagonistischen Effekten mittels Schild-Analyse

Markus Michaelis (University of Leipzig, 2017)

Folding Kinetics of Riboswitches

Felix Kühnl (University of Leipzig, 2016)

Differential integration of genes involved in cognitive disorders into co-expression networks of human brains

Janine Rauch (University of Leipzig, 2016)

Population Structure in Aboriginal Australiens - a genetic perspective on uniparental markers

Enrico Macholdt (University of Leipzig, 2016)

Using dynamic modeling to infer microbial interaction networks from flow cytometry data

Lukas Hirsch (University of Leipzig, 2016)

The genetic relationship between modern and archaic humans

Steffi Grothe (University of Leipzig, 2016)

Strukturelle Analyse von Transkriptions-intermediaten synthetischer Riboswitches

Frauke Olthoff (University of Leipzig, 2016)

Evolution of DNA methyltranferases in Neotera

Oliver Scheer (University of Leipzig, 2016)

Analyse von artifiziellen Substraten für die tRNA-Nukleotidyltransferase

Lisa Duchstein (University of Leipzig, 2015)

Processed Small RNAs in Archaea and BHB Elements

Sarah Berkemer (University of Leipzig, 2015)

Alignment of Words

Nancy Retzlaff (University of Leipzig, 2015)

Hidden Treasures in unspliced EST data

Jan Engelhardt (University of Leipzig, 2014) [ Details ]

Role of random monoallelically expressed genes in the development of Alzheimer's disease

Kanton, Sabina (University of Leipzig, 2014)

Evolutionärer Vergleich von Bindungsstellen des KAP1 bei Mensch und Schimpanse

Sandra Gerstl (University of Leipzig, 2014)

A Lagranian Particle Approach to fluid image warping and image registration

Christian Ludborz (University of Leipzig, 2014)

Functional characterization of ZNF542 and ZEB2 in primates

Lisa Falkowski (University of Leipzig, 2014)

Oriented Graph Grammers and Stereochemistry

Fabian Externbrink (University of Leipzig, 2014)

TiBi-3D a Guide through the World of Epigenetics

Daniel Gerighausen (University of Leipzig, 2014) [ Details ]

RNA structure prediction of PKR activators

Tobias Mede (University of Leipzig, 2013)

Comparative Transcriptomics of Long Non-Coding RNAs

Anne Nitsche (University of Leipzig, 2012)

A homolgy based annotation pipeline for small nucleolar RNAs in Deuterostomia

Sebastian Bartschat (University of Leipzig, 2011)

Ultra-Conserved Regions Analyzing the Tip of the Iceberg

Sven Findeiß (University of Leipzig, 2008) [ Details ]

Detection of Orthologs and Paralogs from Local Syntenic Blocks

Jörg Lehmann (University of Leipzig, 2007) [ Details ]

Tracing the TIRs - Expanding the repertoire of known TIR domain containing proteins

Alexander Donath (University of Leipzig, 2007) [ Details ]

Evolution of Spliceeosomal RNAs in Metazoan Animals

Manuela Lindemeyer (University of Leipzig, 2006)

Noncoding RNA Detection Using Comperative Genomics

Dominic Rose (University of Leipzig, 2006) [ Details ]

Detection of conserves non-coding RNAs in the pig EST data and related mammals

Stefan Seemann (University of Leipzig, 2006)

BBQ in Tanimoto Scores: Novel Scoring Schemes for cis-Regulatory Module Discovery

Peter Menzel (University of Leipzig, 2006) [ Details ]

MicroRNA Detection using Comparative Genomics

Jana Hertel (University of Leipzig, 2005)

MSc theses prepared in Leipzig for other institutions

In silico Analysis of Canine and Feline Parvovirus Evolution

Jennifer Hetzel (University of Vienna, 2004)

Molekulare Evolution der Vertebraten snoRNAs

Bettina Müller (FH Weihenstephan, 2004)

Genomic Surveys for RNA Genes

Andrea Tanzer (University of Vienna, 2004)

Picking Up the Trail of Phylogenetic Footprints: The Story of Tracker and Its First Tracings

Sonja J. Prohaska (University of Vienna, 2004)

Discovery of Transcription Factor Binding Sites

Claudia Fried (University of Vienna, 2004)

BSc theses written at University of Leipzig

Simulation of Phylogenetic Networks and Analsysis of Their Clustering Systems

Jeremias Frohn (University of Leipzig, 2023)

Training and evaluation of a support vector regression model for standardized RNA folding energies

Siegfried Zötzsche (University of Leipzig, 2017)

Cliquen in Co-Graphen

Marius Brunnert (University of Leipzig, 2015)

orthoDeprime: A Tool for Heuristic Cograph Editing on Estimated Ortholgy Graphs

Felix Kühnl (University of Leipzig, 2014)

BSc theses prepared in Leipzig for other institutions

Diploma theses written at University of Leipzig

Clustering and phylogenetic analysis of food recipes

Peter Binder (University of Leipzig, 2015)

Diploma theses prepared in Leipzig for other institutions