Bioinformatics Leipzig

• Published papers
• Supplemental material
• Working papers
• PhD/MSc/BSc/Diploma theses
• Posters
• Books

Publications - PhD/MSc/BSc/Diploma theses

PhD theses written at University of Leipzig

Annotation of Small Proteins

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

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

The Folding Kinetics of RNA

Exploration of Chemical Space

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

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

Computational Characterization of Long Non-coding RNAs

Evolution of DNA methylation across Metazoa

Unraveling the genetic secrets of ancient Baikal amphipods

Segmentation of Heterogeneous Multivariate Genome Annotation Data

Gene Family Histories - Theory and Algorithms

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

Studying Evoltunionary Change - Transdisciplinary Advances in Understanding and Measuring Evolution

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

Comparative Genomics in Distant Taxa

The marvelou World of tRNAs

Improved Workflows for RNA Homology Search

A Parametric Model for the Analysis and Quantification of Fovel Shapes

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

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

Adaptive Evolution of Long Non-Coding RNAs

Sequences Signature and Genome Rearrangements in Mitogenomes

High quality gene annotation for deep phylogenetic analysis

Understanding divergent evolution through comparative genomics

Linguistic Diversity Through Data

Sequences Signature and Genome Rearrangements in Mitogenomes

Insights into the Evolution of small nucleolar RNAs

Boolean Implivations in Transcriptomics

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

Exploring the transiptome with high-throughput sequencing data

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

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

BOOLEAN FUNCTIONS AND DISCRETE DYNAMICS: Analytic and Biological Application

Rhythms and Evolution: Effects of Timing on Survival

Expanding the SnoRNA Interaction Network

Gene regulatory factors in the evolutionary history of humans

Computational investigations into the evolution of mitochondrial genomes

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

(Relaxed) Product Structures of Graphs and Hypergraphs

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

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

The Dynamic Epigenome - Analysis of the Distribution of Histone Modifications

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

High-troughput sequencing and small non-codings RNAs

The Orthology Road

Stochastic Tree Models for Macroevolution

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

Evolutionary Analysis of the Protein Domain Distribution in Eukaryotes

Perturbations in Boolean Networks

Computational Studies on the Evolution of Metabolism

Molecular Morphology

Transcriptional Regulatory Elements

The long and the short of computational ncRNA prediction

Local Prime Factor Decomposition of Approximate Strong Product Graphs

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

Structured non-coding RNAs

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

Generation of metabolic networks through reaction atom maps

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

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

Evolution of Mammalian Adhesion GPCR Splicing Patterns

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

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

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

Extraxting Table Information from Medical Literature using Neurl Networks

Dynamische Simulation und Analyse mikrobieller Gemeinschaftsmodelle

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

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

A search for self-splicing introns in interrupted bacterial genes

Visualization and characterization of cross-feeding networks of microbial communities

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

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

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

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

RAP: Ribozeq Analysis Pipeline

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

Partially Local Multi-Way Alignments

Constructing event-labeled rooted median graphs from generalized orthology relations

Inference of Best Matches from Evolutionary Distance Data

Automatic Dialect Classification in Spoken German

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

Inference of gene regulatory networks from time series

Evaluating Clustering Methods for Transcriptomic Fingerprints

Analyses of an Unknown Endosymbiont Found in Placozoa sp H23

The Ecotoxicogenomic Self-Organizing Map of Fathead Minnow

Evaluation of different muscle models through neuroevolution of human locomotion

Computational analysis of neandertal contribution to modern human developmental phenotypes

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

Development of a universal methylation-based cancer classifier

Detection of rearrangements in cancer genome with ChIP-seq data

Visualization of synteny-based orthology data

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

Partition function algorithm applied to prediction of paralog evolution

SOM portrayal of the blood transcriptome

Host prediction in RNA viruses

Planares Zeichnen von RNA-Sekundärstrulturen

NGS Data Analysis within the Scope of Molecular Diagnostics

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

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

Folding Kinetics of Riboswitches

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

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

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

The genetic relationship between modern and archaic humans

Strukturelle Analyse von Transkriptions-intermediaten synthetischer Riboswitches

Evolution of DNA methyltranferases in Neotera

Analyse von artifiziellen Substraten für die tRNA-Nukleotidyltransferase

Processed Small RNAs in Archaea and BHB Elements

Alignment of Words

Hidden Treasures in unspliced EST data

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

Evolutionärer Vergleich von Bindungsstellen des KAP1 bei Mensch und Schimpanse

A Lagranian Particle Approach to fluid image warping and image registration

Functional characterization of ZNF542 and ZEB2 in primates

Oriented Graph Grammers and Stereochemistry

TiBi-3D a Guide through the World of Epigenetics

RNA structure prediction of PKR activators

Comparative Transcriptomics of Long Non-Coding RNAs

A homolgy based annotation pipeline for small nucleolar RNAs in Deuterostomia

Ultra-Conserved Regions Analyzing the Tip of the Iceberg

Detection of Orthologs and Paralogs from Local Syntenic Blocks

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

Evolution of Spliceeosomal RNAs in Metazoan Animals

Noncoding RNA Detection Using Comperative Genomics

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

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

MicroRNA Detection using Comparative Genomics

MSc theses prepared in Leipzig for other institutions

In silico Analysis of Canine and Feline Parvovirus Evolution

Molekulare Evolution der Vertebraten snoRNAs

Genomic Surveys for RNA Genes

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

Discovery of Transcription Factor Binding Sites

BSc theses written at University of Leipzig

Simulation of Phylogenetic Networks and Analsysis of Their Clustering Systems

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

Cliquen in Co-Graphen

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

BSc theses prepared in Leipzig for other institutions

Diploma theses written at University of Leipzig

Clustering and phylogenetic analysis of food recipes

Diploma theses prepared in Leipzig for other institutions