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Former Members

Julia Bayer

Julia Bayer - master student (2015)

The aim of my research internship is to find target mRNAs and their corresponding proteins of former identified microRNAs from next generation sequencing data in niche model organisms. For example, I compare and link different microRNA targeting databases to get the best matches and subsequently map the identified targets to the transcriptome and proteome of regenerating hearts in the newt Notophthalmus viridescens.

 

Nina Hofmann

Nina Hofmann - bachelor student (2015)

In preparation for my bachelor thesis in bioinformatics at the University for Applied Sciences (THM) in Gießen I am doing a research internship which focuses on development, improvement and evaluation of bioinformatics software. Specifically, I'm working on a tool which offers the opportunity to add new information, such as new transcripts or genes, to a still existing transcriptome assembly without the necessary of a complete new assembly and annotation. In the end the tool will be usable for real data. Contact

 

Thomas Licht

Thomas Licht - master student (2015)

As a bioinformatics master student at the Goethe University Frankfurt am Main, I am interested in alternative RNA splicing, detection and scoring of RNA binding sites. One of our proteins of interest is able to re-include commonly skipped exons during alternative splicing. Driven by wetlab generated data for single target genes, I postulate general rules for potential binding sites and develop scoring functions for genome wide binding screenings. Contact

 

Marc Bruckskotten

Marc Bruckskotten - phd student (2014)

Marcs work focused on biocomputational analysis, integration and data-mining of high-throughput datasets derived from several omics-approaches. During his diploma he developed a statistical method to detect and analyze specific enrichments and representations of high-throughput datasets within Gene Ontology. His PhD project was dedicated to develop a repository and data-warehouse for a new model organism, which lacks genome information, like the newt Notophthalmus viridescens. The developed bioinformatics database comprises assemblies of de novo transcriptome and proteome data, expression information from several methods, annotation and functional characterization. Besides this integration of data the repository allows a structured data-mining and analysis of certain organisms without a known genome characterized only by different high-throughput datasets. Marc is now staff scientist at the MPI for Terrestrial Microbiology.

 

Marie-Theres Arend

Marie-Theres Arend - masters thesis and internship (2014)

Marie helped our group to set up a Galaxy server, a web-based platform for data intensive biomedical research. She integrated several in-house developed tools, including the miRNA pipeline, enabling us and other researchers to efficiently access these tools without the need of using the command line.
Additionally, Marie wrote her masters thesis about the evaluation and comparison of de novo transcriptome assembly algorithms. One objective was to optimize the complete reconstruction of the transcriptome of non-model organisms

 

Mario Herzog

Mario Herzog - bachelor student (2013)

Mario focused his work on identification of microRNAs in next-generation sequencing data from regenerating hearts in the newt Notophthalmus viridescens. He developed a pipeline to quantify expression of miRNAs at different time points with the goal to reflect the ongoing regeneration process.

 

Stephan Neese

Stephan Neese - bachelor student (2013)

During his bachelor, Stephan developed an approach to correct for frameshifts in de novo sequence assemblies. He used hidden Markov models to calculate the per-readingframe coding potential of translated nucleotide sequences. Transitions from regions of high to regions of low coding potential were then used to detect possible frameshifts.

 

Nicole Schnell - diploma student (2011)

For her diploma, Nicole developed a pipeline for quantitative analysis of phospho peptides. She integrated SILAC, mass spectrometry, MaxQuant and phospho databases to quantify phosphorylated proteins and discover new phosphorylation sites. Nicole is now employed in the lipidomics & proteomics facility at CECAD Cologne.

 

Bodo Vossen - diploma student (2011)

During his diploma, Bodo worked out how to set up a productive galaxy environment and how to customize it to make existing programs written by different researchers available for all researchers in the institute. Furthermore, he expanded the galaxy codebase to integrate programs on the fly into galaxy, including automated program validation and integration.

 

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