Phd student
Office: Haus 26, 4th floor, Room 402
Goethe University and Uniklinikum Frankfurt
Theodor-Stern-Kai 7
60590 Frankfurt am Main
+49 69 6301 86208 
n.baumgarten|em.uni-frankfurt.deAbout Me
I mainly work on projects that analyse the binding behavior of Transcription Factors (TFs) using epigenomics and genome variation data, which aim for a better understanding of gene regulation. For instance, I develop a method that prioritizes SNPs observed in non-coding genomic regions as targets of one or several TFs. In addition, the method jointly identifies TF-gene pairs for whom the TF binding affinity is influenced by the SNP.
Short CV
I received a Bachelor and Master in Computational Molecular Biology/Bioinformatics from the Saarland University. During my master studies I worked as a Hiwi in the group of Prof. Dr. Jörn Walter (Genetic/Epigenetic, Saarland University) and for an internship I joined the group of Dr. Mathias Wegner at the Alfred-Wegener Institute, List (Sylt). Since July 2018 I am a PhD student in Prof. Schulz's group.
Publications
*shared first authorship ^shared last authorship
[5] Baumgarten N*, Hecker D*, Karunanithi S*, Schmidt F, List M, Schulz MH^
EpiRegio: Analysis and retrieval of regulatory elements linkedto genes.,
Nucleic Acids Research (in press), full text
[4] N Baumgarten, F Schmidt, MH Schulz
Improved linking of motifs to their TFs using domain information,
full text
[3] F Schmidt, A Marx, M Hebel,M Wegner, N Baumgarten, M Kaulich, J Göke, J Vreeken, MH Schulz
Integrative analysis of epigenetics data identifies gene-specific regulatory elements,
[preprint]
[2] F Schmidt, F Kern, P Ebert, N Baumgarten, MH Schulz
TEPIC 2 - An extended framework for transcription factor binding prediction and integrative epigenomic analysis,
Bioinformatics, bty856, full text
[1] SC Mueller, C Backes, A Gress, N Baumgarten OV Kalinina, O Kohlbacher, E Meese, A Keller
BALL-SNPgp-from genetic variants toward computational diagnostics,
Bioinformatics, Volume 32, Issue 12, 15 June 2016, Pages 1888–1890, full text
Poster Presentations
Nina Baumgarten, Florian Schmidt and Marcel H. Schulz
A statistical approach detecting genetic variation as the cause of far-away transcription regulation
ISMB/ECCB 2019, Switzerland, Basel, July 21-25, 2019.
Nina Baumgarten, Florian Schmidt and Marcel H. Schulz
Domain Information improves motif enrichment analysis for ChIP-seq data
17th European Conference on Computational Biology, Athens, Greece, Sep 8-12, 2018.