[HTML][HTML] Single cell sequencing reveals endothelial plasticity with transient mesenchymal activation after myocardial infarction

…, M Furtado, N Rosenthal, N Baumgarten… - Nature …, 2021 - nature.com
Endothelial cells play a critical role in the adaptation of tissues to injury. Tissue ischemia
induced by infarction leads to profound changes in endothelial cell functions and can induce …

EpiRegio: analysis and retrieval of regulatory elements linked to genes

N Baumgarten, D Hecker, S Karunanithi… - Nucleic Acids …, 2020 - academic.oup.com
A current challenge in genomics is to interpret non-coding regions and their role in transcriptional
regulation of possibly distant target genes. Genome-wide association studies show …

TEPIC 2—an extended framework for transcription factor binding prediction and integrative epigenomic analysis

F Schmidt, F Kern, P Ebert, N Baumgarten… - …, 2019 - academic.oup.com
Prediction of transcription factor (TF) binding from epigenetics data and integrative analysis
thereof are challenging. Here, we present TEPIC 2 a framework allowing for fast, accurate …

[HTML][HTML] DOT1L regulates chamber-specific transcriptional networks during cardiogenesis and mediates postnatal cell cycle withdrawal

P Cattaneo, MGB Hayes, N Baumgarten… - Nature …, 2022 - nature.com
Mechanisms by which specific histone modifications regulate distinct gene networks remain
little understood. We investigated how H3K79me2, a modification catalyzed by DOT1L and …

[PDF][PDF] Circular RNA circPLOD2 regulates pericyte function by targeting the transcription factor KLF4

SF Glaser, A Brezski, N Baumgarten, M Klangwart… - Cell Reports, 2023 - cell.com
Circular RNAs are generated by backsplicing and control cellular signaling and phenotypes.
Pericytes stabilize capillary structures and play important roles in the formation and …

TF-Prioritizer: a Java pipeline to prioritize condition-specific transcription factors

…, LL Willruth, O Lazareva, K Yuan, N Baumgarten… - …, 2023 - academic.oup.com
Background Eukaryotic gene expression is controlled by cis-regulatory elements (CREs),
including promoters and enhancers, which are bound by transcription factors (TFs). Differential …

Integrative analysis of epigenetics data identifies gene-specific regulatory elements

F Schmidt, A Marx, N Baumgarten, M Hebel… - Nucleic acids …, 2021 - academic.oup.com
Understanding how epigenetic variation in non-coding regions is involved in distal gene-expression
regulation is an important problem. Regulatory regions can be associated to genes …

A statistical approach for identifying single nucleotide variants that affect transcription factor binding

N Baumgarten, L Rumpf, T Kessler, MH Schulz - iScience, 2024 - cell.com
Non-coding variants located within regulatory elements may alter gene expression by
modifying Transcription Factor (TF) binding sites, thereby leading to functional consequences. …

CVD-associated SNPs with regulatory potential drive pathologic non-coding RNA expression

C Zhu, N Baumgarten, M Wu, Y Wang, AP Das, J Kaur… - bioRxiv, 2023 - biorxiv.org
Background Cardiovascular diseases (CVDs) are the leading cause of death worldwide.
Genome-wide association studies (GWAS) have identified many single nucleotide …

A statistical approach to identify regulatory DNA variations

N Baumgarten, L Rumpf, T Kessler, MH Schulz - bioRxiv, 2023 - biorxiv.org
Non-coding variations located within regulatory elements may alter gene expression by
modifying Transcription Factor (TF) binding sites and thereby lead to functional consequences …