[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 …
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 …
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
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 …
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 …
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 …
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 …
including promoters and enhancers, which are bound by transcription factors (TFs). Differential …
Integrative analysis of epigenetics data identifies gene-specific regulatory elements
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 …
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
Non-coding variants located within regulatory elements may alter gene expression by
modifying Transcription Factor (TF) binding sites, thereby leading to functional consequences. …
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 …
Genome-wide association studies (GWAS) have identified many single nucleotide …
A statistical approach to identify regulatory DNA variations
Non-coding variations located within regulatory elements may alter gene expression by
modifying Transcription Factor (TF) binding sites and thereby lead to functional consequences …
modifying Transcription Factor (TF) binding sites and thereby lead to functional consequences …