Marcel H. Schulz
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View article: The transaminase-ω-amidase pathway senses oxidative stress to control glutamine metabolism and α-ketoglutarate levels in endothelial cells
The transaminase-ω-amidase pathway senses oxidative stress to control glutamine metabolism and α-ketoglutarate levels in endothelial cells Open
Oxidative stress is a major driver of cardiovascular disease; however, the fast changes in cellular metabolism caused by short-lived reactive oxygen species (ROS) remain ill-defined. Here, we characterized changes in the endothelial cell m…
View article: Epigenetic control of metabolic identity across cell types
Epigenetic control of metabolic identity across cell types Open
Background Constraint-based network modeling is a powerful genomic-scale approach for analyzing cellular metabolism, capturing metabolic variations across tissues and cell types, and defining the metabolic identity essential for identifyin…
View article: TripLexicon: prediction and analysis of gene regulatory RNA–DNA interactions
TripLexicon: prediction and analysis of gene regulatory RNA–DNA interactions Open
Motivation Non-coding RNA (ncRNA) plays a crucial role in gene regulation, including by forming sequence-specific RNA–DNA interactions at gene regulatory elements. One form of interaction takes place via the formation of RNA:DNA:DNA triple…
View article: Decoding heart failure subtypes with neural networks via differential explanation analysis
Decoding heart failure subtypes with neural networks via differential explanation analysis Open
Single-cell transcriptomics offers critical insights into the molecular mechanisms of heart failure (HF) with reduced or preserved ejection fraction. However, understanding these mechanisms is hindered by the growing complexity of single-c…
View article: Vascular Niches Are the Primary Hotspots in Cardiac Aging
Vascular Niches Are the Primary Hotspots in Cardiac Aging Open
BACKGROUND: Aging is a major, yet unmodifiable, cardiovascular risk factor and is associated with vascular alterations, increased cardiac fibrosis, and inflammation, all of which contribute to impaired cardiac function. However, the microe…
View article: Cystine import and oxidative catabolism fuel vascular growth and repair via nutrient-responsive histone acetylation
Cystine import and oxidative catabolism fuel vascular growth and repair via nutrient-responsive histone acetylation Open
Endothelial metabolism underpins tissue regeneration, health, and longevity. We uncover a nuclear oxidative catabolic pathway linking cystine to gene regulation. Cells preparing to proliferate upregulate the SLC7A11 transporter to import c…
View article: Quantifying Components in a Model Vaccine with Machine-Learning-Augmented Raman Spectroscopy
Quantifying Components in a Model Vaccine with Machine-Learning-Augmented Raman Spectroscopy Open
Vaccination is a highly efficient strategy in controlling infections. Aluminum-containing adjuvants have long been used to enhance immunogenicity, but quantification of adsorbed antigens remains analytically challenging. This study uses Ra…
View article: Pipeline Olympics: continuable benchmarking of computational workflows for DNA methylation sequencing data against an experimental gold standard
Pipeline Olympics: continuable benchmarking of computational workflows for DNA methylation sequencing data against an experimental gold standard Open
DNA methylation is a widely studied epigenetic mark and a powerful biomarker of cell type, age, environmental exposures, and disease. Whole-genome sequencing following selective conversion of unmethylated cytosines into thymines via bisulf…
View article: A cell type-specific expression atlas of small and total RNA in the heart after myocardial infarction
A cell type-specific expression atlas of small and total RNA in the heart after myocardial infarction Open
Acute myocardial infarction (AMI) is a leading cause of mortality worldwide. MicroRNAs (miRNAs), among other small non-coding RNAs, shape the transcriptome and control cellular functions. Although single-cell technologies are now available…
View article: Harnessing machine learning models for epigenome to transcriptome association studies
Harnessing machine learning models for epigenome to transcriptome association studies Open
Understanding how epigenome variation contributes to gene expression in disease and development is a fundamental challenge. Regulatory regions show cell type-specific epigenome activity and differ in their location, size, and distance to t…
View article: <scp>STAT3</scp> expression is reduced in cardiac pericytes in <scp>HFpEF</scp> and its loss reduces cellular adhesion and induces pericyte senescence
<span>STAT3</span> expression is reduced in cardiac pericytes in <span>HFpEF</span> and its loss reduces cellular adhesion and induces pericyte senescence Open
Heart failure with preserved ejection fraction (HFpEF) accounts for half of heart failure cases and is characterised by reduced pericyte coverage. While the contributions of other cardiac cell types to HFpEF are well‐studied, the role of p…
View article: GeneCOCOA: Detecting context-specific functions of individual genes using co-expression data
GeneCOCOA: Detecting context-specific functions of individual genes using co-expression data Open
Extraction of meaningful biological insight from gene expression profiling often focuses on the identification of statistically enriched terms or pathways. These methods typically use gene sets as input data, and subsequently return overre…
View article: Decoding heart failure subtypes with neural networks via differential explanation analysis
Decoding heart failure subtypes with neural networks via differential explanation analysis Open
Single-cell transcriptomics offers critical insights into the molecular mechanisms of heart failure with reduced or preserved ejection fraction. However, understanding these mechanisms is hindered by the growing complexity of single-cell d…
View article: Cell type-specific epigenetic regulatory circuitry of coronary artery disease loci
Cell type-specific epigenetic regulatory circuitry of coronary artery disease loci Open
Coronary artery disease (CAD) is the leading cause of death worldwide. Recently, hundreds of genomic loci have been shown to increase CAD risk, however, the molecular mechanisms underlying signals from CAD risk loci remain largely unclear.…
View article: Revealing microRNA regulation in single cells
Revealing microRNA regulation in single cells Open
MicroRNAs (miRNAs) are key regulators of gene expression and control cellular functions in physiological and pathophysiological states. miRNAs play important roles in disease, stress, and development, and are now being investigated for the…
View article: Long non-coding RNAs direct the SWI/SNF complex to cell type-specific enhancers
Long non-coding RNAs direct the SWI/SNF complex to cell type-specific enhancers Open
The coordination of chromatin remodeling is essential for DNA accessibility and gene expression control. The highly conserved and ubiquitously expressed SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodeling complex plays a central …
View article: Detection of statistically robust interactions from diverse RNA-DNA ligation data
Detection of statistically robust interactions from diverse RNA-DNA ligation data Open
Chromatin-localized RNAs play diverse roles in gene regulation and nuclear architecture. Mapping genome-wide RNA-DNA interactions is possible using a variety of molecular methods, including using bridging oligonucleotides to ligate RNA and…
View article: Pipeline Olympics: continuable benchmarking of computational workflows for DNA methylation sequencing data against an experimental gold standard
Pipeline Olympics: continuable benchmarking of computational workflows for DNA methylation sequencing data against an experimental gold standard Open
DNA methylation is a widely studied epigenetic mark and a powerful biomarker of cell type, age, environmental exposures, and disease. Whole-genome sequencing following selective conversion of unmethylated cytosines into thymines via bisulf…
View article: A systematic analysis of circRNAs in subnuclear compartments
A systematic analysis of circRNAs in subnuclear compartments Open
CircRNAs are an important class of RNAs with diverse cellular functions in human physiology and disease. A thorough knowledge of circRNAs including their biogenesis and subcellular distribution is important to understand their roles in a w…
View article: The transaminase-ω-amidase pathway is a redox switch in glutamine metabolism that generates α-ketoglutarate
The transaminase-ω-amidase pathway is a redox switch in glutamine metabolism that generates α-ketoglutarate Open
Summary Oxidative stress is caused by short-lived molecules and metabolic changes belong to the fastest cellular responses. Here we studied how the endothelial cell metabolome reacts to acute oxidative challenges (menadione or H 2 O 2 ) to…
View article: Metabolic alterations drive inflammatory phenotypes in CHIP-associated heart failure
Metabolic alterations drive inflammatory phenotypes in CHIP-associated heart failure Open
Summary Mutations in DNA methyltransferase 3 alpha (DNMT3A) are the most frequent driver of clonal hematopoiesis of indeterminate potential (CHIP), and associated with higher risk of cardiovascular disease and pro-inflammatory activation o…
View article: Epigenetic control of metabolic identity across cell types
Epigenetic control of metabolic identity across cell types Open
Background Constraint-based network modeling is a powerful genomic-scale approach for analyzing cellular metabolism, capturing metabolic variations across tissues and cell types, and defining the metabolic identity essential for identifyin…
View article: GeneCOCOA: Detecting context-specific functions of individual genes using co-expression data
GeneCOCOA: Detecting context-specific functions of individual genes using co-expression data Open
Extraction of meaningful biological insight from gene expression profiling often focuses on the identification of statistically enriched terms or pathways. These methods typically use gene sets as input data, and subsequently return overre…
View article: Long non-coding RNAs direct the SWI/SNF complex to cell-specific enhancers
Long non-coding RNAs direct the SWI/SNF complex to cell-specific enhancers Open
The coordination of chromatin remodeling is essential for DNA accessibility and gene expression control 1 . The highly conserved and ubiquitously expressed SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodeling complex plays a centr…
View article: An AI-based cell segmentation pipeline for studying immune markers from brightfield microscopy images
An AI-based cell segmentation pipeline for studying immune markers from brightfield microscopy images Open
Background : Cell segmentation is a essential task in analysing the tumormicroenvironment (TME), which encompasses vascular cells and cells of theinnate and adaptive immune system in and around the tumor. The impact of theTME on survival a…
View article: Improved integration of single-cell transcriptome data demonstrates common and unique signatures of heart failure in mice and humans
Improved integration of single-cell transcriptome data demonstrates common and unique signatures of heart failure in mice and humans Open
Background Cardiovascular research heavily relies on mouse (Mus musculus) models to study disease mechanisms and to test novel biomarkers and medications. Yet, applying these results to patients remains a major challenge and often results …
View article: Multiomics analysis identifies novel facilitators of human dopaminergic neuron differentiation
Multiomics analysis identifies novel facilitators of human dopaminergic neuron differentiation Open
Midbrain dopaminergic neurons (mDANs) control voluntary movement, cognition, and reward behavior under physiological conditions and are implicated in human diseases such as Parkinson’s disease (PD). Many transcription factors (TFs) control…
View article: Dataset of single nucleotide polymorphisms of immune-associated genes in patients with SARS-CoV-2 infection
Dataset of single nucleotide polymorphisms of immune-associated genes in patients with SARS-CoV-2 infection Open
The SARS-CoV-2 pandemic has affected nations globally leading to illness, death, and economic downturn. Why disease severity, ranging from no symptoms to the requirement for extracorporeal membrane oxygenation, varies between patients is s…
View article: The challenges of research data management in cardiovascular science: a DGK and DZHK position paper—executive summary
The challenges of research data management in cardiovascular science: a DGK and DZHK position paper—executive summary Open
The sharing and documentation of cardiovascular research data are essential for efficient use and reuse of data, thereby aiding scientific transparency, accelerating the progress of cardiovascular research and healthcare, and contributing …