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Articles by Markus Joppich
Immunothrombolytic monocyte-neutrophil axes dominate the single-cell landscape of human thrombosis and correlate with thrombus resolution
Keywords immunothrombosis thrombosis immune landscape neutrophils monocytes innate immunity single-cell multi-omics immunothrombolysis thrombus resolution immunothrombotic dysregulation thromboinflammation stroke immune-cell plasticity organ ischemia Introduction Thrombosis and thromboembolism are a major global cause of morbidity and mortality by leading to myocardial infarction, stroke, and venous thromboembolism.1,2 Simultaneously, anti-thrombotic therapies carry a relevant risk of...
PLO(SC)2: Plots and Scripts for scRNA-seq analysis
Abstract scRNA-seq analysis has become a standard technique for studying biological systems. As costs decrease, scRNA-seq experiments become increasingly complex. While typical scRNA-seq analysis frameworks provide basic functionality to analyze such data sets, downstream analysis and visualization become a bottleneck. Standard plots are not always suitable to provide specific insight into such complex data sets and should be extended to provide camera-ready, meaningful plots.
Text Mining miRNA-gene Interactions for the mx-plore Platform
Abstract miRNAs are post-transcriptional regulators which bind to the specific mRNA of expressed genes and induce increased mRNA degradation, thereby reducing the gene expression of their target genes. miRNAs perform their regulatory functions in a context-specific manner. Several databases contain collections of miRNA-target interactions, which are either experimentally validated, derived from high-throughput experiments, or computationally predicted or captured from existing literature.
PICASO: Profiling Integrative Communities of Aggregated Single-cell Omics data
Abstract Various single-cell modalities covering transcriptomics, epigenetic and spatio-temporal changes in health and disease phenotypes are used in an exploratory way to understand biological systems at single-cell resolution. However, the vast amount of such single-cell data is not systematically linked to existing biomedical data. Networks have previously been used to represent harmonized biomedical data.
Resident and recruited macrophages differentially contribute to cardiac healing after myocardial ischemia
Request a detailed protocol After sorting, cells were proceeded for single-cell capture, barcoding and library preparation using Chromium Next GEM single cell 3′ (v3.1, 10× Genomics) according to the manufacturer’s specifications. Pooled libraries were sequenced on an Illumina HiSeq1500 sequencer (Illumina, San Diego, USA) in paired-end mode with asymmetric read length of 28 + 91 bp and a single indexing read of 8 bp.
Multiomic analyses uncover immunological signatures in acute and chronic coronary syndromes - Nature Medicine
Abstract Acute and chronic coronary syndromes (ACS and CCS) are leading causes of mortality. Inflammation is considered a key pathogenic driver of these diseases, but the underlying immune states and their clinical implications remain poorly understood. Multiomic factor analysis (MOFA) allows unsupervised data exploration across multiple data types, identifying major axes of variation and associating these with underlying molecular processes.
Peripheral priming induces plastic transcriptomic and proteomic responses in circulating neutrophils required for pathogen containment
Research Article HEALTH AND MEDICINE Rainer Kaiser https://orcid.org/0000-0003-1750-3395 rainer.kaiser@med.uni-muenchen.de, Christoph Gold https://orcid.org/0009-0008-8994-1021, [...] , Markus Joppich https://orcid.org/0000-0002-6665-8951, Quentin Loew, [...] , Anastassia Akhalkatsi, Tonina T.
Immunothrombolytic monocyte-neutrophil axes dominate the single-cell landscape of human thrombosis
Abstract Thrombotic diseases remain the major cause of death and disability worldwide with insufficient preventive and therapeutic strategies available. In the last decades a prominent inflammatory component has been identified as a key driver in the initiation and propagation of thrombosis, named thromboinflammation.
Resident and recruited macrophages differentially contribute to cardiac healing after myocardial ischemia
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Tryptophan usage by Helicobacter pylori differs among strains
Abstract Because of its association with severe gastric pathologies, including gastric cancer, Helicobacter pylori has been subject of research for more than 30 years. Its capacity to adapt and survive in the human stomach can be attributed to its genetic flexibility. Its natural competence and its capacity to turn genes on and off allows H. pylori to adapt rapidly to the changing conditions of its host.
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