A5074661143- RNA and protein synthesis mechanisms
- Immune Cell Function and Interaction
- RNA Research and Splicing
- SARS-CoV-2 and COVID-19 Research
- T-cell and B-cell Immunology
- RNA modifications and cancer
- Single-cell and spatial transcriptomics
- Immunodeficiency and Autoimmune Disorders
- Cancer-related molecular mechanisms research
- Monoclonal and Polyclonal Antibodies Research
- CAR-T cell therapy research
- MicroRNA in disease regulation
- Cancer Genomics and Diagnostics
- Viral Infections and Immunology Research
- Heat shock proteins research
- Advanced biosensing and bioanalysis techniques
- Genomics and Phylogenetic Studies
- Metallurgy and Material Forming
- RNA Interference and Gene Delivery
- Sarcoma Diagnosis and Treatment
- interferon and immune responses
- COVID-19 Clinical Research Studies
- Scientific Computing and Data Management
- Genetic Mapping and Diversity in Plants and Animals
- Immunotherapy and Immune Responses
German Cancer Research Center
2025
Heidelberg University
2025
Heinrich Heine University Düsseldorf
2025
Düsseldorf University Hospital
2025
Deutschen Konsortium für Translationale Krebsforschung
2025
Max Planck Institute of Immunobiology and Epigenetics
2022-2023
Max Delbrück Center
2020-2022
UNSW Sydney
2017-2020
Juno Therapeutics (Germany)
2017
Howard Hughes Medical Institute
2008-2015
often contribute new sequence elements to conserved lncRNAs d Syntenic counterparts of hundreds mammalian were found in fish and urchin
ABSTRACT Bioremediation is an important approach to waste reduction that relies on biological processes break down a variety of pollutants. This made possible by the vast metabolic diversity microbial world. To explore this for breakdown plastic, we screened several dozen endophytic fungi their ability degrade synthetic polymer polyester polyurethane (PUR). Several organisms demonstrated efficiently PUR in both solid and liquid suspensions. Particularly robust activity was observed among...
The post-transcriptional fate of messenger RNAs (mRNAs) is largely dictated by their 3′ untranslated regions (3′ UTRs), which are defined cleavage and polyadenylation (CPA) pre-mRNAs. We used poly(A)-position profiling sequencing (3P-seq) to map poly(A) sites at eight developmental stages tissues in the zebrafish. Analysis over 60 million 3P-seq reads substantially increased improved existing UTR annotations, resulting confidently identified UTRs for >79% annotated protein-coding genes...
Detailed knowledge of the molecular biology severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is crucial for understanding viral replication, host responses, and disease progression. Here, we report gene expression profiles three SARS-CoV- SARS-CoV-2-infected human cell lines. SARS-CoV-2 elicited an approximately two-fold higher stimulation innate immune response compared to SARS-CoV in epithelial line Calu-3, including induction miRNA-155. Single-cell RNA sequencing...
Abstract Motivation The B-cell receptor (BCR) performs essential functions for the adaptive immune system including recognition of pathogen-derived antigens. vast repertoire and variation BCR sequences due to V(D)J recombination somatic hypermutation necessitates single-cell characterization sequences. Single-cell RNA sequencing presents opportunity simultaneous capture paired heavy light chains transcriptomic signature. Results We developed VDJPuzzle, a novel bioinformatic tool that...
Abstract The coronavirus disease 2019 (COVID-19) pandemic, caused by the novel severe acute respiratory syndrome 2 (SARS-CoV-2), is an ongoing global health threat with more than two million infected people since its emergence in late 2019. Detailed knowledge of molecular biology infection indispensable for understanding viral replication, host responses, and progression. We provide gene expression profiles SARS-CoV SARS-CoV-2 infections three human cell lines (H1299, Caco-2 Calu-3 cells),...
SARS-CoV-2, responsible for the ongoing global pandemic, must overcome a conundrum faced by all viruses. To achieve its own replication and spread, it simultaneously depends on subverts cellular mechanisms. At early stage of infection, SARS-CoV-2 expresses viral nonstructural protein 1 (NSP1), which inhibits host translation blocking mRNA entry tunnel ribosome; this interferes with binding mRNAs to ribosome. Viral mRNAs, other hand, blockade. We show that NSP1 enhances expression containing...
The generation of distinct messenger RNA isoforms through alternative processing modulates the expression and function genes, often in a cell-type-specific manner. Here, we assess regulatory relationships between transcription initiation, splicing, 3′ end site selection. Applying long-read sequencing to accurately represent even longest transcripts from end, quantify mRNA Drosophila tissues, including transcriptionally complex nervous system. We find that heads, as well human cerebral...
Abstract Background Tiling arrays have been the tool of choice for probing an organism's transcriptome without prior assumptions about transcribed regions, but RNA-Seq is becoming a viable alternative as costs sequencing continue to decrease. Understanding relative merits these technologies will help researchers select appropriate technology their needs. Results Here, we compare two platforms using matched sample poly(A)-enriched RNA isolated from second larval stage C. elegans . We find...
The influenza polymerase cleaves host RNAs ∼10–13 nucleotides downstream of their 5′ ends and uses this capped fragment to prime viral mRNA synthesis. To better understand process cap snatching, we used high-throughput sequencing determine the A/WSN/33 (H1N1) mRNAs. sequences provided clear evidence for nascent-chain realignment during transcription initiation revealed a strong influence template on frequency realignment. After accounting extra inserted through realignment, analysis...
Abstract We present Bioconda ( https://bioconda.github.io ), a distribution of bioinformatics software for the lightweight, multiplatform and language-agnostic package manager Conda. Currently, offers collection over 3000 packages, which is continuously maintained, updated, extended by growing global community more than 200 contributors. improves analysis reproducibility allowing users to define isolated environments with defined versions, all are easily installed managed without...
<title>Abstract</title> Spinal ependymoma and myxopapillary are the two most common spinal ependymal tumor types that feature distinct histological characteristics, genetic alterations DNA methylation profiles. Their distinction may be difficult in individual cases molecular diagnostic assessment, particular methylome profiling, then required to assign correct diagnosis. Expression of homeobox gene HOXB13 at mRNA protein levels has been reported as a frequent finding serve marker for these...
Abstract Spinal ependymoma and myxopapillary are the two most common spinal ependymal tumor types that feature distinct histological characteristics, genetic alterations DNA methylation profiles. Their distinction may be difficult in individual cases molecular diagnostic assessment, particular methylome profiling, then required to assign correct diagnosis. Expression of homeobox gene HOXB13 at mRNA protein levels has been reported as a frequent finding serve marker for these tumors. Here, we...
ETV6::RUNX1, the most common oncogenic fusion in pediatric B cell precursor acute lymphoblastic leukemia (BCP-ALL), induces a clinically silent preleukemic state that can persist carriers for over decade and may progress to overt upon acquisition of secondary lesions. The mechanisms contributing quiescence ETV6::RUNX1+ cells still remain elusive. In this study, we identify linker histone H1-0 as critical mediator by employing human -induced pluripotent stem (hiPSC) models engineered using...
Abstract Tumor-infiltrating lymphocytes (TILs) are critical to anti-cancer immune responses, but their diverse phenotypes and functions remain poorly understood challenging study. We therefore developed a single-cell barcoding technology for deep characterization of TILs without the need cell-sorting or culture. Our emulsion-based method captures full-length, natively paired B-cell T-cell receptor (BCR TCR) sequences from among millions input cells. validated with 3 million B-cells healthy...
ABSTRACT A diverse T cell repertoire is a critical component of the adaptive immune system, providing protection against invading pathogens and neoplastic changes, relying on recognition foreign antigens neoantigen peptides by receptors (TCRs). However, statistical properties function pool in an individual, under normal physiological conditions, are poorly understood. In this study, we report comprehensive, quantitative characterization from over 1.9 million cells, yielding 200,000 high...
Abstract The B-cell receptor (BCR) performs essential functions for the adaptive immune system including recognition of pathogen-derived antigens. Cell-to-cell variability BCR sequences due to V(D)J recombination and somatic hypermutation (SHM) necessitates single-cell characterization sequences. Single-cell RNA sequencing (scRNA-seq) presents opportunity simultaneous capture sequence transcriptomic signature a detailed understanding dynamics an response. We developed VDJPuzzle 2.0,...
ABSTRACT SARS-CoV-2, responsible for the ongoing global pandemic, must overcome a conundrum faced by all viruses. To achieve its own replication and spread, it simultaneously depends on subverts cellular mechanisms. At early stage of infection, SARS-CoV-2 expresses viral nonstructural protein 1 (NSP1), which inhibits host translation blocking mRNA entry tunnel ribosome; this interferes with binding mRNAs to ribosome. Viral mRNAs, other hand, blockade. We show that NSP1 enhances expression...
Abstract During manufacturing of an exemplary CD19-directed CAR-T cell product, patient T cells were transduced with a viral vector encoding the CD19-directed, 41BBζ endodomain-containing chimeric antigen receptor (CAR) construct, enabling permanent genetic modification target cells. Lentiviral transduction self-inactivating (SIN) can offer certain advantages in safety and consistency over other DNA delivery methods. Although integration patterns wildtype HIV-1 have been well-characterized...