A5000077668- RNA Research and Splicing
- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- Genomics and Chromatin Dynamics
- Genomics and Phylogenetic Studies
- Cancer-related molecular mechanisms research
- Single-cell and spatial transcriptomics
- Plant Molecular Biology Research
- Gene expression and cancer classification
- Molecular Biology Techniques and Applications
- Machine Learning in Bioinformatics
- MicroRNA in disease regulation
- CRISPR and Genetic Engineering
- Cell Image Analysis Techniques
- Chromosomal and Genetic Variations
- Photosynthetic Processes and Mechanisms
- RNA regulation and disease
- Immunotherapy and Immune Responses
- Epigenetics and DNA Methylation
- Gene Regulatory Network Analysis
- Plant nutrient uptake and metabolism
- Plant Reproductive Biology
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Natural Language Processing Techniques
- SARS-CoV-2 and COVID-19 Research
Max Delbrück Center
2015-2024
Humboldt-Universität zu Berlin
2015-2024
Iowa State University
2022-2023
Humboldt State University
2015-2021
Heinrich Heine University Düsseldorf
2021
Duke University
2008-2018
Duke University Hospital
2006-2018
Duke Medical Center
2006-2018
Berlin Institute of Health at Charité - Universitätsmedizin Berlin
2016-2018
Center for Systems Biology
2011-2013
Transcriptional programs that regulate development are exquisitely controlled in space and time. Elucidating these underlie is essential to understanding the acquisition of cell tissue identity. We present microarray expression profiles a high-resolution set developmental time points within single Arabidopsis root comprehensive map nearly all types. These type-specific transcriptional signatures often predict previously unknown cellular functions. A computational pipeline identified dominant...
Abstract Crosslinking and immunoprecipitation (CLIP) protocols have made it possible to identify transcriptome-wide RNA-protein interaction sites. In particular, PAR-CLIP utilizes a photoactivatable nucleoside for more efficient crosslinking. We present an approach, centered on the novel PARalyzer tool, mapping high-confidence sites from deep-sequencing data. show that delineates with high signal-to-noise ratio. Motif finding identifies sequence preferences of RNA-binding proteins, as well...
Epstein-Barr virus (EBV) is a ubiquitous human herpesvirus linked to number of B cell cancers and lymphoproliferative disorders. During latent infection, EBV expresses 25 viral pre-microRNAs (miRNAs) induces the expression specific host miRNAs, such as miR-155 miR-21, which potentially play role in oncogenesis. To date, only limited miRNA targets have been identified; thus, miRNAs pathogenesis and/or lymphomagenesis not well defined. Here, we used photoactivatable ribonucleoside-enhanced...
Regnase-1 and Roquin are RNA binding proteins essential for degradation of inflammation-related mRNAs maintenance immune homeostasis. However, their mechanistic relationship has yet to be clarified. Here, we show that, although regulate an overlapping set via a common stem-loop structure, they function in distinct subcellular locations: ribosome/endoplasmic reticulum processing-body/stress granules, respectively. Moreover, specifically cleaves degrades translationally active requires the...
Abstract Efforts to precisely identify tumor human leukocyte antigen (HLA) bound peptides capable of mediating T cell-based rejection still face important challenges. Recent studies suggest that non-canonical tumor-specific HLA derived from annotated non-coding regions could elicit anti-tumor immune responses. However, sensitive and accurate mass spectrometry (MS)-based proteogenomics approaches are required robustly these peptides. We present an MS-based analytical approach characterizes...
Complex patterns of cell-type–specific gene expression are thought to be achieved by combinatorial binding transcription factors (TFs) sequence elements in regulatory regions. Predicting mammals has been hindered the oftentimes unknown location distal To alleviate this bottleneck, we used DNase-seq data from 19 diverse human cell types identify proximal and at genome-wide scale. Matched allowed us separate genes into classes up-regulated, down-regulated, constitutively expressed genes. CG...
In all multicellular organisms, transcriptional networks orchestrate organ development. The Arabidopsis root, with its simple structure and indeterminate growth, is an ideal model for investigating the spatiotemporal signatures underlying developmental trajectories. To map gene expression dynamics across root cell types time, we built a comprehensive, organ-scale atlas at single-cell resolution. addition to estimating progressions in pseudotime, employed mathematical concept of optimal...
Deep sequencing of ribosome footprints (ribosome profiling) maps and quantifies mRNA translation. Because ribosomes decode every 3 nt, the periodic property could be used to identify novel translated ORFs. However, due limited resolution existing methods, 3-nt periodicity is observed mostly in a global analysis, but not individual transcripts. Here, we report protocol applied Arabidopsis that over 90% main reading frame thus offers super-resolution profiles for transcripts precisely define...
Protein subcellular localization is fundamental to the establishment of body axis, cell migration, synaptic plasticity, and a vast range other biological processes. occurs through three mechanisms: protein transport, mRNA localization, local translation. However, relative contribution each process neuronal polarity remains unknown. Using neurons differentiated from mouse embryonic stem cells, we analyze RNA expression translation rates in isolated bodies neurites genome-wide. We quantify...
Abstract Recent methodological advances allowed the identification of an increasing number RNA-binding proteins (RBPs) and their sites. Most those methods rely, however, on capturing associated to polyadenylated RNAs which neglects RBPs bound non-adenylate RNA classes (tRNA, rRNA, pre-mRNA) as well vast majority species that lack poly-A tails in mRNAs (including all archea bacteria). We have developed Phenol Toluol extraction (PTex) protocol does not rely a specific sequence or motif for...
Brassinosteroids are plant steroid hormones that regulate diverse processes, such as cell division and elongation, through gene regulatory networks vary in space time. By using time series single-cell RNA sequencing to profile brassinosteroid-responsive expression specific different types developmental stages of the Arabidopsis root, we identified elongating cortex a site where brassinosteroids trigger shift from proliferation elongation associated with increased wall–related genes. Our...
Understanding how the expression of transcription factor (TF) genes is modulated essential for reconstructing gene regulatory networks. There increasing evidence that sequences other than upstream noncoding can contribute to modulating expression, but frequently they do so remains unclear. Here, we investigated regulation TFs expressed in a tissue-enriched manner Arabidopsis roots. For 61 TFs, created GFP reporter constructs driven by each TF’s sequence (including 5′UTR) fused alone or...
Computational methods for automated genome annotation are critical to our community's ability make full use of the large volume genomic sequence being generated and released. To explore accuracy these feature prediction tools in genomes higher organisms, we evaluated their performance on a large, well-characterized contig from Adh region Drosophila melanogaster . This experiment, known as Genome Annotation Assessment Project (GASP), was launched May 1999. Twelve groups, applying...