A5066553079- Genomics and Chromatin Dynamics
- Genomic variations and chromosomal abnormalities
- RNA Research and Splicing
- Chromosomal and Genetic Variations
- RNA modifications and cancer
- Chromatin Remodeling and Cancer
- Genetics, Bioinformatics, and Biomedical Research
- Genomics and Phylogenetic Studies
- Developmental Biology and Gene Regulation
- Cancer Genomics and Diagnostics
- RNA and protein synthesis mechanisms
- Marine and coastal plant biology
- Evolution and Genetic Dynamics
- Genomics and Rare Diseases
- Echinoderm biology and ecology
- Molecular Biology Techniques and Applications
- Proteoglycans and glycosaminoglycans research
- Plant Molecular Biology Research
- Estrogen and related hormone effects
- Single-cell and spatial transcriptomics
- vaccines and immunoinformatics approaches
- Environmental DNA in Biodiversity Studies
- Immunotherapy and Immune Responses
- interferon and immune responses
- Cytokine Signaling Pathways and Interactions
University Medical Center of the Johannes Gutenberg University Mainz
2019-2024
Johannes Gutenberg University Mainz
2016-2024
Translationale Onkologie an der Universitätsmedizin der Johannes Gutenberg-Universität Mainz
2023
Max Planck Institute for Molecular Genetics
2016-2019
Institute of Molecular Biology
2016-2017
Max Planck Society
2015
Institut de Biologie de l'École Normale Supérieure
2015
Inserm
2015
Charité - Universitätsmedizin Berlin
2014
Freie Universität Berlin
2014
The human genome is highly organized in the three-dimensional nucleus. Chromosomes fold locally into topologically associating domains (TADs) defined by increased intra-domain chromatin contacts. TADs contribute to gene regulation restricting interactions of regulatory sequences, such as enhancers, with their target genes. Disruption can result altered expression and associated genetic diseases cancers. However, it not clear which extent TAD regions are conserved evolution whether disruption...
Abstract Background Recent data from genome-wide chromosome conformation capture analysis indicate that the human genome is divided into conserved megabase-sized self-interacting regions called topological domains. These domains form regulatory backbone of and are separated by boundary elements or barriers. Copy-number variations can potentially alter domain architecture deleting duplicating barriers thereby allowing enhancers neighboring to ectopically activate genes causing misexpression...
The classical DNA recognition sequence of the glucocorticoid receptor (GR) appears to be present at only a fraction bound genomic regions. To identify sequences responsible for recruitment this transcription factor (TF) individual loci, we turned high-resolution ChIP-exo approach. We exploited signal by determining footprint profiles TF binding single-base-pair resolution using ExoProfiler, computational pipeline based on motifs. When applied our GR and few available public data sets, find...
Paralog genes arise from gene duplication events during evolution, which often lead to similar proteins that cooperate in common pathways and protein complexes. Consequently, paralogs show correlation expression whereby the mechanisms of co-regulation remain unclear. In eukaryotes, are regulated part by distal enhancer elements through looping interactions with promoters. These can be measured genome-wide chromatin conformation capture (Hi-C) experiments, revealed self-interacting regions...
The sea urchin larval skeleton offers a simple model for formation of developmental patterns. calcium carbonate is secreted by primary mesenchyme cells (PMCs) in response to largely unknown patterning cues expressed the ectoderm. To discover novel ectodermal cues, we performed an unbiased RNA-Seq-based screen and functionally tested candidates; thereby identified several skeletal cues. Among these, show that SLC26a2/7 ventrally sulfate transporter promotes ventral accumulation sulfated...
<h3>Background</h3> Clinical evaluation of CNVs identified via techniques such as array comparative genome hybridisation (aCGH) involves the inspection lists known and unknown duplications deletions with goal distinguishing pathogenic from benign CNVs. A key step in this process is comparison individual9s phenotypic abnormalities those associated Mendelian disorders genes affected by CNV. However, because often there not much about these human genes, an additional source data that could be...
Abstract Motivation Neoantigens are promising targets for cancer immunotherapies and might arise from alternative splicing. However, detecting tumor-specific splicing is challenging because many non-canonical splice junctions identified in tumors also appear healthy tissues. To increase tumor-specificity, we focused on caused by somatic mutations as a source neoantigen candidates individual patients. Results We developed the tool splice2neo with multiple functionalities to integrate...
Knowledge of the three-dimensional structure genome is necessary to understand how gene expression regulated. Recent experimental techniques such as Hi-C or ChIA-PET measure long-range chromatin interactions genome-wide but are experimentally elaborate, have limited resolution and data only available for a number cell types tissues.While ChIP-seq was not designed detect interactions, formaldehyde treatment in protocol cross-links proteins with each other DNA. Consequently, also regions that...
Abstract Background The human genome is highly organized in the three-dimensional nucleus. Chromosomes fold locally into topologically associating domains (TADs) defined by increased intra-domain chromatin contacts. TADs contribute to gene regulation restricting interactions of regulatory sequences, such as enhancers, with their target genes. Disruption can result altered expression and associated genetic diseases cancers. However, it not clear which extent TAD regions are conserved...
ChIP-nexus, an extension of the ChIP-exo protocol, can be used to map borders protein-bound DNA sequences at nucleotide resolution, requires less input and enables selective PCR duplicate removal using random barcodes. However, use barcodes additional preprocessing mapping data, which complicates computational analysis. To date, only a very limited number software packages are available for analysis have not yet been systematically tested compared on ChIP-nexus data. Here, we present...
Abstract Background Our understanding of the nuclear chromatin structure has increased hugely during last years mainly as a consequence advances in conformation capture methods like Hi-C. The unprecedented resolution genome-wide interaction maps shows functional consequences that extend initial thought an efficient DNA packaging mechanism: gene regulation, repair, chromosomal translocations and evolutionary rearrangements seem to be only peak iceberg. One key concept emerging from this...
Abstract Embryonic development is arguably the most complex process an organism undergoes during its lifetime, and understanding this complexity best approached with a systems-level perspective. The sea urchin has become highly valuable model for developmental specification, morphogenesis, evolution. As non-chordate deuterostome, occupies important evolutionary niche between protostomes vertebrates. Lytechinus variegatus (Lv) Atlantic species that been well studied, which provided insights...
Abstract We present a computational method to gain knowledge of the three-dimensional structure genome from ChIP-seq datasets. While not designed detect contacts, protocol cross-links proteins with each other and DNA. Consequently, genomic regions that interact protein binding-site via chromatin looping are coimmunoprecipitated sequenced. This produces minor signals around CTCF motif pairs at loop anchor regions. Together sequence features, these predict whether anchors or not. Our method,...
Abstract Splicing is dysregulated in many tumors and may result tumor-specific transcripts that can encode neoantigens, which are promising targets for cancer immunotherapy. Detecting splicing challenging because non-canonical splice junctions identified tumor transcriptomes also appear healthy tissues. Here, we developed splice2neo to integrate the predicted effects from somatic mutations with detected RNA-seq individual patients. Splice2neo excludes tissue samples, annotates resulting...
On 30 November 2016, over 70 junior researchers in computational biology from diverse countries met Mainz, Germany, for the 1st Student Symposium on Computational Genomics. Overall, symposium was a great success and featured four outstanding keynote lectures, nine selected student talks, 38 poster presentations. This report briefly highlights scientific outcomes activities of this student-driven event.