Carl Herrmann
A5045118783- Cancer Genomics and Diagnostics
- Neuroblastoma Research and Treatments
- Genomics and Chromatin Dynamics
- Epigenetics and DNA Methylation
- Genomics and Phylogenetic Studies
- Bioinformatics and Genomic Networks
- Single-cell and spatial transcriptomics
- Cancer-related molecular mechanisms research
- Gene expression and cancer classification
- RNA modifications and cancer
- Cancer, Hypoxia, and Metabolism
- Protein Degradation and Inhibitors
- Black Holes and Theoretical Physics
- Glioma Diagnosis and Treatment
- Multiple Myeloma Research and Treatments
- Genetics, Bioinformatics, and Biomedical Research
- Chromosomal and Genetic Variations
- Immune Cell Function and Interaction
- Circular RNAs in diseases
- Acute Myeloid Leukemia Research
- Evolution and Genetic Dynamics
- Cancer-related gene regulation
- Cosmology and Gravitation Theories
- Particle physics theoretical and experimental studies
- Genetic Associations and Epidemiology
Heidelberg University
2016-2025
University Hospital Heidelberg
2018-2025
Heidelberg University
2020-2024
Harvard University
2024
Massachusetts General Hospital
2024
German Cancer Research Center
2014-2023
DKFZ-ZMBH Alliance
2014-2021
Aix-Marseille Université
2009-2015
Inserm
2004-2015
Theories and Approaches of Genomic Complexity
2011-2015
The discovery of drivers cancer has traditionally focused on protein-coding genes
Abstract Transcriptional reprogramming of proliferative melanoma cells into a phenotypically distinct invasive cell subpopulation is critical event at the origin metastatic spreading. Here we generate transcriptome, open chromatin and histone modification maps cultures; integrate this data with existing transcriptome DNA methylation profiles from tumour biopsies to gain insight mechanisms underlying key event. This shows thousands genomic regulatory regions states, identifying SOX10/MITF...
RSAT (Regulatory Sequence Analysis Tools) is a modular software suite for the analysis of cisregulatory elements in genome sequences.Its main applications are (i) motif discovery, appropriate to genome-wide data sets like ChIP-seq, (ii) transcription factor binding (quality assessment, comparisons and clustering), (iii) comparative genomics (iv) regulatory variations.Nine new programs have been added 43 described 2011 NAR Web Software Issue, including tool extract sequences from list...
RSAT (Regulatory Sequence Analysis Tools) comprises a wide collection of modular tools for the detection cis-regulatory elements in genome sequences. Thirteen new programs have been added to 30 described 2008 NAR Web Software Issue, including an automated sequence retrieval from EnsEMBL (retrieve-ensembl-seq), two novel motif discovery algorithms (oligo-diff and info-gibbs), 100-times faster version matrix-scan enabling scanning genome-scale sets, series facilities random model generation...
ChIP-seq is increasingly used to characterize transcription factor binding and chromatin marks at a genomic scale. Various tools are now available extract motifs from peak data sets. However, most approaches only as command-line programs, or via website but with size restrictions. We present peak-motifs , computational pipeline that discovers in sequences, compares them databases, exports putative sites for visualization the UCSC genome browser generates an extensive report suited both naive...
Integrative analysis of multi-omics layers at single cell level is critical for accurate dissection cell-to-cell variation within certain populations. Here we report scCAT-seq, a technique simultaneously assaying chromatin accessibility and the transcriptome same cell. We show that combined signatures enable construction regulatory relationships between cis-regulatory elements target genes single-cell resolution, providing new dimension features helps direct discovery patterns specific to...
Abstract Long non-coding RNAs (lncRNAs) are a growing focus of cancer genomics studies, creating the need for resource lncRNAs with validated roles. Furthermore, it remains debated whether mutated can drive tumorigenesis, and such functions could be conserved during evolution. Here, as part ICGC/TCGA Pan-Cancer Analysis Whole Genomes (PCAWG) Consortium, we introduce Cancer LncRNA Census (CLC), compilation 122 GENCODE causal roles in phenotypes. In contrast to existing databases, CLC requires...
Multi-omics datasets represent distinct aspects of the central dogma molecular biology. Such high-dimensional profiles pose challenges to data interpretation and hypothesis generation. ActivePathways is an integrative method that discovers significantly enriched pathways across multiple using statistical fusion, rationalizes contributing evidence highlights associated genes. As part ICGC/TCGA Pan-Cancer Analysis Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing from...
Abstract Aberrant expression of MYC transcription factor family members predicts poor clinical outcome in many human cancers. Oncogenic profoundly alters metabolism and mediates an antioxidant response to maintain redox balance. Here we show that MYCN induces massive lipid peroxidation on depletion cysteine, the rate-limiting amino acid for glutathione (GSH) biosynthesis, sensitizes cells ferroptosis, oxidative, non-apoptotic iron-dependent type cell death. The high cysteine demand...
Exacerbated pro-inflammatory immune response contributes to COVID-19 pathology. However, despite the mounting evidence about SARS-CoV-2 infecting human gut, little is known antiviral programs triggered in this organ. To address gap, we performed single-cell transcriptomics of SARS-CoV-2-infected intestinal organoids. We identified a subpopulation enterocytes as prime target and, interestingly, found lack positive correlation between susceptibility infection and expression ACE2. Infected...
Abstract Circulating tumor cells (CTCs) drive metastasis, the leading cause of death in individuals with breast cancer. Due to their low abundance circulation, robust CTC expansion protocols are urgently needed effectively study disease progression and therapy responses. Here we present establishment long-term CTC-derived organoids from female metastatic Multiomics analysis along preclinical modeling xenografts identified neuregulin 1 (NRG1)–ERBB2 receptor tyrosine kinase 3 ( ERBB3 /HER3)...
The field of regulatory genomics today is characterized by the generation high-throughput data sets that capture genome-wide transcription factor (TF) binding, histone modifications, or DNAseI hypersensitive regions across many cell types and conditions. In this context, a critical question how to make optimal use these publicly available datasets when studying transcriptional regulation. Here, we address in Drosophila melanogaster for which large number are available. We developed...
ChIP-seq has become a widely adopted genomic assay in recent years to determine binding sites for transcription factors or enrichments specific histone modifications. Beside detection of enriched bound regions, an important question is differences between conditions. While this common analysis gene expression, which large number computational approaches have been validated, the same particularly challenging owing complexity data terms noisiness and variability. Many different tools developed...
The broad clinical spectrum of neuroblastoma ranges from spontaneous regression to rapid progression despite intensive multimodal therapy. This diversity is not fully explained by known genetic aberrations, suggesting the possibility epigenetic involvement in pathogenesis. In pursuit this hypothesis, we took an integrative approach analyze methylomes, transcriptomes, and copy number variations 105 cases neuroblastoma, complemented primary tumor- cell line-derived global histone modification...
Article24 March 2016Open Access Transparent process Environment-induced epigenetic reprogramming in genomic regulatory elements smoking mothers and their children Tobias Bauer orcid.org/0000-0002-4961-3639 Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany Search for more papers by this author Saskia Trump Department Environmental Immunology, Helmholtz Centre Leipzig - UFZ, Leipzig, Naveed Ishaque Heidelberg Personalized Oncology, DKFZ-HIPO,...
Abstract Chromosome 17q gains are almost invariably present in high-risk neuroblastoma cases. Here, we perform an integrative epigenomics search for dosage-sensitive transcription factors on marked by H3K27ac defined super-enhancers and identify TBX2 as top candidate gene. We show that is a constituent of the recently established core regulatory circuitry with features cell identity factor, driving proliferation through activation p21-DREAM repressed FOXM1 target genes. Combined MYCN/TBX2...
Abstract The catalog of cancer driver mutations in protein-coding genes has greatly expanded the past decade. However, non-coding are less well-characterized and only a handful recurrent mutations, most notably TERT promoter have been reported. Here, as part ICGC/TCGA Pan-Cancer Analysis Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 across 38 tumor types, we perform multi-faceted pathway network analyses 2583 genomes 27 types compiled by PCAWG...