CancerEpiSys is an interdisciplinary research consortium that involves the project partners listed below.
Benedikt Brors is head of the group "Computational Oncology" in the Division of Theoretical Bioinformatics at the DKFZ. He has
- developed models for predictive and prognostic classification of tumor samples in a number of different cancer entities, and on meta and cross-study analysis of transcriptomic data,
- is coordinating bioinformatics analyses in the German ICGC-PedBrain consortium on sequencing of tumor genomes, transcriptomes and methylomes of pediatric brain cancers, and
- is PI of work packages dealing with the analysis of genome-wide sequencing data within the ICGC projects on malignant lymphoma and on early-onset prostate cancer.
Roland Eils is a mathematician by training and has been working in the field of computational biology over more than 15 years since his PhD. He has
- unraveled for the first time a structure-function relationship of chromosomal organization,
- developed the first computational systems for spatio-temporal structure analysis in living cells,
- discovered that chromosomal organization is inherited through the cell cycle,
- developed a simulation framework for signal transduction networks in apoptosis, and
- has developed a novel method for reverse engineering gene regulatory networks from gene expression data.
Thomas Höfer is a theoretical biophysicist working on elucidating the dynamics of cellular regulatory networks by modeling and model-driven experiments. He has
- proposed molecular mechanisms for cellular calcium oscillations and waves subsequently confirmed experimentally,
- developed the first experimentally-based mathematical models of the NFAT signal transduction pathway and the GATA-3/T-bet gene-regulatory networks governing T cell differentiation,
- devised a comprehensive theoretical framework for multi-site protein phosphorylation in signaling,
- discovered spatio-temporal signaling patterns in multi-cellular cytokine networks.
Peter Lichter leads the division Molecular Genetics at the DKFZ in Heidelberg. He coordinates several research initiatives including the NGFN-PLUS Brain Tumor Network and the German ICGC contribution on pediatric brain tumors. He has
- pioneered technologies in (cyto)genetics, including FISH protocols, array-based comparative genomic hybridization (arrayCGH) and array-based DNA methylation screening (aPRIMES),
- elucidated epigenetic tumor pathomechanisms in medulloblastoma and glioblastoma tumor cells with stem-cell characteristics, analyzed the interaction of malignant cells with their micro-environment, and the therapeutic targeting of tumor-specific molecular changes,
- contributed to understanding mechanisms for resistance to therapy, and the translation of knowledge about prognostic and predictive markers into routine clinical settings, and
- developed novel tumor patient stratification schemes based on genetic profiles and to the elucidation of molecular pathomechanisms in brain tumors and B cell lymphomas.
Daniel Mertens was trained as a biochemist and currently focuses on the underlying pathomechanism of CLL. As head of the cooperation unit “Mechanisms of Leukemogenesis” between the University Ulm and the DKFZ, he is working on the translation of research on the epigenomic pathomechanism of CLL into clinical applications. He
- characterized transcriptional deregulation in CLL patients,
- identified an epigenetic tumor suppressor in the most commonly affected region, 13q14.3, and
- leads a project within the Helmholtz Systems Biology Initiative (SB Cancer) that studies the microenvironment response of CLL cells and models the associated transcription networks.
Christoph Plass is the head of the DKFZ Division Toxicology and Cancer Risk Factors. He is member of the epigenomics special emphasis panel of the NIH, Bethesda, USA. He
- has made major contributions to studies of aberrant DNA methylation in tumorigenesis,
- has shown with his group that human malignancies are characterized by extensive promoter CpG island methylation with non-random and tumor-type specific patterns,
- is elucidating the molecular mechanisms by which epigenetic and genetic alterations cooperate during the initiation and progression of malignant cell growth, and
- studies how environmental stimuli are processed by the epigenome and processed to the onset and severity of malignancies, as well as treatment response and treatment outcome.
Karsten Rippe has conducted interdisciplinary research that combines molecular/cell biology and physics to investigate the relation between chromatin organization and cellular functions. He has
- elucidated mechanisms of chromatin (re)organization mediated by histone chaperones and chromatin remodeling complexes in combination of in vivo and in vitro experiments using e.g. fluorescence and atomic force microscopy/spectroscopy and analytical ultracentrifugation,
- conducted cell biology studies to elucidate the control of the dynamic chromatin conformation and DNA accessibility changes via the histone acetylation state, and
- performed modeling studies and developed quantitative descriptions of chromatin organization.
Stephan Stilgenbauer is department deputy medical director of the department of Internal Medicine III at the University Hospital Ulm, a reference laboratory in the German CLL study group for international clinical studies. He is
- coordinator of 3 international clinical trials on CLL, and co-investigator in 24 current clinical trials,
- pioneered genetic prognostic markers in CLL that are now being used in state-of-the-art molecular diagnostics, and
- develops novel treatment strategies applicable to chemoresistant and high-risk CLL.
Martin Vingron is a director at the Max-Planck-Institut für molekulare Genetik where he heads the Computational Molecular Biology Department. He is Professor at the Freie Universität, teaching in the context of the bioinformatics curriculum, and speaker of the International Max Planck Research School for Computational Biology and Scientific Computing. In 2004 Vingron received the Max Planck Research Award in the field of Bioinformatics and he is a member of the German Academy of Sciences Leopoldina. Together with his group members, he has contributed significantly to the development of
- a theory of statistical significance of sequence alignment and data base searching,
- normalization and analysis methods for microarray gene expression data,
- processing methods for next generation sequencing in expression and splicing analysis, and
- a quantitative connection between histone modification states and gene expression levels.