Projects

Introducing the PIs

» Suzana Atanasoski
» Christian Beisel
» Dagmar Iber
» Erik van Nimwegen
» Savas Tay
» Verdon Taylor

Suzana Atanasoski is a Professor in the Department of Biomedicine at the University of Basel. During her PhD thesis at the University Hospital of Zurich and Cold Spring Harbor Laboratories, New York, she studied and characterized transcription factors involved in brain development. During her post-doctorate at the ETH Zurich, she discovered that Schwann cells switch their requirements for cell cycle proteins and signaling pathways in vivo in a context-dependent manner. Further, she identified the proto-oncogene Ski as a novel player in controlling myelination, thereby contributing substantially to the understanding of the molecular mechanisms that control nerve development, regeneration, and neuropathies. In 2006, she was awarded a professorship by the Swiss National Science Foundation and started working on cortical development. Her group has recently determined the role of Ski in specifying callosal projections neurons, and has further discovered that subtypes of Ski-deficient progenitor cells exhibit altered cell cycle characteristics during corticogenesis. With her expertise in Ski signaling and on cell cycle proteins during cortical development, her group aims at contributing towards establishing and validating computational tools and novel models for transcription factor networks and signaling pathways that are critical in early phases of brain development.

 

Christian Beisel is senior scientist at the Department of Biosystems Science and Engineering (D-BSSE) of ETH Zurich in Basel and head of the Quantitative Genomics Facility (QGF). He received his diploma degree and PhD in biology from the University of Heidelberg. Both studies were honored as best thesis in 1999 and 2004, respectively. He was awarded a PhD fellowship by the German National Science Foundation (DFG) and is a scholarship holder of the Klaus-Tschira Foundation since 2001. He pursued his postdoctoral research with Renato Paro between 2003 and 2006 before he joined D-BSSE. Christian Beisel’s research is dedicated to the deciphering of gene regulatory processes underlying cellular differentiation, stem cell renewal, and in the development of cancer by means of proteomics and genomics approaches. Over the recent years he set up microarray platforms to correlate gene expression profiles with chromatin signatures and he established the QGF at the D-BSSE, the next-generation genomics core facility of the Basel life science community, collaborating with researchers in state-of-the-art genomics and high-throughput sequencing approaches.

 

Dagmar Iber is Assistant Professor for Computational Biology at the Department of Biosystems Science and Engineering of ETH Zurich in Basel. Her research focuses on the development of quantitative, predictive models for cellular signaling networks. Close collaborations with experimental laboratories permit a cycle of model testing and improving. Validated models are then used to further investigate the biological system and to address more general questions regarding the evolution and the design of cellular signaling networks. The ultimate goal of her research is a comprehensive understanding of the dynamics and evolution of complex cellular signaling networks and how they interact in space. Her initial focus was on bacterial systems because quantitative data can be more easily obtained. Here she developed a detailed model that defined the mechanism by which different cell fates are induced in sister cells during sporulation in B. subtilis. She subsequently focused on eukaryotic systems where cellular networks are more complex. She showed by example of the TGFβ network that these networks are highly plastic such that small changes in the parameter values and protein concentrations can fundamentally alter the response. While this explains the many different response types observed in nature it also highlights the need for sufficient data to arrive at a predictive model. Currently, she mainly works on the spatio-temporal organization of signaling during development. Here she focuses on limb development (supported by iPhD position), bone development (supported by Sinergia grant), branching morphogenesis (supported by ETH fellowship), dorso-ventral patterning, and lately ovarian follicle development.

 

Erik van Nimwegen (Associate Professor, Biozentrum, University of Basel, and group leader, Swiss Institute of Bioinformatics) was trained as theoretical physicist and has been working on the computational biology of gene regulation and transcription regulation since the late 1990s. Besides well-recognized theoretical work on evolutionary dynamics and identification of genomic laws in bacteria, much of his work has focused on developing Bayesian probabilistic methods for the reconstructing genome-wide transcription regulatory networks, combining high-throughput data with comparative genomic analysis. In collaboration with researchers at the Riken Institute in Japan annotated promoters genome-wide in human and mouse, and developed the computational modeling methods that successfully reconstructed the core transcriptional regulatory network of a differentiating human cell line. His extensive work on the comparative analysis of transcription regulatory networks in bacteria and eukaryotes lead to fundamental insights in the architecture of the regulatory processes in these two kingdoms. Current work in his lab aims on the one hand to understand principles of bacterial evolution and on the other hand to unravel gene expression regulatory networks in mammals.

 

Savas Tay is a tenure-track assistant professor of Bioengineering at the Department of Biosystems Science and Engineering (D-BSSE), ETH Zurich. During his PhD work, he also developed a new method for nanofabrication with polymer materials and applied it to photonic devices, a plasmonic thermal emitter for bio-sensing applications, and novel materials for infrared imaging. During his postdoctoral work he developed new microfluidic and computational analysis methods to investigate signalling pathways in single-cells, especially the NF-κB pathway. Using high-throughput microfluidic live-cell imaging and stochastic modelling, he developed the most comprehensive mathematical model of the NF-κB pathway to date. He also investigated how cells migrate in their “social context” using single-cell analysis techniques and developed an agent-based computer model, capturing emergent features of collective cell migration. He used microfluidic single-cell analysis to investigate how cells respond to bacterial endotoxin, and identified quantitative differences in the way cells process signals from the “self” and the pathogens. Before transitioning into Biological research, he developed the world’s first updateable holographic three-dimensional display. Tay Group’s current research interests are developing Microfluidics based technologies for single-cell analysis and automated biological assays, and applying them to important problems in neurobiology, cell signalling, immunology and developmental biology using an integrated Systems Biology approach.

Verdon Taylor is Professor of Embryology and Stem Cell Biology in the Department of Biomedicine of the University of Basel. During his PhD he studied the role of receptor tyrosine kinases in neural stem cell development and differentiation, identifying 15 novel genes by degenerative PCR screening. During his postdoctoral work he studied the role of EMP-family members in the murine development and in the peripheral nervous system. He examined glial lineage development in the peripheral nervous system and the regulation of Schwann cell development. As a junior group leader his group studied the role of Notch signaling in the development of the embryonic nervous system. The generated the first conditional knockout of Notch1 in the central nervous system using conditional genetics and developed concomitant gene inactivation and lineage tracing. His group also generated one of the key analyses of Notch signaling in the adult mouse brain, a study which induce an interest in adult neurogenesis. As an independent junior group leader of the Max Planck Society his interests continued in the role of Notch and its targets in the regulation of neural stem cell fate in the differentiation in the embryonic and adult nervous systems. His group has identified novel targets of the Notch pathway in neural stem cells and studies the function of these in neural development and neurogenesis. Recently, his group identified a novel function for the Dorsha and the miRNA microprocessor in the regulation of neurogenesis by directly regulating mRNA stability. He has continued to develop genetic tools and state of the art procedure to analyze and trace neural stem cells in the developing brain.