Workshop 1: Learning from perturbation effects

Reverse engineering of biological networks is a key for the understanding of biological systems and for identifying new drug targets. Perturbation techniques, like target specific inhibitors and RNA interference, open tremendous possibilities to detect so far unknown interdependencies from, possibly multidimensional, effects. At the same time computational methods being able to derive network hypotheses from such complex data play a crucial role. This workshop aims to bring together computational scientists working with various approaches for this challenging task. The goal is to give an overview over different computational methods in the field and to strengthen and initiate new cooperations.

Organizer

Prof. Dr. Holger Fröhlich, Bonn-Aachen International Center for IT (B-IT), Bonn, Germany
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http://www.abi.bit.uni-bonn.de

Program

Session 1: Models for RNAi-Screening Data

  1. Niko Beerenwinkel, ETH Zurich (D-BSSE), Basel, Switzerland, Computational approaches to reconstruct signaling networks of pathogen entry from RNAi screens [slides]. Email: This e-mail address is being protected from spambots. You need JavaScript enabled to view it
  2. Mirko Birbaumer, ETH Zurich, Zurich, Switzerland, From Vesicle Features to Cellular Phenotypes: Statistical Clustering in Image-based High-Throughput RNAi Screens [slides]. Email: This e-mail address is being protected from spambots. You need JavaScript enabled to view it
  3. Lars Kaderali, University of Heidelberg, Bioquant, Germany, Reconstructing Signaling Pathways with Probabilistic Boolean Threshold Networks [slides]. Email: This e-mail address is being protected from spambots. You need JavaScript enabled to view it

Coffee Break

Session 2: Models for Static Perturbation Effects I

  1. Florian Markowetz, Cancer Research UK Cambridge Research Institute, Cambridge, UK, The end of the screen is the beginning of the experiment: pathway integration of hits in genome-wide RNAi screens [slides]. Email: This e-mail address is being protected from spambots. You need JavaScript enabled to view it
  2. Holger Fröhlich, University of Bonn, Bonn-Aachen International Center for IT (BIT), Germany, Demo Session: Nested Effects Models at Work [slides]. Email: This e-mail address is being protected from spambots. You need JavaScript enabled to view it
  3. Charles Vaske, Princeton University, USA, Predicting and expanding biological pathways using a Factor Graph Nested Effects Model [slides]. Email: This e-mail address is being protected from spambots. You need JavaScript enabled to view it

Lunch

Session 3: Models for Static Perturbation Effects II

  1. Lan Zagar, University of Ljubljana, Slovenia, Inference of epistasis from yeast genome-scale genetic interaction map [slides]. Email: This e-mail address is being protected from spambots. You need JavaScript enabled to view it
  2. Achim Tresch, Gene Center Munich, Ludwig-Maximilians University Munich, Germany, Modeling Combinatorial Interventions in Transcriptional Networks [slides]. Email: This e-mail address is being protected from spambots. You need JavaScript enabled to view it
  3. Nicole Radde, University of Stuttgart, Germany, A statistical Bayesian framework for identification of biological networks from perturbation experiments [slides]. Email: This e-mail address is being protected from spambots. You need JavaScript enabled to view it
  4. Marloes Maathuis, ETH Zurich, Switzerland, Predicting perturbation effects in large-scale systems from observational data [slides]. Email: This e-mail address is being protected from spambots. You need JavaScript enabled to view it

Coffee Break

Session 4: Models For Dynamic Perturbation Effects

  1. Rainer Spang, University of Regensburg, Germany, Dynamic Nested Effects Models [slides]. Email: This e-mail address is being protected from spambots. You need JavaScript enabled to view it
  2. Christian Bender, German Cancer Research Center, Heidelberg, Germany, Dynamic Deterministic Effects Propagation Networks [slides]. Email: This e-mail address is being protected from spambots. You need JavaScript enabled to view it
  3. Sven Nelander, Sahlgrenska-CMR/ Wallenberg Laboratory and Gothenburg Mathematical Modeling Center, Sweden, Human transcriptional networks revealed by endogenous perturbations in cancer tumors [slides]. Email: This e-mail address is being protected from spambots. You need JavaScript enabled to view it