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Visualization for Molecular Biology

Guest lecture held by Alexander Lex from Harvard University.
This course will be offered only once in summer semester 2013. Appointments will be blocked in May.

Introduction
Molecular biology has been going through a significant transformation from a predominantly wet-lab based science to an increasingly computational science. The development of powerful data acquisition methods such as next-generation sequencing allows unprecedented insight into the processes underlying all living things with the potential to revolutionize not only our understanding of these fundamental processes but also to change the way in which we treat diseases.

In this lecture we will discuss current and future approaches that address this shift to a data-driven science using visualization. We will discuss the various data sources and types and the appropriate visualization techniques. The lecture has a hands-on component where students are expected to develop visualization solutions in small teams. After this course students will not only understand the challenges of visualizing biological data, but will also be able to design visualizations on their own.

Please see the course website for further information.

Contents
In particular, this course will discuss the following constitutive topics:

  • Introduction to molecular biology
  • Data acquisition methods
  • Genome Visualization (sequence visualization)
  • Omics Visualization (mRNA, protein expression, etc.)
  • Pathway Visualization (biological processes)
  • Visualizing Phylogenetics (relationships between species)
  • Visualizing Clinical Data
  • Visualizing Macromolecular Structures (protein structure, etc.)

Selected Readings

  1. Visualizing genomes: techniques and challenges. Nature Methods Volume 7 No 3s, pp S5 - S15, Cydney B Nielsen, Michael Cantor, Inna Dubchak, David Gordon & Ting Wang, doi:10.1038/nmeth.1422
  2. Visualization of multiple alignments, phylogenies and gene family evolution. Nature Methods Volume 7 No 3s, pp S16 - S25. James B Procter, Julie, Thompson, Ivica Letunic, Chris Creevey, Fabrice Jossinet & Geoffrey J Barton, doi:10.1038/nmeth.1434
  3. Visualization of macromolecular structures. Nature Methods Volume 7 No 3s, pp S42 - S55. Seán I O'Donoghue, David S Goodsell, Achilleas S Frangakis, Fabrice Jossinet, Roman A Laskowski, Michael Nilges, Helen R Saibil, Andrea Schafferhans, Rebecca C Wade, Eric Westhof & Arthur J Olson, doi:10.1038/nmeth.142
  4. Visualization of omics data for systems biology. Nature Methods Volume 7 No 3s, pp S56 - S68. Nils Gehlenborg, Seán I O'Donoghue, Nitin S Baliga, Alexander Goesmann, Matthew A Hibbs, Hiroaki Kitano, Oliver Kohlbacher, Heiko Neuweger, Reinhard Schneider, Dan Tenenbaum & Anne-Claude Gavin, doi:10.1038/nmeth.1436