Category: 2010 WS Online Lectures

A model-based approach to personalised medicine – Gilles Clermont

The discipline of systems medicine seeks to adapt tools inspired from systems engineering and systems biology to solving problems of translational relevance. Model-based interpretation of empirical evidence and model-guided design of experiments, or clinical trials, plays an important role in … Read more


Information integration approaches to network modeling – John Quackenbush

Two trends are driving innovation and discovery in biological sciences: technologies that allow holistic surveys of genes, proteins, and metabolites and the growing realisation that analysis and interpretation of the resulting requires an understanding of the complex phenotypic and environmental … Read more


Decomposition of gene expression state space trajectories to model cell fate transitions – Jessica Mar

. Representing and analysing complex networks remains a roadblock to creating dynamic network models of biological processes and pathways. The study of cell fate transitions can reveal much about the transcriptional regulatory programs that underlie these phenotypic changes and give … Read more


Dynamic protein-protein interaction networks in yeast – Marc Wilkins

This presentation will explore protein-protein interaction networks, specifically that of yeast Saccharomyces cerevisiae, and ask what can these teach us? A specific focus will be on data quality and the nature of interactions captured in current data sets, from a … Read more


Algorithms and computation for large systems II: applications and analysis – Michael Langston

We will discuss innovative algorithms for biological pathway isolation. Coexpression analysis, data integration, the use of model organisms, and a variety of applications to human health serve as examples. Noisy data is a constant concern. Download


Algorithms and computation for large systems I: algorithms and implementations – Michael Langston

We will explore the use of novel algorithms and powerful computational platforms in the analysis of high-throughput biological data. Fixed-parameter tractability provides a unifying principle for strategic problem reduction and efficient combinatorial search. Download


Statistical modeling of dynamic gene networks in cancer II – Can dynamic gene networks predict novel therapeutic targets and clinical outcomes? – Seiya Imoto

Transcriptomic analysis is commonly performed in a time-dependent manner to uncover the temporal response of RNA expressions to a dosed chemical compound. By using drug response time-course gene expression data measured by microarray or RNA-seq technologies, statistical time-series analysis can … Read more


Statistical modeling of dynamic gene networks in cancer I – Models and algorithms for estimating dynamic gene networks – Seiya Imoto

Transcriptomic analysis is commonly performed in a time-dependent manner to uncover the temporal response of RNA expressions to a dosed chemical compound. By using drug response time-course gene expression data measured by microarray or RNA-seq technologies, statistical time-series analysis can … Read more


Analysing RNA-seq: from reads to results – Alicia Oshlack

High-throughput sequencing of the transcriptome leads to the production of millions of short reads which need to be analysed in order to make biological inference. RNA-seq data are complex and the analysis involves a series of steps for which research … Read more


Technologies: classical and next gen approaches – Mark Crowe

For most of the 35 years since its invention, the dye-terminator or Sanger method has been the dominant approach for DNA sequencing, and current capillary electrophoresis platforms using this technique are still considered the gold standard in terms of both … Read more