Category: 2012 WS Online Lectures

Constraint-based reconstruction and analysis of metabolic and regulatory networks – Lars Nielsen

Implicit  in  the  collection  of  high  ‐  throughput  data  is  an  assumption  that  computational  models  ultimately  will  facilitate  biological  discovery,  reconciliation  of  heterogeneous  data  types,  identify  inconsistencies  and  enable  the  systematic  generation  of  hypotheses.  Current  naïve  statistical  models  fall  well  … Read more

Essential graph theory for biologists

One of the simplest yet most useful structures in mathematics is the graph. The essence of a graph is to model pairwise relations between objects by defining a set of vertices or nodes, and edges that connect the vertices. Graphs … Read more

Machine learning in anger – Stefan Maetschke

Next ‐ generation sequencing technologies drive an exponential growth of data that require advanced computational methods for their analysis and annotation. This presentation will give an introduction to machine learning with a focus on the representation, visualisation and classification of … Read more

Modelling the ecological implications of complex dispersal networks – Mikael Boden

In patchy environments, the ecological dynamics of obligate dispersers are driven by their connectivity patterns. Opportunistic analyses have revealed strong, consistent and complex structure within these patterns, but we have yet to synthesise the results into a coherent framework, and … Read more

Word-based approaches to discover transcription factor binding motifs in full-size ChIP-seq datasets – Jacques van-Helden

ChIP ‐ seq has become a method of choice to study binding preferences of transcription factors, and localisation of epigenetic regulatory marks at a genomic scale. There is a crucial need for specialised software tools to make sense of these … Read more

Understanding transcription with NGS – a biologist’s perspective – Michael Tallack

Erythropoiesis, the development of red blood cells (erythrocytes), requires precise control of erythroid specific gene expression by several intensely studied transcription factors. Among this set of transcription factors is the zinc ‐ finger transcription factor KLF1 (for Kruppel ‐ like … Read more

Understanding genetic regulation in the era of massively parallel sequencing: how many sites should a transcription factor bind? – Jacques van-Helden

The turn from the 20th to the 21st Century was marked by a drastic change in the scale at which biologists study regulatory networks. When I was a PhD student, a typical thesis would consist in analysing the regulation of … Read more

NGS sequence analysis for regulation and epigenomics – Tim Bailey

This presentation will give a quick overview of the primary challenges and opportunities inherent in the analysis of next ‐ generation sequence analysis data. To make the most of the unprecedented detail and flexibility in DNA ‐ , RNA ‐ … Read more

RNA-seq analysis pipelines – 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 … Read more

Differential expression analysis of RNA-seq read counts – Gordon Smyth

This presentation will focus on gene ‐ level analysis of RNA ‐ seq experiments. From a software point of view, the talk will describe an R ‐ based pipeline for the analysis of RNA ‐ seq data using the Rsubread, … Read more