Praktikum Netzwerk- und Expressionsdaten-Analyse (SS2012)

In this course models will be reconstructed from expression data. The simplest models are sets of genes with related functions that exhibit significant signals in the experiments (panels 1+2). Pathway models help to understand the complex relationships between genes (panel 3). Finally, simulation models are constructed. Experimental measurements can then be compared to a simulation to evaluate the correctness of a model (panel 4).

For the inference of gene regulatory networks from mRNA expression data, many different approaches with their specific performances, data requirements, and inherent biases have been developed. Approaches are assessed via annually conducted community-wide challenges, the Dialogue on Reverse Engineering Assessment and Methods (DREAM).

The tutors of this course were recognized as best performer in two of these international challenges. The course focuses on the analysis and integration of expression and network data. The students will develop new methods for the inference of networks and are encouraged to participate in the upcoming DREAM challenges.

The course has three parts:

1. Seminar and methods
2. Implementation of a novel approach to network inference
3. Application on current data and writing of a manuscript

Please note: During the seminar part, talks might take place on tuesday and thursday to speed up the basic introduction

Ein detaillierter Zeitplan mit verlinktem Material ist auf der passwortgeschützte Seite
zu finden.

Termin	Thema	Vortragender
24.04.	Einführungsveranstaltung	Prof. Ralf Zimmer
03.05.	Expressionsdaten, Eine Übersicht	Dr. Robert Küffner
on demand	DREAM - Der Wettbewerb 2011	tba
tba	Expressiondaten, Analyse-Verfahren	tba
tba	Netzwerkbasierte Analysen und Modelle	tba
tba	Studentische Vorträge
tba	Studentische Vorträge
tba	Milestone A, Abnahme des Basissystems	Plenum
tba	Milestone B, Abnahme Prototypen	Plenum
tba	SEMESTERENDE	-
tba	Milestone C, Abnahme Blockphasenkonzepte	Plenum
tba	Endabnahme	Plenum

• Prof. Dr. Ralf Zimmer
• PD Dr. Robert Küffner
• Tobias Petri
• Gergely Csaba

• Grundstudium Bioinformatik (Bachelor oder Diplom)
• Bioinformatik Programmierpraktikum
• Genomorientiertes Programmierpraktikum

Allgemein

• Bioconductor Workshops
• BioConductor Course
• Affymetrix white papers

R

• An Introduction to R
• R for Beginners
• Using R for Data Analysis and Graphics
• R Reference Card

R und Expressionsdatenanalyse

• Center for Plant Biology

Einführende Literatur

• passwortgeschützte Literatur