Programme (pre)

Course Registration

Organizational and practical introduction

Opening Overview Seminar:
“From Genomes to Systems”

Speaker: Peer Bork

Session 1:

"Homology-Based Sequence Analysis: Domains, Their Function And The Biological context"

The main concepts and approaches in classical sequence analysis will be reviewed, with a particular focus towards the characterization of novel protein domains. This will be coupled with text mining concepts for quickly obtaining the relevant biological context in sequence analysis-based discoveries.  Text mining will be further scaled up to global knowledge extraction on particular topics.

Lecture 1:
Francesca Ciccarelli

Lecture 2:
Miguel Andrade

Practical Session
(Teachers: Francesca Ciccarelli, Miguel Andrade)

Session 2:

"Functional Genomics I: Protein Structures and Protein Complexes"

Proteins interact with each other in three dimensions, forming complexes and mediating processes. This session introduces high-throughput protein interaction screens, resulting interaction networks, as well as 3D modelling techniques.

Lecture 1: Roland Krause

Lecture 2: Rebecca Wade

Practical Session

(Teachers: Roland Krause and Rebecca Wade)

Social Event:

guided visit to an ancient Mayan archaeological site (over lunch time). The lectures in the morning will be slightly shorter, and the practical session will be resumed following the site visit and extended into the later evening accordingly.

Session 3:

"Comparative Genome Analysis: Mining Genome Evolution"

Comparisons of genomes reveal tightly linked evolutionary constraints and functional features that go beyond individual genes. Current comparative genomics-based approaches and their relevance to generating biological hypotheses will be reviewed and discussed.

Lecture 1:
Enrique Merino

Lecture 2:
Enrique Morett

Practical Session

(Teachers: Enrique Merino and Enrique Morett)

Session 4:

"Functional Genomics II: Genomic Context, mRNA Expression and Data Integration"

Exploitation of genomic context enables elucidation of biological processes and cellular networks. Functional relationships between genes can be enhanced by integrating other types of data such as those on expression and localization.

Lecture 1:
Martijn Huynen

Lecture 2:
Jan Korbel

Practical Session

(Teachers: Jan Korbel and Martijn Huynen)

Social event
(drinks/snacks and outing if time permitted)

Session 5:

"Towards Complex Biological Systems: Molecular Analysis of Ecosystems to Decipher the Basics of Biology on Earth"

From a forward looking introduction into spatio-temporal systems within single cells, concepts and tools to analyze entire ecosystems by using metagenomics approaches will be explored. The knowledge from Sessions 1 through 4 will be utilized to provide functional insights of complex microbial communities coming from diverse habitats such as soil and water.

Lecture 1:
Peer Bork

Lecture 2:
Christian von Mering

Practical Session

(Teachers: Christian von Mering, Peer Bork)

• Summary and Discussions: the participants will present and discuss the obtained results from a original research project carried out. In case of an “enlightening” discovery, an outline for a potential manuscript will be established.

• Feedback session: participants and teachers will give detailed feedback on the course.

• Concluding Remarks: the organizers will summarize the most relevant take home messages.

• End of the Course