|Lead by||Thomas Lengauer|
|Assistants||Yassen Assenov, Lars Feuerbach, Konstantin Halachev|
|Initial meeting||Monday, April 26, 2010 at 12:00 in Campus E1 4 (MPI building), Room 024|
|Review submission||before Friday, October 1, 2010, 23:59|
|Presentations||October 12 and 13, 2010 in Campus E1 4 (MPI building), Room 021|
Epigenetic research aims to understand heritable gene regulation that is not directly encoded in the DNA sequence. Epigenetic mechanisms such as DNA methylation and histone modifications modulate the packaging of the DNA in the nucleus and thereby influence gene expression. Various bioinformatic challenges arise from the analysis of epigenetic data, and computational methods have already played a role in solving important epigenetic problems. In this seminar, we introduce the basic concepts of epigenetics and we summarize relevant computational and bioinformatic work performed in this area.
This is an integrated seminar that combines Master Seminar and Proseminar topics. It can be attended by students at the Bachelor, as well as at the Master level in Bioinformatics and Computer Science. The language is English. The seminar is going to take place as a two-day Blockseminar on October 12 and 13. If you consider participating in the seminar, you need to attend the initial meeting on Thursday, April 22.
For a successful completion, every participant must:
Prof. Lengauer has written guidelines for scientific presentations. They are available in English (Word PDF) and in German (Word PDF). They are really helpful; please read them carefully before you start working on our presentation.
The topics that are going to be discussed in the seminar are listed below. Click on a topic title to see a short description.
Methodologies for quantifying DNA methylation
In this seminar, we are going to discuss three techniques for detection of DNA methylation: methylated DNA immunoprecipitation, methylation sensitive restriction enzymes and reduced-representation bisulfite sequencing. We will present the computational challenges posed by the different methodologies, as well as their limitations.
Inter-individual, cell cycle and tissue-specific methylation
DNA methylation changes dynamically during development and differentiation of mammalian organisms. The methylation patterns are also influenced by aging, viruses, dietary folate, environmental factors and cancer. In this seminar, we are going to introduce methods for identification and quantification of inter-individual, tissue-specific and disease-specific methylation.
Methylation in diseases
Epigenetic alterations have been identified as causal events for common diseases such as cancer and autoimmune disorders. In this seminar, we are going to comment on the development of panels of biomarkers that will allow early detection of cancer and other diseases, as well as prediction of therapy response.
CpG islands are genomic regions that contain an elevated frequency of CpG sites. They are usually located near gene promoters and are hot spots for epigenetic signaling by DNA methylation. However, the exact definition of CpG islands and the mechanism that govern their biological function are open research questions. In this seminar, we are going to introduce density-based, as well as more advanced CpG island annotation algorithms and summarize their drawbacks and advantages. Furthermore, recent findings on the function of CpG island promoters will be reviewed.
Histone molecules undergo a number of post-translational modifications which alter their interaction with DNA and nuclear proteins. Histone modifications act in diverse biological processes such as gene regulation, DNA repair and chromosome condensation (mitosis). In this seminar, we are going to introduce techniques for detecting histone modifications based on chromatin immunoprecipitation, and discuss the applied statistical frameworks for deciphering the complex histone alphabet.
Evolution of DNA methylation
Environmental factors, genome-wide DNA methylation levels and generation times have influenced the co-evolution of genomes and epigenomes of the vertebrate lineage. In this seminar, we are going to introduce the major epigenomic similarities and differences between non-vertebrates and several vertebrate subgroups such as mammals, birds and fish.
The mouse as lab model system is genetically relatively close to the human genome, but its epigenomic similarity is nearly uncharacterized. In this seminar, we are going to discuss the methodologies and results of two comparative studies on epigenetic features in mouse and human.
Induced pluripotent cells
Recently it has been shown that adult cells could be reprogrammed to pluripotency thus revealing the potential that every adult cell be used for tissue-specific individualized research, advanced medicine testing, regenerative medicine and others.
Most of the computational efforts, methods and software in the field are data driven. Once a new dataset or technology is out methods and analysis specific for it are being developed. In this seminar, we will present EpiGRAPH - an attempt to provide the field with general software that will allow for initial integration and analysis of new datasets without the need of developing new methods.
Please note that the number of participants is limited to 20. If you would like to attend the seminar, send an email with subject
Computational Epigenetics to Yassen, and include the following information:
Publications related to each topic are available in the password protected area.