Development of algorithms to decipher the complexity of chromation organization

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Project Description

Cells control gene expression by means of dynamic changes in chromatin. Different functional chromatin states are the result of highly combinatorial patterns of DNA- methylation, histone modifications, sequence specific DNA - binding proteins and chromatin accessory factors. The advent of large-scale, high- throughput experiments has resulted in the generation of an immense array of genome association data ( enrichment profiles) of chromatin components. Computational epigenetics is an interdisciplinary area of research that involves the development of computational methods to analyze and conceptionalize large scale epigenomic data.  At the Chromatin Biochemistry lab, we are developing computational methods for integrative analysis of Big-Data from ,odENCODE (1) to better understand the complexity of (epi) gennomic information. Decoding the increasingly large volumes of Bid-Data sets involves deciphering signal patterns and to systematically quantify the localization of these signal intensities.  ​​
Program - BioScience
Division - Biological and Environmental Sciences and Engineering
Field of Study - ​computational biology, bioinformatics, informatics

About the
Researcher

Wolfgang Fischle

Professor, Bioscience

Wolfgang Fischle
To sustain life in different environments, cells and organisms must adjust to different conditions and external cues. In contrast to immediate and mostly transient responses to short-term stimuli, processes of long-term adaptation require lasting changes in gene expression patterns. Such epigenetic changes are controlled on the level of chromatin, the packaging form of eukaryotic genomes. Here, different chemical modifications are associated with distinct functional states of chromatin.

Prof. Fischle's research aims to gain detailed and molecular understanding of fundamental epigenetic processes. In particular, he is investigating how modifications and small cellular molecules interplay to direct different structural and functional states of chromatin. To address these problems, Prof. Fischle is applying highly interdisciplinary approaches. These include advancing technologies for establishing and analyzing complex chromatin systems in vitro (biochemistry and biophysics), molecular and cellular biology for studying essential chromatin components and global analysis of modules of epigenetic regulation.

Desired Project Deliverables

​Develop (or assist/apply) computational method for segmentation of genomes using a combination of epigenomic datasetsApplication of machine learning techniques to predict the​ 3D architecture of epigenomic segments Maintain good log (CVS), submit progress in writing and present results Final report summarizing and explaining all project work.