Domain Cooccurence Distribution of Genetic Regulation Activation from an Evolutionary Perspective

(This Research was supported by DAAD fellowship).

I'm collaborating with Prof Peter Stadler and Jun.Prof Sonja Prohaska at Interdisciplinary Center of Bioinformatics, University of Leipzig. Here are the summary of my work:

The emergence multicellular organisms was facilitated by dramatic increases in the complexity of gene regulatory mechanism. At the level of transcriptional regulation, this can be clearly seen in the massive expansion of transcription factor families and the pervasive combinatorial control of genes by multiple transcription factors in higher organism. One other mechanism is the large and growing class of ~22 nucleotide-long non-coding RNA, known as microRNAs (miRNAs). Crystallography reveals, that the fundamental unit of protein structure is the domain. MiRNAs are of great interest, since translational regulation must have existed in the RNA world before the invention of DNA and transcription respectively. Transcription factors are interesting because all domains of life have at least parts of them and they are involved in many regulatory processes in the cell. The goal of this project is to elucidate how gene regulatory networks evolve and understand the basic principles that underly their evolution. Large-scale studies of the origins and evolution of regulatory mechanisms require quantitative estimates of the abundance and co-occurrence of functional protein domains in the genomes of very diverse organism. Current databases, such as SUPERFAMILY , are not able to provide such quantitative data because of species-specific differences and biases in the existing transcript and protein annotations on which they are based. Our objective is to show, that the combination of de novo gene predictors and subsequent HMM-based annotation of SCOP domains in the predicted peptides leads to consistent estimates with acceptable accuracy.

My Dissertation:

'Evolutionary Analysis of Protein Domain Distribution in Eukaryotes'.(2012). [available online].It is also deposited at Indonesian Institute of Science Thesis Repository and Figshare.

Selected Publications on this project: