Ilya Ioshikhes

Our research is focused on gene regulation. It includes several related projects and studies on chromatin, transcription factor (TF) interactions with DNA, promoter analysis and microRNAs. Specific projects include algorithms for mapping TF binding sites and cis-regulatory modules, nucleosome mapping, the study of the influence of histone variants on chromatin architecture, chromatin modeling, and the development of algorithms for mapping miRNA targets. Other areas of bioinformatics, such as the human milk metagenome, are also part of our area of interest. Our goal is the mathematical modeling of gene regulation processes on various levels, combined with position prediction of regulatory elements.

The Ioshikhes lab accepts students from graduate programs in Bioinformatics, Biochemistry, Microbiology and Immunology, Mathematics and Statistics.

Research Program

The study of the regulation of gene expression is a fundamental problem in molecular biology. Transcriptional regulation is maintained through the interactions of various transcription factors (TFs) with the protein components of base transcriptional complexes. The DNA sequences of the promoters, enhancers and other regulatory regions of the genes contain specific binding sites for transcription factors and other components of the transcription machinery. These sites serve as a scaffold to bring various TFs into close proximity to each other to facilitate their interaction and form active DNA-protein regulation complexes. In our research, we focus on the investigation of interactions between promoters and transcription factor complexes and the discovery of gene regulatory modules in the proximal promoter sequences and long gene regulatory regions.

To be properly understood, promoter machinery must be studied within its chromatin context. Current and planned directions of our research in this area include the refinement of nucleosome sequence patterns in new experimental data; a comparative analysis of common nucleosomes and those with histone modifications (H2A.Z, CENP-A and others); the analysis of species-specific and tissue-specific chromatin structures; an analysis of the relationship between specific mechanisms of chromatin remodelling and alternative types of chromatin architecture; and an analysis of the interaction of nucleosomes with TFs and other regulatory elements. Our research also includes algorithm development for mapping microRNA targets, the study of the human milk metagenome and other projects.

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