Ali Sharifi Zarchi

Assistant Professor

CellNet, identity of the cells revealed by algorithms

  Computer Engineering Department, Floor 1, Class 101
  Wednesday, 30 December 2015
  10:30 - 11:30


Our body consists of more than 200 cell types and tissues that are originated from a single cell, the fertilized egg. Although some tissues have a limited repair ability after an injury by regeneration of the damaged cells, a number of critically important organs such as the central nervous system or heart are unable to regenerate. To treat the patients who have lost some organ or tissue, it is required to produce a huge number of cells of the desired types. Hence it is very important to understand how the cells differentiate from each other and how to convert a cell type to another.

Cell engineering is a new branch of science that aims to generate the required cell types (e.g. nerves or heart cells) from the available cells (e.g. skin or blood cells) of our body by manipulating the gene regulatory network, a network of causal interactions among the genes. The challenge is to identify a small set of genes that can restate the cell.

In this talk, we will have a glance over some mathematical models for better understanding of mechanisms that determine the identity of the cells. We will also review a few algorithms which are widely used to discover the regulatory network of the genes and to find out the tissue-specific subnetworks. Finally, we will learn about a new algorithmic tool, called CellNet, that helps the scientists to engineer the cells.


Ali Sharifi-Zarchi received his Bachelor and Master degrees from the Sharif University of Technology in Computer Engineering, and his Ph.D. degree in bioinformatics form the Institute of Biochemistry and Biophysics in the University of Tehran under the supervision of Dr. Mehdi Sadeghi and Dr. Hamid Pezeshk. Now he is doing bioinformatics research at Royan Institute and is an assistant prof. of bioinformatics at the department of computer engineering at the Sharif University of Technology.