Saeed Saberi

Saeed now works at BC Cancer Agency

Contact: ssaberi[at]

Position/Role: Post-Doctoral Fellow

Research Interests: Bioinformatics, next-generation sequencing data management and HI-C/ChIP-seq analysis



Major research activities/interests: I am strongly driven by the question of how high-throughput technologies can be used to address different biological questions. I create different tools to find and visualize meaningful, biologically relevant patterns in large datasets. I am working specifically on epigenetic modifications and their relation to different types of cancer including Malignant Rhabdoid Tumour (MRT). Using resources from both CHiBi and BC Genome Science Centre (GSC), I have been investigating the epigenetic regulatory alterations contributing to oncogenesis in MRT.  The key oncogenic mutation in MRT is thought to be SWI/SNF complex catalytic member Smarcb1. SWI/SNF complex modifies nucleosome positioning across the chromatin and its aberrant behaviour results in vast changes in the transcriptomic landscape.  I have been analyzing the genomic distribution of DNA modifications and nucleosome positioning using high-throughput data from methods such as ChIP-seq, whole genome bisulfite sequencing (WGBS) and ATAC-seq methods. I am also involved in many other collaborative projects with groups in BC GSC, BC cancer agency and UBC.


Background: I achieved my MSc. in Sharif University of Technology (SUT) studying complex systems and seismic wave data in particular. I received my PhD at Simon Fraser University (SFU) under supervision of Dr. Eldon Emberly. I have studied Hi-C data in Drosophila Melanogaster to find the relationships between 3D conformation of chromosomes, enhancer-promoter interactions and gene expression. Currently, I am a post-doctorate fellow in Dr. Martin Hirst’s  lab at UBC.


All publications




J. Pon, S. Saberi et al.MEF2B Mutations in Non-Hodgkin Lymphoma Deregulate Cell Migration by Decreasing Transcriptional Activation of MEF2B Target Genes”,  In revision at Nature Communication.


K. Scheu, R. Gill, S. Saberi, P. Meyer, and E. Emberly, “Localization of aggregating proteins in bacteria depends on the rate of addition, Invited paper at Frontiers in microbiology, 2014.


S. Saberi, P. Farre, O. Cuvier, E. Emberly, “Identifying DNA Interaction Profiles from HI-C Data”, Accepted at Biomedical Journal.


S. Saberi, E. Emberly, “Self-organized protein localization and DNA segregation in cells”, PloS One, 2013.


S. Saberi, E. Emberly, “Chromosome Driven Spatial Patterning of Proteins in Bacteria”, PloS Computational Biology, 2010.


P. Manshour, S. Saberi, M. Sahimi, J. Peinke, A. F. Pacheco, M. R. RahimiTabar, Turbulent-Like Behavior of Seismic Time Series, Physical Review Letter, 2009.


In progress:


S. Saberi, D Bogdanoff and Martin Hirst Nucleosome positioning alteration in Rhabdoid Tumour leads to cancer phenotype, In progress.


E. Chun, A. Musavi, S Saberi, Misha Bilenky, M. Hirst and M. Marra, “Genome-wide molecular landscape of malignant renal and extra-renal rhabdoid tumours”, In progress.