ETH - BSSE - CBG Pejman Mohammadi

Our paper Reliable detection of subclonal
single-nucleotide variants in tumor cell populations appeared in Nature Communications today (see also ETH Life). In this work, we present the deepSNV algorithm and demonstrate its capability to detect subclonal mutations present in only 1/10,000 cells.

Gerstung et al. (2012) Nat Commun 3:811. DOI: 10.1038/ncomms1814.

ETH Zurich, D-BSSE
Computational Biology Group (CBG)
Office: 7.48
Mattenstrasse 26
CH-4058 Basel, SWITZERLAND
Phone: +41 61 387 3205
Fax: +41 61 387 3992
E-Mail:firstname.lastname@bsse.ethz.ch

Current Research Project

24 hours in life of HIV-1

The sequence of viral events taking place upon infection of the cell by Human Immunodeficiency Virus type 1 (HIV-1) has been studied in detail. The cellular responses to the infection have also been subject to studies from various perspectives: the general and viral protein-specific host expression reprogramming, the antiviral defence program, and also HIV-specific miRNA response. There is a need for a more complete picture of the viral life cycle that integrates viral and host events under the paradigm of new quantitative technologies.

My part is to devise the theoretical means to reach this goal. The work includes developing computational pipelines, and novel mathematical models for in-depth analysis and systematic integration of the experimental data. The analysis will (hopefully!) provide a reference and scaffold for in vivo large-scale genome and cellular screens.

I work in close collaboration with the scientists at Institute for Microbiology of the University of Lausanne, at: Amalio Telenti Lab and Angela Ciuffi Lab.

Areas of Research Interests

Integrative analysis of biological systems
Statistical machine learning and Bayesian data analysis
Computational immunology and auto-immune disorders

Teaching

I assist the course 626-002-00L Bioinformatics.

Academic Background

2010-Now	Doctoral candidate here at D-BSSE of ETH Zurich, Since June 2010.
2010	M.Sc. in Bioinformatics, awarded with distinction Thesis: Bayesian Integrative Modeling of Metabolic and Transcriptional Data Using Pathway Information. Aalto university, school of science and technology, Helsinki, Finland.
2008-2010	Research assistant – Biological data fusion. Visit My Old Homepage for details. Statistical Machine Learning and Bioinformatics Group, Prof. Samuel Kaski, Aalto University. My research was affiliated with Plant Stress Group at University of Helsinki BioCenter, on the oxidative stress in Arabidopsis Thaliana.
2008	B.Sc. in Software Engineering Thesis: Protein 3D structure prediction and contact maps. Isfahan University of Technology, Iran.
2007-2008	Research assistant – Structural bioinformatics Bioinformatics Research Group at Institute for Studies in Theoretical Physics and Mathematics (IPM), Tehran, Iran.
2006-2008	Research assistant – Algorithmic data mining Data Mining and Bioinformatics Laboratory, Isfahan University of Technology.
2003	High school degree in Maths and Physics. National Organization for the Development of Exceptional Talents (NODET), Isfahan, Iran.

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