Dr. Ali Salehzadeh-Yazdi

To unveil and quantify the principles of genotype-phenotype associations, I use different metabolic modeling approaches

Research interest

Biological systems contain many highly interconnected processes that function in a coordinated fashion to produce cellular behavior. Therefore, understanding the biological networks and their crosstalk properties is important to put an accurate interpretation on the complex nature of biological systems.

Metabolism is a complex network of dynamical biochemical reactions empowering organisms to grow, reproduce, maintain their integrity, defend against harmful environments and facilitate communication between different life forms. To illustrate the genotype-phenotype relationship of metabolism requires the use of computational models. These models can be used to answer the questions in metabolic engineering, drug development and personalized medicine.

Representation and modeling of metabolic networks have different levels of abstraction, predictive power, advantages and limitations. topological, constraint-based and kinetic approaches.

"I am interested in all three kinds of metabolic modelling approaches and integration of experimental data (transcriptome, metabolome, proteome, regulome, epigenome and phenome) for reconstruction and analysis tissue-specific models."

Here, we are engineering Streptomyces coelicolor as an expression superhost for heterologous cryptic gene clusters, for antibiotic production. For this, constraint-based and kinetic modelling is applied in combination with integration of experimental data.


Research Projects

BESTER: Bioprocesses for the optimized, integrated production of butyl esters from sustainable resources

The BESTER project will develop new bioprocesses for the production of butyl esters for the bio-based chemicals market. The in situ enzymatic esterification of butyric acid (HBu) and butanol (BuOH), produced by C. acetobutylicum, to butyl butyrate (BuB) with simultaneous extraction of the ester has been successfully shown by TU Delft (NL), using a single bioreactor setup (5g/L BuB yield).


SYSTERACT: Systematic Rebuilding of Actinomycetes for Natural Product Formation

The main objective of the SYSTERACT project is through an integrated and interdisciplinary approach to develop the model actinomycete Streptomyces coelicolor into a "Superhost" for the efficient heterologous production of bioactive compounds, enabling a faster discovery of new antibiotics from environmental microbial resources (microbial strains and metagenomes). Central to this approach will be an iterative Systems Biology process, combining microbiology, genetics, biochemistry, and fermentation technology with modelling.


Academic background


Postdoctoral Fellow
Department of Systems Biology & Bioinformatics, University of Rostock, Germany


Research assistant in Hematology-Oncology and Stem Cell Transplantation Research Center
Tehran University of Medical Sciences, Tehran, Iran


Ph.D in Biophysics
University of Tehran, Tehran, Iran


Master's degree in Biophysics
University of Tehran, Tehran, Iran


Bachelor's degree in Cell and molecular biology - Genetics
Shahid Chamran University of Ahvaz, Ahvaz, Iran


Selected publications

A systematic survey of centrality measures for protein-protein interaction networks

Ashtiani M, Salehzadeh-Yazdi A, Razaghi-Moghadam Z, Hennig H, Wolkenhauer O, Mirzaie M and Jafari M

BMC Systems Biology 12:80 (2018)

Evolution of computational models in BioModels Database and the Physiome Model Repository

Scharm M, Gebhardt T, Touré V, Bagnacani A, Salehzadeh-Yazdi A, Wolkenhauer O, Waltemath D

BMC Systems Biology 12:53 (2018)

Unveiling network-based functional features through integration of gene expression into protein networks

Jalilia M, Gebhardt T, Wolkenhauer O, Salehzadeh-Yazdi A

Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease

Comprehensive functional enrichment analysis of male infertility

Razavi SM, Sabbaghian M, Jalili M, Divsalar A, Wolkenhauer O, Salehzadeh-Yazdi A

Nature Scientific Reports

Meta-Analysis of Gene Expression Profiles in Acute Promyelocytic Leukemia Reveals Involved Pathways

Jalili M, Salehzadeh-Yazdi A, Mohammadi S, Yaghmaie M, Ghavamzadeh A, Alimoghaddam K

International Journal of Hematology Oncology and Stem Cell Research

Evolution of centrality measurements for the detection of essential proteins in biological networks

Mahdi Jalili, Ali Salehzadeh-Yazdi, Shailendra Gupta, Olaf Wolkenhauer, Marjan Yaghmaie, Osbaldo Resendis-Antonio and Kamran Alimoghaddam (2016)

Frontiers in Physiology

Cancerome: A hidden informative subnetwork of the diseasome

Mahdi Jalili, Ali Salehzadeh-Yazdi, Marjan Yaghmaie, Ardeshir Ghavamzadeh, Kamran Alimoghaddam (2016)

Impairment of DNA Methylation Maintenance Is the Main Cause of Global Demethylation in Naive Embryonic Stem Cells

Ferdinand von Meyenn, Mario Iurlaro, Ehsan Habibi, Ning Qing Liu, Ali Salehzadeh-Yazdi, Fa´tima Santos, Edoardo Petrini, Ineˆs Milagre, Miao Yu, Zhenqing Xie, Leonie I. Kroeze, Tatyana B. Nesterova, Joop H. Jansen, Hehuang Xie (2016)

Molecular Cell


  • Genome-scale metabolic reconstruction and analysis
  • Kinetic modeling
  • Data integration