SBI – Department of Systems Biology and Bioinformatics
Faculty of Computer Science and Electrical Engineering
University of Rostock
Ulmenstrasse 69 | 18057 Rostock
+49 381 498-7571
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.
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).
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.
Research assistant in Hematology-Oncology and Stem Cell Transplantation Research Center
Ph.D in Biophysics
Master's degree in Biophysics
Bachelor's degree in Cell and molecular biology - Genetics
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
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)
- Genome-scale metabolic reconstruction and analysis
- Kinetic modeling
- Data integration