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
My research interest/plan is tackling genotype-phenotype relationship by using graph theory, constraint-based modeling and dynamical analysis with focus on metabolic traits and protein interaction functional features at cellular, tissue and organism levels. In my work I am covering a broad range of Systems Biology topics. Some areas of special interest of mine are the followings:
Network biology: Particularly focused on network reconstruction, analysis, and comprehension of complex behavior in biological systems. For example, we developed (CentiServer) a comprehensive resource and web application for centrality indices. We also constructed an integrated human disease network and extracted the cancerome as a cancer-related subnetwork.
Data integration: Working on integration of experimental data (transcriptome, metabolome, proteome, regulome, fluxome, epigenome and phenome) for reconstruction and analysis tissue-specific model. For example, to evaluate alterations in cancer cell metabolism (Warburg effect), we integrated different cancer cell’s gene expression into the human GEM. In another study, we analyzed reciprocal associations of metabolism and epigenetics by data integration. We also published a comprehensive review about the identification of network-based functional features through integration of gene expression into protein networks. Furthermore, in an omics integrative approach, we integrated gene expression and genomic aberration data for pre- and post-invasive samples and investigated the evolutionary role of further genetic changes in later stages compared to the early ones. We found that single gene alterations and copy-number alterations work together in forward and backward evolution manners to fine-tune the signaling pathways operating in tumors.
Method development: As a contribution to method development, I provided input to CytoKavosh (a Cytoscape plug-in which allows discovering network motifs), HomoTarget (an algorithm for prediction of microRNA targets in Homo sapiens), CentiServer (a comprehensive centrality resource and web application for centrality measures calculation) and GEMtractor (a platform for trimming and extracting genome-scale metabolic models).
Metabolic modelling approaches: Using a wide range of modelling techniques, from constraint-based approaches to differential equation models, to understand the complexity of cellular metabolism.
A benchmark of context-specific models for the assessment of cancer metabolic heterogeneity.
A platform for trimming and extracting genome-scale metabolic models (GEMs)
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).
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
Enzyme-constrained models and omics analysis of Streptomyces coelicolor reveal metabolic changes that enhance heterologous production
Sulheim S, Kumelj T, van Dissel D, Salehzadeh-Yazdi A, Du Ch, P. van Wezel G, Nieselt K, Almaas E, Wentzel A, Kerkhoven E
GEMtractor: Extracting Views into Genome-scale Metabolic Models
Scharm M, Wolkenhauer O, Jalili M, Salehzadeh-Yazdi A
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)
Applications of genome-scale metabolic models and data integration in systems medicine
Salehzadeh-Yazdi A, Wolfien M, Wolkenhauer O
Nova (2019), chapter in Focus on Systems Theory Research
ISBN 13 (online): 9781536145618
Awards and Distinctions
- Metabolic grant award winner of the first NanoString grant program in Metabolism - (2019)
- Invited speaker for 16th International Conference on Molecular Systems Biology (ICMSB) - (2019)