Dr. Ali Salehzadeh-Yazdi

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

Research interest

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. Furthermore, 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.

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.

My current projects focus on systems medicine and biotechnology projects (SYSTERACT, BESTER and SASKit).

Projects

Research Projects

GEMtractor

A platform for trimming and extracting genome-scale metabolic models (GEMs)

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SASKit: Senescence-Associated Systems diagnostics Kit for cancer and stroke
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).

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Academic background

2016

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

2012-2016

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

2008-2014

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

2003-2006

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

1999-2003

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

 

Selected publications

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

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

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

Services

  • Member of the editorial board for Frontiers in Physiology
  • Associate editor for IEEE/Access
  • Reviewer Board Member of Metabolites (MDPI)
  • Reviewer for MDPI Journals (Metabolites, Molecules, Processes, JCM, ijms, Medicina, and applsci)
  • Reviewer for Scientific Report, PLOS ONE, IEEE/ACM Transaction, and The journal of cellular biochemistry)

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)