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. 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.

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


Research Projects


A benchmark of context-specific models for the assessment of cancer metabolic heterogeneity.



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


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

A European standardization framework for data integration and data-driven in silico models for personalised medicine.



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).


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 Metabolic Model of Intestinal Secretions: The Link between Human Microbiota and Colorectal Cancer Progression

Salahshouri P, Emadi-Baygi M, Jalili N , Khan F.M, Wolkenhauer O and Salehzadeh-Yazdi A

Exploring the Metabolic Heterogeneity of Cancers: A Benchmark Study of Context-Specific Models

Jalili M, Scharm M, Wolkenhauer O, Damaghi M and Salehzadeh-Yazdi A

Towards biomarkers for outcomes after pancreatic ductal anocarcinoma and ischemic stroke, with focus on (co-)morbidity and aging / cellular senescence (SASKit): protocol for a prospective cohort study

Henze L, Walter U, Murua Escobar H, Junghanß C, Jaster R, Köhling R, Lange F, Salehzadeh-Yazdi A, Wolkenhauer O, Hamed M, Barrantes I, Palmer D, Möller S, Kowald A, Heussen N, Fuellen G

Metabolic function-based normalization improves transcriptome data-driven reduction of genome-scale metabolic models

Salehzadeh-Yazdi A, Jalili M, Scharm M, Wolkenhauer O

Construction of a three-component regulatory network of transcribed ultraconserved regions for the identification of prognostic biomarkers in gastric cancer

Khalafiyan A, Emadi-Baygi M, Wolfien M, Salehzadeh-Yazdi A, Nikpour P

Computational Models for Clinical Applications in Personalized Medicine—Guidelines and Recommendations for Data Integration and Model Validation

Collin CB, Gebhardt T, Golebiewski M, Karaderi T, Hillemanns M, Khan FM, Salehzadeh-Yazdi A, Kirschner K, Krobitsch S, EU-STANDSPM consortium, Kuepfer L

MDPI JPM (2022)

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

Omics Integration Analyses Reveal the Early Evolution of Malignancy in Breast Cancer

Sarhadi Sh, Salehzadeh-Yazdi A, Damaghi M, Zarghami N, Wolkenhauer O and Hosseini H

Cancers 2020, 12(6), 1460

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

Jalili M, Salehzadeh-Yazdi A, Gupta S, Wolkenhauer O, Yaghmaie M, Resendis-Antonio O and Alimoghaddam K

Frontiers in Physiology

Cancerome: A hidden informative subnetwork of the diseasome

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

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


  • Member of the editorial board for Frontiers in Physiology
  • Associate editor for IEEE/Access
  • Reviewer Board Member of Metabolites (MDPI)
  • Reviewer Board Member of Cancers (MDPI)

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)
  • Guest editor of the journal of personalized medicine (MDPI) - "Special Issue "Systems Medicine and Bioinformatics"