Tehran University of Medical Sciences
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Yazdan Asgari

Contact Information
http://yazdan59.ir
Academic Rank
Assistant Professor
School
Advanced Technologies in Medicine
Medical Biotechnology
About
CV last edited on: 2020/17/05

1.

Postdoctoral fellowship


Bioinformatics, Institute for Research in Fundamental Sciences-IPM, Tehran, Iran, 2015-2016
Supervisor:Dr. M. Sadeghi
2.


Researcher , Institute of Plant Genetics and Crop Plant Research-IPK, Gatersleben, Germany, 2011
Supervisor:Prof. Falk Schreiber
3.

Ph.D


Bioinformatics, University of Tehran, Tehran, Iran, 2014
Thesis Title:Modeling Cancer as a Metabolic Disease
Supervisor:Prof. Falk Schreiber, Dr. A. Masoudi-Nejad
4.


Researcher , University of Lethbridge, Lethbridge-AB, Canada, 2008
Supervisor:Prof. Marc Roussel
5.

M.Sc


Physical Chemistry, Khaje Nasir Toosi University of Technology, Tehran, Iran, 2004
Thesis Title:Cellular Automata and Reaction-Diffusion Systems
Supervisor:M. Ghaemi, M.G. Mahjani
6.

B.Sc


Applied Chemistry, University of Kashan, Kashan, Iran, 2002
1.

Persian


Speaking: Native, Reading: Native, Writing: Native
2.

English


Speaking: Good, Reading: Good, Writing: Good

1.

Ph.D. - Bioinformatics


2016-Now see the details by clicking the "courses" in the "Links" part of the page, .
2.

Ph.D. - Medical Informatics


2016-Now see the details by clicking the "courses" in the "Links" part of the page, .
3.

Ph.D. - Applied Statistics


2018/2019 .
4.

Ph.D. - Protein Engineering


2016-Now see the details by clicking the "courses" in the "Links" part of the page, .
5.

Ph.D. - Computational and Systems Biology


2016-Now see the details by clicking the "courses" in the "Links" part of the page, .
6.

Ph.D. - Systems Biology for Tissue Engineering Students


2018-Now see the details by clicking the "courses" in the "Links" part of the page, .
7.

Ph.D. - Analysis of Metabolic Networks


Spring Semester - 2015/2016 University of Tehran,.
8.

M.Sc. - Bioinformatics


2016-Now see the details by clicking the "courses" in the "Links" part of the page, .
9.

M.Sc. - Medical Informatics


2016-Now see the details by clicking the "courses" in the "Links" part of the page, .
10.

M.Sc. - Research Method


2016-Now see the details by clicking the "courses" in the "Links" part of the page, .

English

1.

Integration of Metabolic Knowledge for Genome-scale Metabolic Reconstruction, Invited chapter in “Biological Knowledge Discovery Handbook: Preprocessing, Mining and Post processing of Biological Data”


Authors: A. Masoudi-Nejad, A. Salehzadeh-Yazdi, S. Akbari, Y. Asgari
English, Publisher: John Wiley & Sons, Inc, 2014, Original

Papers

English

1.

Evidence for enhancer noncoding RNAs (enhancer-ncRNAs) with gene regulatory functions relevant to neurodevelopmental disorders


Authors: Yazdan Asgari, Julian Ik-Tsen Heng, Nigel Lovell, Alistair Forrest, Hamid Alinejad-Rokny
https://www.biorxiv.org/content/10.1101/2020.05.16.087395v1, Year. 2020,
2.

iMM1860: A new reconstruction of mouse genome-scale metabolic model


Authors: S. Khodaee, Y. Asgari, M. Totochi, M.H. Karimi-Jafari
Scientific Reports, Vol.10, No.1, Year. 2020, Page:1-13,
3.

Reconstruction and Analysis of Cattle Metabolic Networks in Normal and Acidosis Rumen Tissue


Authors: M. Gholizadeh, J. Fayazi, Y. Asgari, H. Zali, L. Kaderali
Animals, Vol.10, No.3, Year. 2020, Page:469,
4.

, Transcriptomic Changes in the Rumen Epithelium in Beef Cattle after Induction of Acidosis


Authors: J. Fayazi, M. Gholizadeh, H. Zali, Y. Asgari
Archives of Razi Institute, Vol.75, No.1, Year. 2020, Page:109-121,
5.

Thioredoxin is a potential pathogenesis attribute of Malassezia globosa and Malassezia sympodialis in pityriasis versicolor


Authors: S. Aghaei Gharehbolagh, S. Mahmoudi, Y. Asgari, H. Rahimi, S. Agha Kuchak Afshari, F. Noorbakhsh, S. Rezaie
Gene Reports, Vol.17, Year. 2019, Page:100468,
6.

The Significance of Noise in the Evolution of Negative and Positive Cooperativity in Protein Complexes


Authors: M. Taheri, K. Nouri, Y. Asgari, Z. Zabihinpour, M. Sadeghi
MATCH Communications in Mathematical and in Computer Chemistry, Vol.81, No.1, Year. 2019, Page:177-192,
7.

MGL_3741 gene contributes to pathogenicity of Malassezia globosa in pityriasis versicolo


Authors: S. Aghaei Gharehbolagh, P. Kordbacheh, S.J. Hashemi, R. Daie Ghazvini, Y. Asgari, S. Agha Kuchak Afshari, S.M. Seyedmousavi, S. Rezaie
Mycoses, Vol.61, No.12, Year. 2018, Page:938-944,
8.

Identification of candidate genes and proteins in aging skeletal muscle (sarcopenia) using gene expression and structural analysis


Authors: G. Shafiee, Y. Asgari, A. Soltani, B. Larijani, R. Heshmat
PeerJ, Vol.5, No.6, Year. 2018, Page:e5239,
9.

Exploring candidate biomarkers for lung and prostate cancers using gene expression and flux variability analysis


Authors: Y. Asgari, P. Khosravi, Z. Zabihinpour, M. Habibi
Integrative Biology, Vol.10, No.113, Year. 2018, Page:113-120,
10.

SCAN-Toolbox: Structural COBRA Add-oN (SCAN) for Analysing Large Metabolic Networks


Authors: Y. Asgari, Z. Zabihinpour, A. Masoudi-Nejad
Current Bioinformatics, Vol.13, No.1, Year. 2018, Page:100-107,
11.

Analysis of the enzyme network involved in cattle milk production using graph theory


Authors: S. Ghorbani, M. Tahmoores pur, A. Masoudi-Nejad, M. Nasiri, Y. Asgari
Molecular Biology Research Communications, Vol.4, No.2, Year. 2015, Page:93-103,
12.

CentiServer: A Comprehensive Resource, Web-Based Application and R Package for Centrality Analysis


Authors: M. Jalili, A. Salehzadeh-Yazdi, Y. Asgari, S. Arab, M. Yaghmaie, A. Ghavamzadeh, and K. Alimoghaddam
Plos One, Vol.10, No.11, Year. 2015, Page:e0143111,
13.

Alterations in cancer cells metabolism: the Warburg effect and metabolic adaptation


Authors: Y. Asgari, Z. Zabihinpour, A. Salehzadeh-Yazdi, F. Schreiber, A. Masoudi-Nejad
Genomics, Vol.105, Year. 2015, Page:275-281,
14.

Metabolic Cancer Biology: Structural-based analysis of cancer as a metabolic disease, new sights and opportunities for disease treatment


Authors: A. Masoudi-Nejad, Y. Asgari
Seminars in Cancer Biology, Vol.30, Year. 2015, Page:21-29,
15.

Computational analysis of reciprocal association of metabolism and epigenetics in the budding yeast: a genome-scale metabolic model (GSMM) approach


Authors: A. Salehzadeh-Yazdi, Y. Asgari, A.A. Sabouri, A. Masoudi-Nejad
PloS one, Vol.9, No.11, Year. 2014, Page:e111686,
16.

Network-based approach reveals Y chromosome influences prostate cancer susceptibility


Authors: P. Khosravi, V. H. Gazestani, Y. Asgari, B. Law, M. Sadeghi, B. Goliaei
Computers in Biology and Medicine, Vol.54, Year. 2014, Page:24-31,
17.

Controllability in Cancer Metabolic Networks According to Drug Targets as Driver Nodes


Authors: Y. Asgari, A. Salehzadeh-Yazdi, F. Schreiber, A. Masoudi-Nejad
PloS one, Vol.8, No.11, Year. 2013, Page:e79397,
18.

Cellular Automata Simulation of a Bistable Reaction-Diffusion System: Microsocopic and Macroscopic Approaches


Authors: Y. Asgari, M. Ghaemi, M.G. Mahjani
Iran. J. Chem. & Chem. Eng, Vol.30, No.1, Year. 2011, Page:143-150,
19.

Pattern Formation of the FitzHugh-Nagumo Model: Cellular Automata Approach


Authors: Y. Asgari, M. Ghaemi, M.G. Mahjani
Iran. J. Chem. & Chem. Eng, Vol.30, No.1, Year. 2011, Page:135-142,
20.

Computer simulation study of the Levy flight process


Authors: M. Ghaemi, Z. Zabihinpour, Y. Asgari
Physica A, Vol.388, Year. 2009, Page:1509-1514,
21.

Lattice gas automata simulation of 2-D site percolation diffusion: Configuration dependence of the theoretically-expected crossover of diffusion regime


Authors: M. Ghaemi, N. Rezaei-Ghaleh, Y. Asgari
Lect. Notes in Comp. Sci, Vol.5191, Year. 2008, Page:274-281,
22.

Obtaining the critical point and shift exponent for the anisotropic two-layer Ising and Potts models: Cellular Automata approach


Authors: Asgari, M. Ghaemi
Physica A, Vol.387, No.8-9, Year. 2008, Page:1937-1946,
23.

Constructing the critical curve for the two-layer Potts models using Cellular Automata


Authors: Y. Asgari, M. Ghaemi
J. Theor. Comp. Chem, Vol.5, No.2, Year. 2006, Page:141-150,
24.

Calculation of the critical point for the two-layer Ising and Potts models using Cellular Automata


Authors: Y. Asgari, M. Ghaemi, M.G. Mahjani
Lect. Notes in Comp. Sci, Vol.3305, Year. 2004, Page:709-718,

Farsi

1.

Reconstruction and topological analysis of metabolic network in the bovine rumen tissue


Authors: M. Gholizadeh, J. Fayazi, Y. Asgari, H. Zali
Veterinary Researches & Biological Products, No.125, Year. 2019, Page:106-117,
2.

Reconstruction and topology analysis of metabolic network involved in Bos Taurus milk production


Authors: S. Ghorbani, M. Tahmoores pur, A. Masoudi-Nejad, M. Nasiri, Y. Asgari
Animal Sciences Journal, Vol.110, Year. 2016, Page:167-180,

Abstracts and Presentations

English

1.

Screening of potential therapy targets for hepatocellular carcinoma using analysis of gene expression profile


3rd international and 11th national biotechnology congress
Location: Tehran, Iran,
Date: 2019-Type : Presentaion, Lecturer,
2.

What is Life


Location: School of Biological Sciences, Institute for Research in Fundame,
Date: 2016-Type : Presentaion, Lecturer,
3.

Next Generation Sequencing


Location: School of Biological Sciences, Institute for Research in Fundame,
Date: 2016-Type : Presentaion, Lecturer,
4.

Fixed Random Effects in Statistical Models with R


Location: School of Biological Sciences, Institute for Research in Fundame,
Date: 2016-Type : Presentaion, Lecturer,
5.

Reconstruction of context-specific metabolic models for mouse Hematopoietic Stem and Progenitor Cells


6th Conference on Bioinformatics
Location: University of Tehran,
Date: 2016-Type : Poster, Lecturer,
6.

Introduction to MATLAB Programming


1st Summer School in Bioinformatics: Gene Expression Analysis
Location: Institute for Research in Fundamental Sciences,
Date: 2015-Type : Presentaion, Lecturer,
7.

Human Objective Function


6th International Workshop on Biological Knowledge Discovery and Data Mining
Location: Valencia, Spain,
Date: 2015-Type : Poster, Lecturer,
8.

Metabolomic Applications as Biomarkers in Oncology


Iranian Cancer Genetics Congress
Location: Shariati Hospital, Tehran, Iran,
Date: 2013-Type : Presentaion, Lecturer,
9.

Biophysical Interpretation of Hubs in Protein-Protein Interaction Networks


EMBO Meeting
Location: Barcelona, Spain,
Date: 2010-Type : Poster, Lecturer,
10.

Corresponding states theory and thermodynamic properties of alkali metals


9th Iranian Physical Chemistry Seminar
Location: Rasht, Zibakenar, Iran,
Date: 2006-Type : Poster, Lecturer,
11.

Calculation of the critical point for the two-layer Ising model using Cellular Automata


7th Iranian Physical Chemistry Seminar
Location: Isfahan University of Technology, Isfahan, Iran,
Date: 2005-Type : Poster, Lecturer,
12.

Simulation of FitzHugh-Nagumo models as a reaction-diffusion system using Cellular Automata


7th Iranian Physical Chemistry Seminar
Location: Isfahan University of Technology, Isfahan, Iran,
Date: 2005-Type : Poster, Lecturer,
13.

Cellular Automata and reaction-diffusion systems


14th Iranian Chemistry and Chemical Engineering Congress
Location: Tehran, Iran,
Date: 2004-Type : Poster, Lecturer,
14.

Application of Cellular Automata in pattern formation


First Iranian Bioinformatics Conference
Location: Tehran, Iran,
Date: 2003-Type : Presentaion, Lecturer,
1.

Programming


  • C
  • C++
  • MATLAB
  • R
  • Python (in progress)
  • Mathematica (in progress)
2.

Network Skills


  • Network+
  • CCNA
  • CWNA
  • MCSA
1.

انجمن علمی بیوانفورماتیک ایران


Activity Type:عضو هیئت مدیره
1397
1. Available Projects
  • Finding mechanism of specific cancer-related proteins using systems biology approaches
  •  
  • Metabolic modeling of engineered stem cells (or a specific cell line) for higher protein/exosome production
  •  
  • Finding candidate genes/pathways for cancer diagnosis based on investigation of metabolic reprogramming in cancer cells using tissue-specific metabolic models
  •  
  • Exploring enhancer-like RNAs (eRNAs) functions using genomic data analysis
  •  
  • Systems Biology of drug-resistance tumors
  •  
  • Non-invasive biomarker discovery in cancers using Systems Biology methods
  •  
  • Identification of important genes/proteins of cancers by network analysis (for example using GEO/TCGA data and/or ceRNA Network)
  •  
  • Electrochemical DNA/RNA biosensor for detecting cancers & using an artificial neural network for the evaluation of parameters

Selected guided publications would be available for each project on request.

For ongoing projects you could see the "Research Group" section of the web page.

2. Research Interests
  • Bioinformatics
    • Systems Biology
    • Metabolic Networks (Genome-Scale Models, Structural Analysis, Constraint-based Modeling, Kinetic Modeling)
  • Complex Systems
    • Reaction-Diffusion Systems
    • Cellular Automata (CA)
    • Random Walks - Anomalous Diffusion
    • Nonlinear Dynamics
  • Philosophy of Science
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