Group Leader

 Ali Masoudi-Nejad, Ph.D.   





Ali Masoudi-Nejad

Associate Professor of Systems Biology and Bioinformatics


علی مسعودی نژاد

دانشیار سیستم بیولوژی و بیوانفورماتیک

Ali Masoudi-Nejad received his Ph.D. in genomics with Prof. Takashi Endo from Kyoto University, Japan. He then did his first Post-Doc with Prof. Robbie Waugh at James Hutton Institute in Scotland and Prof. Paul H. Dear from MRC-LMB, Cambridge, UK. He returned to the Kyoto University and did two consecutive Post-Docs with Prof. Minoru Kanehisa, co-founder of The GenBank and founder of the KEGG and Prof. Susumu Goto in bioinformatics and systems biology. He then returned to Iran in 2006 and founded the Laboratory of Systems Biology and Bioinformatics, LBB ( at University of Tehran.


He is now associate professor of systems biology and bioinformatics. His main research interest focuses on:


  • Computational systems biology
  • Cancer modeling and network biology
  • Analysis of biological networks
  • Drug-Target  and disease networks
  • Controllability and observability in biological networks
  • Genome-scale pathway modeling
  • Bioinformatics algorithms
  • MicroRNA and RNAi pathway reconstruction
  • Cancer stem cell modeling and network biology
  • MicroRNA and TF regulatory network
Name and Surname Ali Masoudi-Nejad
Nationality Persian (Iranian)
Date of Birth 22/May/1967
Languages Persian ( (پارسی, Kurdish (کوردی) , English (انگلیسی) , Japanese (日本語)
2005-2006 Associate Researcher, Bioinformatics Center, Kyoto University, Japan
2006-2011 Assistant Professor of Systems Biology and Bioinformatics, University of Tehran, Iran
Current Associate Professor of Systems Biology and Bioinformatics, University of Tehran, Iran. 


Academic Degrees & Research
Ph.D.        Molecular Genetics and Genomics, Kyoto University, Japan
Post-Doc-1 Genome Dynamics, MRC-LMB Cambridge and James Hutton Institute, UK
Post-Doc-2 Bioinformatics, Bioinformatics Center, Kyoto University. Japan
Post-Doc-3 Systems Biology, Laboratory of Bioknowledge Systems, Bioinformatics Center,   Institute for Chemical Research, Kyoto University, Japan




1        Computational Genomics (Ph.D. Course)

2        Introduction to Bioinformatics (M.Sc. and Ph.D. Course)

3        Advanced Bioinformatics (Ph.D. Course)

4        Genome Structure and Function (Ph.D. Course)

5        Biological Databases (Ph.D. Course)

6        Computational Molecular Biology (M.Sc. and Ph.D. Course)

7        Seminar in Bioinformatics (Ph.D. Course)

8        Seminar in Systems Biology (Ph.D. Course)



1        Head of the Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, 2010-now

2        Director of the study program in charge of the curriculum for Ph.D. Program in Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran

3        Director of the study program in charge of the curriculum for Master Program in Bioinformatics



  1. Japanese Monbugakosho Ph.D. scholarship award (1999-2002)
  2. James Hutton Institute & Leverhulme Foundation Post-Doctoral award (2002-2003)
  3. Japanese JSPS Post-Doctoral award (2003-2005)
  4. Kyoto University, Bioinformatics Center  COE 21th century award (2005-2006)
  5. German DAAD Visiting Professorship award (summer 2010)
  6. German DAAD Visiting Professorship award (summer 2012)
  7. JundiShapur Iran-France collaborative research program (2012)


Scientific Networks











Prof. Dr. Ina Koch University of  Frankfurt, Germany
Prof. Steven Haggarty Harvard University & MIT, USA
Prof. Frank Emmert-Streib Queen’s University Belfast, UK
Prof. Alexandre  Bonvin Utrecht University, Netherlands
Dr. Björn Junker IPK Gatersleben, Germany
Prof. Dr. Falk Schreiber Halle University, Germany
Dr. Ruy Jáuregui Helmholtz Zentrum für Infektionsforschung, Germany
Prof. Susumu Goto Kyoto University, Japan
Prof. Takashi R. Endo Kyoto University, Japan
Prof. Minoru Kanehisa Kyoto University, Japan
Prof. Siamak Bahram Université de Strasbourg, France



Editorial Activity


1        Seminar in Cancer Biology (Guest Editor), IF= 7.43

2        Genes and Genetic Systems (Associate Editor)

3        Current Bioinformatics (Associate Editor)

4        Frontiers in Bioinformatics and Computational Biology (Review Editor)

5        In Silico Pharmacology (Editor)

6        Biomedical Engineering and Computational Biology (Editor)

7        Journal of Proteomics & Bioinformatics (Editor)

8        Computational and Mathematical Methods in Medicine (Editor)

9        Comparative and Functional Genomics (Editor)

10    Systems Pharmacology (Assistant Editor)

11    MicroRNA (Associate Editor)

12    International Journal On Advances in Life Sciences

13    International Journal On Advances in Intelligent Systems



Reviewer for International Journals  

1        Bioinformatics

2        Seminar in Cancer Biology

3        BMC Systems Biology

4        Nucleic Acids Research

5        Briefing in Bioinformatics

6        BMC Genomics

7        IEEE/ACM Transactions on Computational Biology and Bioinformatics

8        PLOS ONE

9        BMC Bioinformatics

10    OMICS: Journal of Integrative Biology

11    DNA Research

12    Molecular Genetics and Genomics

13    Genes and Genetic Systems

14    Digital Signal Processing

15    Frontiers in Bioinformatics and Computational Biology

16    Computer Methods and Programs in Biomedicine

17    Information Systems

18    Evolutionary Bioinformatics

19    Cancer Informatics

20    Journal of Proteomics & Bioinformatics

21    International Journal of  Data Mining and Bioinformatics

22    Journal of Genetics and Genomics

23    Computational and Mathematical Methods in Medicine

24    International Journal of Genomics (Comparative and Functional Genomics)



1- Books   

Edited Books:

  1. Ali Masoudi-Nejad, Zahra Narimani, Nazanin Hosseinkhan. (Editors). Next Generation Sequencing and Sequence Assembly: methodologies and algorithms. SpringerBriefs in Systems Biology. 2013
  2. Ali Masoudi-Nejad, Alireza Meshkin. (Editors). Gene Prioritization: rationale, methodologies and algorithms. SpringerBriefs in Systems Biology. 2014.
  3. Ali Masoudi-Nejad, Gholamreza Bidkhori, Ali Najafi. (Editors). Genome Scale Modeling of Biological Systems. SpringerBriefs in Systems Biology. 2014.



Contributed Chapters in Books:

  1. Ali Masoudi-Nejad, Ali Salehzadeh, Shiva Akbari, Yazdan Asgari. Integration of Metabolic Knowledge for Genome-scale Metabolic Reconstruction. Invited chapter in book “Biological Knowledge Discovery Handbook: Preprocessing, Mining and Post processing of Biological Data “. ISBN: 978-1-1181-3273-9.  Wiley 2013.
  2. Ali Masoudi-Nejad, Susumu Goto, Takashi Endo and Minoru Kanehisa. KEGG/EGENES resource for plant bioinformatics in post-sequence era. Invited chapter in book “Plant Bioinformatics”. Humana Press, USA 2007.
  3. Bahman Yari, Daryanaz Dargahi, Nima Aghaeepour and Ali Masoudi-Nejad. Support Vector Clustering: From Local Constraint to Global Stability. Invited chapter in book ” Foundations of Computational Intelligence Volume 6: Data Mining “. Springer 2009.
  4. Saeed Omidi and Ali Masoudi-Nejad.  Network Evolution: Theory and Mechanisms. Invited chapter in book “Computational Network Analysis”. Springer 2009.
  5. Ali Masoudi-Nejad, Takashi Endo. Novel gene mapping technology for post-genome era. Invited chapter in book “Chromosome Mapping Research Developments”. Nova Publisher, USA 2008.
  6. Hamid Ravaee, Ali Masoudi-Nejad and Ali Moeini.  Finding Protein Complexes via Fuzzy Learning Vector Quantization Algorithm. Invited chapter in book “Protein-Protein Interactions – Computational and Experimental Tools”. InTech 2012.




2- Submitted Papers

  1. Ali Masoudi-Nejad, Yazdan Asgari (2013) Metabolic Cancer Biology: Structural Perspective. INVITED REVIEW. Seminar in Cancer Biology. Under Review
  2. Ali Masoudi-Nejad, Gholamreza Bidkhori, Saman Ashtiani, Edwin Wang (2013) Genome-Scale Cancer Modeling. INVITED REVIEW. Seminar in Cancer Biology. Under Review
  3. Edwin Wang, Ali Masoudi-Nejad (2013) Cancer Networks. INVITED REVIEW. Seminar in Cancer Biology. Under Review
  4. Ali Masoudi-Nejad, Alireza Meshkin (2013) Agent-based approaches to cancer modeling: rationales for using holonic agent-based modeling. INVITED REVIEW. Seminar in Cancer Biology. Under Review
  5. Yazdan Asgari, Ali Salehzadeh-Yazdi, Zahra Zabihinpour, Falk Schreiber, Ali Masoudi-Nejad (2013) SCAN-Toolbox : Structural COBRA Add-oN (SCAN) for Metabolic Networks. Genomics. Under Review
  6. Peyman Zarrineh, Aminael Sánchez-Rodríguez, Nazanin Hosseinkhan, Zahra Narimani,  Ali Masoudi-Nejad, Kathleen Marchal (2013) Genome-scale co-expression network comparison between Escherichia coli, Bacillus subtilis, and Salmonella enetica serovar Typhimurium reveals conservation and divergence in their regulatory networks and explains their dissimilar lifestyles. PLOS ONE. Under Review.
  7. Ali Najafi, Gholamreza Bidkhori, Ina Koch, Ali Masoudi-Nejad (2013) Genome Scale Modeling in Systems Biology: algorithms and resources. Current Genomics. Under Review
  8.  Javad Zahiri, , Morteza Mohammad-Noori, Reza Ebrahimpour, Ali Masoudi-Nejad (2014)  LocFuse: Human Protein-Protein Interaction Prediction via Classifier Fusion Using Localization Information. Bioinformatics. Submited
  9. Balal sadeghi, Hamed Ahmadi, Mohammadreza Nassiri, Ali Masoudi-Nejad (2014) BosFinder: A Novell Pre-MicroRNA Gene Prediction algorithm in Bos taurus. Animal Genetics. Submited
  10. Isar Nassiri, Ali Masoudi-Nejad, Mahdi Jalili, Ali Moeini (2013) Sensitivity Analysis of the Brain’s Signalling Network Flow: finding the optimal region of the systems for perturbation.Genomics. Submited.
  11. Reza Shamsaee, Mahmood Fathy, Gholamreza Bidkhori, Ali Masoudi-Nejad (2013) LuCaSim:  a toolbox for Lung Cancer Modeling and Simulation. Current Vascular Pharmacology. Submited
  12. Alireza Meshkin†, Mahdi Heidari†, Ali Masoudi-Nejad (2013) Drug Prioritization: a network-based approach for finding optimal cocktail drug combination.
  13. Ali Najafi, Ali Masoudi-Nejad, Mostafa Ghanei, Mohamad-Reza Nourani, Ali Moeini (2013) Pathway Reconstruction of Airway Remodeling in Chronic Lung Diseases: a systems biology approach. PLOS ONE. Under Review
  14. Ali Salehzadeh-Yazdi, Yazdan Asgari, Ali Akbar Saboury,  Ali Masoudi-Nejad (2013) Computational analysis of reciprocal association of metabolism and epigenetics in budding yeast. PLOS ONE. Under review
  15. Mehran Aflakparast, Abbas Gerami, Shyam Visweswaran, Ali Masoudi-Nejad (2012) Informative Bayesian Model Selection‎: ‎A‎ Method for Identifying Interactions in Genome-Wide Data. Genomics. Under Review
  16. Nazanin Hosseinkhan, Peyman Zarrineh, Ali Masoudi-Nejad (2013) Comparative Analysis of genome-scale expression network in resident microorganisms in lung. Current Genomics. Under Review
  17. Ali Najafi, Ali Masoudi-Nejad, Mostafa Ghanei, Gholamreza Bidkhori, Ali Moeini, and Mohamad-Reza Nourani (2013) Computational modelling of molecular airway remodeling pathway in chronic lung disease. PLOS ONE. Under Review




2- Published/Accepted Papers


  1. Yazdan Asgari, Ali Salehzadeh-Yazdi, Falk Schreiber, Ali Masoudi-Nejad (2013) Controllability in metabolic cancer networks according to drug targets as driver nodes. PLOS ONE 8(11): e79397.
  2. Sadegh Azimzadeh, Ali Masoudi-Nejad (2013) Human RNAi Pathway: crosstalk with organelles and cells. Functional and Integrative Genomics. DOI: 10.1007/s10142-013-0344-1. REVIEW
  3. Ali Masoudi-Nejad, Zaynab Mousavian, Joseph H. Bozorgmehr (2013) Drug-Target and Disease Networks: polypharmacology in the post-genomic era. In Silico Pharmacology. 1:17
  4. 4.       Gholamreza Bidkhori, Zahra Narimani, Saman Hosseini Ashtiani, Ali Moeini, Ali Masoudi-Nejad (2013) Reconstruction of integrated genome-scale coexpression network revealed key modules in lung adenocarcinoma. PLOS ONE. 8 (7), e67552
  5. Mehran Aflakparast, Hamid Salimi,  Abbas Gerami, Marie-Pierre Dubé, Shyam Visweswaran, Ali Masoudi-Nejad (2013) Cuckoo Search Epistasis: A New Method for exploring Significant Genetic Interactions. Heredity. Accepted
  6. Gholamreza Bidkhori,  Ali Moeini, Ali Masoudi-Nejad (2012) Modeling of tumor progression in non-small-cell lung cancer  (NSCLC) and intrinsic resistance to TKI in loss of PTEN expression. PLOS ONE. 7(10): e48004
  7. Javad Zahiri, Joseph Hannon Bozorgmehr, Ali Masoudi-Nejad (2013) Computational Prediction of Protein–Protein Interaction Networks: algorithms and resources. Current Genomics. 14 (6): 397-414. REVIEW
  8. Mahdieh Sadat Ghasemi, Hossein Seidkhani, Faeze Tamimi, Maseud Rahgozar, Ali Masoudi-Nejad (2014) Centrality Measures in Biological Networks. Current Bioinformatics. 9: 11-37. REVIEW
  9. 9.       Mahdieh Sadat Ghasemi, Gholamreza Bidkhori, Maseud Rahgozar, Ali Masoudi-Nejad (2013) C-element: a New Clustering Algorithm to Find High Quality Functional Modules in PPI Networks. PLOS ONE. 8(9):e72366
  10. Sahand Khakabimamaghani, Iman Sharafuddin, Norbert Dichter, Ina Koch and Ali Masoudi-Nejad (2013) QuateXelero: an accelerated exact network motif detection algorithm. PLOS ONE. 18;8(7):e68073
  11. Isar Nassiri, Ali Masoudi-Nejad, Mahdi Jalili, Ali Moeini (2013)  Discovering dominant pathways and signal–response relationships in signaling networks. Genomics. S0888-7543(13)00149-3
  12. Javad Zahiri, Morteza Mohammad-Nouri, Reza Ebrahimpour, and Ali Masoudi-Nejad (2013) PPIevo: Protein-Protein Interaction Prediction from Evolutionary Information. Genomics. S0888-7543(13)00121-3
  13. Ali Najafi, Ali Masoudi-Nejad, Mostafa Ghanei, Mohamad Reza Nourani (2013) Microarray gene expression analysis of human airway in patients exposed to sulfur mustard. Genomics.
  14. Sedigheh Mahdavi, Ali Salehzadeh-Yazdi, Ali Mohades, Ali Masoudi-Nejad (2013) Computational Structure Analysis of Biomacromolecule Complexes by Interface Geometry. Computational Biology and Chemistry. 25;47C:16-23
  15. Hamed Ahmadi, Ali Ahmadi, Sadegh Azimzadeh-Jamalkandi, Mahdi Aliyari Shoorehdeli, Ali Salehzadeh-Yazdi, Gholamreza Bidkhori, Ali Masoudi-Nejad (2012) HomoTarget: a New Algorithm for Prediction of MicroRNA Targets in Homo sapiens. Genomics. 101(2):94–100
  16. Isar Nassiri, Ali Masoudi-Nejad, Mahdi Jalili, Ali Moeini (2012) Normalized Similarity Index: An adjusted index to prioritize article citations. Journal of Informetrics. 7:91-98
  17. Isar Nasiri, Ali Masoudi-Nejad, Mahdi Jalili, Ali Moeni (2012) Nonparametric Simulation of Signal Transduction Networks with Semi-Synchronized Update. PLOS ONE. 7(6):e39643
  18. Ali Masoudi-Nejad, Alireza Meshkin, Behzad Haji-Eghrari, Gholamreza Bidkhori (2012) Candidate Gene Prioritization. Molecular Genetics and Genomics. 287(9):679-98
  19. Ali Masoudi-Nejad, Mitra Anasariola, Ali Salehzadeh-Yazdi, Sahand Khakabi (2012) CytoKavosh: a Cytoscape Plug-in for Finding Network Motifs in Large Biological Networks. PLOS ONE. 7(8): e43287
  20. Isar Nassiri, Esmael Azadian, Roozbeh Sharafi, Ali Masoudi-Nejad (2013) Co-Occurrence: a Gene Reference Resource for Coincidental Patterns of Gene Mutations in Human Cancers. Journal of Proteomics and Bioinformatics. 6(9):197-201.
  21. Isar Nassiri, Esmaeel Azadian, Ali Masoudi-Nejad (2013) A Sequence Motif Associated with Intrinsic Mutation Hot-Spots in Human Cancers. Journal of Proteomics and Bioinformatics. 6(9):173-186.
  22. 22.  Siavash Ghavami, Farshad Lahouti, Ali Masoudi-Nejad (2012) Modeling and Analysis of Abnormality Detection in Biomolecular Nano-Networks. Nano Communication Networks. 3(4): 229–241
  23. Ali Masoudi-Nejad, Falk Schreiber, Zahra Razaghi MK (2012) Building Blocks of Biological Networks: A Review on Major Network Motif Discovery Algorithms. IET Systems Biology. 6 (5) 164-174
  24. Ali Masoudi-Nejad, Sara Movahedi, Ruy Jáuregui (2011) Genome-scale computational analysis of DNA curvature and repeats in Arabidopsis and rice uncovers plant-specific genomic properties. BMC Genomics. 12:214
  25. Sedigheh Mahdavi, Ali Mohades, Ali Salehzadeh Yazdi, Ali Masoudi-Nejad (2012) Computational Analysis of RNA-Protein Interaction  interfaces via the Voronoi Diagram. Journal of Theoretical Biology. 293:55-64
  26. Ehsan Habibi, Ali Masoudi-Nejad, Steven Haggarty (2011) Emerging Roles of Epigenetic Mechanisms in Parkinson’s disease. Functional and Integrative Genomics. 11:523–537
  27. 27.  Reza Shamsaee, Mahmud Fathy, Ali Masoudi-Nejad (2013) Extracting a Cancer Model by Ant Colony Optimization Algorithm. International Journal of Data Mining and Bioinformatics. 7(6):1-13
  28. Sadegh Azimzadeh, Ali Masoudi-Nejad (2011) RNAi Pathway Integration in Caenorhabditis elegans Development. Functional and Integrative Genomics. 11:389-405
  29. Maryam Darabi, Ali Masoudi-Nejad, Ghorbanali Nemat-Zadeh (2012) Bioinformatics Study of the 3-hydroxy-3-methylglotaryl-Coenzyme A Reductase (HMGR) Gene in Gramineae. Molecular Biology Reports. DOI: 10.1007/s11033-012-1761-2
  30. Zahra Zamani, Amirhossein Hajihosseini, Ali Masoudi-Nejad (2010) Computational methodologies for analyzing, modeling and controlling gene regulatory networks. Biomedical Engineering and Computational Biology. 2:47–62.
  31. Azimzadeh, S., Masoudi-Nejad, Ali (2009) Reconstruction of Arabidopsis thaliana Fully-Integrated Small RNA Pathway. Functional & Integrative Genomics. 9:419-432.
  32. Razaghi, A.,  Ahrabian, H.,…. Masoudi-Nejad, Ali (2009) Kavosh: A New Algorithm for Finding Network Motifs. BMC Bioinformatics. 4:10:318.
  33. Omidi, S., Schreiber, F., Masoudi-Nejad, Ali (2009) MODA: An Efficient Algorithm for Network Motif Discovery in Biological Networks. Genes and Genetic Systems. 84:385-395
  34. Katayoun Samimi-Rad., Mohsen Nasiri Toosi., Ali Masoudi-Nejad.,  Ali Najafi., Ramin Rahimnia., Fatemeh Asgari., Alireza Namazi Shabestari., Gholamreza Hassanpour., Seyed-Moayed Alavian., Freshteh Asgari (2012) Molecular epidemiology of hepatitis C virus among injection drug users in Iran. Archives of Virology. DOI 10.1007/s00705-012-1369-9
  35. Askary, A., Masoudi-Nejad, A., Mizbani, A., Naderi-Parizi, S., Purmasjedi, M (2009) N4: A Precise and Highly Sensitive Promoter Predictor Using Neural Network fed by Nearest Neighbors. Genes and Genetic Systems. 84: 425-430
  36. R. Daie Ghazvini., H. Mirhendi., S. A. Ghiasian., A. Masoudi-Nejad., H. Shokri., M. Soltani., S. Haddadi., A. R. Khosravi (2011) Genotyping of Fusarium verticillioides strains producing fumonisin B1 in feed associated with animal health problems. Iranian Journal of Veterinary Research (IJVR). 8:309-316
  37. Masoudi-Nejad, A., Goto, S., Endo, TR and Kanehisa, M (2007) Bioinformatics Resources for Plant Genomics Research. Methods Mol Biol. 406:437-458.
  38. Nasr-Isfahani, S., Mirsafian, A., Masoudi-Nejad, A (2008) A New Approach for Touching Cells Segmentation. IEEE BioMedical Engineering and Informatics. 1:816-820
  39. Masoudi-Nejad, A.,  Susumu Goto, Ruy Jauregui, Masumi Ito, Shuichi Kawashima,Yuki Moriya, Takashi R. Endo and Minoru Kanehisa (2007) EGENES: Transcriptome-based plant database of genes with metabolic pathway information and EST indices in KEGG. Plant Physiology. 144: 857-866       
  40. 40.  Masoudi-Nejad, A.,  Koichiro Tonomura, Shuichi Kawashima, Masumi Itoh, Minoru Kanehisa, Takashi Endo and Susumu Goto (2006) EGassembler: online bioinformatics service for large-scale processing, clustering and assembling ESTs and genomic DNA fragments. Nucleic Acids Research. 34: W459-W462.
  41. Masoudi-Nejad, A., Nasuda, S., R. Waugh., Marrie-Therese Bihoreau., Endo, T.R. (2005) an alternative to radiation hybrid mapping for large-scale genome analysis in barley. Molecular Genetics and Genomics. 274: 589–594.
  42. Ali Salehzadeh-Yazdi, Shiva  Akbari-Birgani, Ali  Masoudi-Nejad (2011) Diabetes and Systems Biology. JICS.  8(3): 63-67
  43. Rahimi A. A. , Bahmani M. Kh. , Masoudi-Nejad A. , Saadati M. , Khosravi A. , Shafie Khani A (2010) Application of near-infrared spectroscopy and support vector machine in detection of HIV-1 infection. Kowsar Medical Journal, 15 (1) :23-29 فارسی
  44. Mostafa Hadian Dehkordi, Ali Masoudi-Nejad, Mohamad Nouri (2010) gpALIGNER: a fast algorithm for global pairwise alignment of DNA sequences. IJCCE. Accepted
  45. Monireh Cheniany, Hassan Ebrahimzadeh, Ali Masoudi-Nejad (2011) Effect of expression of chalcone synthase gene on flavonoids content and rooting ability in Juglans regia L. Plant Cell, Tissue and Organ Culture. DOI 10.1007/s11240-011-0072-y
  46. Reza Shamsaee, Mahmood Fathy, Ali Masoudi-Nejad (2010) Integration and Reduction of Microarray Data Using Information Theory Approach. IJCCE. 29(4):19-29
  47.  Daie Ghazvini, R. Mirhendi, H. Ghiasian, S. A. Masoudi-Nejad, A. Shokri, H. Soltani, M. Haddadi, S and Khosravi, A. R. (2011) Genotyping of Fusarium verticillioides strains producing fumonisin B1 in feed associated with animal health problems. Iranian Journal of Veterinary Research. 12(4): 309- 316
  48. Hesam T. Dashti, Ali Masoudi-Nejad (2010) Mining Biological Repetitive Sequences Using Support Vector Machines and Fuzzy SVM. IJCCE. 29(4):1-18
  49. Hesam T. Dashti, Ali Masoudi-Nejad  (2010) Finding Exact and Solo LTR-Retrotransposons in Biological Sequences Using SVM. IJCCE. Accepted
  50. Sedigheh Mahdavi, Ali Mohades Khorasani, Samad Jahandideh, Ali Masoudi-Nejad (2010) Recognition Protein-RNA Interaction interfaces via the Voronoi Diagram. JICS. 7:S1-A61
  51.  Khosravi A, Behzad F, Sabokbar A, Shokri H, Haddadi S, Masoudi-Nejad A (2010) Molecular typing of Epidermophyton floccosum isolated from patients with dermatophytosis by RAPD-PCR. J Basic Microbiol. 1:S68-S73
  52. Monireh Cheniany, Hassan Ebrahimzadeh, Ali Masoudi-Nejad, Kourosh Vahdati and Charles Leslie. Effect of endogenous phenols and some antioxidant enzyme activities on rooting of Persian walnut. African Journal of Plant Science. 4(12): 479-487
  53. Yazdi-Samadi, B., Masoudi-Nejad, A., Abd-Mishani, S., Sarblouki, M. (2003) Quantitative Study of Seed Storage Proteins (HMW-GS) in Wheat Using Electrophoresis and Laser Scanning Densitometry. Physiology and Molecular Biology of Plants. 7:61-66.
  54. Tsuchida, M., Fukushima, T., Shuhei Nasuda, S., Masoudi-Nejad, A., Ishikawa, G., Nakamura, T., and Takashi R. Endo (2008) Dissection of rye chromosome 1R in common wheat. Genes and Genetics System. 83: 43-53.
  55. Haddadi, S., Khosravi, A.R., Rostami, M., Masoudi-Nejad, A.,  Soltani, S., Soltani, M. (2008) Molecular Typing of Iranian Cladosporium Isolates Using RAPD-PCR. Journal of Biotechnology.  7(4): 1-6.
  56. Modarressi, M.H., Ranjzad, F., Tavallaei,M ., ,Asadi, A., Zaim-Kohan, H., Masoudi-Nejad, A  (2008) Importance of 273rd residue in proteolytic processing for production of functional TSGA10 protein. Bioscience Hypotheses. 1:336-373.
  57. Masoudi-Nejad, A., Nasuda, S., Kawabe, A., Endo, T.R. (2002) Molecular cloning, sequencing and chromosomal mapping of a 1A-encoded omega-gliadin gene from wheat. Genome. 45: 661–669.
  58. Masoudi-Nejad, A., Nasuda, S., McIntosh, R.A., Endo, T.R. (2002) Transfer of rye chromosome segments to wheat by a gametocidal system. Chromosome Research. 10:349-57.
  59. Endo, T. R., Masoudi-Nejad, A., Nasuda, S., McIntosh, R. A. (2001) Separation of rust resistance genes from Sec-1 on rye chromosome 1R by the gametocidal recombination. Chromosome Research. 9:33-43.
  60.  Masoudi-Nejad, A. (2000) Wheat storage protein. Wheat Information Service. 92:33.


Congress/Symposium سخنرانیها

Keynote Speech  سخنرانیهای کلیدی

  1. Ali Masoudi-Nejad, 2013. Systems Biology: Making sense of the Biological systems by Integration of Post-Genomics High-Throughput Data. International Symposium on Programming and Systems (ISPS 2013) Algeria, 22- 24 April. Algeria
  2. Ali Masoudi-Nejad, Cognitive Systems Biology (2012) Cognitive Science; application in high stress condition. 16 May 2012 (17 Ordibehesht). Shahid Beheshti University of Medical Science, Tehran, Iran
  3. Ali Masoudi-Nejad, Systems Biology and Health: Toward Systems Medicine. First National Conference of Application of Basic Sciences in Medicine. Tehran, Beheshti, 10-12 March 2011 (18-19 Esfand 1389).
  4. Ali Masoudi-Nejad, Systems Biology and Diabetes. Symposium on Biophysics and Bioinformatics of Diabetes: Amyloid Frontier. Departments of Biological Sciences and Condensed Matter Physics, IASBS, Zanjan. 17  January 2011.
  5. Ali Masoudi-Nejad, From Complexity of Biological Systems to Systems Biology and Systems Medicine. 11th Iranian Congress of Genetics, 22‐24 May 2010 (1‐3 Khordad, 1389), Tehran, Iran.
  6. Ali Masoudi-Nejad, Genes, Genetics Systems, Systems Biology and Synthetic Biology; It is all about making sense of biological systems. 2th Iranian Congress of Bioinformatics, 9-10Oct., 2008, (9-1 Mehr 1387) Tehran, Iran
  7. Ali Masoudi-Nejad, Bioinformatics in the post-genomics era: Towards Biology of the Systems. 5th Iranian Congress of Biotechnology, 10-15 Nov., 2008, (1-3 Aban 1386) Tehran, Iran.
  8. Ali Masoudi-Nejad, Genes to post-genomics era: From Biological Systems to Systems Biology. 10th Iranian Congress of Genetics, 21-23 May 2008 (1-3 Khordad, 1387), Tehran, Iran.
  9. Ali Masoudi-Nejad, Wheat storage protein: past, present and the future. The joint meeting of the 5th Japanese Society of Molecular Biology of Triticeae and the 27th Japanese Genetics Symposium, October 7-9, 2000, Japan.


Regular Presentation سخنرانیهای شفاهی و معمولی

1        Mahdieh Ghasemi, Maseud Rahgozar, Gholamreza Bidkhori and Ali Masoudi-Nejad (2013) Finding High Quality Functional Modules in Homo sapiens Tissue Specific PPI Networks. 12th IEEE/ACIS International Conference on Computer and Information Science (ICIS 2013). Toki Messe. June 16-20, 2013. Niigata, Japan

2        Iman Sharafuddin, Mehrdad Mirzaei, Masoud Rahgozar and Ali Masoudi-Nejad, 2013. Protein-Protein Interaction Network Clustering Using Particle Swarm Optimization.  International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO 2013). 18-20 March, 2013. Granada, Spain

3        Rezvan Zendehdel, Ali Masoudi-Nejad, Farshad H. Shirazi, 2013. Predicting Biomarker for Cytotoxicity Using Partial Least Square-Fourier Transform Infrared Spectroscopy (PLS FTIR). Progress in Electromagnetics Research Symposium (PIERS 2013), March 25-28, Taipei, Taiwan.

4        Ali  Masoudi-Nejad, G. Bidkhori (2012) Modeling of tumor progression in non-small-cell lung cancer (NSCLC).  4th Conference on Systems Biology of Mammalian Cells. 9–11 July 2012 in Leipzig, Germany.

5        J. Zahiri, M. H. Karimi-Jafari, R. Ebrahimpour, Ali Masoudi-Nejad, A. Emamjomeh, O. Yaghoubi (2012) Using GO annotation clustering to improve protein-protein interaction prediction.  4th Conference on Systems Biology of Mammalian Cells. 9–11 July 2012 in Leipzig, Germany.

6        G. Bidkhori, Z. Narimani, Ali Masoudi-Nejad (2012) Reconstruction of CNV-related co-expression network in non small cell lung cancer (NSCLC) .4th Conference on Systems Biology of Mammalian Cells. 9–11 July 2012 in Leipzig, Germany.

7        J. zahiri, R. Ebrahimpour, M.H. Karimi-Jafari, Ali Masoudi-Nejad, A. Emamjomeh (2012) A novel ensemble learning method for protein protein interaction prediction .4th Conference on Systems Biology of Mammalian Cells. 9–11 July 2012 in Leipzig, Germany.

8        Ali Salehzadeh-Yazdi, Ali Masoudi-Nejad, Ali Akbar Saboury, Shiva Akbari-Birgani (2012) Hubs and Non-Hubs in Protein-Protein Interaction Networks: A Biophysical Interpretation.  BIOKDD ’12 as part of 23rd International Conference on Database and Expert Systems Applications – DEXA 2012. Vienna (Austria) September 3 – 6, 2012

9        Hamid ravaee, Ali Masoudi-Nejad (2011) Finding Protein Complexes via Fuzzy Learning Vector Quantization Algorithm. The Third International Conference on Bioinformatics, Biocomputational Systems and Biotechnologies BIOTECHNO May 22-27,  Venice/Mestre, Italy

10    Ali Masoudi-Nejad, Sadegh Azimzadeh jamalkandi. Small RNA Based Silencing in Caenorhabditis elegans Development: a Fully-Integrated Pathway. The 4th Annual Congress of Molecular Diagnostic, September 22-24 Beijing, China

11    Hamid Ravaee, Ali Masoudi-Nejad, Saeed Omid, Ali Moini (2010) Improved Immune Genetic Algorithm for Clustering Protein-Protein Interaction Network. IEEE International Conference on Bioinformatics and Bioengineering (BIBE2010).  31 May-3 June, Philadelphia, PA, USA.  Oral Presentation

12    Ali Masoudi-Nejad (2010) Biological Network and Network Motifs. 4th World Congress of Gene, 1-4 December, China

13    Ali Masoudi-Nejad, Ali Salehzadeh Yazdi, Ehsan Habibi, Yazdan Asgari, Fatemeh Miri Disfani, Ali Akbar Sabouri and Samad Jahandideh (2010) Biophysical Interpretation of Hubs in Protein-Protein Interaction Networks. EMBO Meeting 2010. Barcelona, Spain.

14    Sara Movahedi, Ali Masoudi-Nejad, Ruy Jauregui (2008) Genome Scale Analysis of Curvature, CpG Island and Repeats in Arabidopsis and Rice. XX International Congress of Genetics. 12 – 17 July, Berlin, Germany.

15    Hesam T. Dashti, Ali Masoudi-Nejad, Nasim Jamali (2008) Using Support Vector Machines in Biological Sequences Assembly. 5th International Symposium on Integrative Bioinformatics. 20-22 August, Wittenberg, Germany.

16    Shirin Nasr Isfahani, Ali Masoudi-Nejad (2008) A New Approach for Touching Cells Segmentation. International Conference on BioMedical Engineering and Informatics (BMEI2008), 27-30 May,  Sanya, Hainan, China

17    Ali Masoudi-Nejad, Ruy Jauregui, Shuichi Kawashima, Susumu Goto, Minoru Kanehisa and Takashi R. Endo (2004) The kingdom of Plantae EST Indices: a resource for plant genomics community. Genome Informatics 2004. PP-102. The 15th International Conference on Genome Informatics December 16-18, 2004, Yokohama Pacifico, Japan.

18    Cheniany, Monireh., Ebrahimzade, Hasan., Vahdati, Kourosh., Masoudi-Nejad, Ali. Endogenous Phenolic Contents, Peroxidase and Polyphenoloxidase Activities in Shoot Microcuttings from Persian Walnut (Juglans regia L.) Cultivars. The 6th International Walnut Symposium, February 25-27, 2009, Melbourne, Australia

19    Ali Masoudi-Nejad, Takashi Endo and Robbie Waugh. (2004) efficient method to amplify the all of a minute amount of DNA sample from plants; Implementation for single cell/chromosome analysis and high throughput gene mapping. ICBP 2004. A01-022. The 5th International Conference on Biological Physics August 23-27, 2004, Gothenburg, Sweden.

20    Ali Masoudi-Nejad, Paul. H. Dear and Robbie. Waugh (2004) A Technology for Ultra Rapid Mapping of Complex Genomes. The 9th International Genetics Symposium June 20-26, 2004. Brno Trade Fairs, Brno, Czech Republic.

21    Ali Masoudi-Nejad (2000) Wheat storage protein: Past, present and future. The 5th Japanese Society of Molecular Biology of Triticeae and the 27th Japanese Wheat Genetics Symposium, October 7-9, 2000. Gifu, Japan.

22    Ali Masoudi-Nejad, Minoru Kanehisa and Susumu Goto. (2006) Eassembler: Online Bioinformatics Tool for Large-Scale Clustering and assembling ESTs and Genomic DNA. The Applied Computing. February 25-28, 2006, San Sebastian, Spain.

23    Ali Masoudi-Nejad, Minoru Kanehisa and Susumu Goto. (2006) EGENES: Plant Metabolic Pathway Information Database, a Bioinformatics Resource for Plant Research Community. Genomes to Systems Conference. March 22-24, 2006, Manchester International Convention Center, UK.

24    Luke Ramsay, Nicola Bonar, Malcolm Macaulay, Ali Masoudi-Nejad, Roger P. Wise, Robbie Waugh. (2006) Use of Flanking Loci To Characterise Variation At The Mla Disease Resistance Locus In Barley. Plant & Animal Genomes XIV Conference. January 14-18, 2006 Town & Country Convention Center, San Diego, CA, USA.

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