Ali Masoudi-Nejad

Associate Professor of Systems Biology and Bioinformatics

 

アリ

マスウヂ - ネジャド

 

علی مسعودی نژاد

دانشیار سیستم بیولوژی

 و بیوانفورماتیک

دانشگاه تهران

Ali Masoudi-Nejad, Ph.D.

Ali Masoudi-Nejad received his Ph.D. in genetics/genomics with Prof. Takashi Endo from Kyoto University (京都大学), 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 at NCBI and founder of the KEGG and Prof. Susumu Goto in bioinformatics and systems biology, respectively. He then returned to Iran in 2006 and founded the Laboratory of Systems Biology and Bioinformatics, LBB (http://LBB.ut.ac.ir) at the 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
  • Bioinformatics
  • Systems biology and brain
  • Systems biology approach to anti-cancer therapy
  • Analysis of biological networks
  • Drug-target and disease networks
  • Genome-scale network reconstruction and pathway modeling
  • MicroRNA and RNAi pathway reconstruction
  • Genome Scale lncRNA analysis
  • Protein-Protein interaction networks

Name and Surname

Ali Masoudi-Nejad                      

Nationality     

Persian (Iranian)

Date of Birth

22/May/1967

Languages      

Persian, Kurdish, English, Japanese

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.

Background

  • Ph.D. Molecular Genetics and Genomics, Kyoto University, Japan
    Post-Doc (1st) Genome Dynamics, MRC-LMB Cambridge and James Hutton Institute, UK
    Post-Doc (2nd) Bioinformatics, Bioinformatics Center, Kyoto University. Japan
    Post-Doc (3rd) 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 Head of the Department of Bioinformatics, KISH international campus, University of Tehran, 2014-now
    3 Director of the study program in charge of the curriculum for Ph.D. Program in Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran
    4 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 (2010)
    6. German DAAD Visiting Professorship award (2012)
    7. JundiShapur Iran-France collaborative research program (2012)

Collaborators

Louxin  Zhang

National University of Singapore

Neda Jahanshad

Keck School of Medicine of USC, USA

Madelaine Daianu

UCLA, USA

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

Prasun J. Mishra

National Cancer Institute, USA

Dr. Björn Junker

IPK Gatersleben, Germany

Prof. Dr. Falk Schreiber

Halle University, Germany

Prof.  Fernando Silva

University of Porto, Portugal

Prof. Albert Rizvanov

Kazan Federal University, Russia

Prof. Takashi R. Endo

Kyoto University, Japan

Prof. Minoru Kanehisa

Kyoto University, Japan

Dr. Ruy Jáuregui

Helmholtz Zentrum für Infektionsforschung, Germany

Prof. Susumu Goto

Kyoto University, Japan

Editorial Activity
Reviewer for International Journals
Edited Books
Contributed Chapters
  • 1 Seminar in Cancer Biology (Guest Editor), Impact Factor of 9.15
    http://www.journals.elsevier.com/seminars-in-cancer-biology/
    2 Seminars in Cell and Developmental Biology(Guest Editor), Impact Factor of 6.43
    http://www.journals.elsevier.com/seminars-in-cell-and-developmental-biology/
    3 Current Bioinformatics (Associate Editor) , Impact Factor of 2.1
    http://www.benthamscience.com/cbio/EBM.htm
    4 Frontiers in Bioinformatics and Computational Biology
    www.frontiersin.org/people/AliMasoudi_Nejad/33966
    5 Genes and Genetic Systems (Associate Editor) , Impact Factor of 1.1
    http://www.jstage.jst.go.jp/browse/ggs
    6 In Silico Pharmacology (Editor)
    http://www.in-silico-pharmacology.com/about/edboard
    7 Biomedical Engineering and Computational Biology (Editor)
    http://www.la-press.com/biomedical-engineering-and-computational-biology-journal-j170
    8 MicroRNA (Associate Editor)
    http://www.benthamscience.com/mirna/EBM.htm

  • 1 Bioinformatics
    2 Seminar in Cancer Biology
    3 Seminars in Cell and Developmental Biology
    4 BMC Systems Biology
    5 Nucleic Acids Research
    6 Briefing in Bioinformatics
    7 BMC Genomics
    8 IEEE/ACM Transactions on Computational Biology and Bioinformatics
    9 PLOS ONE
    10 Physica A
    11 BMC Bioinformatics
    12 OMICS: Journal of Integrative Biology
    13 DNA Research
    14 Molecular Genetics and Genomics
    15 Molecular Biology Reports
    16 Genes and Genetic Systems
    17 Digital Signal Processing
    18 Frontiers in Bioinformatics and Computational Biology
    19 Computer Methods and Programs in Biomedicine
    20 Information Systems
    21 Evolutionary Bioinformatics
    22 Cancer Informatics
    23 Computational and Structural Biotechnology
    24 Journal of Proteomics & Bioinformatics
    25 International Journal of Data Mining and Bioinformatics
    26 Journal of Genetics and Genomics
    27 Computational and Mathematical Methods in Medicine
    28 International Journal of Genomics
    29 Journal of Computational and Graphical Statistics
    30 Future Medicinal Chemistry

  • 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, Gholamreza Bidkhori, Saman Hosseini Ashtiani, Ali Najafi. (Editors). Microscopic Scale of the Cancer Systems Biology. SpringerBriefs in Systems Biology. 2014

  • 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. John Wiley 2014.
    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.

Published/Accepted Papers

  • 1. Zaynab Mousavian, Abbas Nowzari-Dalini, Ronald W. Stam, Yasir Rahmatallah, Ali Masoudi-Nejad (2016) Network-based expression analysis reveals key genes related to glucocorticoid resistance in infant acute lymphoblastic leukemia. Cellular Oncology. DOI: 10.1007/s13402-016-0303-7 2. Reza Mohammadi,Jalil, Fallah-Mehrabadi, Gholamreza Bidkhori, Javad Zahiri, Mohammad Javad Niroomande, Ali Masoudi-Nejad (2016) A systems biology approach to reconcile metabolic network models with application to Synechocystis sp. PCC 6803 for biofuel production. Molecular Biosystems. DOI: 10.1039/C6MB00119J 3. Hamid Beiki, Ardeshir N Javaremi, Abbas Pakdel, Ali Masoudi-Nejad, Zhi-Liang Hu, James M Reecy (2016) Large-scale Gene Co-expression Network as a Source of Functional Annotation for Bovine Genes. BMC Genomics. DOI: 10.1186/s12864-016-3176-2 4. Zaynab Mousavian, Kaveh Kavousi, Ali Masoudi-Nejad (2016) Information Theory in Systems Biology: Signaling and Metabolic Networks. Seminars in Cell and Developmental Biology. DOI: 10.1016/j.semcdb.2015.12.007 5. Morteza Kouhsar, Zahra Razaghi-Moghadam Kashani, Zaynab Mousavian, Ali Masoudi-Nejad (2016) CeFunMO: a centrality based method for discovering functional motifs with application in biological networks. Computers in Biology and Medicine. DOI: 10.1016/j.compbiomed.2016.07.009 6. Zaynab Mousavian, Jose Diaz, Ali Masoudi-Nejad (2016) Information Theory in Systems Biology: Gene Regulatory and Protein-Protein Interaction Networks. Seminars in Cell and Developmental Biology. DOI: 10.1016/j.semcdb.2015.12.006 7. Zaynab Mousavian, SahandKhakabimamaghani, KavehKavousi, Ali Masoudi-Nejad (2015) Drug-Target Interaction Prediction from PSSM based Evolutionary Information. Journal of Pharmacological and Toxicological Methods. DOI: 10.1016/j.vascn.2015.11.002 8. Ali Masoudi-Nejad, Hector Zenil (2016) Flow of Information in Biological Systems. Seminars in Cell and Developmental Biology. DOI: 10.1016/j.semcdb.2016.03.004 9. Marzieh Dehghan-Shasaltaneh, Nasser Naghdi, Samira Choopani, Leila Alizadeh, Bahram Bolouri, Ali Masoudi-Nejad, Gholam Hossein Riazi (2016) Determination of the Best Concentration of Streptozotocin to Create a Diabetic Brain Using Histological Techniques. J Mol Neurosci. 2016 May;59(1):24-35. DOI: 10.1007/s12031-015-0702-7. 10. Atefeh Seyeddokht, Ali Asghar Aslaminejad, Ali Masoudi-Nejad, Mohammadreza Nassiri, Javad Zahiri, Balal Sadeghi (2016) Computational Detection of piRNA in Human Using Support Vector Machine. Avicenna J Med Biotechnol. 2016 Jan-Mar;8(1):36-41. 11. Mostafa Rezaei-Tavirani, Mona Zamanian-Azodi, Sepideh Rajabi, Ali Masoudi-Nejad, Mohammad RostamiNejad, Sara Rahmatirad (2016) Protein Clustering and Interactome Analysis in Parkinson and Alzheimer's Diseases.Arch Iran Med. 2016 Feb;19(2):101-9. DOI: 0161902/AIM.007. 12. Hamid Beiki, Ardeshir N Javaremi, Abbas Pakdel, Ali Masoudi-Nejad, Zhi-Liang Hu, James M Reecy )2016( Large-scale Gene Co-expression Network as a Source of Functional Annotation for Bovine Genes. BMC Genomics. ACCEPTED 13. Marzieh Dehghan-Shasaltaneh, Hossein Lanjanian, Gholam H. Riazi, Ali Masoudi-Neja (2016) The importance of α-CT and salt bridges in the formation of insulin and its receptor complex by computational simulation. Iranian Journal of Pharmaceutical Research. ACCEPTED. 14. Sadegh Sulaimany, Mohammad Khansari, Peyman Zarrineh, Madelaine Daianu, Neda Jahanshad, Paul M. Thompson, Ali Masoudi-Nejad (2015) Predicting Brain Network Changes in Alzheimer’s Disease with Link Prediction Algorithms. Molecular Biosystems. REVISED. 15. Yazdan Asgari, Zahra Zabihinpour, Ali Masoudi-Nejad (2014) SCAN-Toolbox : Structural COBRA Add-oN (SCAN) for Metabolic Networks. Current Bioinformatics. ACCEPTED. 16. Mahdieh Ghasemi, Faeze Tamimi, Zahra Narimani, Maseud Rahgozar, Ali Masoudi-Nejad (2016) NetCentra: A Program for Analyzing the Network Centrality in Biological, Social and Other Networks. SUBMITTED. 17. Isar Nassiri, Ali Masoudi-Nejad, Mahdi Jalili, Ali Moeini (2016) Sensitivity Analysis of the Brain's Signaling Network Flow: finding the optimal region of the systems for perturbation. SUBMITTED. 18. Reza Shamsaee, Mahmood Fathy, Gholamreza Bidkhori, Ali Masoudi-Nejad (2016) LuCaSim: a toolbox for Lung Cancer Modeling and Simulation. SUBMITTED. 19. Hamid Beiki, Abbas Pakdel, Ardeshir Nejati, Javaremi, Ali Masoudi-Nejad, James Reecy (2016) Cattle Bacterial Stress Response Network and its Functional Modules. BMC Immunology. SUBMITTED.
  • 1. Ali Masoudi-Nejad, Edwin Wang (2014) Cancer Modeling and Network Biology: accelerating toward personalized medicine. Seminar in Cancer Biology. doi: 10.1016/j.semcancer.2014.06.005 2. Ali Masoudi-Nejad, Yazdan Asgari (2014) Metabolic Cancer Biology: structural-based analysis of cancer as a metabolic disease, new sights and opportunities for disease treatment. Seminar in Cancer Biology. doi:10.1016/j.semcancer.2014.01.007 3. Edwin Wang, Naif Zaman, Shauna Mcgee, Jean-Sébastien Milanese, Ali Masoudi-Nejad, Maureen O'Connor (2014) Predictive Genomics: a cancer hallmark network framework for predicting tumor clinical phenotypes using genome sequencing data. Seminar in Cancer Biology. doi: 10.1016/j.semcancer.2014.04.002 4. Yazdan Asgari, Zahra Zabihipour, Falk Schreiber, Ali Masoudi-Nejad (2015) Alterations in cancer cells metabolism: the Warburg effect and metabolic adaptation. Genomics. doi: 10.1016/j.ygeno.2015.03.001 5. Ali Najafi, Ali Masoudi-Nejad, Mostafa Ghanei, Gholamreza Bidkhori, Mohamad-Reza Nourani, Ali Moeini (2015) Computational modeling of core regulatory elements controlling airway remodeling pathway in chronic lung diseases. PLOS ONE. Accepted 6. Nazanin Hosseinkhan, Peyman Zarrineh, Hassan Rokni-Zadeh, Mohammad Reza Ashouri, Ali Masoudi-Nejad (2015) Co-expressional conservation in virulence and stress related genes of three Gamma Proteobacterial species: Escherichia coli, Salmonella enterica and Pseudomonas aeruginosa. Molecular Biosystems. 11:3137-3148 7. Aida Shakouri Motlagh, Saman Hosseini Ashtiani, Hamid Keshvari, Masoumeh Firouzi, Ali Najafi, Ali Masoudi-Nejad (2015) Reconstruction of gene regulatory network reveals key apoptotic pathways and candidate survival genes after traumatic spinal cord injury. Genomics. Under Review 8. Habib MotieGhader, Sajjad Gharaghani, Yosef Masoudi- Sobhanzadeh, , Ali Masoudi-Nejad (2015) Novel hybrid Algorithms using Learning Automata and Genetic Algorithm for feature selection in QSAR: anti cancer case study. 9. Habib MotieGhader, Yosef Masoudi- Sobhanzadeh, Sajjad Gharaghani, Ali Masoudi-Nejad (2015) Feature selection in QSAR using Cuckoo Optimization Algorithm on anti-cancer data.
  • 1. Mehran Aflakparast, Hamid Salimi, Abbas Gerami, Marie-Pierre Dubé, Shyam Visweswaran, Ali Masoudi-Nejad (2014) Cuckoo Search Epistasis: a new method for exploring significant genetic interactions. Nature's Heredity. 112(6):666-74 2. Mehran Aflakparast, Joseph H. Bozorgmehr, Shyam Visweswaran, Ali Masoudi-Nejad (2014) Informative Bayesian Model Selection‎: ‎A‎ Method for Identifying Interactions in Genome-Wide Data. Molecular Biosystems. 10: 2654 3. Ali Najafi, Ali Masoudi-Nejad, Mostafa Ghanei, Mohamad Reza Nourani (2013) Microarray gene expression analysis of human airway in patients exposed to sulfur mustard. Journal of Receptors and Signal Transduction. 34(4):283-9 4. Ali Masoudi-Nejad, Zaynab Mousavian (2014) Drug-Target Interaction Prediction via Chemogenomic Space: Learning-Based Methods. Expert Opinion on Drug Metabolism and Toxicology. 10(9):1273-1287 5. Ali Masoudi-Nejad, Gholamreza Bidkhori, Saman Hosseini Ashtiani, Joseph H Bozorgmehr, Edwin Wang (2014) Cancer Systems Biology and Modeling: microscopic scale and multiscale approaches. Seminar in Cancer Biology. doi: 10.1016/j.semcancer.2014.03.003 6. Balal Sadeghi, Hamed Ahmadi, Mohammadreza Nassiri, Ali Masoudi-Nejad (2014) BosFinder: a Novell Pre-MicroRNA Gene Prediction algorithm in Bos taurus. Animal Genetics. 45(4):479-84 7. Ali Najafi, Gholamreza Bidkhori, Joseph H. Bozorgmehr, Ina Koch, Ali Masoudi-Nejad (2014) Genome Scale Modeling in Systems Biology: algorithms and resources. Current Genomics. 15 (2): 130-159 8. Ali Najafi, Ali Masoudi-Nejad, Mostafa Ghanei, Mohamad-Reza Nourani, Ali Moeini (2014) Pathway Reconstruction of Airway Remodeling in Chronic Lung Diseases: a systems biology approach. PLOS ONE. 9(6):e100094 9. Peyman Zarrineh, Aminael Sánchez-Rodríguez, Nazanin Hosseinkhan, Zahra Narimani, Ali Masoudi-Nejad, Kathleen Marchal (2014) 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. 9(8): e102871 10. Reza Shamsaee, Mahmood Fathy, Ali Masoudi-Nejad (2014) Weighted-Directed Networks: merging weight and direction into scale free biological network. Current Bioinformatics. 9:1426-1445 11. Javad Zahiri, Morteza Mohammad-Noori, Reza Ebrahimpour, Ali Masoudi-Nejad (2014) LocFuse: Human Protein-Protein Interaction Prediction via Classifier Fusion Using Localization Information. Genomics. DOI:10.1016/j.ygeno.2014.10.006 12. Ali Salehzadeh-Yazdi, Yazdan Asgari, Ali Akbar Saboury, Ali Masoudi-Nejad (2014) Computational analysis of reciprocal association of metabolism and epigenetics in the budding yeast: a genome-scale metabolic model (GSMM) approach. PLOS ONE. DOI: 10.1371/journal.pone.0111686 13. Ali Salehzadeh-Yazdi, Yazdan Asgari, Ali Akbar Saboury, Ali Masoudi-Nejad (2014) Integrative Systems Biology: Integration of epigenetics data into kinetics modeling in Yeast. Functional & Integrative Genomics. DOI:10. 14. Nazanin Hosseinkhan, Peyman Zarrineh, Ali Masoudi-Nejad (2014) Analysis of Genome-scale Expression Network in Four Major Bacterial Residents of Cystic Fibrosis Lung. Current Genomics. 15: 408-418
  • 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, Esmaeel Azadian, Ali Masoudi-Nejad (2013) Human RNAi Pathway: crosstalk with organelles and cells. Functional and Integrative Genomics. 14(1):31-46 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. 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. 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 6. Mahdieh Sadat Ghasemi, Hossein Seidkhani, Faeze Tamimi, Maseud Rahgozar, Ali Masoudi-Nejad (2013) Centrality Measures in Biological Networks. Current Bioinformatics. 9:426-441 7. 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 8. 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 9. 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 10. 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 11. 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 12. Isar Nassiri, Esmaeel 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. 13. 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. 14. 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
  • 1. 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 2. 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 3. 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 4. 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 5. 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 6. 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 7. 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 8. 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 9. 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 10. 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. 157(10):1959-1965
  • 1. 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 2. Ehsan Habibi, Ali Masoudi-Nejad, Steven Haggarty (2011) Emerging Roles of Epigenetic Mechanisms in Parkinson's disease. Functional and Integrative Genomics. 11:523–537 3. Sadegh Azimzadeh, Ali Masoudi-Nejad (2011) RNAi Pathway Integration in Caenorhabditis elegans Development. Functional and Integrative Genomics. 11:389-405 4. 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. 5. Azimzadeh, S., Masoudi-Nejad, Ali (2009) Reconstruction of Arabidopsis thaliana Fully-Integrated Small RNA Pathway. Functional & Integrative Genomics. 9:419-432. 6. Razaghi, A., Ahrabian, H.,…. Masoudi-Nejad, Ali (2009) Kavosh: A New Algorithm for Finding Network Motifs. BMC Bioinformatics. 4:10:318. 7. 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 8. 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 9. 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 10. Masoudi-Nejad, A., Goto, S., Endo, TR and Kanehisa, M (2007) Bioinformatics Resources for Plant Genomics Research. Methods Mol Biol. 406:437-458. 11. Nasr-Isfahani, S., Mirsafian, A., Masoudi-Nejad, A (2008) A New Approach for Touching Cells Segmentation. IEEE BioMedical Engineering and Informatics. 1:816-820 12. 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 13. 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. 14. 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. 15. Ali Salehzadeh-Yazdi, Shiva Akbari-Birgani, Ali Masoudi-Nejad (2011) Diabetes and Systems Biology. JICS. 8(3): 63-67 16. 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 17. Mostafa Hadian Dehkordi, Ali Masoudi-Nejad, Mohamad Nouri (2010) gpALIGNER: a fast algorithm for global pairwise alignment of DNA sequences. IJCCE. Accepted 18. 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 19. Reza Shamsaee, Mahmood Fathy, Ali Masoudi-Nejad (2010) Integration and Reduction of Microarray Data Using Information Theory Approach. IJCCE. 29(4):19-29 20. 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 21. Hesam T. Dashti, Ali Masoudi-Nejad (2010) Mining Biological Repetitive Sequences Using Support Vector Machines and Fuzzy SVM. IJCCE. 29(4):1-18 22. Hesam T. Dashti, Ali Masoudi-Nejad (2010) Finding Exact and Solo LTR-Retrotransposons in Biological Sequences Using SVM. IJCCE. Accepted 23. Sedigheh Mahdavi, Ali Mohades Khorasani, Samad Jahandideh, Ali Masoudi-Nejad (2010) Recognition Protein-RNA Interaction interfaces via the Voronoi Diagram. JICS. 7:S1-A61 24. 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 25. 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 26. 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. 27. 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. 28. 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. 29. 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. 30. 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. 31. 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. 32. 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. 33. Masoudi-Nejad, A. (2000) Wheat storage protein. Wheat Information Service. 92:33.
Member of International Conference Scientific Committee
Coordinating Workshop /Training Course
Congress/Symposium
  • 1 5th International Workshop on Biological Processes & Petri Nets (BioPPN 2014). June 24, 2014 . Germany. http://www-dssz.informatik.tu-cottbus.de/BME/BioPPN2014#organizers
    2 Applied Computing 2013. IADIS International Conference. 23 – 25 October 2013. Fort Worth, Texas, USA. http://www.computing-conf.org/committees
    3 The Third International Conference on Advances in Information Mining and Management. IMMM 2013. November 17 - 22, 2013 - Lisbon, Portugal.
    http://www.iaria.org/conferences2013/ComIMMM13.html
    4 20th Iranian Conference on Biomedical Engineering (ICBME 2013). University of Tehran, School of Electrical and Computer Engineering, Tehran, Iran. December 18 to 20, 2013
    http://www.icbme.ir/en/commitee-tech.htm
    5 Applied Computing 2012, 19 – 21 October, Madrid, Spain
    http://www.computing-conf.org/index.php/committees-page
    6 3rd International Conference on Proteomics & Bioinformatics (Proteomics-2013) July 15-17, USA http://www.omicsgroup.com/conferences/proteomics-bioinformatics-2013/
    7 The Second International Conference on Advances in Information Mining and Management (IMMM 2012), October 21 - 26, 2012 - Venice, Italy
    http://www.iaria.org/conferences2012/ComIMMM12.html
    8 International Symposium on Integrative Bioinformatics, 2011, Netherland
    (http://www.bioinformatics.nl/ib2011/organizers.php)
    9 The 2011 International Conference on Bioinformatics & Computational Biology (BIOCOMP'2011). http://www.worldacademyofscience.org/worldcomp11/ws/conferences/biocomp11/committee/?searchterm=masoudi-nejad
    10 The 2011 International Conference on Genetic and Evolutionary Methods (GEM'2011). http://www.worldacademyofscience.org/worldcomp11/ws/conferences/gem11/committee/?searchterm=masoudi-nejad
    11 First International Conference on Advances in Information Mining and Management, 2011, UK (http://www.iaria.org/conferences2011/ComIMMM11.html)
    12 Applied Computing, 2006, 2007, 2008, 2009, 2010, 2011, 2012
    (http://www.computing-conf.org/ )
    13 The 2011 International Conference on Modeling, Simulation and Visualization Methods (MSV'2011). http://www.worldacademyofscience.org/worldcomp11/ws/conferences/msv11/committee/?searchterm=masoudi-nejad
    14 The 2011 International Conference on Image Processing, Computer Vision, and Pattern Recognition (IPCV'2011).
    http://www.worldacademyofscience.org/worldcomp11/ws/conferences/ipcv11/committee/?searchterm=masoudi-nejad
    15 International Symposium on Integrative Bioinformatics, 2008
    (http://meetings.ipk-gatersleben.de/ib08/)
    16 BIOCOMP'10 - The 2010 International Conference on Bioinformatics & Computational Biology.http://www.world-academy-of-science.org/worldcomp10/ws/conferences/biocomp10/committee
    17 IKE'10 - The 2010 International Conference on Information and Knowledge Engineering
    http://www.world-academy-of-science.org/worldcomp10/ws/conferences/ike10/committee
    18 MSV'10 - The 2010 International Conference on Modeling, Simulation and Visualization Methods.http://www.world-academy-of-science.org/worldcomp10/ws/conferences/msv10/committee
    19 CSC'10 - The 2010 International Conference on Scientific Computing
    http://www.world-academy-of-science.org/worldcomp10/ws/conferences/csc10/committee
    20 GEM'10 - The 2010 International Conference on Genetic and Evolutionary Methods
    http://www.world-academy-of-science.org/worldcomp10/ws/conferences/gem10/committee
    21 MSV'09 - The 2009 International Conference on Modeling, Simulation and Visualization Methods.http://www.world-academy-of-science.org/worldcomp09/ws/conferences/msv09/committee
    22 GEM'09 - The 2009 International Conference on Genetic and Evolutionary Methods.
    http://www.world-academy-of-science.org/worldcomp09/ws/conferences/gem09/committee
    23 ICAI'09 - The 2009 International Conference on Artificial Intelligence.
    http://www.world-academy-of-science.org/worldcomp09/ws/conferences/icai09/committee
    24 The 10th Asian Bioethics Conference & 4th UNESCO Asia- Pacific School of Ethics Roundtable. Tehran - 26-29 April 2009.
    http://abc10iran.tums.ac.ir/english/content/?contentID=76
    25 BIOCOMP'08 - The 2008 International Conference on Bioinformatics & Computational Biology. http://www.world-academy-of-science.org/worldcomp08/ws/conferences/biocomp08/committee

  • 1. Winter Course on Biophysics & Biochemistry Simulation, 2008, joint with Barcelona National Computing Center & Institute of Biochemistry and Biophysics, University of Tehran, 12 Feb.-12 March. Iran
    2. Application of Electrophoresis in Plant Science, 1998, Univeristy of Zahedan, 31 March to 10 April. Zahedan, Iran
    3. Advanced Bioinformatics, 2011, Research Center of Biotechnology, Zanjan University, Fe

  • Keynote Speech
    1. Lahijan systems Microbiology
    2. 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
    3. 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
    4. 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).
    5. 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.
    6. 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.
    7. 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
    8. 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.
    9. 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.
    10. 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
    1 Hamid Beiki, Ardeshir N Javaremi, Abbas Pakdel, Ali Masoudi-Nejad, Zhi-Liang Hu, James M Reecy. 2016. Large-scale gene co-expression network as a source of functional annotation for bovine genes. 35th International Society for Animal Genetics Conference. 23-27 July, Salt Lake City, Utah, USA
    2 Ali Masoudi-Nejad, Reza Shamsaee, Mahmoud Fathy, 2014.LuCaSim: a computational framework for lung cancer modeling and simulation.5th Conference on Systems Biology of Mammalian Cells (www.sbmc2014.de). May 12th–14th. Berlin.Germany.
    3 Ali Masoudi-Nejad, Javad Zahiri , et al. 2014.Human Protein-Protein Interaction Prediction via Clas-sifier Fusion Using Proteins Localization Information.5th Conference on Systems Biology of Mammalian Cells (www.sbmc2014.de). May 12th–14th. Berlin.Germany.
    4 Ali Masoudi-Nejad, nazanin Hosseinkhan, et al. , 2014.Comparative Analysis of genome-scale expression network in resident microorganisms in lung .5th Conference on Systems Biology of Mammalian Cells (www.sbmc2014.de). May 12th–14th. Berlin.Germany.
    5 Ali Masoudi-Nejad, Alireza meshkin , 2014.Agent-Based Approaches to Cancer Modeling: rationale, classification and successes.5th Conference on Systems Biology of Mammalian Cells (www.sbmc2014.de). May 12th–14th. Berlin.Germany.
    6 Ali Masoudi-Nejad, Ali najafi, et al. 2014.Computational modeling of core regulatory elements controlling airway remodeling pathway in chronic lung diseases.5th Conference on Systems Biology of Mammalian Cells (www.sbmc2014.de). May 12th–14th. Berlin.Germany.
    7 Ali Masoudi-Nejad, Isar Nassiri, et al. 2014.Sensitivity Analysis of the Brain's Signalling Network Flow.5th Conference on Systems Biology of Mammalian Cells (www.sbmc2014.de). May 12th–14th. Berlin.Germany.
    8 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
    9 Mahdieh Ghasemi, Maseud Rahgozar, Gholamreza Bidkhori and Ali Masoudi-Nejad (2013) A New Clustering Algorithm to Find Functional Modules in Protein-Protein Interaction Networks. Tenth International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB 2013). 20-22 june. Valrose Castle, Nice, France
    10 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
    11 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.
    12 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.
    13 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.
    14 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.
    15 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.
    16 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
    17 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
    18 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
    19 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
    20 Ali Masoudi-Nejad (2010) Biological Network and Network Motifs. 4th World Congress of Gene, 1-4 December, China
    21 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.
    22 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.
    23 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.
    24 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
    25 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.
    26 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
    27 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.
    28 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.
    29 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.
    30 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.
    31 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.
    32 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.