Affiliation: Laboratory of Systems Biology and Bioinformatics (LBB), University of Tehran
Location: Tehran, Iran
Analysis of Biological Networks
1- Invited Book Chapters for international publisher
1. 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.
2. 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.
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.
2- Published Papers
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
3. Sadegh-Azimzadeh, Ali Masoudi-Nejad (2011) RNAi Pathway Integration in Caenorhabditis elegans Development. Functional and Integrative Genomics. accepted
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. REVIEW
5. Azimzadeh, S., Masoudi-Nejad, A (2009) Reconstruction of Arabidopsis thaliana Fully-Integrated Small RNA Pathway. Functional & Integrative Genomics. 9:419-432. REVIEW
6. Razaghi, A., Ahrabian, H., Masoudi-Nejad, A (2009) Kavosh: A New Algorithm for Finding Network Motifs. BMC Bioinformatics. 4:10:318.
7. Omidi, S., Schreiber, F., Masoudi-Nejad, A (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. Masoudi-Nejad, A., Goto, S., Endo, TR and Kanehisa, M (2007) Bioinformatics Resources for Plant Genomics Research. Methods Mol Biol. 406:437-458.
10. Nasr-Isfahani, S., Mirsafian, A., Masoudi-Nejad, A (2008) A New Approach for Touching Cells Segmentation. IEEE BioMedical Engineering and Informatics. 1:816-820
11. 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
12. 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.
13. 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.
14. Mostafa Hadian Dehkordi, Ali Masoudi-Nejad, Mohamad Nouri (2010) gpALIGNER: a fast algorithm for global pairwise alignment of DNA sequences. IJCCE. Accepted
15. Reza Shamsaee, Mahmood Fathy, Ali Masoudi-Nejad (2010) Integration and Reduction of Microarray Data Using Information Theory Approach. IJCCE. 29(4):18-29
16. Hesam T. Dashti, Ali Masoudi-Nejad (2010) Mining Biological Repetitive Sequences Using Support Vector Machines and Fuzzy SVM. IJCCE. 29(4):1-17
17. Hesam T. Dashti, Ali Masoudi-Nejad (2010) Tackling Repeat Finding Problem in Biological Systems using SVM. Under Revision in IJCCE.
18. Sedigheh Mahdavi, Ali Mohades Khorasani, Samad Jahandideh, Ali Masoudi-Nejad (2010) Recognition Protein-RNA Interaction interfaces via the Voronoi Diagram. JICS. 7:S1-A61
19. 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
20. 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.
21. 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.
22. 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.
23. 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.
24. 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.
25. 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.
26. 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.
27. Masoudi-Nejad, A. (2000) Wheat storage protein. Wheat Information Service. 92:33.
28. 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
- Transfer of rye chromosome segments to wheat by a gametocidal systemA Masoudi-Nejad
Laboratory of Plant Genetics, Graduate School of Agriculture, Kyoto University, Japan
Chromosome Res 10:349-57. 2002..Thus, the 3C gametocidal system was demonstrated to be effective in transferring small rye chromosome segments...
- An alternative to radiation hybrid mapping for large-scale genome analysis in barleyAli Masoudi-Nejad
Laboratory of Plant Genetics, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake cho, 606 8502 Sakyo Ku, Kyoto, Japan
Mol Genet Genomics 274:589-94. 2005..In addition, mapping results are cumulative when using the same mapping set with new markers. The GC lines will be available from the National Bioresources Project-KOMUGI ( http://www.nbrp.jp/index.jsp )...
- EGassembler: online bioinformatics service for large-scale processing, clustering and assembling ESTs and genomic DNA fragmentsAli Masoudi-Nejad
Laboratory of Bioknowledge Systems, Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho Uji, Kyoto 611 0011, Japan
Nucleic Acids Res 34:W459-62. 2006..The service provides an excellent bioinformatics tool to research groups in wet-lab as well as an all-in-one-tool for sequence handling to bioinformatics researchers...
- Dissection of rye chromosome 1R in common wheatMasashi Tsuchida
Laboratory of Plant Genetics, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
Genes Genet Syst 83:43-53. 2008....
- Kavosh: a new algorithm for finding network motifsZahra Razaghi Moghadam Kashani
Laboratory of Systems Biology and Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
BMC Bioinformatics 10:318. 2009..Existing algorithms for finding network motifs are extremely costly in CPU time and memory consumption and have practically restrictions on the size of motifs...
- Reconstruction of Arabidopsis thaliana fully integrated small RNA pathwaySadegh Azimzadeh Jamalkandi
Laboratory of Systems Biology and Bioinformatics LBB, Institute of Biochemistry and Biophysics IBB and COE in Biomathematics, College of Science, University of Tehran, Tehran, Iran
Funct Integr Genomics 9:419-32. 2009..We present a fully integrated pathway connecting ncRNA entities such as miRNAs, siRNAs, ta-siRNAs, and nat-siRNAs, to each other within Arabidopsis thaliana...
- MODA: an efficient algorithm for network motif discovery in biological networksSaeed Omidi
Laboratory of Systems Biology and Bioinformatics LBB, Institute of Biochemistry and Biophysics and Center of Excellence in Biomathematics, University of Tehran, Iran
Genes Genet Syst 84:385-95. 2009..The MODA source code is freely available at: http://LBB.ut.ac.ir/Download/LBBsoft/MODA/..
- N4: a precise and highly sensitive promoter predictor using neural network fed by nearest neighborsAmjad Askary
Laboratory of Systems Biology and Bioinformatics LBB, Institute of Biochemistry and Biophysics and COE in Biomathematics, University of Tehran, Tehran, Iran
Genes Genet Syst 84:425-30. 2009....
- Molecular typing of Epidermophyton floccosum isolated from patients with dermatophytosis by RAPD-PCRAlireza Khosravi
Mycology Research Center, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
J Basic Microbiol 50:S68-73. 2010..RAPD-PCR provided a rapid and practical tool for identification of E. floccosum isolates, which was independent of morphological characteristics, and enhanced laboratory diagnosis of dermatophytosis...