Dr. Ali Masoudi-Nejad received his Ph.D. in genomics with Prof. Takashi Endo from Kyoto University (京都大学) Japan. He then achieved his first Post-Doc in computational genomics with Prof. Robbie Waugh at James Hutton Institute in Dundee, Scotland and Prof. Paul H. Dear from MRC-LMB, Cambridge, UK. He returned to the Kyoto University and completed two consecutive Post-Docs with Prof. Minoru Kanehisa (co-founder of The GenBank at NCBI and founder of the KEGG Database) and Prof. Susumu Goto (http://www.dbcls.rois.ac.jp/members-en.html) in bioinformatics and systems biology, respectively.
He 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 an Associate Professor of systems biology and bioinformatics. Prof. Masoudi-Nejad has supervised about 25 Ph.D. and 30 M.Sc. students. He has served as guest editor for different high impact journals such as Seminar in Cancer Biology, and Seminars in Cell and Developmental Biology. He has also published several book chapters and edited two books with Springer (Next Generation Sequencing and Sequence Assembly: Methodologies and Algorithms, Microscopic Scale of the Cancer Systems Biology). His main research interest focuses on:
Computational systems biology
Cancer systems biology
Network-based biomarker development
Drug repositioning & Drug-target networks analysis
Non-coding RNA analysis
Controllability in biological networks
Network biology and Omic’s interaction networks
Brain & biological networks analysis
Personalized medicine
Big Data and data integration in systems biology
Bioinformatics and algorithm development
Genome scale analysis of none-coding RNA
Selected Publications
- 1.Pournoor E., Mousavian Z., Dalini A.N. Ali Masoudi-Nejad (2020) Identification of key components in colon adenocarcinoma using transcriptome to interactome multilayer framework. Sci. Rep. doi: 10.1038/s41598-020-59605-z. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 2.Poorinmohammad N., Hamedi J. Ali Masoudi-Nejad (2020) Genome-scale exploration of transcriptional regulation in the nisin Z producer Lactococcus lactis subsp. lactis IO-1. Sci. Rep. doi: 10.1038/s41598-020-59731-8. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3.Hooshmand S.A., Jamalkandi S.A., Alavi S.M. Ali Masoudi-Nejad (2020) Evaluation of pre-training of deep belief network for distinguishing of drug/non drug-like in drug discovery. Mol. Divers. doi: 10.1007/s11030-020-10065-7. [DOI] [PubMed] [Google Scholar]
- 4.Abbasi K., Poso A., Ghasemi J., Amanlou M. Ali Masoudi-Nejad (2019) Deep Transferable Compound Representation Across Domains and Tasks for Low Data Drug Discovery. J. Chem. Inf. Model. doi: 10.1021/acs.jcim.9b00626. [DOI] [PubMed] [Google Scholar]
- 5.Kouhsar M., Jamalkandi S.A., Moeini A. Ali Masoudi-Nejad (2019) Detection of novel biomarkers for early detection of Non-Muscle-Invasive Bladder Cancer using Competing Endogenous RNA network analysis. Sci. Rep. doi: 10.1038/s41598-019-44944-3. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6.Masoudi-Sobhanzadeh Y., Omidi Y., Amanlou M. Ali Masoudi-Nejad (2019) Trader as a new optimization algorithm predicts drug-target interactions efficiently. Sci. Rep. doi: 10.1038/s41598-019-45814-8. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7.Khosravi A., Kouhsar M., Goliaei B. B. Jayaram, Ali Masoudi-Nejad (2019) Systematic Analysis of Genes and Diseases by PheWAS Associated Networks. Comput. Biol. Med. doi: 10.1016/j.compbiomed.2019.04.037. [DOI] [PubMed] [Google Scholar]
- 8.Masoudi-Sobhanzadeh Y., Motieghader H. Ali Masoudi-Nejad (2019) FeatureSelect: A software for feature selection based on machine learning approaches. BMC Bioinformatics. doi: 10.1186/s12859-019-2754-0. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9.Pournoor E. NaserElmi, Ali Masoudi-Nejad (2019) CatbNet: A Multi Network Analyzer for Comparing and Analyzing the Topology of Biological Networks. Curr. Genomics. doi: 10.2174/1389202919666181213101540. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10.Masoudi-Sobhanzadeh Y., Omidi Y. MassoudAmanlou, Ali Masoudi-Nejad (2019) DrugR+: A comprehensive relational database for drug repurposing, combination therapy and replacement therapy. Comput. Biol. Med. doi: 10.1016/j.compbiomed.2019.05.006. [DOI] [PubMed] [Google Scholar]
- 11.Masoudi-Sobhanzadeh Yosef, Omidi Yadollah, Amanlou Massoud. Ali Masoudi-Nejad. 2019.
- 12.Mortezaei Z., Cazier J-B., Mehrabi A.A. Ali Masoudi-Nejad (2018) Novel Putative Drugs and Key Initiating Genes for Neurodegenerative Disease Determined Using Network-based Genetic Integrative Analysis. J. Cell. Biochem. doi: 10.1002/jcb.27825. [DOI] [PubMed] [Google Scholar]
- 13.Hosseinkhan N. ZaynabMousavian, Ali Masoudi-Nejad (2018) Comparison of pseudomonas aeruginosa and staphylococcus aureus gene co-expression networks reveals conservation in some aspects of virulence. Gene. doi: 10.1016/j.gene.2017.10.005. [DOI] [PubMed] [Google Scholar]