Trader

Yosef Masoudi-Sobhanzadeh, Yadollah Omidi, Massoud Amanlou, Ali Masoudi-Nejad (2019) Trader as a new optimization algorithm predicts drug-target interactions efficiently. Scientific Reports. DOI: 10.1038/s41598-019-45814-8.

DrugR+

Yosef Masoudi-Sobhanzadeh, Yadollah Omidi, MassoudAmanlou, Ali Masoudi-Nejad (2019) DrugR+: A comprehensive relational database for drug repurposing, combination therapy and replacement therapy. Computers in Biology and Medicine. DOI: 10.1016/j.compbiomed.2019.05.006.

FeatureSelect

Yosef Masoudi-Sobhanzadeh, Habib Motieghader, Ali Masoudi-Nejad (2019) FeatureSelect: A software for feature selection based on machine learning approaches. BMC Bioinformatics. DOI: 10.1186/s12859-019-2754-0

Kavosh

Razaghi, A., Ahrabian, H., Abbas Nowzari, Masoudi-Nejad, Ali (2009) Kavosh: A New Algorithm for Finding Network Motifs. BMC Bioinformatics. 4:10:318.

EGENES

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

Egassembler

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.

CatbNet

Ehsan Pournoor, NaserElmi, Ali Masoudi-Nejad (2019) CatbNet: A Multi Network Analyzer for Comparing and Analyzing the Topology of Biological Networks. Current Genomics. DOI: 10.2174/1389202919666181213101540

CytoKavosh

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

QuateXelero

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

C-element

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

HomoTarget

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

LocFuse

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

SCAN-Toolbox

YazdanAsgari, Zahra Zabihinpour, Ali Masoudi-Nejad (2018) SCAN-Toolbox: Structural COBRA Add-oN (SCAN) for Metabolic Networks. Current Bioinformatics. 2018, 13, 100-107

PPIevo

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

MODA

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

BosFinder

Balal Sadeghi, Hamed Ahmadi, MohammadrezaNassiri, Ali Masoudi-Nejad (2014) BosFinder: a Novell Pre-MicroRNA Gene Prediction algorithm in Bostaurus. AnimalGenetics.45(4):479-84

RPINBASE

Mahsa Torkamanian-Afshar, Hossein Lanjanian, Sajjad Nematzadeh, Maryam Tabarzad, Ali Najafi, Farzad Kiani, Ali Masoudi-Nejad (2020) RPINBASE: An Online Toolbox to Extract Features for Predicting RNA-Protein Interactions. Genomics. DOI:10.1016/j.ygeno.2020.02.013.

N4

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

CeFunMO

Morteza Kouhsar, Zahra Razaghi-MoghadamKashani, ZaynabMousavian, Ali Masoudi-Nejad (2016) CeFunMO: a centrality based method for discovering functional motifs with application in biological networks. Computers in Biology and Medicine. 76:154-9