Kavosh

Razaghi, A., Ahrabian, H., Abbas Nowzari, Masoudi-Nejad, Ali (2009) Kavosh: A...

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.  

FeatureSelect

Yosef Masoudi-Sobhanzadeh, Habib Motieghader, Ali Masoudi-Nejad (2019)...

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  

DrugR+

Yosef Masoudi-Sobhanzadeh, Yadollah Omidi, MassoudAmanlou, Ali Masoudi-Nejad...

EGENES

Masoudi-Nejad, A., Susumu Goto, Ruy Jauregui, Masumi Ito, Shuichi...

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:...

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  

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

Razaghi, A., Ahrabian, H., Abbas Nowzari, Masoudi-Nejad, Ali (2009) Kavosh: A...

CeFunMO

Razaghi, A., Ahrabian, H., Abbas Nowzari, Masoudi-Nejad, Ali (2009) Kavosh: A...