New scoring schema for finding motifs in DNA Sequences. - Fatemeh Zare-Mirakabad; Hayedeh Ahrabian; Mehdi Sadeghi; Abbas Nowzari-Dalini; Bahram Goliaei (BMC Bioinform., 2009)

A Constant Time Algorithm for DNA Add. - Haydeh Ahrabian; Abbas Nowzari-Dalini; Fatemeh Zare-Mirakabad (Int. J. Found. Comput. Sci., 2009)

RNA-RNA interaction prediction using genetic algorithm. - Soheila Montaseri; Fatemeh Zare-Mirakabad; Nasrollah Moghadam Charkari (Algorithms Mol. Biol., 2014)

Evaluating the accuracy of protein design using native secondary sub-structures. - Marziyeh Movahedi; Fatemeh Zare-Mirakabad; Seyed Shahriar Arab (BMC Bioinform., 2016)

Robust Multiple Model adaptive control with fuzzy posterior Probability Combination. - Fatemeh Zare-Mirakabad; Mohammad Hosein Kazemi (Control. Intell. Syst., 2017)

Evaluating the quality of SHAPE data simulated by k-mers for RNA structure prediction. - Soheila Montaseri; Fatemeh Zare-Mirakabad; Mohammad Ganjtabesh (J. Bioinform. Comput. Biol., 2017)

Assessing the impact of exact reads on reducing the error rate of read mapping. - Farzaneh Salari; Fatemeh Zare-Mirakabad; Mehdi Sadeghi; Hassan Rokni-Zadeh (BMC Bioinform., 2018)

The assessment of efficient representation of drug features using deep learning for drug repositioning. - Mahroo Moridi; Marzieh Ghadirinia; Ali Sharifi-Zarchi; Fatemeh Zare-Mirakabad (BMC Bioinform., 2019)

The assessment of histone acetylation marks in the vicinity of transcription factor binding sites in human CD4 + T cells using information theory methods. - Nafiseh Banirazi Motlagh; Bahram Mohammadpour Esfahani; Behnoosh Ashrafi; Fatemeh Zare-Mirakabad (Comput. Biol. Chem., 2020)

EIA-CNDP: An exact iterative algorithm for critical node detection problem. - Javad Rezaei; Fatemeh Zare-Mirakabad; Seyyed Ali MirHassani; Sayed-Amir Marashi (Comput. Oper. Res., 2021)

Protein sequence profile prediction using ProtAlbert transformer. - Armin Behjati; Fatemeh Zare-Mirakabad; Seyed Shahriar Arab; Abbas Nowzari-Dalini (Comput. Biol. Chem., 2022)

DrugRep-KG: Toward Learning a Unified Latent Space for Drug Repurposing Using Knowledge Graphs. - Zahra Ghorbanali; Fatemeh Zare-Mirakabad; Mohammad Akbari; Najmeh Salehi; Ali Masoudi-Nejad (J. Chem. Inf. Model., 2023)

DrugRep-HeSiaGraph: when heterogenous siamese neural network meets knowledge graphs for drug repurposing. - Zahra Ghorbanali; Fatemeh Zare-Mirakabad; Najmeh Salehi; Mohammad Akbari; Ali Masoudi-Nejad (BMC Bioinform., 2023)

A novel data augmentation approach for influenza A subtype prediction based on HA proteins. - Mohammad Amin Sohrabi; Fatemeh Zare-Mirakabad; Saeed Shiri Ghidary; Mahsa Saadat; Seyed-Ali Sadegh-Zadeh (Comput. Biol. Medicine, 2024)

Molecular landscape of endometrioid Cancer: Integrating multiomics and deep learning for personalized survival prediction. - Behnaz Haji Molla Hoseyni; Hossein Lanjanian; Yasaman Zohrab Beigi; Mahdieh Salimi; Fatemeh Zare-Mirakabad; Ali Masoudi-Nejad (Comput. Biol. Medicine, 2025)