Publications

Fariba Davanian, Iman Adibi, Mahnoosh Tajmirriahi, Mehdi Rejali, Mehdi Paykan Heyrati, Matin Ghasemi, Seyed Hassan Alavi, Kiarash Mokhtari Dizaji, Mohammad Heydari Rad, Zahra Ghorbanali, Morteza Hajiabadi, Ali Sedaghi, Elnaz Rezaee Khaniki, Hoorieh Sabzevari, Seyedeh-Parisa Zarei, Ali Bavafa, Mahdi Bazargani, Farnaz Sedighin, Hossein Rabbani (2026). Diagnosing Multiple Sclerosis from Magnetic Resonance Imaging Images: Highlights from the Second Isfahan Artificial Intelligence Event 2024. Journal of Medical Signals & Sensors.

Cite DOI

Maryam Mehrabani, Amir Lakizadeh, Alireza Fotuhi Siahpirani, Mahdieh Salimi, Fatemeh Zare-Mirakabad, Ali Masoudi-Nejad (2025). SynergyGraph: predicting cell line specific drug combination synergy scores using knowledge graph representation and hypergraph modeling. Scientific Reports.

PDF Cite DOI github

Mahsa Sa'adat, Fatemeh Zare-Mirakabad, Milad Besharatifard (2025). SiaScoreNet: a siamese neural network-based model integrating prediction scores for HLA-peptide interaction prediction. Bioinformatics Advances.

PDF Cite DOI github

Milad Besharatifard, Fatemeh Zare-Mirakabad (2025). A Siamese Neural Network for Predicting snoRNA-Disease Association. 2025 33rd International Conference on Electrical Engineering (ICEE).

Cite DOI

Maryam Nazarloo, Mahsa Sa'adat, Fatemeh Zare-Mirakabad (2025). PHLA-SiNet: A novel peptide-HLA binding prediction model using heterogeneous Siamese neural networks. Computers in Biology and Medicine.

Cite DOI

Zahra Ghorbanali, Fatemeh Zare-Mirakabad, Bahram Mohammadpour (2025). DRP-VEM: Drug repositioning prediction using voting ensemble. AUT Journal of Mathematics and Computing.

PDF Cite Project DOI

Sara Mohammadzadeh, Zahra Ghorbanali, Mohammad Amin Sohrabi, Fatemeh Zare-Mirakabad (2025). Prediction of human-virus protein-protein interaction using heterogeneous siamese neural network. Modares Journal of Biotechnology.

PDF Cite

Maryam Ghobakhloo, Zahra Ghorbanali, Fatemeh Zare-Mirakabad, Roya Abbaszadeh, Mohammad Taheri-Ledari, Bahman Zeynali (2025). SimPep and OP-AND: A deep learning framework and curated database for predicting osteogenic peptides. PLOS Computational Biology.

PDF Cite Project DOI github

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

Cite DOI

Reyhaneh Ebrahimi, Seyed Hassan Alavi, Fayaz Soleymani, Fatemeh Zare-Mirakabad (2025). Targeting Protein in Neurodegenerative Diseases: A Computational Approach. 4th International & 13th Iranian Conference on Bioinformatics.

Cite CIVILICA

Sobhan Ahmadian Moghadam, Zahra Ghorbanali, Hesam Montazeri, Fatemeh Zare-Mirakabad (2025). Integrating Biological Networks and Deep Learning for Microbe -Disease Prediction. 4th International & 13th Iranian Conference on Bioinformatics.

Cite CIVILICA

Seyed Hassan Alavi, Zahra Ghorbanali, Fatemeh Zare-Mirakabad (2025). In-silico drug generation using masked language modeling. 4th International & 13th Iranian Conference on Bioinformatics.

Cite CIVILICA

Fateme Mirza-Abolhassani, Sobhan Ahmadian Moghadam, Fatemeh Zare-Mirakabad, Kaveh Kavousi (2025). Identification of driver genes in glioblastoma based on single-cell gene expression data using integrated pseudotime and phylogenetic analysis. 4th International & 13th Iranian Conference on Bioinformatics.

Cite CIVILICA

Masoud Madavifara, Fatemeh Zare-Mirakabad (2025). Enhancing Predictive Accuracy of CRISPR-Cas9 on-target efficiency using Deep Learning and Active Learning Optimization for Small Datasets. 4th International & 13th Iranian Conference on Bioinformatics.

Cite CIVILICA

Masoud Madavifara, Milad Beshartifarda, Fatemeh Zare-Mirakabad (2025). Discovering Moonlighting Proteins with AI and Explainability. 4th International & 13th Iranian Conference on Bioinformatics.

Cite CIVILICA

Z. Vahdani, F. Darvishi, Fatemeh Zare-Mirakabad (2025). Designing Guide RNAs Considering Essential Genes for Genome Editing of Yarrowia lipolytica Using Deep Learning in the CRISPR System. 4th International & 13th Iranian Conference on Bioinformatics.

Cite CIVILICA

Amir Zarghami, Milad Besharatifard, Fatemeh Zare-Mirakabad (2025). A novel approach to find Biomarkers affecting Autism Spectrum Disorder (ASD) Using Machine Learning. 4th International & 13th Iranian Conference on Bioinformatics.

Cite CIVILICA

Mahsa Sa'adat, Fatemeh Zare-Mirakabad, Ali Masoudi-Nejad, Mohammad Farahanchi Baradaran, Nazanin Hosseinkhan (2024). HLAPepBinder: An Ensemble Model for The Prediction Of HLA-Peptide Binding. Iranian Journal of Biotechnology.

PDF Cite DOI github

Nikta Gohari Sadr, Armin Behjati, Fatemeh Zare-Mirakabad (2024). RNA-Protein interaction prediction using transformers and asymmetric Siamese neural network. Cellular and Molecular Research (Iranian Journal of Biology).

PDF Cite DOI

Mohammad Amin Sohrabi, Fatemeh Zare-Mirakabad, Saeed Shiri Ghidary, Mahsa Sa'adat, Seyed-Ali Sadegh-Zadeh (2024). A novel data augmentation approach for influenza A subtype prediction based on HA proteins. Computers in Biology and Medicine.

PDF Cite DOI github

Fateme Bahgeri, Cholamreza Pazuki, Fatemeh Zare-Mirakabad, Mahsa Sa'adat, Zahra Ghorbanali (2024). Enhancing Predictive Accuracy of Biomolecules Partition Coefficients in Aqueous Two-Phase Systems Using Machine Learning. 3rd International & 12th Iranian Conference on Bioinformatics.

Cite CIVILICA

Zahra Seraj, Fatemeh Zare-Mirakabad (2024). Antimicrobial resistance prediction in Acinetobacter baumannii using collaborative matrix factorization. 2nd International and 11th National Iranian Conference on Bioinformatics.

Cite CIVILICA

Reyhaneh Mortezaee, Fatemeh Zare-Mirakabad (2024). A Siamese neural network for immunotherapy response prediction. 3rd International & 12th Iranian Conference on Bioinformatics.

Cite CIVILICA

Milad Besharatifard, Zahra Ghorbanali, Fatemeh Zare-Mirakabad (2024). Adverse drug reaction prediction using voting ensemble training approach. AUT J Math Comput.

PDF Cite DOI

Alireza Shariatmadar Taleghani, Yasaman Zohrab Beigi, Fatemeh Zare-Mirakabad, Ali Masoudi-Nejad (2023). Exploring ceRNA networks for key biomarkers in breast cancer subtypes and immune regulation. Scientific Reports.

PDF Cite DOI

Mehdi Paykan Heyrati, Zahra Ghorbanali, Mohammad Akbari, Ghasem Pishgahi, Fatemeh Zare-Mirakabad (2023). BioAct-Het: A heterogeneous siamese neural network for bioactivity prediction using novel bioactivity representation. ACS omega.

PDF Cite DOI github

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

PDF Cite DOI github

Fayaz Soleymani Babadi, Zahra Razaghi-Moghadam, Fatemeh Zare-Mirakabad, Zoran Nikoloski (2023). Prediction of metabolite–protein interactions based on integration of machine learning and constraint-based modeling. Bioinformatics advances.

PDF Cite DOI github

Zahra Ghorbanali, Fatemeh Zare-Mirakabad, Mohammad Akbari, Najmeh Salehi, Ali Masoudi-Nejad (2023). DrugRep-KG: toward learning a unified latent space for drug repurposing using knowledge graphs. Journal of chemical information and modeling.

PDF Cite DOI github

Milad Besharatifard, Fatemeh Zare-Mirakabad, Zahra Ghorbanali (2023). Predicting Adverse Drug Reactions Using Computational Methods: An Analysis of Drug and Adverse Reaction Features and Representations. 2nd International and 11th National Iranian Conference on Bioinformatics.

Cite CIVILICA

Mahsa Sa'adat, Fatemeh Zare-Mirakabad, Nazanin Hosseinkhan (2023). Improvement of peptide-HLA class I prediction using transformers. 2nd International and 11th National Iranian Conference on Bioinformatics.

Cite CIVILICA

Maryam Rastegari, Najmeh Salehi, Fatemeh Zare-Mirakabad (2023). Biomarker prediction in autism spectrum disorder using a network-based approach. BMC medical genomics.

PDF Cite DOI

Armin Behjati, Fatemeh Zare-Mirakabad, Seyed Shahriar Arab, Abbas Nowzari-Dalini (2022). Protein sequence profile prediction using ProtAlbert transformer. Computational Biology and Chemistry.

Cite DOI

Javad Rezaei, Fatemeh Zare-Mirakabad, Sayed-Amir Marashi, Seyed Ali MirHassani (2022). The assessment of essential genes in the stability of PPI networks using critical node detection problem. AUT Journal of Mathematics and Computing.

PDF Cite Project DOI

Mahsa Sa'adat, Armin Behjati, Fatemeh Zare-Mirakabad, Sajjad Gharaghani (2022). Drug-target binding affinity prediction using transformers. bioRxiv.

PDF Cite Project DOI

Milad Besharatifard, Zahra Ghorbanali, Fatemeh Zare-Mirakabad (2021). The assessment of similarity vectors of fingerprint and UMLS in adverse drug reaction prediction. bioRxiv.

PDF Cite Project DOI

Javad Rezaei, Fatemeh Zare-Mirakabad, Seyed Ali MirHassani, Sayed-Amir Marashi (2021). EIA-CNDP: An exact iterative algorithm for critical node detection problem. Computers & Operations Research.

Cite DOI

Najmeh Salehi, Bahareh Attaran, Fatemeh Zare‐Mirakabad, Bahareh Ghadiri, Maryam Esmaeili, Mohadeseh Shakaram, Mohammad Tashakoripour, Mahmoud Eshagh Hosseini, Marjan Mohammadi (2020). The outward shift of clarithromycin binding to the ribosome in mutant<i>Helicobacter pylori</i>strains. Helicobacter.

Cite DOI

Farzaneh Salari, Fatemeh Zare-Mirakabad, Mehdi Sadeghi (2020). A new hash function and its use in read mapping on genome. AUT Journal of Mathematics and Computing.

PDF Cite DOI

Najmeh Salehi, Bahareh Attaran, Fatemeh Zare-Mirakabad, Bahareh Ghadiri, Maryam Esmaeili, Mohadeseh Shakaram, Mohammad Tashakoripour, Mahmoud Eshagh Hosseini, Marjan Mohammadi (2020). The outward shift of clarithromycin binding to the ribosome in mutant Helicobacter pylori strains. Helicobacter.

PDF Cite DOI

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

Cite DOI

Farzaneh Salari, Fatemeh Zare-Mirakabad, Mohammad Hossein Alavi, Léa Girard, Mahya Ghafari, René De Mot, Hassan Rokni-Zadeh (2020). Draft genome sequence of Pseudomonas aeruginosa strain LMG 1272, an atypical white line reaction producer. Microbiology Resource Announcements.

PDF Cite DOI

Fazeleh S Mohseni-Salehi, Fatemeh Zare-Mirakabad, Mehdi Sadeghi, Soudeh Ghafouri-Fard (2020). A stochastic model of DNA double-strand breaks repair throughout the cell cycle. Bulletin of Mathematical Biology.

Cite DOI

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

PDF Cite DOI

Marziyeh Movahedi, Fatemeh Zare-Mirakabad, Ali Ramazani, Nagarjun Konduru, Seyed Shahriar Arab (2019). Computational Analysis of Nanoparticle Features on Protein Corona Composition in Biological Nanoparticle-Protein Interactions. 2019 5th Conference on Knowledge Based Engineering and Innovation (KBEI).

Cite DOI

Ali Jalilvand, Behzad Akbari, Fatemeh Zare-Mirakabad, Foad Ghaderi (2019). Disease gene prioritization using network topological analysis from a sequence based human functional linkage network. arXiv preprint arXiv:1904.06973.

PDF Cite DOI

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

PDF Cite DOI

Hossein Bankikoshki, Seyed Ali Seyyedsalehi, Fatemeh Zare-Mirakabad (2018). Dimensionality Reduction of Binding Site Sequence Data on Human Genome Using a Deep Autoencoder Neural Network. Iranian Journal of Biomedical Engineering.

PDF Cite DOI

A Jalilvand, B Akbari, Fatemeh Zare-Mirakabad (2018). S-FLN: A sequence-based hierarchical approach for functional linkage network construction. Journal of theoretical biology.

Cite DOI

Fatemeh Zare-Mirakabad, M Movahedia, N Sarang, S. S Arab (2018). Protein design using native secondary sub-structures and solvent accessibility. 7th Iranian Conference on Bioinformatics.

Cite CIVILICA

Fazeleh S Mohseni-Salehi, Fatemeh Zare-Mirakabad, Soudeh Ghafouri-Fard, Mehdi Sadeghi (2017). The effect of stochasticity on repair of DNA double strand breaks throughout non-homologous end joining pathway. Mathematical Medicine and Biology: A Journal of the IMA.

Cite DOI

Fatemeh Zare-Mirakabad, H Ahrabian, Mehdi Sadeghi, J Mohammadzadeh, S Hashemifar, Abbas Nowzari-Dalini, B Goliaei (2017). PSOMF: An algorithm for pattern discovery using PSO. Proceedings of the Third IAPR International Conferences on Pattern Recognition in Bioinformatics, Melbourne. Australia.

Cite

Soheila Montaseri, Fatemeh Zare-Mirakabad, Mohammad Ganjtabesh (2017). Evaluating the quality of SHAPE data simulated by k-mers for RNA structure prediction. Journal of Bioinformatics and Computational Biology.

Cite DOI

Nafiseh Banirazi Motlagh, Fatemeh Zare-Mirakabad (2017). Transcription Factor Binding Sites Prediction Based on Histone Acetylations using Neural Networks. Cellular and Molecular Research (Iranian Journal of Biology).

PDF Cite

Mohadeseh Lotfi, Fatemeh Zare-Mirakabad, Soheila Montaseri (2017). RNA design using simulated SHAPE data. Genes & genetic systems.

PDF Cite DOI

Hossein Banki-Koshki, S Ali Seyyedsalehi, Fatemeh Zare-Mirakabad (2017). Transcription factor binding sites identification on human genome using an artificial neural network. ICEE.

Cite DOI

Soheila Montaseri, Mohammad Ganjtabesh, Fatemeh Zare-Mirakabad (2016). Evolutionary algorithm for RNA secondary structure prediction based on simulated SHAPE data. PloS one.

PDF Cite DOI

Yousef Seyfari, Farzad Didehvar, Hadi Banaee (2016). Evaluating the Accuracy of Splice Site Prediction based on Integrating Jensen-Shannon Divergence and a Polynomial Equation of Order 2. International Journal of Computer Applications.

PDF Cite DOI

M Mollalo, Master of Science, Fatemeh Zare-Mirakabad (2016). Motif Finding in upstream regulatory regions of co-expressed genes using Cuckoo optimization Algorithm and Simulated Annealing. Tabriz Journal of Electrical Engineering.

PDF Cite

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

PDF Cite Project DOI

Morteza Kouhsar, Fatemeh Zare-Mirakabad, Yousef Jamali (2015). WCOACH: Protein complex prediction in weighted PPI networks. Genes & genetic systems.

PDF Cite Project DOI

Mohadeseh Lotfi, Fatemeh Zare-Mirakabad, Soheila Montaseri (2015). RNA secondary structure prediction based on SHAPE data in helix regions. Journal of theoretical biology.

Cite DOI

Soheila Montaseri, Nasrollah Moghadam-Charkari, Fatemeh Zare-Mirakabad (2014). A genetic approach to accurately predict RNA secondary structure. Cellular and Molecular Research (Iranian Journal of Biology).

PDF Cite

Mohammad Ganjtabesh, Soheila Montaseri, Fatemeh Zare-Mirakabad (2014). Using temperature effects to predict the interactions between two RNAs. Journal of Theoretical Biology.

Cite DOI

Soheila Montaseri, Fatemeh Zare-Mirakabad, Nasrollah Moghadam-Charkari (2014). RNA-RNA interaction prediction using genetic algorithm. Algorithms for Molecular Biology.

PDF Cite DOI

Mohammad Talebzadeh, Fatemeh Zare-Mirakabad (2014). Transcription factor binding sites prediction based on modified nucleosomes. PLoS One.

PDF Cite DOI

Mohammad Ganjtabesh, Fatemeh Zare-Mirakabad, Abbas Nowzari-Dalini (2013). Inverse RNA folding solution based on multi-objective genetic algorithm and Gibbs sampling method. EXCLI journal.

PDF Cite

Hesamedin Torabi Dashti, Fatemeh Zare-Mirakabad, Nima Aghaeepour, Hayedeh Ahrabian, Abbas Nowzari-Dalini (2013). PreRkTAG: Prediction of RNA Knotted Structures Using Tree Adjoining Grammars. Iranian Journal of Biotechnology.

PDF Cite DOI

Soheila Montaseri, Nasrollah Moghadam-Charkari, Fatemeh Zare-Mirakabad (2012). RNA Secondary Structure Prediction Using Heuristic Algorithm. Modares Journal of Biotechnology.

PDF Cite

Soheila Montaseri, Nasrollah Moghadam-Charkari, Fatemeh Zare-Mirakabad (2012). A heuristic approach to RNA–RNA interaction prediction. Journal of Theoretical Biology.

Cite DOI

Mohammad-Reza Sadeghi, Fatemeh Zare-Mirakabad, Maryam Tahmasebi, Mehdi Sadeghi (2012). EPWM: An Extended Position Weight Matrix for Motif Representation in Biological Sequences. basic and applied scientific research.

PDF Cite

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

PDF Cite DOI

Fatemeh Zare-Mirakabad, Hayedeh Ahrabian, Mehdi Sadeghi, Somaieh Hashemifar, Abbas Nowzari-Dalini, Bahram Goliaei (2009). Genetic algorithm for dyad pattern finding in DNA sequences. Genes & genetic systems.

Cite DOI

Haydeh Ahrabian, Abbas Nowzari-Dalini, Fatemeh Zare-Mirakabad (2009). A constant time algorithm for DNA add. International Journal of Foundations of Computer Science.

PDF Cite DOI github