Publications

Seyed Hassan Alavi, Fatemeh Zare-Mirakabad, Sajjad Gharaghani (2026). Which chemical features are captured by ChemBERTa's attention?. Journal of Computer-Aided Molecular Design.

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Zahra Seraj, Zahra Ghorbanali, Fatemeh Zare-Mirakabad, Bahareh Attaran, Sajjad Gharaghani (2026). Exploring feature limitations in antimicrobial resistance prediction: machine learning and deep learning in A. baumannii. Scientific Reports.

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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.

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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.

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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.

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

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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.

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

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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.

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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.

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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.

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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.

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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.

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

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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.

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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.

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

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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.

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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.

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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.

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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).

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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.

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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.

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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.

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

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

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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

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

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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.

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

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

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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).

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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.

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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.

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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.

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

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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.

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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.

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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.

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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.

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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).

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

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

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

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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.

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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.

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

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

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

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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).

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

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

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

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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.

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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.

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

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

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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.

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

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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.

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

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