Publications

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

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

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

Maryam Ghobakhloo, Zahra Ghorbanali, Fatemeh Zare, 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.

Fatemeh Zare, Nasrollah Moghadam Charkari, Soheila Montaseri (2025). RNA Secondary Structure Prediction Using Heuristic Algorithm. Modares Journal of Biotechnology.

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

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

Mohammad Amin Sohrabi, Fatemeh Zare, 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.

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

Elham Arkan, Faranak Aghaz (2024). Preparation of biodegradable Electrospun-nanofibers based on wheat gluten containing doxorubicin as a drug delivery system. **.

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

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

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

Zahra Ghorbanali, Fatemeh Zare, 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.

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

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

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

Javad Rezaei, Fatemeh Zare, 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.

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

Mahsa Sa'adat, Armin Behjati, Fatemeh Zare, Sajjad Gharaghani (2021). TranDTA: Prediction Of Drug–Target Binding Affinity Using Transformer Representations. bioRxiv.

Mahsa Sa'adat, Armin Behjati, Fatemeh Zare, Sajjad Gharaghani (2021). Drug-target binding affinity prediction using transformers. **.

Zahra Ghorbanali, Fatemeh Zare, Bahram Mohammadpour (2021). DRP-VEM: Drug repositioning prediction using voting ensemble. arXiv preprint arXiv:2110.01403.

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

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

Nafiseh Banirazi Motlagh, Bahram Mohammadpour Esfahani, Behnoosh Ashrafi, Fatemeh Zare (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.

Farzaneh Salari, Fatemeh Zare, 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.

Nafiseh Banirazi Motlagh, Fatemeh Zare (2020). Transcription Factor Binding Sites Prediction Based on Histone Acetylations using Neural Networks. Cellular and Molecular Research (Iranian Journal of Biology).

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

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

Marziyeh Movahedi, Fatemeh Zare, 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).

Fazeleh S Mohseni-Salehi, Fatemeh Zare, Soudeh Ghafouri-Fard, Mehdi Sadeghi (2018). 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.

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

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

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

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

Hossein Bankikoshki, Seyed Ali Seyyedsalehi, Fatemeh Zare (2017). Dimensionality Reduction of Binding Site Sequence Data on Human Genome Using a Deep Autoencoder Neural Network. Iranian Journal of Biomedical Engineering.

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

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

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

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

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

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

Mohammad Ganjtabesh, Soheila Montaseri, Fatemeh Zare (2015). Using temperature effects to predict the interactions between two RNAs. Journal of Theoretical Biology.

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

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

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

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

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

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

F Zare Mirakabad, M Sadeghi, H Ahrabian, A Nowzari-Dalini (2009). RNAComp: A new method for RNA secondary structure alignment. Match.

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

Najmeh Salehi, Bahareh Attaran, Fatemeh Zare‐Mirakabad, Bahareh Ghadiri, Maryam Esmaeili, Mohadeseh Shakaram, Mohammad Tashakoripour, Mahmoud Eshagh Hosseini, Marjan Mohammadi (0001). The outward shift of clarithromycin binding to the ribosome in mutant Helicobacter pylori strains. Helicobacter.

Soheila Montaseri, Mohammad Ganjtabesh, Fatemeh Zare, Correlation Coefficient MCC (0001). Supporting Information ESD-Fold: RNA Folding Based on Simulated SHAPE Data. **.

F Zare Mirakabad, H Ahrabian, M Sadeghi, J Mohammadzadeh, S Hashemifar, A Nowzari-Dalini, B Goliaei (0001). PSOMF: An algorithm for pattern discovery using PSO. Proceedings of the Third IAPR International Conferences on Pattern Recognition in Bioinformatics, Melbourne. Australia.

Yousef Seyfari, Farzad Didehvar, Hadi Banaee (0001). 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.

Mohammad-Reza Sadeghi, Fatemeh Zare, Maryam Tahmasebi, Mehdi Sadeghi (0001). EPWM: An Extended Position Weight Matrix for Motif Representation in Biological Sequences. **.

Milad Besharatifard, Zahra Ghorbanali, Fatemeh Zare (0001). Adverse drug reaction prediction using voting ensemble training approach. AUT J Math Comput.

Fazeleh S Mohseni-Salehi, Fatemeh Zare, Mehdi Sadeghi, Soudeh Ghafouri-Fard (0001). A stochastic model of DNA double-strand breaks repair throughout the cell cycle. Bulletin of Mathematical Biology.

Haydeh Ahrabian, Abbas Nowzari-Dalini, Fatemeh Zare (0001). A constant time algorithm for DNA add. International Journal of Foundations of Computer Science.