| WCOACH: Protein complex prediction in weighted PPI networks M Kouhsar, F Zare-Mirakabad, Y Jamali Genes & genetic systems 90 (5), 317-324, 2015 | 36 | 2015 |
| The assessment of efficient representation of drug features using deep learning for drug repositioning M Moridi, M Ghadirinia, A Sharifi-Zarchi, F Zare-Mirakabad BMC bioinformatics 20 (1), 577, 2019 | 30 | 2019 |
| Genetic algorithm for dyad pattern finding in DNA sequences F Zare-Mirakabad, H Ahrabian, M Sadeghi, S Hashemifar, ... Genes & genetic systems 84 (1), 81-93, 2009 | 29 | 2009 |
| DrugRep-KG: toward learning a unified latent space for drug repurposing using knowledge graphs Z Ghorbanali, F Zare-Mirakabad, M Akbari, N Salehi, A Masoudi-Nejad Journal of chemical information and modeling 63 (8), 2532-2545, 2023 | 25 | 2023 |
| Protein sequence profile prediction using ProtAlbert transformer A Behjati, F Zare-Mirakabad, SS Arab, A Nowzari-Dalini Computational Biology and Chemistry 99, 107717, 2022 | 22 | 2022 |
| Transcription factor binding sites prediction based on modified nucleosomes M Talebzadeh, F Zare-Mirakabad PLoS One 9 (2), e89226, 2014 | 22 | 2014 |
| New scoring schema for finding motifs in DNA Sequences F Zare-Mirakabad, H Ahrabian, M Sadeghi, A Nowzari-Dalini, B Goliaei Bmc Bioinformatics 10 (1), 93, 2009 | 19 | 2009 |
| Biomarker prediction in autism spectrum disorder using a network-based approach M Rastegari, N Salehi, F Zare-Mirakabad BMC medical genomics 16 (1), 12, 2023 | 18 | 2023 |
| Drug-target binding affinity prediction using transformers M Saadat, A Behjati, F Zare-Mirakabad, S Gharaghani | 18 | 2021 |
| Evolutionary algorithm for RNA secondary structure prediction based on simulated SHAPE data S Montaseri, M Ganjtabesh, F Zare-Mirakabad PloS one 11 (11), e0166965, 2016 | 15 | 2016 |
| RNA-RNA interaction prediction using genetic algorithm S Montaseri, F Zare-Mirakabad, N Moghadam-Charkari Algorithms for Molecular Biology 9 (1), 17, 2014 | 15 | 2014 |
| DrugRep-HeSiaGraph: when heterogenous siamese neural network meets knowledge graphs for drug repurposing Z Ghorbanali, F Zare-Mirakabad, N Salehi, M Akbari, A Masoudi-Nejad BMC bioinformatics 24 (1), 374, 2023 | 14 | 2023 |
| EIA-CNDP: An exact iterative algorithm for critical node detection problem J Rezaei, F Zare-Mirakabad, SA MirHassani, SA Marashi Computers & Operations Research 127, 105138, 2021 | 11 | 2021 |
| Evaluating the accuracy of protein design using native secondary sub-structures M Movahedi, F Zare-Mirakabad, SS Arab BMC bioinformatics 17 (1), 353, 2016 | 9 | 2016 |
| Exploring ceRNA networks for key biomarkers in breast cancer subtypes and immune regulation A Shariatmadar Taleghani, Y Zohrab Beigi, F Zare-Mirakabad, ... Scientific Reports 13 (1), 20795, 2023 | 8 | 2023 |
| The outward shift of clarithromycin binding to the ribosome in mutant Helicobacter pylori strains N Salehi, B Attaran, F Zare‐Mirakabad, B Ghadiri, M Esmaeili, ... Helicobacter 25 (6), e12731, 2020 | 8 | 2020 |
| BioAct-Het: A heterogeneous siamese neural network for bioactivity prediction using novel bioactivity representation M Paykan Heyrati, Z Ghorbanali, M Akbari, G Pishgahi, F Zare-Mirakabad ACS omega 8 (47), 44757-44772, 2023 | 7 | 2023 |
| Inverse RNA folding solution based on multi-objective genetic algorithm and Gibbs sampling method M Ganjtabesh, F Zare-Mirakabad, A Nowzari-Dalini EXCLI journal 12, 546, 2013 | 7 | 2013 |
| A novel data augmentation approach for influenza A subtype prediction based on HA proteins MA Sohrabi, F Zare-Mirakabad, SS Ghidary, M Saadat, SA Sadegh-Zadeh Computers in Biology and Medicine 172, 108316, 2024 | 6 | 2024 |
| Prediction of metabolite–protein interactions based on integration of machine learning and constraint-based modeling F Soleymani Babadi, Z Razaghi-Moghadam, F Zare-Mirakabad, ... Bioinformatics advances 3 (1), vbad098, 2023 | 6 | 2023 |
