FATEMEH ZARE MIRAKABAD - Amirkabir University of Technology

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Amirkabir University of Technology

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FATEMEH ZARE MIRAKABAD

Associate Professor
Department of Mathematics and Computer Science
Computer Science

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f.zare

aut.ac.ir

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h-index (Scopus):

10.00

Citations (Scopus):

290

Supervised PhD Theses

Thesis title

Date

Learning a unified latent space for drugs and diseases facing drug repurposing problem

ZAHRA GHORBANALI

2023 Oct

Identifying genes and gene products in biochemical networks interdiction

JAVAD REZAEI

2021 Oct

A model of DNA double strand break repair throughout the cell cycle

FAZELEH SADAT MOHSENI SALEHI MONFARED

2020 Jan

Read mapping and reference-based genome assembly using NGS technologies

FARZANEH SALARI

2019 Oct

Supervised MSc Theses

Thesis title

Date

Predicting Relationships Between Microbiota and Diseases Based on Heterogeneous Network

SOBHAN AHMADIAN MOGHADAM

2024 Sep

Prediction of HLA-Peptide interaction Using Neutral Networks

MARYAM NAZARLOO

2024 Feb

Masked language modeling for de novo drug design

SEYYED HASSAN ALAVI
Other Supervisor: SAEED SHIRY GHIDARY

2024 Feb

Feature Extraction from Splice Sites for Coding Region Prediction

ARASH KAZEMI AZARBAIJANI

2024 Feb

Drug target prediction for neurodegenerative disease using PPI network

REYHANEH EBRAHIMI

2024 Feb

Prediction of IC50 for drug targets using pharmacokinetics

MOHAMMAD FARAHANCHI BARADARAN

2024 Jan

Reducing the error rate of read mapping by short-read clustering

SEYEDMOSTAFA MESHKATI
Other Supervisor: M.HASSAN SHIRALI-SHAHREZA

2023 Sep

Modeling Protein Metabolite Interaction Using Metabolic Networks

FAYAZ SOLEYMANI BABADI & Mohammad Akbari
Other Supervisor:

2023 Mar

Classifying influenza A subtypes using deep learning

MOHAMMAD AMIN SOHRABI & SAEED SHIRY GHIDARY
Other Supervisor:

2023 Mar

Prediction of microRNA-disease associations based on integrating different molecular data

SOHRAB SALEHI ARASHLOO
Other Supervisor: ALIREZA MOFIDI

2022 Oct

biomarker prediction for Identifying Esophageal Cancer subtypes using Transcriptomics data

MAHDIS HABIBPOUR FATIDEH & MEHDI GHATEE
Other Supervisor:

2022 Oct

Identification of biomarkers for predicting gestational age

AREZOU PAKSERESHT
Other Supervisor: Mohammad Akbari

2022 Oct

Predicting antimicrobial resistance in bacteria using bacteria-bacteria and antibiotic-antibiotic similarity

ZAHRA SERAJ & M.HASSAN SHIRALI-SHAHREZA
Other Supervisor:

2022 Oct

Lead Compoundes Prediction using homogeneous Feature Space

MEHDI PAYKAN HEYRATI
Other Supervisor: MEHDI ROSTAMI

2022 Jun

Adverse drug reaction prediction with integrating multiple data sources

MILAD BESHARATIFARD

2021 Sep

Prediction of drug-target binding affinity based on fundamental molecular properties

MAHSA SAADAT

2021 Aug

Rna 3D Design

SARA SADAT NOURIZADEH

2021 Aug

Inverse protein Folding Using Learning Methods

AMIN RAHMANI

2021 Apr

Identifying Effective Biomarkers in Autism Spectrum Disorder

MARYAM RASTEGARI

2021 Mar

RNA structure prediction using neural network

PARHAM HAFEZI BAFTI
Other Supervisor: Ali Mohades Khorasani

2020 Feb

prediction of protein-protein interaction sites from geometric features

MAHBOOBRH SHARIFIAN ESFAHANI
Other Supervisor: Ali Mohades Khorasani

2019 Feb

Inverse Protein Folding prediction according to polymers in pdb

AREFE ALIKHANI
Other Supervisor: Mostafa Shamsi

2018 Oct

Tuning the parameters of Hallmarks in Cancer Simulation

MOHAMMAD JAVAD SABAGHZADEH

2018 Oct

Transcription Factor Binding Sites Prediction in human Genome Using Deep Neural Network

HOSSEIN BANKI-KOSHKI & S.ALI SEYYEDSALEHI
Other Supervisor:

2018 Feb

Constructing gene regulatory networks by using microarray data

MAHYA MOSHREF
Other Supervisor: MOHAMMAD EBRAHIM SHIRI AHMAD ABADY

2018 Feb

Phylogenetic tree construction based on clustering

BITA POURMOHSENIN

2017 Oct

pairwise global alignment of protein-protein interaction networks

ZAHRA GHORBANALI

2016 Oct

Pairwise alignment of RNA 3D structures using geometric approaches

SOHA SALEHIAN GHAMSARI & Ali Mohades Khorasani
Other Supervisor:

2016 Oct

Comparing RNA Secondary Structures Based on Image Processing Techniques

MAHDI FARSHI KERMANI

2016 Feb

Controllability Discovery of Biological Networks

FARBOD FARHOUR
Other Supervisor: Farzad Didehvar

2016 Feb

consensus folding prediction of unaligned RNA sequences

MOHAMADREZA VAHEDI
Other Supervisor: Farzad Didehvar

2016 Feb

Identifying splice sites in DNA sequences

SAEED RASTEGAR
Other Supervisor: Ali Mohades Khorasani

2015 Oct

a new model for motif representation based on coding theory

MEHRI BAKHSHIAN

2015 Oct

Reconstruction haplotype from genotype based on parsimony method

SHIVA SHAKIBAPOUR

2014 Oct

haplotype assembly from genome sequence data

MOTAHARE FAROKHNIA

2014 Oct

Inverse RNA folding prediction with SHAPE-directed

MOHADESEH LOTFI

2014 Oct

Association analysis between epigenetic variation and gene transcription

MOHAMMAD TALEBZADEH

2013 Oct

Structural alignment of RNA molecules with pseudoknots

ABBAS MASOUMZADEH TORK

2013 Oct

Reconstructing evolutionary inter relationships of species based on rooted triplets

ALIREZA ZAMANY ZAYNALI
Other Supervisor: SEYYED NASER HASHEMI

2013 Feb

Detecting structural variationin genome

ALI IZADI MOTLAGH

2012 Nov

Dyad motif finding in biological sequence

MOSTAFA POURSALEHIABBASABADI

2012 Oct

Discrimination of rheumatoid arthritis from osteoarthritis using machine learning

SHAHAB GHASEMI NEJAD RAEINI
Other Supervisor: M.HASSAN SHIRALI-SHAHREZA

2026 May

Discovering Autism spectrum disorder biomarkers using gene expression data

AMIR ZARGHAMI
Other Supervisor: DR SAEID REZAKHAH VARNOUSEFADERNAI

2025 Sep

Cell type clustering based on single-cell RNA-seq data and biological pathway information

MITRA AHMADI

2025 Sep

Predicting sgRNA effect on Cas9 cleavage

MASOUD MAHDAVIFAR
Other Supervisor: Mohammad Akbari

2025 Sep

T cell receptor and HLA association prediction using deep learning

SABA ESKANDARI MANJILI
Other Supervisor: M.HASSAN SHIRALI-SHAHREZA

2025 Oct

network-based approach to predict immune checkpoint inhibitors response in cancer patients

REYHANEH MORTEZAEI
Other Supervisor: DR SAEID REZAKHAH VARNOUSEFADERNAI

2025 Mar

Journal Papers

M. Nazarloo, M. Saadat, F. Zare Mirakabad, "PHLA-SiNet: A novel peptide-HLA binding prediction model using heterogeneous Siamese neural networks", Computers In Biology and Medicine, 2025 Sep vol. 197, no. , pp.-, 2025.

Maryam Ghobakhloo, Z. Ghorbanali, F. Zare Mirakabad, Roya Abbaszadeh, Mohammad Taheri-ledari, Bahman Zeynali, "SimPep and OP-AND: A deep learning framework and curated database for predicting osteogenic peptides", Plos Computational Biology, 2025 Aug vol. , no. , pp.-, 2025.

Behnaz Haji Molla Hoseyni, Hossein Lanjanian, Yasaman Zohrab Beig, Mahdieh Salimi, F. Zare Mirakabad, Ali Masoudi-nejad, "Molecular landscape of endometrioid Cancer: Integrating multiomics and deep learning for personalized survival prediction", Computers In Biology and Medicine, 2025 Apr vol. 192, no. 192, pp.1-15, 2025.

Z. Ghorbanali, F. Zare Mirakabad, B. Mohammadpouresfahani, "DRP-VEM: Drug Repositioning Using Voting Ensemble Model", Aut Journal of Mathematics and Computing, 2024 May vol. 1, no. 1, pp.1-1, 2024.

N. Gohari Sadr, A. Behjati, F. Zare Mirakabad, "RNA-Protein interaction prediction using transformers and asymmetric Siamese neural network", , 2024 Mar vol. 37, no. 1, pp.74-91, 2024.

M.A. Sohrabi, F. Zare Mirakabad, Saeed Shiri Ghidary, M. Saadat, Seyed-ali Sadegh-zadeh, "A novel data augmentation approach for influenza a subtype prediction based on HA proteins", Computers In Biology and Medicine, 2024 Mar vol. 172, no. 172, pp.108316-108316, 2024.

M. Besharatifard, Z. Ghorbanali, F. Zare Mirakabad, "Adverse drug reaction prediction using voting ensemble training approach", Aut Journal of Mathematics and Computing, 2024 Jan vol. 5, no. 1, pp.45-60, 2024.

M. Paykan Heyrati, Z. Ghorbanali, M. Akbari, Ghasem Pishgahi, F. Zare Mirakabad, "BioAct-Het: A Heterogeneous Siamese Neural Network for Bioactivity Prediction Using Novel Bioactivity Representation", Acs Omega, 2023 Nov vol. 47, no. 8, pp.44757-44772, 2023.

Alireza Shariatmadar Taleghani, Yasaman Zohrab Beigi, F. Zare Mirakabad, Ali Masoudi?nejad, "Exploring ceRNA networks for key biomarkers in breast cancer subtypes and immune regulation", Scientific Reports, 2023 Nov vol. 20795, no. 13, pp.1-16, 2023.

Z. Ghorbanali, F. Zare Mirakabad, Najmeh Salehi, M. Akbari, Research Open Access Published: 03 October 2023 Drugrep-hesiagraph: When Heterogenous, "DrugRep-HeSiaGraph: when heterogenous siamese neural network meets knowledge graphs for drug repurposing", Bmc Bioinformatics, 2023 Oct vol. 374, no. 24, pp.1-31, 2023.

F. Soleymani Babadi, Zahra Razaghi Moghadam Kashani, F. Zare Mirakabad, Zoran Nikoloski, "Prediction of metabolite-protein interactions based on integration of machine learning and constraint-based modeling", Bioinformatics Advances, 2023 Jul vol. 3, no. 1, pp.1-13, 2023.

Z. Ghorbanali, F. Zare Mirakabad, M. Akbari, Najmeh Salehi, Ali Masoudi-nejad, "DrugRep-KG: Toward Learning a Unified Latent Space for Drug Repurposing Using Knowledge Graphs", Journal of Chemical Information and Modeling, 2023 Apr vol. 10, no. 21, pp.1-20, 2023.

M. Rastegari, Najmeh Salehi, F. Zare Mirakabad, "Biomarker prediction in autism spectrum disorder using a network-based approach", Bmc Medical Genomics, 2023 Jan vol. 16, no. 12, pp.1-13, 2023.

A. Behjati, F. Zare Mirakabad, Shahriar Arab, Abbass Nowzari Dalini, "Protein sequence profile prediction using ProtAlbert transformer", Computational Biology and Chemistry, 2022 Jun vol. 99, no. 107717, pp.1-13, 2022.

J. Rezaei, F. Zare Mirakabad, Sayed-ali Marashi, S. Mirhassani, "The assessment of essential genes in the stability of PPI networks using critical node detection problem", .Aut Journal of Mathematics and Computing, 2022 Feb vol. 3, no. 1, pp.59-76, 2022.

J. Rezaei, F. Zare Mirakabad, S. Mirhassani, Seyed Amir Marashii, "EIA-CNDP: An exact iterative algorithm for critical node detection problem", Computers and Operations Research, 2020 Nov vol. 127, no. 1, pp.105-138, 2020.

Najmeh Salehi, Bahareh Attaran, F. Zare Mirakabad, Bahareh Ghadiri, Maryam Esmaeli, Mohadeseh Shakaram, Mohammad Tashakoripour, Mahmoud Eshagh Hossini, Marjan Mohammadi, "The outward shift of clarithromycin binding to the ribosome in mutant Helicobacter pylori strains", Helicobacter, 2020 Jul vol. 1, no. 1, pp.1-11, 2020.

N. Banirazi Motlagh, B. Mohammadpoor Esfahani, B. Ashrafi, F. Zare Mirakabad, "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, 2020 Mar vol. 86, no. 0, pp.1-9, 2020.

F. Salari, F. Zare Mirakabad, Mohammad Hossein Alavi, Lea Girard, Mahya Ghafari, Rene De Mot, Hassan Roknizahed, "Draft Genome Sequence of Pseudomonas aeruginosa Strain LMG 1272, an Atypical White Line Reaction Producer", Microbiology Resource Announcements, 2020 Feb vol. 9, no. 7, pp.1-3, 2020.

F.S. Mohseni Salehi Monfared, F. Zare Mirakabad, Mehdi Sadeghi, Soudeh Ghafouri-fard, "A Stochastic Model of DNA Double-Strand Breaks Repair Throughout the Cell Cycle", Bulletin of Mathematical Biology, 2020 Jan vol. 0, no. 0, pp.517-539, 2020.

M. Moridi, Marzyeh Gadiri, Ali Sharifi-zarchi, F. Zare Mirakabad, "The assessment of efficient representation of drug features using deep learning for drug repositioning", Bmc Bioinformatics, 2019 Nov vol. 20, no. 577, pp.1-11, 2019.

F. Salari, F. Zare Mirakabad, Mehdi Sadeghi, "A new hash function and its use in read mapping on genome", .Aut Journal of Mathematics and Computing, 2019 Jul vol. 1, no. 1, pp.1-4, 2019.

F. Zare Mirakabad, N. Banirazi Motlagh, "Transcription Factor Binding Sites Prediction Based on Histone Acetylations using Neural Networks", , 2019 Jun vol. 32, no. 4, pp.527-538, 2019.

F. Salari, F. Zare Mirakabad, Mehdi Sadegi, Hassan Roknizadeh, "Assessing the impact of exact reads on reducing the error rate of read mapping", Bmc Bioinformatics, 2018 Nov vol. 19, no. 19, pp.406-421, 2018.

Ali Jalivand, Behzad Akbari, F. Zare Mirakabad, "S-FLN: A sequence-based hierarchical approach for functional linkage network reconstruction", Journal of Theoretical Biology, 2018 Jan vol. 437, no. 437, pp.149-162, 2018.

F.S. Mohseni Salehi Monfared, F. Zare Mirakabad, Soudeh Ghafouri-fard, Mehdi Sadeghi, "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, 2017 Dec vol. 1, no. 1, pp.1-23, 2017.

F. Zare Mirakabad, N. Banirazi Motlagh, "Transcription Factor Binding Sites Prediction Based on Histone Acetylations using Neural Networks", , 2017 Nov vol. 31, no. 1, pp.1-5, 2017.

Soheila Montaseri, F. Zare Mirakabad, Mohammad Genjtabesh, "Evaluating the quality of SHAPE data simulated by k-mers for RNA structure prediction", Journal of Bioinformatics and Computational Biology, 2017 Oct vol. 15, no. 6, pp.1-17, 2017.

H. Bankikoshki, S. Seyyedsalehi, F. Zare Mirakabad, "Dimensionality Reduction of Binding Site Sequence Data on Human Genome Using a Deep Autoencoder Neural Network", Iranian Journal of Biomedical Engineering, 2017 Sep vol. 11, no. 3, pp.219-230, 2017.

M. Lotfi, F. Zare Mirakabad, Soheila Montaseri, "RNA design using simulated SHAPE data", Genes and Genetic Systems, 2017 Aug vol. 0, no. 0, pp.1-10, 2017.

Soheila Montaseri, Mohammad Ganjtabesh, F. Zare Mirakabad, "Evolutionary Algorithm for RNA Secondary Structure Prediction Based on Simulated SHAPE Data", Plos One, 2016 Nov vol. 11, no. 0, pp.1-13, 2016.

Y. Seyfari, F. Didehvar, Hadi Banaee, F. Zare Mirakabad, "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, 2016 Oct vol. 151, no. 5, pp.1-5, 2016.

M. Mollalo, F. Zare Mirakabad, "Motif Finding in upstream regulatory regions of co-expressed genes using Cuckoo optimization Algorithm and Simulated Annealing", , 2016 Sep vol. 46, no. 3, pp.333-344, 2016.

M. Movahedi, F. Zare Mirakabad, Seyed Shahriar Arab, "Evaluating the accuracy of protein design using native secondary sub-structure", Bmc Bioinformatics, 2016 Sep vol. 17, no. 353, pp.1-11, 2016.

Morteza Kouhsar, F. Zare Mirakabad, Yousef Jamali, "WCOACH: protein -protein complex prediction in weighted PPT networks", Genes and Genetic Systems, 2016 Mar vol. 90, no. 0, pp.317-324, 2016.

M. Lotfi, F. Zare Mirakabad, Soheila Montaseri, "RNA secondary structure prediction based on SHAPE data in helix regions", Journal of Theoretical Biology, 2015 May vol. 380, no. 0, pp.178-182, 2015.

Soheila Montaseri, Nasrollah Mogadam Chakeri, F. Zare Mirakabad, "RNA secondary structure prediction based on genetic algorithm", , 2015 Feb vol. 27, no. 3, pp.428-437, 2015.

Mohammad Ganjtabesh, Soheila Montaseri, F. Zare Mirakabad, "using tempreture effects to predict the interactions between two RNAs", Journal of Theoretical Biology, 2015 Jan vol. 364, no. 364, pp.98-102, 2015.

M. Talebzadeh, F. Zare Mirakabad, "Transcription Factor Binding Sites Prediction Based on Modified Nucleosomes", Plos One, 2014 Feb vol. 2, no. 9, pp.1-10, 2014.

Mohammad Gakjtabesh, F. Zare Mirakabad, Abbss Nowzari, "Inverse RNA folding solution based on multi-objective genetic algorithm and gibbs sampling method", Excli Journal, 2013 Jun vol. 12, no. 0, pp.546-555, 2013.

Hesamedin Torabi Dashti, F. Zare Mirakabad, Nima Aghaeepour, Hayedeh Ahrabian, Abbas Nowzari-dalini, "PreRkTAG: Prediction of RNA Knotted Structures Using Tree Adjoining Grammars", Iranian Journal of Biotechnology, 2013 Jan vol. 11, no. 1, pp.3-13, 2013.

M.R. Rafsanjani Sadeghi, F. Zare Mirakabad, M. Tahmasebi, Mahdi Sadeghi, "EPWM: An Extended Position Weight Matrix for Motif Representation in Biological Sequences", Journal of Basic and Applied Scientific Research, 2012 Jul vol. 2, no. 7, pp.7276-7286, 2012.

Siheila Montaseri, Nasrollah Moghadam, F. Zare Mirakabad, "A heuristic approach to RNA-RNA interaction prediction", Journal of Theoretical Biology, 2012 Jan vol. 300, no. 300, pp.206-211, 2012.

Taught Courses

Course title

Description

Headlines

Date

Fundamental of Bioinformatics

4051

Macromolecules Structure Prediction and Modeling

4051

Cellular and Molecular Biology

4051

Design & Analysis of Algorithms

•آشنایی با روش های طراحی الگوریتم•تحلیل پیچیدگی زمانی و فضایی الگوریتم ها•اثبات درستی الگوریتم ها•آشنایی با مفاهیم NP- کامل و الگوریت�

4042

Protein and Nucleic Acid Sequence Analysis

4042

Advanced Algorithms

Understand systematic techniques for algorithm design• Analyze time and space complexity of algorithms• Prove correctness of algorithms• Become familiar with NP-Completeness and approximation algorithms

4042

Advanced Algorithms

4042

Macromolecules Structure Prediction and Modeling

4041

Introduction to the Theory of Computation

4041

Fundamental of Bioinformatics

4041

Protein and Nucleic Acid Sequence Analysis

4032

Design & Analysis of Algorithms

4032