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):

286

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

Drug target prediction for neurodegenerative disease using PPI network

REYHANEH EBRAHIMI

2024 Feb

Feature Extraction from Splice Sites for Coding Region Prediction

ARASH KAZEMI AZARBAIJANI

2024 Feb

Prediction of HLA-Peptide interaction Using Neutral Networks

MARYAM NAZARLOO

2024 Feb

Masked language modeling for de novo drug design

SEYYED HASSAN ALAVI

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

2023 Sep

Classifying influenza A subtypes using deep learning

MOHAMMAD AMIN SOHRABI & SAEED SHIRY GHIDARY

2023 Mar

Modeling Protein Metabolite Interaction Using Metabolic Networks

FAYAZ SOLEYMANI BABADI & Mohammad Akbari

2023 Mar

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

ZAHRA SERAJ & M.HASSAN SHIRALI-SHAHREZA

2022 Oct

Identification of biomarkers for predicting gestational age

AREZOU PAKSERESHT

2022 Oct

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

SOHRAB SALEHI ARASHLOO

2022 Oct

biomarker prediction for Identifying Esophageal Cancer subtypes using Transcriptomics data

MAHDIS HABIBPOUR FATIDEH & MEHDI GHATEE

2022 Oct

Lead Compoundes Prediction using homogeneous Feature Space

MEHDI PAYKAN HEYRATI

2022 Jun

Adverse drug reaction prediction with integrating multiple data sources

MILAD BESHARATIFARD

2021 Sep

Rna 3D Design

SARA SADAT NOURIZADEH

2021 Aug

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

MAHSA SAADAT

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

2020 Feb

prediction of protein-protein interaction sites from geometric features

MAHBOOBRH SHARIFIAN ESFAHANI

2019 Feb

Tuning the parameters of Hallmarks in Cancer Simulation

MOHAMMAD JAVAD SABAGHZADEH

2018 Oct

Inverse Protein Folding prediction according to polymers in pdb

AREFE ALIKHANI

2018 Oct

Constructing gene regulatory networks by using microarray data

MAHYA MOSHREF

2018 Feb

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

HOSSEIN BANKI-KOSHKI & S.ALI SEYYEDSALEHI

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

2016 Oct

consensus folding prediction of unaligned RNA sequences

MOHAMADREZA VAHEDI

2016 Feb

Comparing RNA Secondary Structures Based on Image Processing Techniques

MAHDI FARSHI KERMANI

2016 Feb

Controllability Discovery of Biological Networks

FARBOD FARHOUR

2016 Feb

a new model for motif representation based on coding theory

MEHRI BAKHSHIAN

2015 Oct

Identifying splice sites in DNA sequences

SAEED RASTEGAR

2015 Oct

Inverse RNA folding prediction with SHAPE-directed

MOHADESEH LOTFI

2014 Oct

haplotype assembly from genome sequence data

MOTAHARE FAROKHNIA

2014 Oct

Reconstruction haplotype from genotype based on parsimony method

SHIVA SHAKIBAPOUR

2014 Oct

Structural alignment of RNA molecules with pseudoknots

ABBAS MASOUMZADEH TORK

2013 Oct

Association analysis between epigenetic variation and gene transcription

MOHAMMAD TALEBZADEH

2013 Oct

Reconstructing evolutionary inter relationships of species based on rooted triplets

ALIREZA ZAMANY ZAYNALI

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

2026 May

Predicting sgRNA effect on Cas9 cleavage

MASOUD MAHDAVIFAR

2025 Sep

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

MITRA AHMADI

2025 Sep

Discovering Autism spectrum disorder biomarkers using gene expression data

AMIR ZARGHAMI

2025 Sep

T cell receptor and HLA association prediction using deep learning

SABA ESKANDARI MANJILI

2025 Oct

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

REYHANEH MORTEZAEI

2025 Mar

Journal Papers

Seraj Zahra ، Ghorbanali Zahra ، ZARE MIRAKABAD FATEMEH ، Attaran Bahareh ، Gharaghani Sajjad, "Exploring feature limitations in antimicrobial resistance prediction: machine learning and deep learning in A. baumannii", Scientific Reports, 2026 Jul vol. 1, no. 1, pp.1-40, 2026.

Maryam Mehrabani ، Lakizadeh Amir ، Fotuhi Siahpirani Alireza ، Salimi Mahdieh ، ZARE MIRAKABAD FATEMEH ، Masoudi-Nejad Ali, "SynergyGraph: predicting cell line specific drug combination synergy scores using knowledge graph representation and hypergraph modeling", Scientific Reports, 2025 Dec vol. 16, no. 1, pp.1-14, 2025.

Saadat Mahsa ، ZARE MIRAKABAD FATEMEH ، Besharatifard Milad, "SiaScoreNet: a siamese neural network-based model integrating prediction scores for HLA-peptide interaction prediction", Bioinformatics Advances, 2025 Nov vol. 5, no. , pp.1-13, 2025.

NAZARLOO MARYAM ، SAADAT MAHSA ، ZARE MIRAKABAD FATEMEH, "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 ، Ghorbanali Zahra ، ZARE MIRAKABAD FATEMEH ، 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.

MOHAMMADZADEH SARA ، Ghorbanali Zahra ، ZARE MIRAKABAD FATEMEH, "Prediction of human-virus protein-protein interaction using heterogeneous siamese neural network", , 2025 Jul vol. 16, no. 2, pp.42-57, 2025.

Behnaz Haji Molla Hoseyni ، Hossein Lanjanian ، Yasaman Zohrab Beig ، Mahdieh Salimi ، ZARE MIRAKABAD FATEMEH ، 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.

SAADAT MAHSA ، ZARE MIRAKABAD FATEMEH ، Ali Masoudi-Nejad ، FARAHANCHI BARADARAN MOHAMMAD ، Nazanin Hosseinkhan, "HLAPepBinder: An Ensemble Model for The Prediction Of HLA- Peptide Binding", Iranian Journal of Biotechnology, 2024 Oct vol. 22, no. 4, pp.92-105, 2024.

Ghorbanali Zahra ، ZARE MIRAKABAD FATEMEH ، MOHAMMADPOURESFAHANI BAHRAM, "DRP-VEM: Drug Repositioning Using Voting Ensemble Model", Aut Journal of Mathematics and Computing, 2024 May vol. 1, no. 1, pp.1-1, 2024.

SOHRABI MOHAMMAD AMIN ، ZARE MIRAKABAD FATEMEH ، Saeed Shiri Ghidary ، SAADAT MAHSA ، 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.

GOHARI SADR NIKTA ، BEHJATI ARMIN ، ZARE MIRAKABAD FATEMEH, "RNA-Protein interaction prediction using transformers and asymmetric Siamese neural network", , 2024 Mar vol. 37, no. 1, pp.74-91, 2024.

BESHARATIFARD MILAD ، GHORBANALI ZAHRA ، ZARE MIRAKABAD FATEMEH, "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.

Alireza Shariatmadar Taleghani ، Yasaman Zohrab Beigi ، ZARE MIRAKABAD FATEMEH ، 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.

PAYKAN HEYRATI MEHDI ، GHORBANALI ZAHRA ، Akbari Mohammad ، Ghasem Pishgahi ، ZARE MIRAKABAD FATEMEH, "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.

GHORBANALI ZAHRA ، ZARE MIRAKABAD FATEMEH ، Najmeh Salehi ، Akbari Mohammad ، 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.

SOLEYMANI BABADI FAYAZ ، Zahra Razaghi Moghadam Kashani ، ZARE MIRAKABAD FATEMEH ، 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.

GHORBANALI ZAHRA ، ZARE MIRAKABAD FATEMEH ، Akbari Mohammad ، 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.

RASTEGARI MARYAM ، Najmeh Salehi ، ZARE MIRAKABAD FATEMEH, "Biomarker prediction in autism spectrum disorder using a network-based approach", Bmc Medical Genomics, 2023 Jan vol. 16, no. 12, pp.1-13, 2023.

BEHJATI ARMIN ، ZARE MIRAKABAD FATEMEH ، 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.

REZAEI JAVAD ، ZARE MIRAKABAD FATEMEH ، sayed-Ali Marashi ، MIRHASSANI S.ALI, "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.

REZAEI JAVAD ، ZARE MIRAKABAD FATEMEH ، MIRHASSANI S.ALI ، 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 ، ZARE MIRAKABAD FATEMEH ، 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.

BANIRAZI MOTLAGH NAFISEH ، MOHAMMADPOOR ESFAHANI BAHRAM ، ASHRAFI BEHNOOSH ، ZARE MIRAKABAD FATEMEH, "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.

SALARI FARZANEH ، ZARE MIRAKABAD FATEMEH ، 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.

MOHSENI SALEHI MONFARED FAZELEH SADAT ، ZARE MIRAKABAD FATEMEH ، 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.

MORIDI MAHROO ، Marzyeh Gadiri ، Ali Sharifi-Zarchi ، ZARE MIRAKABAD FATEMEH, "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.

SALARI FARZANEH ، ZARE MIRAKABAD FATEMEH ، 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.

ZARE MIRAKABAD FATEMEH ، BANIRAZI MOTLAGH NAFISEH, "Transcription Factor Binding Sites Prediction Based on Histone Acetylations using Neural Networks", , 2019 Jun vol. 32, no. 4, pp.527-538, 2019.

SALARI FARZANEH ، ZARE MIRAKABAD FATEMEH ، 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 ، ZARE MIRAKABAD FATEMEH, "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.

MOHSENI SALEHI MONFARED FAZELEH SADAT ، ZARE MIRAKABAD FATEMEH ، 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.

ZARE MIRAKABAD FATEMEH ، BANIRAZI MOTLAGH NAFISEH, "Transcription Factor Binding Sites Prediction Based on Histone Acetylations using Neural Networks", , 2017 Nov vol. 31, no. 1, pp.1-5, 2017.

Soheila Montaseri ، ZARE MIRAKABAD FATEMEH ، 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.

BANKIKOSHKI HOSSEIN ، SEYYEDSALEHI S.ALI ، ZARE MIRAKABAD FATEMEH, "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.

LOTFI MOHADESEH ، ZARE MIRAKABAD FATEMEH ، 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 ، ZARE MIRAKABAD FATEMEH, "Evolutionary Algorithm for RNA Secondary Structure Prediction Based on Simulated SHAPE Data", Plos One, 2016 Nov vol. 11, no. 0, pp.1-13, 2016.

SEYFARI YOUSEF ، Didehvar Farzad ، Hadi Banaee ، ZARE MIRAKABAD FATEMEH, "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.

MOVAHEDI MARZIYEH ، ZARE MIRAKABAD FATEMEH ، 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.

MOLLALO MEHRI ، ZARE MIRAKABAD FATEMEH, "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.

Morteza Kouhsar ، ZARE MIRAKABAD FATEMEH ، 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.

LOTFI MOHADESEH ، ZARE MIRAKABAD FATEMEH ، 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 ، ZARE MIRAKABAD FATEMEH, "RNA secondary structure prediction based on genetic algorithm", , 2015 Feb vol. 27, no. 3, pp.428-437, 2015.

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

TALEBZADEH MOHAMMAD ، ZARE MIRAKABAD FATEMEH, "Transcription Factor Binding Sites Prediction Based on Modified Nucleosomes", Plos One, 2014 Feb vol. 2, no. 9, pp.1-10, 2014.

Mohammad Gakjtabesh ، ZARE MIRAKABAD FATEMEH ، 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 ، ZARE MIRAKABAD FATEMEH ، 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.

RAFSANJANI SADEGHI MOHAMMAD REZA ، ZARE MIRAKABAD FATEMEH ، TAHMASEBI MARYAM ، 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 ، ZARE MIRAKABAD FATEMEH, "A heuristic approach to RNA-RNA interaction prediction", Journal of Theoretical Biology, 2012 Jan vol. 300, no. 300, pp.206-211, 2012.

Conference Papers

BESHARATIFARD MILAD ، ZARE MIRAKABAD FATEMEH, "A siamese neural network for predicting snoRNA-disease association,", the 33rd International Conference on Electrical Engineering, May 2025.

AHMADIAN MOGHADAM SOBHAN ، Ghorbanali Zahra ، Hesam Montazeri ، ZARE MIRAKABAD FATEMEH, "Intergrating biological networks and deep learning for microbe-disease prediction,", The 4th International & 13th Iranian Conference on Bioinformatics, Feb 2025.

ALAVI SEYYEDHASSAN ، Ghorbanali Zahra ، ZARE MIRAKABAD FATEMEH, "In-silico drug generation using masked language modeling,", The 4rd International & 13th Iranian Conference on Bioinformatics, Feb 2025.

MAHDAVIFAR MASOUD ، BESHARATIFARD MILAD ، ZARE MIRAKABAD FATEMEH, "Discovering moonlighting proteins with AI and explainabilit,", The 4th International & 13th Iranian Conference on Bioinformatics, Feb 2025.

MAHDAVIFAR MASOUD ، ZARE MIRAKABAD FATEMEH, "Enhancing predictive accuracy of CRISPR-Cas9 on-target efficiency using deep learning and active learning optimization for small datasets,", The 4rd International & 13th Iranian Conference on Bioinformatics, Feb 2025.

EBRAHIMI REYHANEH ، ALAVI SEYYEDHASSAN ، SOLEYMANI BABADI FAYAZ ، ZARE MIRAKABAD FATEMEH, "Targeting protein in neurodegenerative diseases: a computational approch,", The 4rd International & 13th Iranian Conference on Bioinformatics, Feb 2025.

Fateme Mirza-Abolhassani ، AHMADIAN MOGHADAM SOBHAN ، ZARE MIRAKABAD FATEMEH ، Kaveh Kavousi, "Identification of driver genes in glioblastoma based on single-cell gene expression data using integrated pseudotime and phylogenetic analysis,", The 4rd International & 13th Iranian Conference on Bioinformatics, Feb 2025.

Zahra Vahdani ، Farshad Darvishi ، ZARE MIRAKABAD FATEMEH, "Designing guide RNAs considering essential genes for genome editing of yarrowia lipolytica using deep learning in CRISPR system,", The 4rd International & 13th Iranian Conference on Bioinformatics, Feb 2025.

MORTEZAEI REYHANEH ، ZARE MIRAKABAD FATEMEH, "A Siamese neural network for immunotherapy response prediction,", The 3rd International & 12th Iranian Conference on Bioinformatics, Feb 2024.

BAGHERI FATEME ، PAZOUKI GHOLAMREZA ، ZARE MIRAKABAD FATEMEH ، SAADAT MAHSA ، GHORBANALI ZAHRA, "Enhancing Predictive Accuracy of Biomolecules Partition Coefficients in Aqueous Two-Phase Systems Using Machine Learning,", سومین کنفرانس بین المللی و دوازدهمین کنفرانس بیوانفورماتیک ایران, Feb 2024.

SERAJ ZAHRA ، ZARE MIRAKABAD FATEMEH, "Antimicrobial resistance prediction in Acinetobacter baumannii using collaborative matrix factorization,", The 2nd International and 11th National Iranian Conference on Bioinformatics (ICB), Feb 2023.

BESHARATIFARD MILAD ، ZARE MIRAKABAD FATEMEH ، GHORBANALI ZAHRA, "Predicting Adverse Drug Reactions Using Computational Methods: An Analysis of Drug and Adverse Reaction Features and Representations,", The 2nd International and 11th National Iranian Conference on Bioinformatics (ICB), Feb 2023.

SAADAT MAHSA ، ZARE MIRAKABAD FATEMEH ، Nazanin Hosseinkhan, "Improvement of peptide-HLA class I prediction using transformers,", The 2nd International and 11th National Iranian Conference on Bioinformatics (ICB), Feb 2023.

SAADAT MAHSA ، BEHJATI ARMIN ، ZARE MIRAKABAD FATEMEH ، Sajjad Gareghani, "Drug-target Binding Affinity Prediction Using Transformers,", The 1th international and 3rd national conference on Bioinformatics, Jan 2022.

RAHMANI AMIN ، ZARE MIRAKABAD FATEMEH, "An extension of Wang's protein design model using Blosum62 substitution matrix,", 52nd annual mathematics conference, Aug 2021.

MOVAHEDI MARZIYEH ، Ali Ramazani ، Nagarjun Kondure ، ZARE MIRAKABAD FATEMEH ، Shahriar Arab, "Computational Analysis of Nanoparticle Features on Protein Corona Composition in Biological Nanoparticle protein Interaction,", 5th Conference on Knowledge-Based Engineering and Innovation (KBEI-2019), Feb 2019.

ZARE MIRAKABAD FATEMEH ، MOVAHEDI MARZIYEH ، Shahriar Arab ، SARANG NIMA, "protein design using native secondary sub-structures and solvent accessibility,", The 7th Conference on Bioinformatics, 3-5 January 2018, Jan 2018.

BANKI-KOSHKI HOSSEIN ، SEYYEDSALEHI S.ALI ، ZARE MIRAKABAD FATEMEH, "Transcription factor binding sites identification on human genome using an artificial neural network,", 25th Iranian Conference on Electrical Engineering, May 2017.

BANKI-KOSHKI HOSSEIN ، SEYYEDSALEHI S.ALI ، ZARE MIRAKABAD FATEMEH, "Clustering of Gene Expression Temporal Patterns of Yeast Microarray Data Using Data Mining Methods,", 23rd National & 1st International Iranian Conference on Biomedical Engineering, Nov 2016.

Morteza Kouhsar ، ZARE MIRAKABAD FATEMEH ، Yousef Jamali, "Protein complex prediction in weighted protein interaction networks using COACH method and semantic similarity,", the fifth Iranian Conference Bioinformatics, May 2014.

Mohadeseh Lotfi ، ZARE MIRAKABAD FATEMEH ، Alireza hoshyarmanesh ، Soheila Montaseri, "Analyzing SHAPE data on the RNA secondary structure,", The 5th Iranian Conference on Bioinfromatics, May 2014.

Ali Izadi ، ZARE MIRAKABAD FATEMEH, "Detecting structural variants using genetic algorithm,", The fourth Iranian Conference on Bioinformatics, Nov 2012.

ZARE MIRAKABAD FATEMEH ، Farhad Maleki ، Mashsa Torkaman ، Shiva shakibapoor, "a new method for haplotype inference based on maximum parsimony,", The fourth Iranian Conference on Bioinformatics, Nov 2012.

FOROUZESH NEGIN ، KAZEMI MOHAMADREZA ، Mohades Khorasani Ali ، ZARE MIRAKABAD FATEMEH, "A new ranking method for protein binding site prediction based on triangulation entropy,", Moscow Conference on Computational Molecular Biology (MCCMB13), Jul 2012.

MALEKI FARHAD ، Mohades Khorasani Ali ، ZARE MIRAKABAD FATEMEH ، SHIRI AHMAD ABADY MOHAMMAD EBRAHIM ، afsane Bijari, "A PSO Inspired Harmony Search Algorithm,", CICIS'12, IASBS, Zanjan, Iran Third International Conference on Contemporary Issues in Computer and Information Sciences (CICIS 2012), May 2012.

Mohammad GanjTabesh ، ZARE MIRAKABAD FATEMEH ، Hayedeh Ahrabian ، Abbass Nowzari, "MSSRNA: Make a sequence for a given RNA secondary strucutre based on genetic algorithm and gibbs sampling,", International Conference on Operations Research & Optimization, Jan 2012.

Soheila Montaseri ، Nasrollah Mogadam ، ZARE MIRAKABAD FATEMEH, "A heuristic method for prediction the interation netween tow RNAs,", The 42nd Annual Iranian Mathematics Conference, Sep 2011.

BANAEE SEYED HADI ، Mohades Khorasani Ali ، ZARE MIRAKABAD FATEMEH, "Gene Expression Similarity with Polygonal Chain Alignment,", 2nd International Conference on Contemporary Issues in Computer and Information Sciences (CICIS 2011), May 2011.

Taught Courses

Course title

Description

Headlines

Date

Cellular and Molecular Biology

4051

Introduction to the Theory of Computation

4051

Computer Workshop

4051

Computer Workshop

4051

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

Protein and Nucleic Acid Sequence Analysis

4042

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

Macromolecules Structure Prediction and Modeling

4041

Introduction to the Theory of Computation

4041

Fundamental of Bioinformatics

4041

Design & Analysis of Algorithms

4032

Protein and Nucleic Acid Sequence Analysis

4032