FATEMEH ZARE MIRAKABAD
Assistant Professor
Department of Mathematics and Computer Science
Computer Science
Department of Mathematics and Computer Science
Computer Science
Download PDF فارسی
Content
Pepole
CV
Download PDF فارسی
Email:
f.zare
aut.ac.ir
aut.ac.irPhone:
h-index (Scopus):
6
Citations (Scopus):
152
Supervised MSc Theses
#
Thesis title
By
Date
1
Feature Extraction from Splice Sites for Coding Region Prediction
Arash Kazemi Azarbaijani & Fatemeh Zare Mirakabad
February 2024
2
Masked language modeling for de novo drug design
Seyyed Hassan Alavi & Fatemeh Zare Mirakabad
February 2024
3
Drug target prediction for neurodegenerative disease using PPI network
Reyhane Ebrahimi & Fatemeh Zare Mirakabad
February 2024
4
Prediction of HLA-Peptide interaction Using Neutral Networks
Maryam Nazarloo & Fatemeh Zare Mirakabad
February 2024
5
Prediction of IC50 for drug targets using pharmacokinetics
Mohammad Farahanchi Baradaran & Fatemeh Zare Mirakabad
January 2024
6
Reducing the error rate of read mapping by short-read clustering
Seyedmostafa Meshkati & Fatemeh Zare Mirakabad
September 2023
7
Classifying influenza A subtypes using deep learning
Mohammad Amin Sohrabi & Fatemeh Zare Mirakabad
March 2023
8
Modeling Protein Metabolite Interaction Using Metabolic Networks
Fayaz Soleymani Babadi & Fatemeh Zare Mirakabad
March 2023
9
Predicting antimicrobial resistance in bacteria using bacteria-bacteria and antibiotic-antibiotic similarity
Zahra Seraj & Fatemeh Zare Mirakabad
October 2022
10
Prediction of microRNA-disease associations based on integrating different molecular data
Sohrab Salehi Arashloo & Fatemeh Zare Mirakabad
October 2022
11
Identification of biomarkers for predicting gestational age
Arezou Pakseresht & Fatemeh Zare Mirakabad
October 2022
12
biomarker prediction for Identifying Esophageal Cancer subtypes using Transcriptomics data
Mahdis Habibpour Fatideh & Fatemeh Zare Mirakabad
October 2022
13
Lead Compoundes Prediction using homogeneous Feature Space
Mehdi Paykan Heyrati & Fatemeh Zare Mirakabad
June 2022
14
Adverse drug reaction prediction with integrating multiple data sources
Milad Besharatifard & Fatemeh Zare Mirakabad
September 2021
15
Rna 3D Design
Sara Sadat Nourizadeh & Fatemeh Zare Mirakabad
August 2021
16
Prediction of drug-target binding affinity based on fundamental molecular properties
Mahsa Saadat & Fatemeh Zare Mirakabad
August 2021
17
Inverse protein Folding Using Learning Methods
Amin Rahmani & Fatemeh Zare Mirakabad
April 2021
18
Identifying Effective Biomarkers in Autism Spectrum Disorder
Maryam Rastegari & Fatemeh Zare Mirakabad
March 2021
19
RNA structure prediction using neural network
Parham Hafezi Bafti & Fatemeh Zare Mirakabad
February 2020
20
prediction of protein-protein interaction sites from geometric features
Mahboobrh Sharifian Esfahani & Fatemeh Zare Mirakabad
February 2019
21
Inverse Protein Folding prediction according to polymers in pdb
Arefe Alikhani & Fatemeh Zare Mirakabad
October 2018
22
Tuning the parameters of Hallmarks in Cancer Simulation
Mohammad Javad Sabaghzadeh & Fatemeh Zare Mirakabad
October 2018
23
Transcription Factor Binding Sites Prediction in human Genome Using Deep Neural Network
Hossein Banki-Koshki & Fatemeh Zare Mirakabad
February 2018
24
Constructing gene regulatory networks by using microarray data
Mahya Moshref & Fatemeh Zare Mirakabad
February 2018
25
Phylogenetic tree construction based on clustering
Bita Pourmohsenin & Fatemeh Zare Mirakabad
October 2017
26
pairwise global alignment of protein-protein interaction networks
Zahra Ghorbanali & Fatemeh Zare Mirakabad
October 2016
27
Pairwise alignment of RNA 3D structures using geometric approaches
Soha Salehian Ghamsari & Fatemeh Zare Mirakabad
October 2016
28
Controllability Discovery of Biological Networks
Farbod Farhour & Fatemeh Zare Mirakabad
February 2016
29
Comparing RNA Secondary Structures Based on Image Processing Techniques
Mahdi Farshi Kermani & Fatemeh Zare Mirakabad
February 2016
30
consensus folding prediction of unaligned RNA sequences
Mohamadreza Vahedi & Fatemeh Zare Mirakabad
February 2016
31
a new model for motif representation based on coding theory
Mehri Bakhshian & Fatemeh Zare Mirakabad
October 2015
32
Identifying splice sites in DNA sequences
Saeed Rastegar & Fatemeh Zare Mirakabad
October 2015
33
Reconstruction haplotype from genotype based on parsimony method
Shiva Shakibapour & Fatemeh Zare Mirakabad
October 2014
34
haplotype assembly from genome sequence data
Motahare Farokhnia & Fatemeh Zare Mirakabad
October 2014
35
Inverse RNA folding prediction with SHAPE-directed
Mohadeseh Lotfi & Fatemeh Zare Mirakabad
October 2014
36
Association analysis between epigenetic variation and gene transcription
Mohammad Talebzadeh & Fatemeh Zare Mirakabad
October 2013
37
Structural alignment of RNA molecules with pseudoknots
Abbas Masoumzadeh Tork & Fatemeh Zare Mirakabad
October 2013
38
Reconstructing evolutionary inter relationships of species based on rooted triplets
Alireza Zamany Zeynali & Fatemeh Zare Mirakabad
February 2013
39
Detecting structural variationin genome
Ali Izadi Motlagh & Fatemeh Zare Mirakabad
November 2012
40
Dyad motif finding in biological sequence
Mostafa Poursalehiabbasabadi & Fatemeh Zare Mirakabad
October 2012
Journal Papers
Portal Records
1
Milad Besharatifard, Zahra Ghorbanali, Fatemeh Zare Mirakabad, "Adverse drug reaction prediction using voting ensemble training approach", AUT Journal of Mathematics and Computing, January 2024
Vol. 5,
Num. 1,
Page 45-60,
January 2024,
2
Alireza Shariatmadar Taleghani, Yasaman Zohrab Beigi, Fatemeh Zare Mirakabad, Ali Masoudi?Nejad, "Exploring ceRNA networks for key biomarkers in breast cancer subtypes and immune regulation", Scientific Reports, November 2023
Vol. 20795,
Num. 13,
Page 1-16,
November 2023,
3
Mehdi Paykan Heyrati, Zahra Ghorbanali, Mohammad Akbari, Ghasem Pishgahi, Fatemeh Zare Mirakabad, "BioAct-Het: A Heterogeneous Siamese Neural Network for Bioactivity Prediction Using Novel Bioactivity Representation", ACS Omega, November 2023
Vol. 47,
Num. 8,
Page 44757-44772,
November 2023,
4
Zahra Ghorbanali, Fatemeh Zare Mirakabad, Najmeh Salehi, Mohammad 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, October 2023
Vol. 374,
Num. 24,
Page 1-31,
October 2023,
5
Fayaz Soleymani Babadi, Zahra Razaghi Moghadam Kashani, Fatemeh Zare Mirakabad, Zoran Nikoloski, "Prediction of metabolite–protein interactions based on integration of machine learning and constraint-based modeling", Bioinformatics Advances, July 2023
Vol. 3,
Num. 1,
Page 1-13,
July 2023,
6
Zahra Ghorbanali, Fatemeh Zare Mirakabad, Mohammad 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, April 2023
Vol. 10,
Num. 21,
Page 1-20,
April 2023,
7
Maryam Rastegari, Najmeh Salehi, Fatemeh Zare Mirakabad, "Biomarker prediction in autism spectrum disorder using a network-based approach", BMC MEDICAL GENOMICS, January 2023
Vol. 16,
Num. 12,
Page 1-13,
January 2023,
8
Armin Behjati, Fatemeh Zare Mirakabad, Shahriar Arab, Abbass Nowzari Dalini, "Protein sequence profile prediction using ProtAlbert transformer", COMPUTATIONAL BIOLOGY AND CHEMISTRY, June 2022
Vol. 99,
Num. 107717,
Page 1-13,
June 2022,
9
Javad Rezaei, Fatemeh Zare Mirakabad, Sayed-Ali Marashi, S.Ali Mirhassani, "The assessment of essential genes in the stability of PPI networks using critical node detection problem", AUT Journal of Mathematics and Computing, February 2022
Vol. 3,
Num. 1,
Page 59-76,
February 2022,
10
Javad Rezaei, Fatemeh Zare Mirakabad, S.Ali Mirhassani, Seyed Amir Marashii, "EIA-CNDP: An exact iterative algorithm for critical node detection problem", COMPUTERS & OPERATIONS RESEARCH, November 2020
Vol. 127,
Num. 1,
Page 105-138,
November 2020,
11
Najmeh Salehi, Bahareh Attaran, Fatemeh 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, July 2020
Vol. 1,
Num. 1,
Page 1-11,
July 2020,
12
Nafiseh Banirazi Motlagh, Bahram Mohammadpoor Esfahani, Behnoosh Ashrafi, Fatemeh 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, March 2020
Vol. 86,
Num. 0,
Page 1-9,
March 2020,
13
Farzaneh Salari, Fatemeh Zare Mirakabad, Mohammad Hossein Alavi, Lea Girard, Mahya Ghafari, Hassan Roknizahed, Rene De Mot, "Draft Genome Sequence of Pseudomonas aeruginosa Strain LMG 1272, an Atypical White Line Reaction Producer", MICROBIOLOGY RESOURCE ANNOUNCEMENTS, February 2020
Vol. 9,
Num. 7,
Page 1-3,
February 2020,
14
Fazeleh Sadat Mohseni Salehi Monfared, Fatemeh Zare Mirakabad, Mehdi Sadeghi, Soudeh Ghafouri-Fard, "A Stochastic Model of DNA Double-Strand Breaks Repair Throughout the Cell Cycle", BULLETIN OF MATHEMATICAL BIOLOGY, January 2020
Vol. 0,
Num. 0,
Page 517-539,
January 2020,
15
Mahroo Moridi, Marzyeh Gadiri, Ali Sharifi-Zarchi, Fatemeh Zare Mirakabad, "The assessment of efficient representation
of drug features using deep learning for
drug repositioning", BMC BIOINFORMATICS, November 2019
Vol. 20,
Num. 577,
Page 1-11,
November 2019,
16
Farzaneh Salari, Fatemeh Zare Mirakabad, Mehdi Sadeghi, "A new hash function and its use in read mapping on genome", AUT Journal of Mathematics and Computing, July 2019
Vol. 1,
Num. 1,
Page 1-4,
July 2019,
17
Fatemeh Zare Mirakabad, Nafiseh Banirazi Motlagh, "Transcription Factor Binding Sites Prediction Based on Histone Acetylations using Neural Networks", , June 2019
Vol. 32,
Num. 4,
Page 527-538,
June 2019,
18
Farzaneh Salari, Fatemeh Zare Mirakabad, Mehdi Sadegi, Hassan Roknizadeh, "Assessing the impact of exact reads on reducing the error rate of read mapping", BMC BIOINFORMATICS, November 2018
Vol. 19,
Num. 19,
Page 406-421,
November 2018,
19
َAli Jalivand, Behzad Akbari, Fatemeh Zare Mirakabad, "S-FLN: A sequence-based hierarchical approach for functional linkage network reconstruction", JOURNAL OF THEORETICAL BIOLOGY, January 2018
Vol. 437,
Num. 437,
Page 149-162,
January 2018,
20
Fazeleh Sadat Mohseni Salehi Monfared, Fatemeh 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, December 2017
Vol. 1,
Num. 1,
Page 1-23,
December 2017,
21
Fatemeh Zare Mirakabad, Nafiseh Banirazi Motlagh, "Transcription Factor Binding Sites Prediction Based on Histone Acetylations using Neural Networks", , November 2017
Vol. 31,
Num. 1,
Page 1-5,
November 2017,
22
Soheila Montaseri, Fatemeh Zare Mirakabad, Mohammad Genjtabesh, "Evaluating the quality of SHAPE data simulated
by k-mers for RNA structure prediction", Journal of Bioinformatics and Computational Biology, October 2017
Vol. 15,
Num. 6,
Page 1-17,
October 2017,
23
Hossein Bankikoshki, S.Ali Seyyedsalehi, Fatemeh Zare Mirakabad, "Dimensionality Reduction of Binding Site Sequence Data on Human Genome Using a Deep Autoencoder Neural Network", Iranian Journal of Biomedical Engineering, September 2017
Vol. 11,
Num. 3,
Page 219-230,
September 2017,
24
Mohadeseh Lotfi, Fatemeh Zare Mirakabad, Soheila Montaseri, "RNA design using simulated SHAPE data", GENES & GENETIC SYSTEMS, August 2017
Vol. 0,
Num. 0,
Page 1-10,
August 2017,
25
Soheila Montaseri, Mohammad Ganjtabesh, Fatemeh Zare Mirakabad, "Evolutionary Algorithm for RNA Secondary Structure Prediction Based on Simulated SHAPE Data", PLOS ONE, November 2016
Vol. 11,
Num. 0,
Page 1-13,
November 2016,
26
Yousef Seyfari, Farzad Didehvar, Hadi Banaee, Fatemeh 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, October 2016
Vol. 151,
Num. 5,
Page 1-5,
October 2016,
27
Marziyeh Movahedi, Fatemeh Zare Mirakabad, Seyed Shahriar Arab, "Evaluating the accuracy of protein design using native secondary sub-structure", BMC BIOINFORMATICS, September 2016
Vol. 17,
Num. 353,
Page 1-11,
September 2016,
28
Mehri Mollalo, Fatemeh Zare Mirakabad, "Motif Finding in upstream regulatory regions of co-expressed genes
using Cuckoo optimization Algorithm and Simulated Annealing", , September 2016
Vol. 46,
Num. 3,
Page 333-344,
September 2016,
29
Morteza Kouhsar, Fatemeh Zare Mirakabad, Yousef Jamali, "WCOACH: protein -protein complex prediction in weighted PPT networks", GENES & GENETIC SYSTEMS, March 2016
Vol. 90,
Num. 0,
Page 317-324,
March 2016,
30
Mohadeseh Lotfi, Fatemeh Zare Mirakabad, ُSoheila Montaseri, "RNA secondary structure prediction based on SHAPE data
in helix regions", JOURNAL OF THEORETICAL BIOLOGY, May 2015
Vol. 380,
Num. 0,
Page 178-182,
May 2015,
31
Soheila Montaseri, Nasrollah Mogadam Chakeri, Fatemeh Zare Mirakabad, "RNA secondary structure prediction based on genetic algorithm", , February 2015
Vol. 27,
Num. 3,
Page 428-437,
February 2015,
32
Mohammad Ganjtabesh, Soheila Montaseri, Fatemeh Zare Mirakabad, "using tempreture effects to predict the interactions between two RNAs", JOURNAL OF THEORETICAL BIOLOGY, January 2015
Vol. 364,
Num. 364,
Page 98-102,
January 2015,
33
Mohammad Talebzadeh, Fatemeh Zare Mirakabad, "Transcription Factor Binding Sites Prediction Based on
Modified Nucleosomes", PLOS ONE, February 2014
Vol. 2,
Num. 9,
Page 1-10,
February 2014,
34
Mohammad Gakjtabesh, Fatemeh Zare Mirakabad, Abbss Nowzari, "Inverse RNA folding solution based on multi-objective genetic algorithm and gibbs sampling method", EXCLI JOURNAL, June 2013
Vol. 12,
Num. 0,
Page 546-555,
June 2013,
35
Hesamedin Torabi Dashti, Fatemeh Zare Mirakabad, Nima Aghaeepour, Hayedeh Ahrabian, Abbas Nowzari-Dalini, "PreRkTAG: Prediction of RNA Knotted Structures Using Tree Adjoining Grammars", Iranian Journal of Biotechnology, January 2013
Vol. 11,
Num. 1,
Page 3-13,
January 2013,
36
Mohammad Reza Rafsanjani Sadeghi, Fatemeh Zare Mirakabad, Maryam Tahmasebi, Mahdi Sadeghi, "EPWM: An Extended Position Weight Matrix for Motif Representation in Biological Sequences", Journal of Basic and Applied Scientific Research, July 2012
Vol. 2,
Num. 7,
Page 7276-7286,
July 2012,
37
Siheila Montaseri, Nasrollah Moghadam, Fatemeh Zare Mirakabad, "A heuristic approach to RNA-RNA interaction prediction", JOURNAL OF THEORETICAL BIOLOGY, January 2012
Vol. 300,
Num. 300,
Page 206-211,
January 2012,
Conference Papers
Portal Records
1
Fateme Bagheri, Gholamreza Pazouki, Fatemeh Zare Mirakabad, Mahsa Saadat, Zahra Ghorbanali, "Enhancing Predictive Accuracy of Biomolecules Partition Coefficients in Aqueous Two-Phase Systems Using Machine Learning ", سومین کنفرانس بین المللی و دوازدهمین کنفرانس بیوانفورماتیک ایران, February 2024
2
Mahsa Saadat, Armin Behjati, Fatemeh Zare Mirakabad, Sajjad Gareghani, "Drug-target Binding Affinity Prediction Using Transformers ", The 1th international and 3rd national conference on Bioinformatics, January 2022
3
Amin Rahmani, Fatemeh Zare Mirakabad, "An extension of Wang’s protein design model using Blosum62
substitution matrix ", 52nd annual mathematics conference, August 2021
4
Marziyeh Movahedi, Ali Ramazani, Nagarjun Kondure, Fatemeh Zare Mirakabad, 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), February 2019
5
Fatemeh Zare Mirakabad, Marziyeh Movahedi, Shahriar Arab, Nima Sarang, "protein design using native secondary sub-structures and solvent accessibility ", The 7th Conference on Bioinformatics, 3-5 January 2018, January 2018
6
Hossein Banki-Koshki, S.Ali Seyyedsalehi, Fatemeh Zare Mirakabad, "Transcription factor binding sites identification on human genome using an artificial neural network ", 25th Iranian Conference on Electrical Engineering, May 2017
7
Hossein Banki-Koshki, S.Ali Seyyedsalehi, Fatemeh Zare Mirakabad, "Clustering of Gene Expression Temporal Patterns of Yeast Microarray Data Using Data Mining Methods ", 23rd National & 1st International Iranian Conference on Biomedical Engineering, November 2016
8
Mohadeseh Lotfi, Fatemeh Zare Mirakabad, Alireza Hoshyarmanesh, Soheila Montaseri, "Analyzing SHAPE data on the RNA secondary structure ", The 5th Iranian Conference on Bioinfromatics, May 2014
9
Morteza Kouhsar, Fatemeh Zare Mirakabad, Yousef Jamali, "Protein complex prediction in weighted protein interaction networks using COACH method and semantic similarity ", the fifth Iranian Conference Bioinformatics, May 2014
10
Fatemeh Zare Mirakabad, Farhad Maleki, Mashsa Torkaman, Shiva Shakibapoor, "a new method for haplotype inference based on maximum parsimony ", The fourth Iranian Conference on Bioinformatics, November 2012
11
Ali Izadi, Fatemeh Zare Mirakabad, "Detecting structural variants using genetic algorithm ", The fourth Iranian Conference on Bioinformatics, November 2012
12
Negin Forouzesh, Mohamadreza Kazemi, Ali Mohades Khorasani, Fatemeh Zare Mirakabad, "A new ranking method for protein binding site prediction based on triangulation entropy ", Moscow Conference on Computational Molecular Biology (MCCMB13), July 2012
13
Farhad Maleki, Ali Mohades Khorasani, Fatemeh Zare Mirakabad, Mohammad Ebrahim Shiri Ahmad Abady, 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
14
Mohammad Ganjtabesh, Fatemeh Zare Mirakabad, 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, January 2012
15
Soheila Montaseri, Nasrollah Mogadam, Fatemeh Zare Mirakabad, "A heuristic method for prediction the interation netween tow RNAs ", The 42nd Annual Iranian Mathematics Conference, September 2011
16
Seyed Hadi Banaee, Ali Mohades Khorasani, Fatemeh Zare Mirakabad, "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
1
Theory of Computation
Introduces the foundations of computability theory, and complexity theory. Shows the problems which can not be solved by computer. Defines decidability vs undecidability, and Introduces concepts related to computational complexity of problems.
Spring 2024
2
Protein and Nucleic Acid Sequence Analysis
Biological sequence analysis
Spring 2024
3
Computer Prog.
What is C programing language
Spring 2024
4
Introduction to the Theory of Computation
computational models to cluster problems
Fall 2023
5
Fundamental of Bioinformatics
Introdiction to sovle biological probelms by compuationl methods
Fall 2023
6
Macromolecules Structure Prediction and Modeling
modeling and predicting the structure of macromolecules
Fall 2023
7
Fundamental of Bioinformatics
Introdiction to sovle biological probelms by compuationl methods
Fall 2023