IcoBi
  • Back

Fatemeh Zare-Mirakabad

Assistant Professor in Amirkabir University of Technology

    Assistant Professor in Department of Mathematics and Computer Science, Amirkabir University of Technology (Polytechnic Tehran)

    Telephone: +98-21-64545674

    Fax: +98-21-66497930

    E-mail address: f.zare@aut.ac.ir

    Education

    Tehran University 2006-2009  Ph.D. in Bioinformatics

    Thesis: Algorithms for Pattern Finding in Biological Sequences

    Sharif University of Technology 2000-2003  M.Sc. in Computer Science

    Thesis: Use of Markov Chains in Solving Counting Problems

    Amirkabir University of Technology 1992-1996  B.Sc. in Applied Mathematics

     

    Research Interests:

    • Bioinformatics
    • Nanotechnology
    • Biotechnology
    • Genetic
    • Artificial intelligence

     

    Educational Experience:

    Courses in Amirkabir University of Technology:

    Bioinformatics, Theory of Computer Science, Data Structures & Algorithms, Introduction to The theory of Computation, Design & Analysis of Algorithms, Topics in Mathematics & Its Applications, Special Topics (Biological Databases), Compiler, Theory of Automata & Languages, C Programming.

    Courses in Sharif University:

    Graph theory, Discrete mathematics.

    Courses in Shahid Beheshti University:

    Discrete mathematics, Design & Analysis of Algorithms, Compiler, Theory of Automata & Languages, Principles of Computer & Programming, Advanced Programming, Theory of Computation.

    Courses in Shahid Rajaee University:

    Principles of Computer & Programming

     

    Seminars and Workshops:

    • Introduction to Concepts of Computer Science and its Applications, Iranian Bioinformatics Society (IBIS).

     

    Speaking in the scientific community:

    • Bioinformatics Conference of Iran,
    • 2nd International and 10th National Biotechnology,
    • Institute for Research in Fundamental Sciences (IPM).

     

    Research projects:

    • RNA-RNA interaction,’ School of Biological Sciences, IPM – Institute for Research in Fundamental Sciences’.
    • Modeling the process of double strand DNA break repair in the cell cycle, School of Biological Sciences, IPM – Institute for Research in Fundamental Sciences.

     

    Awards and honors:

    • 1st rank in Ph.D.
    • Ranked second among AmirKabir University students.
    • Top Student in Bachelor

     

    Recent Papers:

    • Lotfi, M., Zare-Mirakabad, F., and Montaseri, S. (2017) RNA design using simulated SHAPE data. Genes & Genetic Systems, 16-00067.
    • Montaseri, S., Ganjtabesh, M., and Zare-Mirakabad, F. (2016) Evolutionary algorithm for RNA secondary structure prediction based on simulated SHAPE data. PloS one 11, e0166965.
    • Seyfari, Y., Didehvar, F., Banaee, H., and Zare-Mirakabad, F. (2016b) Evaluating the Accuracy of Splice Site Prediction based on Integrating Jensen-Shannon Divergence and a Polynomial Equation of Order 2. Genome 151.
    • MOLLALO, M., and ZARE, M.F. (2016) MOTIF FINDING IN UPSTREAM REGULATORY REGIONS OF CO-EXPRESSED GENES USING CUCKOO OPTIMIZATION ALGORITHM AND SIMULATED ANNEALING.
    • Movahedi, M., Zare-Mirakabad, F., and Arab, S.S. (2016) Evaluating the accuracy of protein design using native secondary sub-structures. BMC bioinformatics 17, 353.
    • Kouhsar, M., Zare-Mirakabad, F., and Jamali, Y. (2015) WCOACH: Protein complex prediction in weighted PPI networks. Genes & genetic systems 90, 317-324.
    • Lotfi, M., Zare-Mirakabad, F., and Montaseri, S. (2015) RNA secondary structure prediction based on SHAPE data in helix regions. Journal of theoretical biology 380, 178-182.
    • Soheila Montaseri , Nasrollah Mogadam Chakeri, FATEMEH ZARE MIRAKABAD (2015) RNA secondary structure prediction based on genetic algorithm. IRANIAN JOURNAL OF BIOLOGY 27, 428 _ 437.
    • Ganjtabesh, M., Montaseri, S., and Zare-Mirakabad, F. (2015) Using temperature effects to predict the interactions between two RNAs. Journal of theoretical biology 364, 98-102.
    • Montaseri, S., Zare-Mirakabad, F., and Moghadam-Charkari, N. (2014) RNA-RNA interaction prediction using genetic algorithm. Algorithms for Molecular Biology 9, 17.
    • Talebzadeh, M., and Zare-Mirakabad, F. (2014) Transcription factor binding sites prediction based on modified nucleosomes. PloS one 9, e89226.
    • Ganjtabesh, M., Zare-Mirakabad, F., and Nowzari-Dalini, A. (2013) Inverse RNA folding solution based on multi-objective genetic algorithm and Gibbs sampling method. EXCLI journal 12, 546.
    • Torabi Dashti, H., Zare-Mirakabad, F., Aghaeepour, N., Ahrabian, H., and Nowzari-Dalini, A. (2013) PreRkTAG: Prediction of RNA Knotted Structures Using Tree Adjoining Grammars. Iranian Journal of Biotechnology 11, 3-13.
    • Sadeghi, M.-R., Zare-Mirakabad, F., Tahmasebi, M., and Sadeghi, M. (2012) EPWM: An Extended Position Weight Matrix for Motif Representation in Biological Sequences.
    • Montaseri, S., Moghadam-Charkari, N., and Zare-Mirakabad, F. (2012) A heuristic approach to RNA–RNA interaction prediction. Journal of theoretical biology 300, 206-211.
    • Zare-Mirakabad, F., Ahrabian, H., Sadeghi, M., Hashemifar, S., Nowzari- Dalini, A., and Goliaei, B. (2009) Genetic algorithm for dyad pattern finding in DNA sequences. Genes & genetic systems 84, 81-93.
    • Ahrabian, H., Nowzari-Dalini, A., and Zare-Mirakabad, F. (2009) A Constant Time Algorithm for DNA Add. International Journal of Foundations of Computer Science 20, 549-558.
    • Zare-Mirakabada, F., Davoodib, P., Ahrabiana, H., Nowzari-Dalinia, A., Sadeghic, M., and Goliaeia, B. (2009) Finding motifs based on suffix tree. Avanced Modeling and Optimization 11.
    • Zare-Mirakabad, F., Sadeghi, M., Ahrabian, H., and Nowzari-Dalini, A. (2009b) RNAComp: A new method for RNA secondary structure alignment. Match 61, 789.
    • Zare-Mirakabad, F., Ahrabian, H., Sadeghi, M., Nowzari-Dalini, A., and Goliaei, B. (2009b) New scoring schema for finding motifs in DNA Sequences. BMC bioinformatics 10, 93.
    • Ahrabian H, Nowzari-Dalini A., Razaghi M, Zare-Mirakabad F (2007) Parallel generation of the biological trees. The Electronic International Journal Advanced Modeling and Optimization 9, 1-14.

     

    Presented Papers in International and National Conferences: 

    • Identification of transcription factors binding sites on the human genome using artificial neural network, 25th Iranian Conference on Electrical Engineering (ICEE 2017).
    • Time pattern clustering for gene expression of yeast microarray data using data mining methods, 23rd Iranian Conference on Biomedical Engineering (ICBME 2016)
    • Predicting protein complexes in protein weighted networks by COACH and Semantic Similarity methods, the 5th Bioinformatics Conference of Iran, 2015.
    • Analyzing SHAPE data on the RNA secondary structure, The 5th Bioinformatics Conference of Iran, 2015.
    • A new method for Haplotype inference based on Maximum parsimony, The 4th Bioinformatics Conference of Iran, 2013.
    • Genome structural variation discovery by Genetic algorithm, The 4th Bioinformatics Conference of Iran, 2013.
    • A ranking method to predict the position of protein binding based on entropy, Moscow Conference on Computational Molecular Biology (MCCMB13).
    • A PSO Inspired Harmony Search Algorithm, Third International Conference on Contemporary Issues in Computer and Information Sciences (CICIS 2012).
    • MSSRNA: Make a sequence for a given RNA secondary structure based on genetic algorithm and Gibbs sampling, International Conference on Operations Research & Optimization, 2011.
    • Predict the RNA-RNA interaction based on a heuristic method, The 42nd Annual Iranian Mathematics Conference, 2011.
    • Gene Expression Similarity with Polygonal Chain Alignment, 2nd International Conference on Contemporary Issues in Computer and Information Sciences (CICIS 2011)

     

    Theses Supervised:

    • Haplotype assembly
    • RNA-RNA interaction prediction
    • Genome assembly
    • Finding Patterns in Protein-Protein Interaction Networks
    • Building gene expression networks using microarrays data
    • Building phylogenetic trees from frequent clustering
    • Finding the Relationship between Drugs and Diseases Using Learning Algorithms
    • Prediction of transplantation sites of transcription factors on the human genome using deep neural network
    • Predict the risk of stroke based on the degree of fatty liver using neural network
    • Protein-protein interaction prediction based on geometric properties
    • Estimating the basic parameters in cancer Simulation
    • Inverse protein folding Based on polymers in PDB
    • Detection of non-sexual mutations in tumor–normal sequencing
    • Detection cancer cells in a blood test using image processing techniques
    • Construction of gene regulatory networks using multiple data sets
    • Genome assembly and read mapping using reference in the next generation technologies
    • Modeling DNA double-strand breaks repair in the cell cycle
    • Identification of genes and gene products necessary in the destruction of biological networks
    • RNA secondary structure prediction based on ant colony
    • A computational approach to drug discovery using data integration approaches
    • Detection of causality from nonlinear dynamics of short-term micro-array time series data
    • Pairwise alignment of RNA 3D structures using geometric methods
    • Global alignment of protein–protein interaction networks
    • Study and modeling gene-gene interactions in the gene network
    • Complex detection in protein networks based on network topology
    • Prediction of consensus folding in a set of unaligned RNA sequences
    • Comparison of RNA structures based on image processing methods
    • Discovering Controllability in Bio Networks
    • Determining the Computational Complexity of Boolean satisfiability problem with the Special condition and its Applications
    • Classification and clustering high dimensional data by resampling approach
    • Determining the type and boundary of structural Variation in human genome by geometric algorithms
    • Presentation of a new model for motif representation based on coding theory
    • Identification of splicing positions in DNA sequences
    • Detection of Single Nucleotide Polymorphism in the genome sequence
    • Identifying the parameters and structure of large-scale systems with intelligent optimization methods
    • Inverse folding predictions of protein structure
    • Object recognition by the mechanism of the brain’s visual system
    • Phylogenetic tree regeneration for a set of haplotypes
    • Finding relation between Regulation of gene expressions and histone acetylation changes
    • Investigating gene dependency based on synergy
    • Modeling the process of Repairing Double-Strand DNA Breaks during the cell cycle
    • RNA inverse structure folding prediction based on SHAPE-Directed
    • Face Recognition with Processing steps in the visual system approach
    • A method for predicting human reaction times to different visual stimulus
    • Haplotype assembly from genotype data based on parsimony method
    • Using DNA computing methods to solve some of the MAP problems
    • Motif finding based on PSO algorithm
    • Multi-strand protein alignment by exploratory algorithms
    • Simulations of cancer tumor growth
    • Structural equilibrium of RNA molecules with pseudocode
    • Motif finding in biological sequences based on Huffman codes
    • Predicting linked sites in proteins by geometric algorithms
    • Analysis of the relation between epigenetic Modifications and gene transcription
    • Evolutionary Modeling of Tumor Growth Using Cellular Automata
    • Reconstruction of evolutionary relation between creations based on Triad rooted
    • Study of gene expressions regions in Arabidobis genome
    • Finding structural variations in the genome
    • Haplotype inference from genotype data
    • Dyad Motif finding in biological sequences
    • Study of finding Motif algorithms in Biological Sequences
    • Gene prediction algorithms
    • Using Biometric Facial Recognition to identify individuals
    • Detection of folding in protein structure by learning models
    • Classification of Gene Expression Data by Geometric Algorithms
    • Study of coding models on biological sequences
    • Reconstruction of the phylogenetic networks of rooted triplets or unrooted quadruplets.

    \