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.
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