Assistant Professor in Amirkabir University of Technology
Assistant Professor in Amirkabir University of Technology
E-mail address: email@example.com
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
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.
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).
RNA-RNA interaction prediction,
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 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,
پيشگويي تاخوردگي اجماع در يک مجموعه از توالی های RNA غیر متوازن
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 expression 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 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 stimuli,
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 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 expression regions in Arabidobis genome,
Finding structural variations in the genome,
Haplotype assembly from genotype data,
Motif finding based on ant-colony,
Study of Finding Motif algorithms in Biological Sequences,
Gene prediction algorithms,
استفاده از زيست سنج چهره برای تشخيص هويت افراد
Detection of corrosion in protein structure by learning models,
Classification of Gene Expression Data by Geometric Algorithms,
Study of coding models on biological sequences,
بازسازی شبكه های فيلوژنتيكی از مجموعه سه تايی ریشه دار یا چهار تایی بدون ریشه
Papers in International Journals:
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).
“خوشه بندي الگوهاي زماني بيان ژن داده هاي ميکروآرايه مخمّر با استفاده از روشهاي داده کاوی”
بيست و سومين کنفرانس ملي و اولين کنفرانس بين المللي مهندسي زيست پزشکي ايران، 1395
Predicting protein complexes in protein weighted networks by COACH and Semantic Similarity, 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 assembly based on Greedy theory, 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).
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: