dr.zare

Fatemeh Zare-Mirakabad

Assistant Professor

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

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

  • International Computational Biology Workshop of the Amirkabir University of Technology (ICoBi)
  • 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)

Journal Papers

  • Mahsa Saadat, Armin Behjati,Fatemeh Zare Mirakabad, Sajjad Gharaghani, "Drug-Target Binding Affinity Prediction Using Transformers," bioRxiv, 462610, 30 September 2021.
  • Zahra Ghorbanali,Fatemeh Zare Mirakabad, Bahram Mohammadpour, "DRP-VEM: Drug repositioning prediction using voting ensemble," arXiv , 2110.01403, 01 October 2021.
  • Fatemeh Zare Mirakabad, Armin Behjati, Seyed Shahriar Arab, Abbas Nowzari-Dalini, "Protein sequence profile prediction using ProtAlbert transformer," bioRxiv2021.09. 23.461475, 24 September 2021.
  • Javad Rezaei,Fatemeh Zare Mirakabad, Sayed-Amir Marashi, Seyed Ali MirHassani, "The assessment of essential genes in the stability of PPI networks using critical node detection problem," AUT Journal of Mathematics and Computing, 31 August 2021.
  • Javad Rezaei, Fatemeh Zare Mirakabad, Seyed Ali MirHassani, Sayed-Amir Marashi, "EIA-CNDP: An exact iterative algorithm for critical node detection problem," Computers & Operations Research, PP. 105138 V. 127, 01 March 2021.
  • Milad Beshartifard, Zahra Ghorbanali, Fatemeh Zare Mirakabad, "The assessment of similarity vectors of fingerprint and UMLS in adverse drug reaction prediction," bioRxiv, 468509, 01 January 2021.
  • Fatemeh Zare Mirakabad, "TranDTA: Prediction Of Drug Target Binding Affinity Using Transformer Representations," bioRxiv, 462610, 01 January 2021.
  • Najmeh Salehi, Bahareh Attaran, Fatemeh Zare Mirakabad, Bahareh Ghadiri, Maryam Esmaeili, Mohadeseh Shakaram, Mohammad Tashakoripour, Mahmoud Eshagh Hosseini, Marjan Mohammadi, "The outward shift of clarithromycin binding to the ribosome in mutant Helicobacter pylori strains," Helicobacter, PP. e12731, 14 August 2020.
  • Nafiseh Banirazi Motlagh, Bahram Mohammadpour 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, Vol. 86, PP. 107232, 28 February 2020.
  • 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, 16 July 2019 .
  • Farzaneh Salari, Fatemeh Zare Mirakabad, Mohammad Hossein Alavi, Léa Girard, Mahya Ghafari, René De Mot, Hassan Rokni-Zadeh, "Draft Genome Sequence of Pseudomonas aeruginosa Strain LMG 1272, an Atypical White Line Reaction Producer," Microbiology Resource Announcements, Vol. 9, No. 7, 13 February 2020.
  • Fazeleh S Mohseni-Salehi, 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, Vol. 82, No. 1, PP. 1-36, 14 January 2020.
  • Mahroo Moridi, Marzieh Ghadirinia, Ali Sharifi-Zarchi, Fatemeh Zare Mirakabad, "The assessment of efficient representation of drug features using deep learning for drug repositioning," BMC bioinformatics, Vol. 20, No. 1, PP. 577, 14 November 2019.
  • Ali Jalilvand, Behzad Akbari, Fatemeh Zare Mirakabad, Foad Ghaderi, "Disease gene prioritization using network topological analysis from a sequence based human functional linkage network," arXiv preprint arXiv, 15 April 2019.
  • Fazeleh S Mohseni-Salehi, 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, Vol. 35, No. 4, PP. 517–539, 05 December 2018.
  • Farzaneh Salari, Fatemeh Zare Mirakabad, Mehdi Sadeghi, Hassan Rokni-Zadeh, "Assessing the impact of exact reads on reducing the error rate of read mapping," BMC bioinformatics, Vol. 19, PP. 406, 06 November 2018.
  • Ali Jalilvand, Behzad Akbari, Fatemeh Zare Mirakabad, "S-FLN: A sequence-based hierarchical approach for functional linkage network construction," Journal of Theoretical Biology, Vol. 437, PP. 149-162, 21 January 2018.
  • Fazeleh Sadat Mohseni Salehi Monfared, Fatemeh Zare Mirakabad, Soudeh Ghafouri-fard, Mehdi Sadeghi, "The effect of stochasticity on repair of DNA double strand breaks throughoutnon-homologous end joining pathway," Mathematical Medicine And Biology-a Journal Of The Ima, Vol. 1, No. 1, PP. 1 - 23, 05 December 2017.
  • Fatemeh Zare Mirakabad, Nafiseh Banirazi Motlagh, "Transcription Factor Binding Sites Prediction Based on Histone Acetylations using Neural Networks," , Vol. 31, No. 1, PP. 1 - 5, 15 November 2017.
  • Soheila Montaseri, Fatemeh Zare Mirakabad, Mohammad Genjtabesh, "Evaluating the quality of SHAPE data simulatedby k-mers for RNA structure prediction," Journal Of Bioinformatics And Computational Biology, Vol. 15, No. 6, PP. 1 - 17, 25 October 2017.
  • Mohadeseh Lotfi, Fatemeh Zare Mirakabad, Soheila Montaseri, "RNA design using simulated SHAPE data," Genes & Genetic Systems, Vol. 0, No. 0, PP. 1 - 10, 16 August 2017.
  • Soheila Montaseri, Mohammad Ganjtabesh, Fatemeh Zare Mirakabad, "Evolutionary Algorithm for RNA Secondary Structure Prediction Based on Simulated SHAPE Data," Plos One, Vol. 11, No. 0, PP. 1 - 13, 27 November 2016.
  • 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, Vol. 151, No. 5, PP. 1 - 5, 01 October 2016.
  • Mehri Mollalo, Fatemeh Zare Mirakabad, "Motif Finding in upstream regulatory regions of co-expressed genesusing Cuckoo optimization Algorithm and Simulated Annealing," , Vol. 46, No. 3, PP. 333 - 344, 23 September 2016.
  • Marziyeh Movahedi, Fatemeh Zare Mirakabad, Seyed Shahriar Arab, "Evaluating the accuracy of protein design using native secondary sub-structure," Bmc Bioinformatics, Vol. 17, No. 353, PP. 1 - 11, 06 September 2016.
  • Morteza Kouhsar, Fatemeh Zare Mirakabad, Yousef Jamali, "WCOACH: protein -protein complex prediction in weighted PPT networks," Genes & Genetic Systems, Vol. 90, No. 0, PP. 317 - 324, 23 March 2016.
  • Mohadeseh Lotfi, Fatemeh Zare Mirakabad, ?soheila Montaseri, "RNA secondary structure prediction based on SHAPE datain helix regions," Journal Of Theoretical Biology, Vol. 380, No. 0, PP. 178 - 182, 30 May 2015.
  • Soheila Montaseri, Nasrollah Mogadam Chakeri, Fatemeh Zare Mirakabad, "RNA secondary structure prediction based on genetic algorithm," , Vol. 27, No. 3, PP. 428 - 437, 02 February 2015.
  • Mohammad Ganjtabesh, Soheila Montaseri, Fatemeh Zare Mirakabad, "using tempreture effects to predict the interactions between two RNAs," Journal Of Theoretical Biology, Vol. 364, No. 364, PP. 98 - 102, 05 January 2015.
  • Soheila Montaseri, Fatemeh Zare Mirakabad, Nasrollah Moghadam-charkari, "RNA-RNA interaction prediction using genetic algorithm," Algorithms For Molecular Biology, Vol. 9, No. 17, PP. 1 - 7, 22 June 2014.
  • Mohammad Talebzadeh, Fatemeh Zare Mirakabad, "Transcription Factor Binding Sites Prediction Based onModified Nucleosomes," Plos One, Vol. 2, No. 9, PP. 1 - 10, 04 February 2014.
  • Mohammad Gakjtabesh, Fatemeh Zare Mirakabad, Abbss Nowzari, "Inverse RNA folding solution based on multi-objective genetic algorithm and gibbs sampling method," Excli Journal, Vol. 12, No. 0, PP. 546 - 555, 17 June 2013.
  • 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, Vol. 11, No. 1, PP. 3 - 13, 22 January 2013.
  • 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, Vol. 2, No. 7, PP. 7276 - 7286, 26 July 2012.
  • Siheila Montaseri, Nasrollah Moghadam, Fatemeh Zare Mirakabad, "A heuristic approach to RNA-RNA interaction prediction," Journal Of Theoretical Biology, Vol. 300, No. 300, PP. 206 - 211, 30 January 2012.

Conference Papers

  • Hossain 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, Iran (Islamic Republic of), 23 November 2016 - 25 November 2016.
  • Mohadeseh Lotfi, Fatemeh Zare Mirakabad, Alireza Hoshyarmanesh, Soheila Montaseri, "Analyzing SHAPE data on the RNA secondary structure ," The 5th Iranian Conference On Bioinfromatics, Iran (Islamic Republic of), 20 May 2014 - 22 May 2014.
  • 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, Iran (Islamic Republic of), 20 May 2014 - 22 May 2014.
  • Ali Izadi, Fatemeh Zare Mirakabad, "Detecting structural variants using genetic algorithm ," The Fourth Iranian Conference On Bioinformatics, Iran (Islamic Republic of), 06 November 2012 - 07 November 2012.
  • 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, Iran (Islamic Republic of), 06 November 2012 - 07 November 2012.
  • Negin Forouzesh, Mohamadreza Kazemi, Dr. 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), Russian Federation, 23 July 2012 - 27 July 2012.
  • Farhad Maleki, Dr. 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), Iran (Islamic Republic of), 27 May 2012 - 27 May 2012.
  • 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 , Iran (Islamic Republic of), 26 January 2012 - 28 January 2012.
  • Soheila Montaseri, Nasrollah Mogadam, Fatemeh Zare Mirakabad, "A heuristic method for prediction the interation netween tow RNAs," The 42nd Annual Iranian Mathematics Conference, Iran (Islamic Republic of), 05 September 2011 - 08 September 2011.
  • Seyed Hadi Banaee, Dr. 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), Iran (Islamic Republic of), 31 May 2011 - 02 June 2011.

Graduate Students Projects

    MSc Students Projects:


  • Mahya Moshref, Fatemeh Zare Mirakabad, Mohammad Ebrahim Shiri Ahmad Abady, "Constructing gene regulatory networks by using microarray data", MSc, 19 February 2018.
  • Hossain Banki Koshki, S.ali Seyyedsalehi, Fatemeh Zare Mirakabad, "Transcription Factor Binding Sites Prediction in human Genome Using Deep Neural Network", MSc, 14 February 2018.
  • Bita Pourmohsenin, Fatemeh Zare Mirakabad , "Phylogenetic tree construction based on clustering", MSc, 22 October 2017.
  • Mahroo Moridi, Fatemeh Zare Mirakabad , "", MSc, 11 October 2017.
  • Zahra Ghorbanali, Fatemeh Zare Mirakabad , "pairwise global alignment of protein-protein interaction networks", MSc, 23 October 2016.
  • Soha Salehian Ghamsari, Dr. Ali Mohades Khorasani, Fatemeh Zare Mirakabad, "Pairwise alignment of RNA 3D structures using geometric approaches", MSc, 23 October 2016.
  • Mohamadreza Vahedi, Fatemeh Zare Mirakabad, Farzad Didehvar, "consensus folding prediction of unaligned RNA sequences", MSc, 17 February 2016.
  • Mahdi Farshi Kermani, Fatemeh Zare Mirakabad , "Comparing RNA Secondary Structures Based on Image Processing Techniques", MSc, 16 February 2016.
  • Farbod Farhour, Fatemeh Zare Mirakabad, Farzad Didehvar, "Controllability Discovery of Biological Networks", MSc, 10 February 2016.
  • Mehri Bakhshian, Fatemeh Zare Mirakabad , "a new model for motif representation based on coding theory", MSc, 11 October 2015.
  • Saeed Rastegar, Fatemeh Zare Mirakabad, Dr. Ali Mohades Khorasani, "Identifying splice sites in DNA sequences", MSc, 11 October 2015.
  • Mehrdad Karimi, Fatemeh Zare Mirakabad, Mohammad Ebrahim Shiri Ahmad Abady, "", MSc, 04 October 2015.
  • Marziyeh Movahedi, Fatemeh Zare Mirakabad , "", MSc, 01 September 2015.
  • Farnaz Mohammadi, Fatemeh Zare Mirakabad , "", MSc, 16 March 2015.
  • Mohadeseh Lotfi, Fatemeh Zare Mirakabad , "Inverse RNA folding prediction with SHAPE-directed", MSc, 21 October 2014.
  • Majid Changi Ashtiani, Fatemeh Zare Mirakabad , "", MSc, 19 October 2014.
  • Shiva Shakibapour, Fatemeh Zare Mirakabad , "Reconstruction haplotype from genotype based on parsimony method", MSc, 15 October 2014.
  • Motahare Farokhnia, Fatemeh Zare Mirakabad , "haplotype assembly from genome sequence data", MSc, 15 October 2014.
  • Mehri Mollalo, Fatemeh Zare Mirakabad , "", MSc, 20 September 2014.
  • Abbas Masoumzadeh Tork, Fatemeh Zare Mirakabad , "Structural alignment of RNA molecules with pseudoknots", MSc, 22 October 2013.
  • Mohammad Talebzadeh, Fatemeh Zare Mirakabad , "Association analysis between epigenetic variation and gene transcription", MSc, 12 October 2013.
  • Alireza Zamany Zeynali, Fatemeh Zare Mirakabad, Seyyed Naser Hashemi, " Reconstructing evolutionary inter relationships of species based on rooted triplets", MSc, 16 February 2013.
  • Ali Izadi Motlagh, Fatemeh Zare Mirakabad , "Detecting structural variationin genome", MSc, 14 November 2012.
  • Mostafa Poursalehi Abasabadi, Fatemeh Zare Mirakabad , "Dyad motif finding in biological sequence", MSc, 10 October 2012.

Research Interests:

  • Bioinformatics
  • Nanotechnology
  • Biotechnology
  • Genetic
  • Artificial intelligence
  • Algorithm

Research projects:

  • Predict RNA-RNA interaction, School of Biological Sciences, IPM - Institute for Research in Fundamental Sciences.
  • Mathematical modeling of 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