Assistant Data

Mohamad Koohi-Moghadam

*.*****.*@*****.*** (Preferred)

*********@****.****.**.**

*************@*****.**

Address:

ICT Research Institute of ACECR (Academic Center for Education, Culture and Research),

No. 5, Saeedi Avenu, Kalej Intersection, Enghelab Ave., Ferdowsi Sq.,Tehran, Iran.

Phone: +98-911-***-****

Educational Background:

Iran University of Science and Technology (IUST), Tehran, Iran (2009-2011)

M.Sc. Artificial Intelligence

Thesis Title: A New Search Method Based on Evolutionary Algorithms to Identify Suitable

Drug Structure

Supervisor: Dr. A. T. Rahmani

Shahid Bahonar University of Kerman, Kerman, Iran (2004-2009)

B.Sc. Computer Engineering (Software)

Thesis Title: Application of Soft Computing in Bioinformatics

Supervisor: Dr. M. Eftekhari

Objectives and Major Interests:

Computational Biology:

Computer Aided Drug Design

In Silico Biomarker Discovery

Rational Approaches in Drug Delivery

Prediction of Antibiotic Resistance

Personalized Medicine

Achilles Project Data Analysis

Cancer Cell Line Encyclopedia (CCLE) Data Analysis

NCI-60 (Cancer Microarray Project) Data Analysis

Artificial Intelligence:

Graph Mining

Image Processing

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Publication:

M. Koohi-Moghadam, A. T. Rahmani, "Molecular docking with Opposition-based

differential evolution", Proc. ACM Symposium on Applied Computing, Trento, Italy, pp. 1387-

1392, 2012.

M.A. Nikouei Mahani, M. Koohi-Moghadam, H. Nezamabadi-pour, “A Fuzzy Difference

Based Edge Detector,” Iranian Journal of Fuzzy Systems., Vol. 9, No. 6, pp. 69-85, 2012.

Teaching Experience:

Teaching Assistant, “Advanced Programming”, Iran University of Science and Technology.

Fall, 2011.

Teaching Assistant, “Advanced Programming”, Iran University of Science and Technology.

Fall, 2010.

Teaching Assistant, “Introduction to Artificial Intelligence”, Shahid Bahonar University of

Kerman. Fall, 2008.

Teaching Assistant, “Data Structure”, Shahid Bahonar University of Kerman. Fall, 2008.

Teaching Assistant, “Data Structure”, Shahid Bahonar University of Kerman. Fall, 2007.

Job Experience:

“Working in ACECR (Academic Center for Education, Culture and Research)”, Tehran,

Iran, Apr 2011 - NOW.

The Academic Center for Education, Culture and Research (ACECR) is an Iranian public non-

governmental institution that works in different fields of science and technology. I am currently

a member of Advanced Information System group at ICT Research Institute of ACECR. Our

group has three different teams such as bioinformatics, risk and reliability management and

business data mining. I mainly work on rational drug design in this group. I have conducted

some researches about application of computer simulation in drug discovery and biomarker

design. Besides, our team cooperates with Iranian Center for Breast Cancer (ICBC) of ACECR

and Allergy Clinic of ACECR.

“Working in Mobin. Co.”, Tehran, Iran, Feb 2010 – Mar 2011.

This company was responsible to develop the P ersian Search Engine. I mainly worked on

focused web crawler team. In this job position, being familiar with NoSQL database such as

HBase was required. Besides, Hadoop was used for the distributed processing of large data sets

across clusters of computers. I think it was a good experience about work with big data. As

huge amount of data produced every day, Hbase, Hadoop and other NoSQL tools play key role

in today’s bioinformatics data analysis.

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Kerman Robot”, Kerman, Iran, Feb 2007 – 2008.

Working part time in this company, I was a database designer and also a software developer.

This was a small company that developed just simple softwares for small places with maximum

10 users.

Workshop Attending:

“Participate in Two Days Workshop on GPU Programming”, Institute for Research in Fundamental

Sciences (IPM), Tehran, Iran, 2011.

“Participate in Two Days Workshop on Multiple Sequence Alignment and Phylogenetic Tree”,

Institute for Research in Fundamental Sciences (IPM), Tehran, Iran, 2010.

“Participate in Three Days Workshop on Molecular Dynamics with GROMACS”, Research

Center for Sciences and Biotechnology, Tehran, Iran, 2010.

Technical Skills:

Programming Languages Java, C++, QT, CUDA

Programming Tools Eclipse, QT Creator IDE, Intellij Idea,

Visual Studio

Database SQL Server, PostgreSQL, MySQL, HBase

Data Mining Weka, MATLAB

Bioinformatics / AutoDock, Vina, AutoDockTools, Rosetta,

Gromacs, ClustalW2, RNAFold

Chemoinformatics

Linux, Windows

Operating Systems

Word, Excel, PowerPoint

Common Software

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Research and Accomplished Projects:

“Prediction of Cocaine Specific Aptamer with Computer Simulation”, ACECR, Tehran, Iran,

2013.

In this research we tried to predict the best structure of an aptamer-based biomarker to detect

cocaine. Some softwares such as Rosetta and AutoDock have been used to predict the aptamer

structures. Computer simulation not only helps to find the best docking pose between aptamer

and target molecule, but also it is useful in making initial library of SELEX. Using computer

simulation can save a great deal of time and also money.

“In Silico Methods for Biomarker Structure Prediction”, ACECR, Tehran, Iran, 2013.

Researchers use the SELEX method to find the best biomarker structures. This procedure is

very time consuming and in some cases the results are not pleasing. In recent years, the

incorporation of computer simulations into biomarker design projects has been one of the best

ways to optimize biosensors potency. In this research we have investigated about some In Silico

methods and software that are helpful for prediction of new biomarkers.

“Application of Evolutionary Algorithms in Virtual Screening”, ACECR, Tehran, Iran, 2012.

Virtual Screening is the most important stage in discovery of a new drug. In this stage a library

of chemical compounds are selected to hit with ligands. Choosing the best chemical compounds

to enrich the initial library is very critical. In this research, we focused on some evolutionary

algorithms such as Genetic Algorithm (GA) and Differential Evolution (DE) to make the best

initial library.

“Application of GPU Programming in Flexible Docking”, ACECR, Tehran, Iran, 2011.

Computational complexity is the biggest challenge in today’s computational biology. Among

the facilities that have been introduced to speed up the processing time, GPU (Graphics

Processing Unit) is much more interesting. It is a feasibility study about application of GPU in

flexible protein-ligand docking. Computational cost in flexible docking is much more important

than rigid docking.

“Molecular Docking with Opposition-based Differential Evolution”, M.Sc. Thesis, IUST,

Tehran, Iran, 2011.

This is my final thesis in which I have proposed a new algorithm to find the best protein-ligand

complex using Opposition-based Differential Evolution (ODE). Same as other metaheuristic

algorithms, ODE uses a fitness function for evaluating candidate solutions. The evaluation

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function which is used in our study is AutoDock scoring function. Six different protein-ligand

complexes are used to verify the efficiency of ODE. The final results have been published in

the proceedings of the ACM Symposium on Applied Computing (SAC 2012).

“ Prediction of Beta-Lactam Resistance”, IUST, Tehran, Iran, 2011.

In this research, at first we found some proteins that bind to the antibiotic drugs such as

penicillin. About 100 proteins have been extracted from PDB and other protein-ligand

structures database. In continue, we tried to propose a model based on these data to predict the

next mutations of receptor binding site (RBS) a gainst Beta-Lactam. However our final results

are not very good because of lack of data, but I think it was a good research that can be

continued in future.

“NCI-60 (Cancer Microarray Project) Data Analysis”, IUST, Tehran, Iran, 2011.

NCI-60 is a dataset of gene expression profiles of 60 human tumour cell lines. There are a lot of

chemical structures that had been studied as a cancer drug in this project. Each compou nd is

exposed to 60 human tumor cell lines. We tried to find some common substructures among

different compounds. The jCompoundMapper that is an open source Java library for chemical

fingerprints is used in this research.

“Fuzzy Based Edge Detection Algorithm”, IUST, Tehran, Iran 2010.

Image processing is one of my interests besides computational biology. In this research we tried

to find edge of the images with a new fuzzy operation. However, the proposed algorithm is

slower than some others such as Sobel and Canny but its contribution in using a fuzzy

difference operation makes it noticeable. The results of this research have been published in

Iranian Journal of Fuzzy Systems

“Analysis of Gene Expression Data with Soft Computing Algorithms”, Kerman, Iran, 2009.

It was one of my first attempts about biology data analysis. In this research, I tried to analyze

some Gene Expression Data with Weka and Matlab. It was just as a practice to improve my

knowledge about gene expression data. The importance of gene regulatory networks and

protein-protein networks were revealed with doing this research.

“Application of Soft Computing in Bioinformatics”, B.Sc. Thesis, Kerman, Iran, 2008.

This is my B.Sc thesis. In this research, I tried to collect some new issues that were introduced

in bioinformatics and chemoinformatics at that time. Multiple sequence alignment, microarray

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data analysis and ribosome binding sites prediction are some problems that had been

investigated. Besides, the soft computing methods that can be helpful to solve these problems

were proposed. I think it is a good survey in Persian for someone who wants to know about

application of soft computing in boioinformatics.

M.Sc. Courses:

Pattern Recognition

Bioinformatics*

Expert System

Machine Learning

Fuzzy Based Systems

Evolutionary Computing

Distributed Artificial Intelligence

Image Processing

* Institute of Biochemistry and Biophysics (IBB), University of Tehran.

Language Skills:

Persian: Native

English: Fluent

TOEFL Score: 82

Interests:

Persian Poetry

Reading Novels

Being A Critical Thinker!

Reference:

Adel Torkaman Rahamni, Mahdi Eftekhari,

Department of Computer Engineering, Department of Computer Engineering,

Iran University of Science and Technology Shahid Bahonar University of Kerman

Email: rahmani [AT] iust.ac.ir Email: m.eftekhari [AT] uk.ac.ir

Hossein Nezamabadi-pour, Amin Nikanjam,

Department of Electrical Engineering, Department of Computer Engineering,

Shahid Bahonar University of Kerman K. N. Toosi University of Technology

Email: nezam [AT] uk.ac.ir Email : nikanjam [AT] kntu.ac.ir

Mehdi Sadeghi, Mohammad Darzi,

Department of Basic Sciences ICT Research Institute of ACECR,

National Institute of Genetic Engineering Advance Information System Group

and Biotechnology, Email: modarzi [AT] ictrc.ir

Email: sadeghi [AT] nigeb.ac.ir

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