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Alireza Dantism

Hi! I'M Alireza Dantism.

M.Sc. in Bioinformatics from Tarbiat Modares University; Highly experienced and skilled in
structural bioinformatics and building bioinformatics software.

Diligent top-performing student from Tarbiat Modares University with proven problem-solving and communication skills. Honest and hard-working, always willing to learn new skills. with well-balanced hemispheres ready to enjoy creativity and exploration while maintaining a meticulous logic-minded perspective toward bioinformatics and programming, which makes me a good choice for putting out-of-the-box ideas into seemingly methodical problems.
My various projects provide evidence of my computational and perceptual skills, interest in teamwork, hard work, and problem-solving abilities.
As well as this, I have experience teaching programming and bioinformatics topics, and I am very skilled at transferring content in a deep and simple manner.




Education
Oct 2020 - Oct 2022

Master of Science: Bioinformatics

Studied At Tarbiat Modares University - Tehran, Iran

Thesis title: A User-Friendly Web-Based Interface Based on MODELLER

Selected courses: Bioinformatics basics, Cellular and Molecular Biology, Biochemistry, Advanced algorithm, Machine Learning, Modeling and predicting the structure of macromolecules, Systems Biology, Analysis of gene expression data, Drug design, Computational genomics, new topics in bioinformatics.

  • Administrator of computational servers, Structural Bioinformatics Laboratory, Tarbiat Modares University
  • Implement Suffix tree, Smith Water Man, Affine gap penalty, Hirschberg and Needleman–Wunsch algorithm with Python and R in advanced algorithm course
  • Working with some databases for instance RCSB, Omim, Bio Marker, DisProt, UniProt, and ...
  • Implement Naive Bayes, KNN, Decision Tree, and ... with R and Python in machine learning course.
  • Working with MODELLER, Basic modeling, and advanced modeling (multiple templates) for predicting the 3D structure of unknown sequences.
  • Working with AutoDuck Tools, AutoDuck Vina and LigPlus.
  • Molecular dynamics simulation with GROMACS - working on the brucellosis target protein.
  • Working on antibody-specific B cell epitope predictions using machine learning. Study of molecular docking, modeling, investigation, and prevention of brucellosis target protein.

Jan 2018 - Jun 2020

Bachelor of Science: Computer Science

Studied At Shamsipour Technical and Vocational College - Tehran, Iran

Thesis title: Java mobile application for home appliance store with pre-purchase capability

Selected courses: Engineering statistics and probabilities, Mathematical engineering, Discrete mathematics, Machine and assembly language, Design algorithms, System programming, Artificial intelligence.

  • Various projects using C++ and Java

PUBLICATIONS

EasyModel: A User-Friendly Web-Based Interface Based on MODELLER

Author(s):
S. Arab,A. Dantism


PeptiHub: A Curated Repository of Precisely Annotated Cancer-related Peptides with Advanced Utilities for Peptide Exploration and Discovery (Submitted)




SKILLS

Bioinformatics Tools: MODELLER, ClusPro, Haddock, AutoDock, Chimera, Cytoscape, Hyperchem

Programming: R, Python, Matlab, C++, PHP, Perl & Shell Script, Java, Drupal, Html, CSS, JavaScript

GIT (VERSION CONTROL TOOLS): GitHub, GitLab

Operating Systems: Mac, Linux, Windows

Others: LaTeX, SEO, Photoshop, MS Office




ACADEMIC EXPERIENCES

Building a User-Friendly Web-Based Interface Based on MODELLER- EasyModel

Biological data processing: MODELLER

Backend: Python, MySql, PHP

Frontend: HTML, CSS, Bootstrap, Ajax

Designing a cross-reactivity testing tool for diagnostic kit primers

In this study, with having databases of all kinds of genomes, we want to check the available primers and see if there is a complementary relationship with the genomes in the database. As a project, our primer must be specific and if it sticks to another existing gene, cross reactivity will occur and we will check this cross reactivity in silico.
Programming Skills: Python

Detect functional modules of co-expressed genes and networks using WGCNA

Dataset: Human bulk cell RNA-Seq data.

Programming Skills: R

Libraries: Tidyverse, Magrittr, WGCNA, DESeq2, Genefilter

Study of molecular docking, modeling, investigation, and prevention of Brucellosis (2021)

Tarbiat Modares University, Tehran, Iran

PDB Code: 4DLP

Tools: GROMACS, AutoDock Vina

Calculation of cosine similarity between many genes (nucleotide strand) (2021)

Course project at Tarbiat Modares Unviersity

Programming Skills: Matlab

A comparison of the binding affinity of 52𝐸 and 𝐿589 ligands to 5𝑀05 protein (2021)

Course project at Tarbiat Modares University




HONORS

Teacher Assistant of Dr. Seyed Shahriar Arab in courses on the basics of bioinformatics and structural bioinformatics for M.Sc. students.

Tarbiat Modares University, Iran

Teacher Assistant of Dr. Seyed Shahriar Arab in structural bioinformatics course for Ph.D. students.

Tarbiat Modares University, Iran

Full scholarship (tuition waiver) from Tarbiat Modares University, 2020.

Full scholarship (tuition waiver) from Shamsipour Technical and Vocational College, 2017.

Full scholarship (tuition waiver) from Shahid Beheshti Technical and Vocational College, 2015.




RESEARCH INTERESTS

Structures and dynamics of macromolecular assemblies, Homology modelling, Machine learning, R package development, Predicting the three-dimensional structure of macromolecules, Immune system, Gene expression, Algorithm solutions, Programming, Building online bioinformatics tools.




VOLUNTEER ACTIVITIES
2020 - Present

Member of Iranian Bioinformatics Scientific Association

Tarbiat Modares University - Tehran, Iran

2019 - Present

Build a website and support completely free for the Working Children's Charity Association - Ghasedak NGO

Tehran, Iran

2019 - Present
CERTIFICATIONS
Apr 2022 - Python (Digiwise Academy)
Jul 2021 - Preliminary Structural Bioinformatics (Novinzist Informatics)
Aug 2021 - Advanced Structural Bioinformatics (Novinzist Informatics)
Feb 2021 - Digital Marketing Strategy (Digiwise Academy)
Sep 2021 - DevOps Foundation (Digiwise Academy)
May 2021 - Professional Scrum Master I (Digiwise Academy)
Dec 2020 - ITIL4 Foundation (Digiwise Academy)
May 2018 - Android Application Development (Sematec)
May 2018 - Advanced Android (Sematec)
LANGUAGES
English: IELTS on Computer Academic with overall 6.5
English: Duolingo English Test with overall 100
Persian: Native
REFRENCES
Seyed Shahriar Arab - Associate Professor at Tarbiat Modares University, Faculty of Biological Sciences, Department of Bioinformatics.

Parviz Abdolmaleki - Professor at Tarbiat Modares University, Faculty of Biological Sciences, Department of Bioinformatics.