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# 👋 Welcome to My GitHub Pages!
---
layout: default
title: Home
description: "Pedram Torabian - Bioinformatics & Machine Learning Researcher"
---

# Table of Contents
- [About Me](#about-me)
- [My Journey](#-my-journey)
- [Technical Skills](#️-technical-skills)
- [Education](#-education)
- [Professional Experience](#-professional-experience)
- [Awards & Achievements](#-awards--achievements)
- [Featured Projects](#-featured-projects)
- [GitHub Stats](#-github-stats)
- [Get in Touch](#-get-in-touch)

## 👋 Welcome to My GitHub Pages!

## About Me
### About Me

Hello! I'm **Pedram Torabian**, a passionate researcher and data scientist with a strong background in bioinformatics, genomics, and machine learning. Currently pursuing a **Master of Medical Science** at the **University of Calgary**, I leverage my expertise in R, Python, and high-performance computing to analyze complex biological data. My work focuses on spatial transcriptomics, single-cell RNA sequencing (scRNA-seq), and deploying machine learning techniques to uncover insights in cancer research and other genetic disorders.
Hello! I am **Pedram Torabian**, a passionate researcher and data scientist with a strong background in bioinformatics, genomics, and machine learning. I leverage my expertise in R, Python, bash and high-performance computing to analyze complex biological data. My work focuses on spatial transcriptomics (ST), single-cell RNA sequencing (scRNA-seq), and deploying machine learning techniques to uncover insights in cancer research and other genetic disorders.

## 🌱 My Journey
My scientific journey began as a wet lab researcher, where I earned my **Master of Human Genetics** with expertise in genetic engineering, population genetics, and biostatistics. This foundation in experimental biology proved invaluable as I advanced to the **Medical Science Program-Cancer Biology Specialization** at the **University of Calgary**, where I pioneered research in pancreatic ductal adenocarcinoma (PDAC) tumor microenvironment.

At the **Arnie Charbonneau Cancer Institute**, We were among the first researchers to implement spatial transcriptomics (Nature Method of the Year, 2020) in PDAC studies using Visium 10X Genomics technology. This groundbreaking work required mastery of both experimental techniques and advanced computational methods, including single-cell RNA-seq analysis, bulk RNA-seq, protein-protein interaction mapping, and computational functional assessment through ssGSEA.

From the early days of my academic career, I immersed myself in the fascinating realms of genetics and molecular biology. Earning my **Master of Human Genetics** from Iran University, I delved deep into genetic disorders, population genetics, and advanced topics in human genetics. This foundation paved the way for my pursuit of a **Master of Medical Science** at the **University of Calgary**, where I honed my skills in bioinformatics and applied genomics.
My unique strength lies in bridging wet and dry lab expertise, allowing me to approach biological problems with comprehensive insight. I have successfully applied both supervised and unsupervised machine learning algorithms to analyze complex biological datasets. Through leading multiple experimental and computational projects, I have developed strong leadership skills that complement my technical expertise. This dual perspective - combining hands-on laboratory experience with computational proficiency - enables me to drive innovative solutions in modern biological research.

Throughout my career, I've had the privilege of working with esteemed institutions like the **Arnie Charbonneau Cancer Institute** and the **Alberta Machine Intelligence Institute (Amii)**. At the Cancer Institute, I spearheaded projects that integrated machine learning with spatial transcriptomics and single-cell RNA sequencing data, developing classifiers that predict cell identities with remarkable accuracy. My role at Amii involved creating educational content for AI applications in biology, bridging the gap between complex scientific concepts and accessible learning materials.
## 💻 Skills Overview

![R](https://img.shields.io/badge/R-276DC3?style=for-the-badge&logo=r&logoColor=white)
![Python](https://img.shields.io/badge/Python-14354C?style=for-the-badge&logo=python&logoColor=white)
![Git](https://img.shields.io/badge/Git-F05032?style=for-the-badge&logo=git&logoColor=white)

## 🛠️ Technical Skills

Expand All @@ -21,93 +43,119 @@ Throughout my career, I've had the privilege of working with esteemed institutio
- **Bioinformatics Tools:** Seurat, CellPhoneDB, CellChat, DESeq2, Monocle3, ssGSEA, GSVA
- **High-Performance Computing:** Slurm for managing compute jobs on HPC clusters

## 🎓 Education
## 📅 Professional Timeline

```mermaid
gantt
title Career Path
dateFormat YYYY-MM
section Education
Master of Medical Science :2020-07, 2024-10
Master of Human Genetics :2013-09, 2016-02
section Professional
Amii :2024-04, 2024-06
Cancer Institute :2020-07, 2024-10
Razavi Hospital :2016-11, 2019-10
```

### Master of Medical Science
**University of Calgary**
*July 2020 – October 2024*
**GPA:** 3.7/4.0

- **Key Courses:** Intro Bioinformatics Resources, Advanced Bioinformatics, Tumor Microenvironment Dynamics, Intro Biostat Methods, Applied Genomics, Tumor Immunology and Therapy
## 🎓 Education

### Master of Human Genetics
**Iran University**
*September 2013 – February 2016*
**GPA:** 3.5/4.0
- **Master of Medical Science**
- University of Calgary
- July 2020 – October 2024
- GPA: 3.7/4.0
- **Key Courses:** Intro Bioinformatics Resources, Advanced Bioinformatics, Tumor Microenvironment Dynamics, Intro Biostat Methods, Applied Genomics, Tumor Immunology and Therapy

- **Key Courses:** Genetics Engineering, Advanced Topics in Human Genetics, Population Genetics
- **Master of Human Genetics**
- Iran University
- September 2013 – February 2016
- GPA: 3.5/4.0
- **Key Courses:** Genetics Engineering, Advanced Topics in Human Genetics, Population Genetics

## 💼 Professional Experience

### **Content Development Support - Educational Product**
**Alberta Machine Intelligence Institute (Amii)**
*April 2024 – June 2024*

- Created educational content for the "Using AI in Biology & Life Sciences" MOOC, enhancing the learning experience for students and professionals.

### **Research Assistant**
**Arnie Charbonneau Cancer Institute, University of Calgary**
*July 2020 – Present*
- **Content Development Support - Educational Product**
- Alberta Machine Intelligence Institute (Amii)
- April 2024 – June 2024
- Created educational content for the "Using AI in Biology & Life Sciences" MOOC, enhancing the learning experience for students and professionals.

- **Research Assistant**
- Arnie Charbonneau Cancer Institute, University of Calgary
- July 2020 – Present
- *Responsibilities:*
- Machine Learning Classifier Development
- Statistical Analysis
- Single-Cell Analysis
- Data Integration
- Bulk RNA-seq Deconvolution

- **Research Assistant**
- Razavi Hospital, Iran
- November 2016 – October 2019
- *Responsibilities:*
- Led genetic projects
- Authored comprehensive reviews
- Investigated medical conditions

- **Molecular Biologist and Stem Cell Intern**
- November 2011 – May 2012
- *Responsibilities:*
- Mastered laboratory techniques in molecular biology and stem cell biology

- **Machine Learning Classifier Development:** Developed a comprehensive classifier in R and Python for spatial transcriptomics data analysis, utilizing seven algorithms including XGBoost to accurately predict non-annotated cell identities based on differentially expressed genes.
- **Statistical Analysis:** Conducted analyses using Kruskal-Wallis, Mann-Whitney U, and ANOVA tests.
- **Single-Cell Analysis:** Utilized tools such as CellPhoneDB and CellChat for cell communication studies, DESeq2 for gene expression analysis, Monocle3 for pseudotime analysis, and ssGSEA with GSVA.
- **Data Integration:** Analyzed 30 GB of scRNA-seq data from ten samples using Seurat, identifying cell type-specific marker genes and compiling a comprehensive marker gene list.
- **Bulk RNA-seq Deconvolution:** Applied computational deconvolution methods to bulk RNA-seq data from 180 pancreatic cancer samples in TCGA, uncovering gene expression dynamics related to stromal levels in the tumor microenvironment.
## 🏆 Awards & Achievements

### **Research Assistant**
**Razavi Hospital, Iran**
*November 2016 – October 2019*
- **Griffith University Postgraduate Research Scholarship (GUPRS)**
- Awarded $28,092 AUD – December 2019

- Led a genetic generalized epilepsy project, advancing familial genetic profiling and contributing to key research publications.
- Authored a comprehensive review on genetic and epigenetic aspects of Celiac disease.
- Investigated primary non-Hodgkin's lymphoma in atypical sites, providing insights into extra-lymphatic lymphoma detection and treatment.
- **Top 2% Ranking**
- Among participants in the national master's level entrance exam – September 2013

### **Research Assistant**
**Iran University**
*September 2013 – February 2016*
- **Top 1% Ranking**
- Nationwide in the Iran national entrance exam – September 2008

- Led five research projects on genetic disorders including long-QT syndrome, breast cancer, glioblastoma, and Celiac disease.
- Utilized statistical analysis, proteomics, qPCR, and academic writing to guide strategic direction and execution.
## 📂 Featured Projects

### **Molecular Biologist and Stem Cell Intern**
*November 2011 – May 2012*
<details>
<summary><strong>Machine Learning Classifier for Spatial Transcriptomics</strong></summary>

- Mastered laboratory techniques in molecular biology and stem cell biology, including RT-PCR and cell culture.
- Technologies used: R, Python, XGBoost, Seurat
- Key achievements:
- Developed a robust machine learning classifier in R and Python
- Accurately predicted cell identities based on gene expression profiles
- Integrated Seurat for comprehensive data analysis
</details>

## 🏆 Awards & Achievements
<details>
<summary><strong>Single-Cell RNA-seq Data Integration</strong></summary>

- 🏅 **Griffith University Postgraduate Research Scholarship (GUPRS)**
Awarded $28,092 AUD – *December 2019*

- 🥇 **Top 2% Ranking**
Among participants in the national master's level entrance exam – *September 2013*

- 🥇 **Top 1% Ranking**
Nationwide in the Iran national entrance exam – *September 2008*

## 📂 Featured Projects
- Technologies used: R, Seurat
- Key achievements:
- Led analysis of 30 GB of single-cell RNA-seq data from ten samples
- Identified cell type-specific marker genes
- Created comprehensive marker gene list for diverse cellular populations
</details>

### **Machine Learning Classifier for Spatial Transcriptomics**
Developed a robust machine learning classifier in R and Python to analyze spatial transcriptomics data, accurately predicting cell identities based on gene expression profiles. Utilized algorithms like XGBoost and integrated Seurat for data analysis.
<details>
<summary><strong>Computational Deconvolution of Bulk RNA-seq Data</strong></summary>

### **Single-Cell RNA-seq Data Integration**
Led the analysis of 30 GB of single-cell RNA-seq data from ten samples using Seurat, identifying cell type-specific marker genes and compiling a comprehensive marker gene list for diverse cellular population detection.

### **Computational Deconvolution of Bulk RNA-seq Data**
Applied four computational deconvolution methods to bulk RNA-seq data from pancreatic cancer samples in TCGA, uncovering gene expression variations related to stromal levels in the tumor microenvironment, providing insights into cancer progression.
- Technologies used: R, Deconvolution algorithms
- Key achievements:
- Applied four computational deconvolution methods to TCGA data
- Uncovered gene expression variations related to stromal levels
- Provided insights into cancer progression mechanisms
</details>

## 📈 GitHub Stats

![Pedram's GitHub Stats](https://github-readme-stats.vercel.app/api?username=Pedramto89&show_icons=true&theme=radical)
![Top Langs](https://github-readme-stats.vercel.app/api/top-langs/?username=Pedramto89&layout=compact&theme=radical)

![Visitors](https://visitor-badge.laobi.icu/badge?page_id=Pedramto89.Pedramto89)

## 📫 Get in Touch

I'm always open to discussing innovative research, collaborations, or new opportunities. Feel free to reach out via:

- [🔗 LinkedIn](https://www.linkedin.com/in/pedram-torabian)
- [📧 Email](mailto:pedram.torabian@ucalgary.ca)
- [🐱 GitHub](https://github.com/Pedramto89)

---
- [LinkedIn](https://www.linkedin.com/in/pedram-torabian)
- [Email](mailto:pedram.torabian@ucalgary.ca)
- [GitHub](https://github.com/Pedramto89)

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