👋 Welcome to My GitHub Pages!

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.

🌱 My Journey

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.

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.

🛠️ Technical Skills

Programming Languages: R, Python, Bash, Git
Data Analysis: Spatial Transcriptomics, Single-cell RNA-seq, Bulk RNA-seq
Machine Learning: Supervised & Unsupervised Techniques, XGBoost
Statistical Analysis: Kruskal-Wallis Test, Mann-Whitney U Test, ANOVA
Bioinformatics Tools: Seurat, CellPhoneDB, CellChat, DESeq2, Monocle3, ssGSEA, GSVA
High-Performance Computing: Slurm for managing compute jobs on HPC clusters

🎓 Education

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

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

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.

Research Assistant

Razavi Hospital, Iran
November 2016 – October 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.

Research Assistant

Iran University
September 2013 – February 2016

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.

Molecular Biologist and Stem Cell Intern

November 2011 – May 2012

Mastered laboratory techniques in molecular biology and stem cell biology, including RT-PCR and cell culture.

🏆 Awards & Achievements

🏅 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

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.

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.

📈 GitHub Stats

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📫 Get in Touch

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