From 3b3628aecd2afe86d64efdb3d2b1755363a9fc4b Mon Sep 17 00:00:00 2001 From: Pedram Torabian Date: Thu, 7 Nov 2024 23:51:56 -0700 Subject: [PATCH] Update README.md --- README.md | 131 +++++++++++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 130 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index cb01615..2f93b54 100644 --- a/README.md +++ b/README.md @@ -1 +1,130 @@ -# Pedramto89.github.io \ No newline at end of file +# Pedram Torabian + +![GitHub followers](https://img.shields.io/github/followers/Pedramto89?label=Followers&style=social) +![LinkedIn](https://img.shields.io/badge/LinkedIn-Connect-blue?logo=linkedin&style=for-the-badge) +![Email](https://img.shields.io/badge/Email-pedram.torabian@ucalgary.ca-cyan?logo=gmail&style=for-the-badge) + +📞 **Phone:** (403) 890-9177 +📧 **Email:** [pedram.torabian@ucalgary.ca](mailto:pedram.torabian@ucalgary.ca) +🔗 **LinkedIn:** [linkedin.com/in/pedram-torabian](https://www.linkedin.com/in/pedram-torabian) +🐱 **GitHub:** [Pedramto89](https://github.com/Pedramto89) + +--- + +## 🔍 About Me + +I'm **Pedram Torabian**, a passionate researcher and data scientist specializing 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. + +--- + +## 💼 Work 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. + +--- + +## 🎓 Education + +### **Master of Medical Science** +**University of Calgary** +*July 2020 – October 2024* +**GPA:** 3.7/4.0 + +- **Selected 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 + +- **Selected Courses:** Genetics Engineering, Advanced Topics in Human Genetics, Population Genetics + +--- + +## 🏆 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* + +--- + +## 🛠️ Technical Skills + +- **Programming Languages:** R, Python, Bash, Git +- **Data Analysis:** Spatial Transcriptomics, scRNA-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 + +--- + +## 📂 Projects + +### **Machine Learning Classifier for Spatial Transcriptomics** +- **Description:** Developed a machine learning classifier using R and Python to analyze spatial transcriptomics data, accurately predicting cell identities based on gene expression profiles. +- **Technologies:** R, Python, XGBoost, Seurat + +### **Single-Cell RNA-seq Data Integration** +- **Description:** Analyzed 30 GB of single-cell RNA-seq data using Seurat to identify cell type-specific marker genes and develop a comprehensive marker gene list. +- **Technologies:** Seurat, R, Python + +### **Computational Deconvolution of Bulk RNA-seq Data** +- **Description:** Applied computational deconvolution methods to bulk RNA-seq data from pancreatic cancer samples in TCGA, revealing gene expression dynamics in the tumor microenvironment. +- **Technologies:** R, Python, TCGA data + +--- + +## 📈 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) + +--- + +## 📫 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) or email me at [pedram.torabian@ucalgary.ca](mailto:pedram.torabian@ucalgary.ca). + +---