Your Resume Title

Education

Direct Ph.D. in Computational Biology | 2019 – Present

Department of Molecular Genetics, University of Toronto, ON, Canada

Bachelor of Science in Cell and Molecular Biology| 2014 - 2018

University of Tehran, Tehran, Iran

Diploma in Life Sciences Discipline | 2010 – 2014

Farzanegan 2 High School, Tehran, Iran (NODET - National Organization for Development of Exceptional Talents)

Research Experience

Academic Research Experience

University of Toronto | Jan 2020 – Present

Terrence Donnelly Centre - Supervisor: Dr. Gary Bader

Using statistical and machine learning approaches, developed a computational framework to identify interpretable signals in multifactorial single-cell maps.
Developing a scalable linear mixed effect model for single-cell transcriptomics group-based differential expression.
Constructed the first multi-strain single-cell atlas of the rat liver along with performing inter-strain comparison in rat liver transplant model (Collaboration with MacParland Lab)

Sharif University of Technology | July 2018 – Aug 2019

Bioinformatics Research Group - Supervisor: Dr. Ali Sharifi-Zarchi

Investigating the genomic principles of small RNA sorting into exosomes using machine learning and deep learning methods (Collaboration with Goodarzi Lab, University of California, San Francisco)
Analyzing ctDNA samples of breast cancer patients by Variant Calling methods to detect the driver genes and investigate druggable mutations
Investigating the statistical properties of ctDNA data for designing a ctDNA read Simulator

EMBL Heidelberg | June 2017 - Sep 2017

Structural and Computational Biology Unit - Supervisor: Dr. Janosch Hennig

Investigating 3D structure of TRIM25 protein by employing integrated structural biology techniques (NMR, X-ray crystallography) along with wet lab procedures for protein expression

University of Tehran | Mar 2017 - July 2018

Biotechnology Department - Supervisor: Dr. Sayed Amir Marashi

Investigating the relation between E. coli metabolic gene co-expression and metabolic flux correlation using microarray gene expression data and E. coli’s metabolic network model sampling results

Industrial Research Experience

Biossil Co. | Feb 2024 – May 2024 | Part-time

Computational R&D group

Employing machine learning methods to analyze omics and text-based data for drug repurposing

Pardis Gene Technology Co. | Dec 2018 - June 2019 | Part-time

Bioinformatics R&D Group

Analyzed donor-derived cfDNA data of solid organ transplant patients for monitoring of graft status and earlier detection of acute rejection episodes
Designed an individual identification SNP panel for the Iranian population based on the Iranome database

Publications

Pouyabahar, D.*, Xu, C.J.*, et al. (2024). Fast and scalable single-cell differential expression using mixed effect models. Manuscript In preparation.
Pouyabahar, D., et al. (2024). Interpretable single-cell factor decomposition using sciRED. In Review [BIORXIV/2024/605536].
Pouyabahar, D.*, Chung, S.W.* et al. (2023). A rat liver cell atlas reveals intrahepatic myeloid heterogeneity. iScience, 26(11), 108213.
Zirak, B.*,…, Pouyabahar, D.*, et al. (2024). Revealing the grammar of small RNA secretion using interpretable machine learning. Cell Genomics, 4(4).
Clarke, Z.A.*, …, Pouyabahar, D.*, et al. (2021). Tutorial: guidelines for annotating single-cell transcriptomic maps using automated and manual methods. Nature Protocols, 16(6), 2749-2764.
Lim, A., Pouyabahar, D., et al. (2023). Single-cell transcriptome analysis reveals CD34 as a novel marker of human sinoatrial node pacemaker cardiomyocytes. In revision at Nature Communications.
McEvoy, C.M., et al. (2022). Single-cell profiling of healthy human kidney reveals features of sex-based transcriptional programs and tissue-specific immunity. Nature Communications, 13(1), 7634.
Kozlowski, H.N., et al. (2023). Genotyping SARS-CoV-2 Variants Using Ratiometric Nucleic Acid Barcode Panels. Analytical Chemistry, 95(14), 5877-5885.

Presentations

Oral Presentations

Interpretable single-cell factor decomposition using sciRED.
ISMB Conference | RegSys Track Flash Talk | July 2024
Modeling sources of variation in single-cell transcriptomic maps.
Donnelly Centre Postdoctoral Talks | June 2024
High dimensional analysis in single-cell transcriptomics: Thinking beyond tradition.
PANORAMICS - Donnelly Centre | July 2023
Single-cell profiling reveals strain-specific differences in rat intrahepatic macrophage inflammatory potential.
Sheila Sherlock Research Day | Oct 2022
Guidelines for annotating single-cell transcriptomic maps using automated and manual methods.
10x Genomics Webinar | co-presented with Tallulah Andrews and Zoe Clarke | Dec 2021

Poster Presentations

ISMB Conference | July 2024
CCBR retreat | June 2022, June 2023, June 2024
5th Annual PRiME Symposium | Feb 2024
Keystone Symposium | Single-Cell Biology: Genomics, Technologies, and Disease | Jan 2024
Medicine by Design’s Annual Symposium | Dec 2020, Dec 2021, Dec 2023
Data Science Research Day | Data Science Institute | Sep 2023
GLBIO Conference | May 2023
Molecular Genetics retreat | University of Toronto | Sep 2022
ISMB Conference | Virtual | July 2022
Canadian Liver Meeting | Virtual | May 2021, May 2022

Honors & Awards

Awarded Doctoral Student Fellowship | Data Science Institute - UofT | $25,000/year | 2022 - 2025
Awarded SGS Conference Grant | University of Toronto | Keystone conference | 2024
Awarded Jennifer Dorrington Graduate Research Award | Donnelly Centre - UofT | 2024
Awarded SGS Conference Grant | University of Toronto | GLBIO conference | 2022
Awarded Cecil Yip Doctoral Research Award | Donnelly Centre - UofT | 2020
Finalist for Delta Kappa Gamma World Fellowships (top 10 among all UofT female international students) | 2022
Ranked 1st among all Biological Science students (~100 students) | University of Tehran | 2014-2018
Awarded Direct entrance award for Graduate Education | University of Tehran | 2018
Accepted at EMBL fully funded summer internship program | EMBL | 2017

Teaching Experience & Course Development

Course Instructor

Data Science Bootcamp Session for SUDS (Summer Undergraduate Data Science Research)

Introduction to Unix Shell, Git, and GitHub | Data Science Institute - UofT | May 2024, April 2023

Data Science & Machine Learning Certificates

Introduction to Data Science | Data Science Institute - UofT | Nov 2023

Analysis using R workshop | Canadian Bioinformatics Workshops

Dimensionality reduction | June 2023

Teaching Assistance

Genomic Methodologies (MMG3003Y) | University of Toronto | Winter - Summer 2024
Genomics (MMG1001) | Head TA | University of Toronto | Fall 2023, 2022, 2021
Single Cell RNA-seq Analysis | Canadian Bioinformatics Workshops | July 2023, June 2024
Programming for Biologists (MMG1004) | University of Toronto | Spring 2023, 2022, 2021
Foundations of Data Science | Data Science Institute - UofT | Winter 2023, Summer 2022
Introduction to Computer Programming (CSC108) | University of Toronto | Fall 2022, Winter 2022
eCampus Ontario Introductory Coding for Genomics | University of Toronto | Fall 2021 - Winter 2022

Curricular review and assessment of course content

Biochemistry | University of Tehran | Fall 2017
Structural Biochemistry | University of Tehran | Fall 2016

Mentorship & Extracurricular Activities

Undergraduate Bioinformatics Project Mentor | BCB330Y1 Mentor

Exploring Genetic Basis of Transcriptomic Variation in Rat Liver Transplant Models | Sep 2023 - May 2024

Research Exploration Opportunity Program by STEM Fellowship

Graduate mentor | STEM Fellowship charity | March 2022 and March 2021

GLSE February Shadowing Program

Graduate mentor | Temerty Faculty of Medicine – U of T | Feb 2022

Rotation student Mentorship | Molecular Genetics department rotation program

Factor decomposition of an immune scRNA-seq dataset | Sep 2022
SNV identification based on human liver scRNA-seq atlas | Sep 2023

Molecular Genetics Department’s Steward

CUPE 3902 Unit 1 | University of Toronto | Dec 2021 – Jan 2023

Bahar Charity Student Club

Child sponsorship program | University of Toronto | Winter 2020 – Winter 2022