Delaram Pouyabahar

Education

• Ph.D. in Computational Biology, University of Toronto, 2019–2025
• B.Sc. in Cell & Molecular Biology, University of Tehran, 2014–2018
• Diploma in Life Sciences, Farzanegan 2 (NODET), Tehran, 2010–2014

Academic Research Experience

Postdoctoral Researcher

University of Toronto, Terrence Donnelly Centre for Cellular and Biomolecular Research | May 2025 – Present
Supervisor: Dr. Aleksandrina Goeva

• Developing a machine learning method to identify spatially localized disease-associated cell states across multi-sample spatial transcriptomics datasets.

Graduate Student Researcher

University of Toronto, Terrence Donnelly Centre for Cellular and Biomolecular Research | Jan 2020 – April 2025
Supervisor: Dr. Gary Bader

• Developed computational frameworks to extract interpretable biological and technical signals from multi-sample single-cell datasets using statistical and machine learning approaches.
• Designed a scalable linear mixed-effects model for group-based differential expression analysis in large-scale single-cell RNA-seq studies.
• Built the first multi-strain single-cell atlas of the rat liver and performed inter-strain comparisons in a rat liver transplant model in collaboration with the MacParland Lab.

Research Assistant (Bioinformatics)

Sharif University of Technology, Tehran, Iran | July 2018 – August 2019
Supervisor: Dr. Ali Sharifi-Zarchi

• Investigated the genomic principles of small RNA sorting into exosomes using machine learning and deep learning approaches (in collaboration with the Goodarzi Lab, UCSF).
• Analyzed ctDNA samples from breast cancer patients using variant calling pipelines to identify driver mutations and druggable targets.
• Explored the statistical characteristics of ctDNA data to guide simulation tool development.

Visiting Research Intern (Structural Biology)

EMBL, Heidelberg, Germany | June 2017 – September 2017
Supervisor: Dr. Janosch Hennig

• Investigated TRIM25 protein structure using NMR spectroscopy and X-ray crystallography.
• Conducted protein expression and purification to support structure analysis.

Undergraduate Research Assistant (Systems Biology)

University of Tehran | March 2017 – July 2018
Supervisor: Dr. Sayed Amir Marashi

• Explored the relationship between metabolic gene co-expression and flux correlation in E. coli using microarray data and metabolic network sampling.

Industrial Research Experience

Part-Time Research Scientist (Computational R&D)

Biossil Inc., Toronto, ON | February 2024 – May 2024
Supervisor: Dr. Alexander Mosa

• Applied machine learning techniques to analyze omics and biomedical text data for drug repurposing initiatives.

Part-Time Research Intern (Bioinformatics R&D)

Pardis Gene Technology Co., Tehran, Iran | December 2018 – June 2019
Supervisor: Dr. Ali Sharifi-Zarchi

• Analyzed donor-derived cell-free DNA (cfDNA) from solid organ transplant patients to monitor graft health and enable earlier detection of acute rejection episodes.
• Designed an individual identification SNP panel for the Iranian population based on the Iranome database.

Publications

• Xu, C.J.*, Pouyabahar, D.*, et al. (2025) FLASH-MM: Fast and scalable single-cell differential expression using mixed effect models. https://doi.org/10.1101/2025.04.08.647860
• Pouyabahar, D., Andrews, T. & Bader, G.D. (2025). Interpretable single-cell factor decomposition using sciRED. Nature Communications, 16, 1878.
• 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.A., Pouyabahar, D., et al. (2024). Single-cell transcriptome analysis reveals CD34 as a marker of human sinoatrial node pacemaker cardiomyocytes. Nature Communications, 15, 10206.
• 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.

Oral Presentations

• Advanced computational methods for single-cell transcriptomics. Guest Lecturer | Advanced Omics Methods - MMG1328H | Graduate Course - UofT | April 2025
• 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 | University Health Network | Oct 2022
• Guidelines for annotating single-cell transcriptomic maps using automated and manual methods. 10x Genomics Webinar | Dec 2021 | co-presented with Tallulah Andrews and Zoe Clarke

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 and Funding

• Eric and Wendy Schmidt Postdoctoral Fellowship, Broad Institute of MIT and Harvard - 2025
• Doctoral Student Fellowship, Data Science Institute, University of Toronto - 2022–2025
• SGS Summer Conference Grant, University of Toronto - ISMB Conference, 2024
• SGS Winter Conference Grant, University of Toronto - Keystone Conference, 2024
• Jennifer Dorrington Graduate Research Award, Donnelly Centre, University of Toronto - 2024
• SGS Spring Conference Grant, University of Toronto - GLBIO Conference, 2022
• Cecil Yip Doctoral Research Award, Donnelly Centre, University of Toronto - 2020
• Delta Kappa Gamma World Fellowship Finalist (Top 10 among all UofT female international students) - 2022
• Ranked 1st, Biological Sciences (~100 students), University of Tehran - 2014–2018
• Direct Entrance Award for Graduate Education, University of Tehran - 2018
• Fully Funded Summer Internship, European Molecular Biology Laboratory (EMBL) - 2017

Teaching Experience and Course Development

Course Instructor

• Data Science Bootcamp Session for SUDS | Intro 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

• Pathway and Network Analysis | Canadian Bioinformatics workshops | Nov 2024
• Genomic Methodologies (MMG3003Y) | University of Toronto | Winter - Summer 2024
• Genomics (MMG1001) | Head TA | University of Toronto | Fall 2021, 2022, 2023
• Single Cell RNA-seq Analysis | Canadian Bioinformatics workshops | July 2023, June 2024
• Programming for Biologists (MMG1004) | University of Toronto | Spring 2021, 2022, 2023
• Foundations of Data Science | Data Science Institute - UofT | Summer 2022, Winter 2023
• Introduction to Computer Programming (CSC108) | University of Toronto | Winter 2022, Fall 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 & Service

• Review Service: Scientific Reports (2025), LMRL Workshop, ICLR 2025, Biology Direct (2025), Pacific Symposium on Biocomputing (PSB) (2024), Nature Biotechnology (Co-review, 2024)
• Undergraduate Bioinformatics Project Mentor | BCB330Y1 Supervisor | 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 | 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
• Rotation student Mentorship | Molecular Genetics department rotation program | 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