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

Eric and Wendy Schmidt Postdoctoral Fellow

Broad Institute of MIT and Harvard, Schmidt Center | Feb 2026 – Present

Development and application of machine learning models for protein sequence analysis to study immunological mechanisms and predict viral evolution.

Postdoctoral Researcher

University of Toronto, Terrence Donnelly Centre for Cellular and Biomolecular Research | May 2025 – Jan 2026
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

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

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. (2026) FLASH-MM: fast and scalable single-cell differential expression analysis using linear mixed-effects models. Nature Communications. https://doi.org/10.1038/s41467-026-69063-2
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

Modeling sources of variation to interpret single-cell transcriptomic maps. ISCB regional group - Iran | Invited speaker | Nov 2025
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: LMRL Workshop, ICLR 2026, BMC Bioinformatics (2025), Scientific Reports (2025), LMRL Workshop, ICLR 2025, Biology Direct (2025), Pacific Symposium on Biocomputing (PSB) (2024), Nature Biotechnology (Co-review, 2024)
Undergraduate Research Mentor | University of Toronto | Benchmarking case–control differential cell–cell interaction inference methods in single-cell transcriptomics datasets | Jun 2025 – Present
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

Delaram Pouyabahar

Education

Academic Research Experience

Eric and Wendy Schmidt Postdoctoral Fellow

Broad Institute of MIT and Harvard, Schmidt Center | Feb 2026 – Present

Postdoctoral Researcher

University of Toronto, Terrence Donnelly Centre for Cellular and Biomolecular Research | May 2025 – Jan 2026Supervisor: Dr. Aleksandrina Goeva

Graduate Student Researcher

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

Research Assistant (Bioinformatics)

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

Visiting Research Intern (Structural Biology)

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

Undergraduate Research Assistant (Systems Biology)

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

Industrial Research Experience

Part-Time Research Scientist (Computational R&D)

Biossil Inc., Toronto, ON | February 2024 – May 2024

Part-Time Research Intern (Bioinformatics R&D)

Pardis Gene Technology Co., Tehran, Iran | December 2018 – June 2019

Publications

Oral Presentations

Poster Presentations

Honors and Funding

Teaching Experience and Course Development

Course Instructor

Teaching Assistance

Mentorship & Service

University of Toronto, Terrence Donnelly Centre for Cellular and Biomolecular Research | May 2025 – Jan 2026
Supervisor: Dr. Aleksandrina Goeva

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

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

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

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