Curriculum vitae.
Dayag Sheykhkarimli, Ph.D.
Vancouver, BCdayag.sheykhkarimli@ubc.caLinkedInGoogle Scholar
Research summary
Molecular and computational biology focused on measuring relationships between proteins and cells. Doctoral research developed and applied sequencing-based assays for proteome-scale interaction mapping across five organisms, including co-first authorship of a reference map of SARS-CoV-2-human contacts. Current work explores molecular recording and how cellular context and history change what a measurement can reveal. Experimental design is paired with reproducible R and Python analysis for high-throughput and single-cell sequencing. A recurring question is how the representation of an experiment shapes what can be learned from its output.
Education
Ph.D., Molecular Genetics — University of Toronto
2022Thesis: “Sequencing protein interaction dynamics at proteome scale.” Advisor: Dr. Frederick P. Roth.
B.Sc., Honours with Distinction — University of Toronto
2014Double major in Molecular Genetics and Human Biology; Minor in Cinema Studies.
Research experience
Postdoctoral Fellow (NRC & NSERC Fellow) — SBME, University of British Columbia
2024 – presentPrincipal Investigator: Dr. Nozomu Yachie
- Developing sequencing-based approaches to measure molecular interactions in cellular context.
- Investigating molecular recording as a way to preserve cellular histories alongside their molecular parts.
- Combining experimental design with reproducible analysis of high-throughput and single-cell data.
Visiting Scientist (MITACS/JSPS Fellow) — Osaka University, Japan
May – Aug 2024Engineered mouse primary neurons and performed in vitro fertilization related surgeries in collaboration with Dr. Y. Lu
Postdoctoral Fellow — Donnelly Centre, University of Toronto
2022 – 2024Principal Investigator: Dr. Frederick P. Roth
Ph.D. student — Department of Molecular Genetics, University of Toronto
2016 – 2022Principal Investigator: Dr. Frederick P. Roth
- Developed and benchmarked fluorescence and messenger BFG-Y2H assays for pooled proteome-scale protein-interaction mapping and minute-scale measurement of interaction dynamics across perturbations.
- Co-first author of the SARS-CoV-2–human contactome; designed high-throughput screening workflows and integrated the virus–host interaction map with tissue-expression and COVID-19 host-genetic data.
- Managed large barcoded ORF collections, automated quality-control workflows, and sequencing analyses across human, yeast, fly, and pathogen interactome projects; coordinated external collaborators and supervised trainees.
Research Assistant — Donnelly Centre, University of Toronto
2013 – 2015Drosophila genetic screen for regulators of sperm development (Dr. Julie Brill); early development of sequencing-based protein-interaction assays (Dr. Frederick P. Roth).
Undergraduate Summer Research Student — University of Toronto, University of Szeged
2012Quantum ab initio simulations to characterize molecular aging of proteins (Dr. Imre G. Csizmadia, Dr. Bela Fiser).
Selected publications
* denotes first or co-first author. A complete, up-to-date list is available on Google Scholar.
Peer-reviewed articles
- Strauss S-K, …, Sheykhkarimli D, …, Pilpel Y. Quantitative genetics of natural S. cerevisiae strains upon mating reveal heritable determinants of fitness and differential mating affinities. Cell Reports 45(2), 116972 (2026).
- Mount H-O, …, Sheykhkarimli D, …, Ensminger AW. A comprehensive two-hybrid analysis to explore the Legionella pneumophila effector–effector interactome. mSystems 9(12), e01004-24 (2024).
- Kim D-K*, …, Sheykhkarimli D*, …, Falter-Braun P. A proteome-scale map of the SARS-CoV-2–human contactome. Nature Biotechnology 41(1), 140–149 (2023).
- Tang H-W, …, Sheykhkarimli D, …, Mohr SE. Next-generation large-scale binary protein interaction network for Drosophila. Nature Communications 14, 2162 (2023).
- van Loggerenberg W, …, Sheykhkarimli D, …, Roth FP. Systematically testing human HMBS missense variants to reveal mechanism and pathogenic variation. The American Journal of Human Genetics 110(10), 1769–1786 (2023).
- Luck K, …, Sheykhkarimli D, …, Vidal M. A reference map of the human binary protein interactome. Nature 580(7803), 402–408 (2020).
- Kim D-K, …, Sheykhkarimli D, …, Roth FP. A comprehensive, flexible collection of SARS-CoV-2 coding regions. G3: Genes, Genomes, Genetics 10(9), 3399–3402 (2020).
- Yachie N, …, Sheykhkarimli D, …, Roth FP. Pooled-matrix protein interaction screens using Barcode Fusion Genetics. Molecular Systems Biology 12(4), 863 (2016).
- Sheykhkarimli D*, …, Fiser B. Molecular ageing: free radical–initiated epimerization of thymopentin — a case study. The Journal of Chemical Physics 140(20), 205102 (2014).
Manuscripts in preparation
Sheykhkarimli D*, ..., Roth, F.P. Environmental protein interaction dynamics at proteome scale. In preparation (2026).
Grants, fellowships & awards
NRC H.L. Holmes Award for Postdoctoral Studies, UBC · CA$200,000
2025 – 2027Awarded biennially to a single postdoctoral fellow nationally.
NSERC Postdoctoral Fellowship, UBC · CA$140,000
2024 – 2026Sony Research Award (with N. Yachie) · US$150,000
2024 – 2025DNA “tapes” for recording the developmental plasticity of the mammalian brain.
MITACS Globalink / JSPS Research Fellowship · CA$12,000
2024NIH R21 Exploratory/Developmental Grant (with F. Roth; top 5th percentile) · US$300,000
2021 – 2023High-temporal-resolution protein-interaction mapping at proteome scale.
Best Talk / Poster Awards (cumulative)
2016 – 2024EMBO; GSA Yeast Genetics (×2); CSHL; Donnelly Centre (×3); Dept. of Molecular Genetics (×2).
Faculty of Medicine Merit Scholarship, University of Toronto · CA$2,000
2015State Program for Study of Distinguished Azerbaijani Youth Abroad · US$180,000
2010 – 2014Technical expertise
- Experimental
- Molecular and protein-interaction assay development; genome-wide screens; barcoded lentiviral and pooled phenotypic assays; CRISPR and combinatorial overexpression screens; mammalian cell engineering; human iPSC and primary mouse neuronal culture; molecular cloning; flow cytometry; immunostaining; confocal microscopy; mouse injection and dissection; Illumina and Oxford Nanopore library preparation and sequencing; 10x Genomics/Drop-seq.
- Computational
- R, Python, bash, Nextflow, Git/version control, Linux/HPC; large-scale sequencing-data analysis; network biology; biostatistics; Cytoscape, GraphPad, and FlowJo.
- Languages
- English (fluent); Azerbaijani (native); Russian (intermediate); Turkish (intermediate).
Selected conference presentations
EMBO Workshop on Protein–Protein Interactions — Trieste, Italy
2022Oral presentation: “Proteome-scale mapping of protein-interaction dynamics across environments.”
Cold Spring Harbor Laboratory — Systems Biology / Network Biology
2022, 2023Poster (2022) and talk (2023): systematic interrogation of protein-interaction networks under stress.
GSA Yeast Genetics Meeting
2019, 2021Poster awards (×2): “Barcode fusion genetics for massively parallel interaction screening.”
Donnelly Centre Research Day — University of Toronto
2018, 2020, 2022Talk / poster awards (×3): high-throughput barcode fusion genetics and interactome dynamics.
Dept. of Molecular Genetics Retreat — University of Toronto
2016 – 2021Best-talk awards (×2): protein-interaction dynamics under environmental perturbation.
Teaching & mentorship
Primary Lab Instructor — BMEG 245, “The Fundamental Units of Life,” University of British Columbia
2024 – presentDesigned and taught labs for ~100 students: mammalian cell culture, nuclear/F-actin staining, and hands-on bioinformatics.
Sessional Lecturer — Dept. of Molecular Genetics, University of Toronto
2019 – 2021MGY360 (Undergraduate, Whole-Genome Sequencing & Analysis) and MMG3006 (Graduate, Medical Genomics), including remote delivery during COVID-19.
Teaching Assistant — Dept. of Molecular Genetics, University of Toronto
2018 – 2021MGY360, MMG3006 and MMG1001 (Foundational Genetic Approaches): designed and marked exam questions, supervised tutorials, literature discussions, and laboratories.
Mentorship
Supervised 14+ trainees (8 undergraduate, 2 MSc, 2 PhD, 2 research staff); currently supervising and co-supervising 3 trainees at UBC.
Entrepreneurship & knowledge translation
Co-Founder — Zenbu Tx
2024 – 2025Yachie-Lab spin-off exploring targeted drug delivery. Patent filed: PCT/CA2023/050239. Finalist, e@UBC Venture Founder Program; 2nd place, Amgen Pitch Competition. Experience in IP strategy, stakeholder engagement, and bench-to-bedside commercialization planning.
Selected media
- “Landscape of molecular contacts: How SARS-CoV-2 communicates with human cells” Phys.org, 2022.
- “H.L. Holmes Award supports tissue-mapping research for targeted drug delivery” National Research Council Canada, 2025.