Hamed Najafabadi

Hamed Najafabadi

Assistant Professor, Department of Human Genetics

Email: hamed.najafabadi@mcgill.ca
Phone: (514) 398-5308

740 Dr Penfield Ave, Room 7202
Montréal, Québec, Canada, H3A 0G1

Website

Dr. Najafabadi is an Assistant Professor in Department of Human Genetics, and Principal Investigator of the Computational and Statistical Genomics lab at McGill Genome Center. After obtaining his Master’s degree from University of Tehran, he did his PhD studies at McGill University, where he worked on genomics and bioinformatics analysis of gene regulation in parasitic organisms. He obtained his PhD in 2012 and moved to University of Toronto as a Banting postdoctoral fellow, working on new machine learning approaches to study the gene regulatory programs of human cells. He joined McGill University as an Assistant Professor in 2016, where he currently holds the Canada Research Chair in Systems Biology of Gene Regulation. He is also a member of the McGill PhD program in Quantitative Life Sciences, as well as an associate member of the Rosalind and Morris Goodman Cancer Research Centre.

Research Interests

Genome is a self-extracting program with encoded instructions that tightly control the flow of genetic information. The research in Najafabadi lab encompasses the development of computational and statistical frameworks to decode these regulatory instructions, understand the evolutionary mechanisms that have shaped them, and decipher their role in normal cell function and in human diseases. By developing novel methods based on machine learning and statistical inference, his lab aims to characterize the regulatory factors that govern transcription, RNA splicing, and mRNA stability, and their contribution to neurodegenerative disorders and cancer.

Recent Publications

• Jolma, A, Hernandez-Corchado, A, Yang, AWH, Fathi, A, Laverty, KU, Brechalov, A et al.. GHT-SELEX demonstrates unexpectedly high intrinsic sequence specificity and complex DNA binding of many human transcription factors. bioRxiv. 2024; :. doi: 10.1101/2024.11.11.618478. PubMed PMID:39605368 PubMed Central PMC11601218.
• Razavi, R, Fathi, A, Yellan, I, Brechalov, A, Laverty, KU, Jolma, A et al.. Extensive binding of uncharacterized human transcription factors to genomic dark matter. bioRxiv. 2024; :. doi: 10.1101/2024.11.11.622123. PubMed PMID:39605320 PubMed Central PMC11601254.
• Zhang, W, Sladek, R, Li, Y, Najafabadi, H, Dupuis, J. Accounting for genetic effect heterogeneity in fine-mapping and improving power to detect gene-environment interactions with SharePro. Nat Commun. 2024;15 (1):9374. doi: 10.1038/s41467-024-53818-w. PubMed PMID:39478020 PubMed Central PMC11526169.
• Burban, A, Sharanek, A, Hernandez-Corchado, A, Najafabadi, HS, Soleimani, VD, Jahani-Asl, A et al.. Targeting glioblastoma with a brain-penetrant drug that impairs brain tumor stem cells via NLE1-Notch1 complex. Stem Cell Reports. 2024;19 (11):1534-1547. doi: 10.1016/j.stemcr.2024.09.007. PubMed PMID:39423824 PubMed Central PMC11589194.
• Thivierge, C, Bellefeuille, M, Diwan, SS, Dyakov, BJA, Leventis, R, Perron, G et al.. Paraspeckle-independent co-transcriptional regulation of nuclear microRNA biogenesis by SFPQ. Cell Rep. 2024;43 (9):114695. doi: 10.1016/j.celrep.2024.114695. PubMed PMID:39250314 .
• Madrigal, A, Lu, T, Soto, LM, Najafabadi, HS. A unified model for interpretable latent embedding of multi-sample, multi-condition single-cell data. Nat Commun. 2024;15 (1):6573. doi: 10.1038/s41467-024-50963-0. PubMed PMID:39097589 PubMed Central PMC11298001.
• Apostolides, M, Choi, B, Navickas, A, Saberi, A, Soto, LM, Goodarzi, H et al.. Accurate isoform quantification by joint short- and long-read RNA-sequencing. bioRxiv. 2024; :. doi: 10.1101/2024.07.11.603067. PubMed PMID:39026819 PubMed Central PMC11257535.
• Blackburn, DM, Sahinyan, K, Hernández-Corchado, A, Lazure, F, Richard, V, Raco, L et al.. The E3 ubiquitin ligase Nedd4L preserves skeletal muscle stem cell quiescence by inhibiting their activation. iScience. 2024;27 (7):110241. doi: 10.1016/j.isci.2024.110241. PubMed PMID:39015146 PubMed Central PMC11250905.
• Dehghanzadeh, H, Ghaderi-Zefrehei, M, Mirhoseini, SZ, Esmaeilkhaniyan, S, Haruna, IL, Najafabadi, HA et al.. Retraction Note: A new DNA sequence entropy-based Kullback-Leibler algorithm for gene clustering. J Appl Genet. 2024;65 (4):951. doi: 10.1007/s13353-024-00888-7. PubMed PMID:38922512 .
• Zhang, W, Lu, T, Sladek, R, Li, Y, Najafabadi, H, Dupuis, J et al.. SharePro: an accurate and efficient genetic colocalization method accounting for multiple causal signals. Bioinformatics. 2024;40 (5):. doi: 10.1093/bioinformatics/btae295. PubMed PMID:38688586 PubMed Central PMC11105950.