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James Ellis

Title: Senior Scientist, Developmental and Stem Cell Biology
Designations: PhD
Phone: 416-813-7295
Alternate Contact Name: Tirhas Okubazghi
Alternate Phone: 416-813-6518 ext. 306518
Alternate Email:
U of T Positions: Professor, Department of Molecular Genetics


Dr. Ellis completed his B.Sc. at McGill University and his PhD at the University of Toronto with Dr. Alan Bernstein developing retrovirus vectors for gene targeting. His post-doctoral fellowship studying the beta-globin Locus Control Region was mentored by Dr. Frank Grosveld in London, UK.

Dr. Ellis established his own research team at The Hospital for Sick Children (SickKids) in Toronto in 1994 with a focus on gene therapy for sickle cell anemia. He subsequently developed MECP2 vectors for Rett syndrome, and vectors with reporter genes that mark specific cell types. For example, the EOS vectors express specifically in pluripotent stem cells and facilitate generation of patient induced pluripotent stem (iPS) cells. 

Dr. Ellis’ research theme is to define disease mechanisms using gene delivery to reprogram and manipulate human stem cells. His team uses these cells to study post-transcriptional regulation of gene expression. They develop vectors with reporter genes that mark specific cell types, such as our EOS vectors that express highly in pluripotent stem cells but extinguish during differentiation.  

Their focus is on modeling Rett Syndrome, autism spectrum disorder, and Williams Beuren syndrome using patient specific induced pluripotent stem (iPS) cells. They phenotype the affected cells in vitro and interrogate potential disease pathways using chemical compound screens to identify candidate drugs that may have therapeutic utility.  

The Ellis Lab currently uses these iPS cells in collaborative research teams to model Rett syndrome, autism spectrum disorders, Williams Beuren syndrome, and cardiomyopathies. A new research direction concentrates on post-transcriptional regulation during human neurodevelopment.

Education and experience

  • 2015–Present: Panel on Responsible Conduct of Research (PRCR) member.
  • 2013–2023: Research Integrity Advisor, SickKids
  • 2010–Present: Professor, Department of Molecular Genetics, University of Toronto.
  • 2000–Present: Senior Scientist, SickKids, Toronto.
    Research subjects: iPS cells for modeling human disease, gene silencing of retrovirus vectors in stem cells; regulation and replication of human b-globin transgenes; gene therapy of Sickle Cell Anemia and Rett Syndrome.
  • 2008–2010: Scientific Co-Director, Ontario Human IPS Cell Facility.
  • 1994–2000: Scientist, SickKids Hospital, Toronto.
    Research subjects: Regulation and chromatin structure of human b-globin transgenes; gene silencing of retrovirus vectors in stem cells; gene therapy of b-thalassemia and other blood disorders.
  • 1990–1994: Postdoctoral Fellow at National Institute for Medical Research, London, U.K.
    Supervisor: Dr. Frank Grosveld.
    Research subject: Characterization of the human b-globin locus control region.
  • 1985–1990: PhD (Toronto) - Department of Medical Genetics.
  • 1980–1984: B.Sc. Honours (McGill) - Department of Microbiology and Immunology


  • 2020–2025: CIHR Project grant (PJT168905) To Dr. J. Ellis ($182,835 per year). Post-Transcriptional Regulation of Functionally Significant Gene Sets During Neurodevelopment of Rett Syndrome. 
  • 2020–2021: SickKids HSBC Catalyst Research Grant to Drs. J. Ellis (PI) and A. Zani ($25,000 to J. Ellis). Astrocyte-derived Exosomes to Rescue Rett Syndrome Neurons. 
  • 2019–2022: CIHR ERARE Team Grant (ERT161303) - Transnational Research Projects on Rare Diseases to Dr. J. Ellis (Co-App $125,000 per year). Team PI is H. van Bokhoven in the Netherlands. Identification of converging Molecular Pathways Across Chromatinopathies as Targets for Therapy: IMPACT. 
  • 2018–2021: Ted Rogers Centre for Heart Disease Strategic Innovation grant to Dr. J. Ellis (PI), S. Mital (CoPI), P. Billia, C. Simmons and M. Radisic (Total $1 million - $180,000 per year to SickKids). Precision Therapeutics for MYH7 and MYBPC3 Associated Cardiomyopathies. 
  • 2018–2021: Ontario Brain Institute Grant to Drs. E. Anagnostou, P. Arnold and co-applicants ($138,979 per year to J. Ellis). Province of Ontario Neurodevelopmental Disorders Network (POND).  
  • 2017–2020: SFARI Research grant (#514918) to Dr. J. Ellis (PI) and J. Martinez-Trujillo (US $273,340 per year). Network activity and translational regulation in SHANK2 ASD neurons. 


  1. Zaslavsky K. +, W.-B. Zhang+F, McCready, D.C. Rodrigues, E. DeneaultC. Loo, M. Zhao, P.J. Ross, J. El Hajjar, A. Romm, T. Thompson, A. Piekna, W. Wei, Z. Wang, S. Khattak, M. MufteevP. Pasceri, S.W. Scherer, M.W. Salter* and J. Ellis*2019. SHANK2 mutations associated with Autism Spectrum Disorder cause hyperconnectivity of human neurons. +Co-first authors, *co-corresponding authors. Nature Neuroscience 22:556-564Discussed in Lemprier, Nature Reviews Neurology April 2019; and in Williams, Spectrum News, May 2019. 
  2. Hildebrandt M.R.+, M.S. Reuter+, W. Wei, N. Tayebi, J. Liu, S. Sharmin, J. Mulder, S. Lesperance, P.M. Bauer, R. Mok, C. Kinnear, A. Piekna, A. Romm, J. Howe, P. Pasceri, G. Meng, M. Rozycki, D.C. Rodrigues, E.C. Martinez, M. Szego, J.C. Zuniga-Pflucker, M.K. Anderson, S.A. Prescott, N.D. Rosenblum, B.M. Kamath, S. Mital, S.W. Scherer* and J. Ellis*. 2019. Precision health resource of control iPSC lines for versatile multi-lineage differentiation. +Co-first authors, *co-corresponding authors. Stem Cell Reports 13:1126-41. 
  3. Ross, P.J.+, W. Zhang+, R.S.F. Mok, K. Zaslavsky, E. Deneault, L. D’Abate, D.C. Rodrigues, R.K.C. Yuen, M. Faheem, A. Piekna, W. Wei, P. PasceriR.J. Landa, A. Nagy, B. VargaM.W. Salter, S.W. Scherer and J. Ellis. 2020Synaptic Dysfunction in Human Neurons with Autism-Associated Deletions in PTCHD1-AS+Co-first authors. Biological Psychiatry 87:139-149. Discussed in Buxbaum, Biological Psychiatry 2020. 
  4. Rodrigues D.C., M. Mufteev, R.J. Weatheritt, U. Djuric, K.C.H. Ha, P.J. Ross, W. Wei, A. Piekna, M.A. Sartori, L. Byres, R.S.F. Mok, K. Zaslavsky, P. Pasceri, P. Diamandis, Q. Morris, B.J. Blencowe and J. Ellis2020. Shifts in Ribosome Engagement Impact Key Gene Sets in Neurodevelopment and Ubiquitination in Rett Syndrome Neurons. Cell Reports 30:4179-96. 
  5. Kinnear C., R. Agrawal, C. Loo, A. Pahnke, D.C. Rodrigues, T. Thompson, O. Akinrinade, S. Ahadian, F. Keeley, M. Radisic, S. Mital* and J. Ellis*. 2020. Everolimus rescues the phenotype of elastin insufficiency in patient iPSC-derived vascular smooth muscle cells. *Co-corresponding authors. ATVB 40: 1325-39. 

See a full list of James Ellis' publications

Relevant pages

Scientist looking into a microscope

High-quality stem cells enable researchers to better study almost any disease

Using whole genome sequencing, a collaborative team at SickKids and the University of Toronto has created high-calibre control induced pluripotent stem cells that can be used to study a variety of diseases.

SickKids team discovers overconnected brain cells may cause autism

Typically nerve cells with fewer connections are associated with autism. A team at SickKids found that nerve cells from children with autism can be overconnected and overactive, leading us to think about the causes of autism in a new way.

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