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About Sickkids
About SickKids

James Ellis, PhD

Research Institute
Senior Scientist
Developmental & Stem Cell Biology

University of Toronto
Department of Molecular Genetics

Phone: 416-813-7654 ext. 307295
Fax: 416-813-5252
Email: jellis@sickkids.ca

For more information, visit:

Ellis Lab

Brief Biography

  • 2010 - present: Professor, Department of Molecular Genetics, University of Toronto
  • 2008 - 2010: Scientific Co-Director, Ontario Human Induced Pluripotent Stem Cell Facility
  • 2001-  2009: Associate Professor, Department of Molecular Genetics, University of Toronto
  • 2000 - present: Senior Scientist, SickKids Research Institute, Toronto
  • 1996 - 2000: Assistant Professor, Department of Molecular & Medical Genetics, University of Toronto
  • 1994 - 2000: Scientist, SickKids Research Institute, Toronto
  • 1990 - 1994: Postdoctoral Fellowship at National Institute for Medical Research, London, U.K. Supervisor: Dr. Frank Grosveld
  • 1985 - 1990: PhD at Mount Sinai Hospital and Department of Medical Genetics, University of Toronto. Supervisor: Dr. Alan Bernstein
  • 1980 - 1984: B.Sc. Honours at Department of Microbiology and Immunology, McGill University

Research Interests

  • Induced Pluripotent Stem (iPS) cell reprogramming to model human disease
  • Epigenetics of retrovirus and lentivirus vectors in stem cells

Previous Research Interests

  • ß-globin gene regulation, chromatin structure and DNA replication
  • Gene therapy of ß-thalassemia, sickle cell anemia, and Rett Syndrome

Research Activities

Gene therapy involves gene transfer into stem cells but is hindered by low gene expression levels. Stem cells silence retrovirus vectors by compacting DNA into inaccessible chromatin structures.

Dr. Ellis and his colleagues are characterizing retrovirus and lentivirus silencing pathways in embryonic stem cells. Vectors that resist silencing are being enhanced with insulator elements that block silent chromatin and with modified reporter genes that escape silencing. These vectors are being used for marking iPS cells.

By generating iPS cells from patients, we intend to model human disease and apply them to regenerative medicine.

Future Research Interests

Identify the gene silencing pathway and chromatin modifications that silence retrovirus and lentivirus vector expression in embryonic stem cells and transgenic mice.

Develop retrovirus and lentivirus vectors that escape gene silencing in embryonic stem cells by incorporating Insulator elements and improved promoter/reporter gene combinations. 

Generate patient specific iPS cell lines to model human autism, cystic fibrosis and cardiac disease. These cells may have applications for novel drug screens and regenerative medicine.

External Funding

  • Canadian Institutes of Health Research
  • National Institutes of Health
  • Ontario Brain Institute


For a complete list of publications, please see PubMed

Rival-Gervier S, Lo MY, Khattak S, Pasceri P, Lorincz MC, Ellis J. (2013) Kinetics and epigenetics of retroviral silencing in mouse embryonic stem cells defined by deletion of the D4Z4 element. Molecular Therapy. June 11. 

Han H, Irimia M, Ross PJ, Sung HK, Alipanahi B, David L, Golipour A, Gabut M, Michael IP, Nachman EN, Wang E, Trcka D, Thompson T, O'Hanlon D, Slobodeniuc V, Barbosa-Morais NL, Burge CB, Moffat J, Frey BJ, Nagy A, Ellis J, Wrana JL, Blencowe BJ. (2013) MBNL proteins repress ES-cell-specific alternative splicing and reprogramming. Nature. 498(7453):241-5.

Kinnear C, Chang WY, Khattak S, Hinek A, Thompson T, de Carvalho Rodrigues D, Kennedy K, Mahmut N, Pasceri P, Stanford WL, Ellis J, Mital S. (2013) Modeling and rescue of the vascular phenotype of Williams-Beuren syndrome in patient induced-pluripotent stem cells. Stem Cells Translational Medicine. 2(1):2-15.

Fussner E, Strauss M, Djuric U, Li R, Ahmed K, Hart M, Ellis J, Bazett-Jones DP. (2012) Open and closed domains in the mouse genome are configured as 10 nm fibres.  EMBO Reports. 

Wong AP, Bear C, Chin S, Huan LJ, Pasceri P, Thompson T, Ratjen F, Ellis J, Rossant J. (2012) Directed differentiation of human pluripotent stem cells toward functional CFTR-expressing airway epithelia expressing functional CFTRTR protein. Nature Biotechnology. 30(9):876-82.

Lo MYM, Rival-Gervier S, Pasceri P, Ellis J. (2012) Rapid transcriptional pulsing dynamics of high expressing retroviral transgenes in embryonic stem cells. PLoS One. 7(5):e37130.

Cheung AY, Horvath LM, Carrel L, Ellis J. (2012) X-chromosome inactivation in rett syndrome human induced pluripotent stem cells. Frontiers in Psychiatry. 3:24.

Farra N, Manickaraj AK, Ellis J, Mital S. (2012) Personalized Medicine in the Genomics Era: highlights from an international symposium on heart disease. Future Cardiology. 8(2):157-60. 

Kinoshita T, Nagamatsu G, Kosaka T, Takubo K, Hotta A, Ellis J, Suda T. (2011) Ataxia-telangiectasia mutated (ATM) deficiency decreases reprogramming efficiency and leads to genomic instability in iPS cells. Biochemical & Biophysical Research Communications. 407(2):321-6.

Farra N, Zhang WB, Pasceri P, Eubanks JH, Salter MW, Ellis J. (2012) Rett Syndrome induced pluripotent stem cell derived neurons reveal novel neurophysiology alterations. Molecular Psychiatry. 17(12):1261-71. 

Ross PJ, Ellis J. (2010) Modeling complex neuropsychiatric disease with induced pluripotent stem cells. F1000 Biology Reports. 2:82.

Ellis J, Baum C, Benvenisty N, Mostoslavsky G, Okano H, Stanford WL, Porteus M, Sadelain M. (2010) Benefits of utilizing gene-modified iPS cells for clinical applications. Cell Stem Cell. 7:429-30.

Yantha J, Tsui H, Winer S, Song A, Wu P, Paltser G, Ellis J, Dosch HM. (2010) Unexpected acceleration of Type 1 Diabetes by transgenic expression of B7-H1 in NOD mouse Peri Islet Glia. Diabetes. 59:2588-96.

Belmonte JCI, Ellis J, Hochedlinger K, Yamanaka S. (2009) Induced pluripotent stem cells and reprogramming: seeing the science through the hype.  Nature Reviews Genetics. 10:878-83.

Ramunas J, Montgomery HJ, Kelly L, Sukonnik T, Ellis J, Jervis EJ. (2007) Real time fluorescence tracking of dynamic transgene variegation in stem cells. Molecular Therapy. 15:810-817.

Chen J, Reifsnyder PC, Scheuplein F, Schott WH, Milievsky M, Soodeen-Karamath S, Nagy A, Dosch MH, Ellis J, Koch-Nolte F, Leiter EH. (2005) "Agouti NOD": identification of a CBA-derived Idd locus on Chromosome 7 and its use for chimera production with NOD embryonic stem cells. Mammalian Genome. 16:775-783.

Lam PP, Leung YM, Sheu L, Ellis J, Tsushima RG, Osborne LR, Gaisono HY. (2005) Transgenic mouse over-expressing syntaxin-1A as a diabetes model. Diabetes. 54:2744-2754.

Dalle B, Rubin JE, Alkan O, Sukonnik T, Pasceri P, Yao S, Pawliuk R, Leboulch P, Ellis J. (2005) eGFP reporter genes silence LCRbeta-globin transgene expression via CpG dinucleotides. Molecular Therapy. 11:591-599.

Bharadwaj RR, Trainor CD, Pasceri P, Ellis J. (2003) LCR- regulated transgene expression levels depend on the Oct-1 site in the AT-rich region of beta-globin intron-2. Blood. 101:1603-1610.

Ostermeier GC, Liu Z, Martins RP, Bharadwaj RR, Ellis J, Draghici S, Krawetz SA. (2003) Nuclear matrix association of the human beta-globin locus utilizing a novel approach to quantitative real-time PCR. Nucleic Acids Research. 31(12)3257-66.

Pawliuk R, Westerman K, Fabry ME, Payen E, Tighe R, Bouhassira EE, Acharya SA, Ellis J, London IM, Eaves CJ, Humphries RK, Beuzard Y, Nagel RL, Leboulch P. (2001) Correction of sickle cell disease in transgenic mouse models by gene therapy. Science. 294:2368-71.

Ellis J, Tan-Un KC, Harper A, Michalovich D, Yannoutsos N, Philipsen S, Grosveld F. (1996) A dominant chromatin-opening activity in 5' hypersensitive site 3 of the human beta-globin locus control region. EMBO Journal. 15: 562-568.

Intellectual Property

Hybrid Genes for Gene Therapy in Erythroid Cells

EOS Stem Cell Expression Cassettes