Research Overview

Our research focuses on mechanisms underlying the regulation of gene expression and how these mechanisms are disrupted in human diseases. Most of our research is directed at understanding how alternative splicing is regulated and integrated with other layers of gene expression to control fundamental biological processes. For example, we have recently discovered alternative splicing "switches" with key roles in the regulation of transcriptional programs required for neural cell differentiation, embryonic stem cell pluripotency, and which are important for efficient somatic cell reprogramming. Our research encompasses a wide range of approaches, from bioinformatics and functional genomics to focused molecular,biochemical, and cell biological methods. We have pioneered the development and application of technologies for the genome-wide quantitative profiling of transcriptomes. These efforts have uncovered a remarkable landscape of new regulation that awaits further investigation.

Selected Review Articles

Braunschweig et al. 2013

Braunschweig, U., Gueroussov, S., Plocik, A.M., Graveley, B.R. and Blencowe, B.J (2013) Dynamic integration of Splicing within Gene Regulatory Pathways, Cell, 152:1252-1269.


Irimia and Blencowe, 2012

Irimia, M, Blencowe, B.J. (2012) Alternative splicing: decoding an expansive regulatory layer, Current Opinion in Cell Biology, 24: 3.

Blencowe, 2009

Blencowe, B.J., Ahmad, S. and Lee,L.J.(2009) Current generation high-throughput sequencing: deepening insights into mammalian transcriptomes, Genes and Development 23:1379-1386.


Blencowe, 2006

Blencowe, B.J. (2006) Alternative Splicing: New insights from global analyses, Cell 126:37-47.

Han, 2011

Han, H., Nutiu, R., Moffat, J. and Blencowe, B.J. (2011) SnapShot: High Throughput Sequencing Applications, Cell 146(6):1044-1044.e2.

Gabut, 2008

Gabut, M., Chaudhry, S. and Blencowe, B.J.(2008) SnapShot: The Splicing Regulatory Machinery, Cell 133(1):192-192e1.


Current Research Topics and Selected Publications

Deep surveying of transcriptome complexity and deciphering RNA regulatory codes

Pan et al. 2008
Pan, Q., Shai, O., Lee, L., Frey, B.J., and Blencowe, B.J. (2008). Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat. Genetics. 40:1413-1415.


-Highlighted in Nature and Nature Genetics Editorial, Research Highlight of Nature Review Genetics.
-Highlighted on the journal cover

Barash et al 2010
Barash, Y., Calarco, J.A., Gao, W., Pan, Q., Wang, X., Shai, O., Blencowe, B.J., and Frey, B.J. (2010). Deciphering the splicing code. Nature, 465: 53-59.


-Featured in Nature Editorials, in several News and Views articles in Nature, Nature Biotech, Cell Res, and numerous media reports including CBC,and Toronto Star
-Featured on the journal cover
-Recommended by Faculty of 1000
-Featured in a Nature Biotech article "Trends in Computational Biology-2010"

Discovery and characterization of splicing regulators and exon networks with critical roles in development

Calarco et al. 2009
Calarco, J., Superina, S., O'Hanlon, D., Gabut, M., Raj, B., Pan, Q., Skalska, U., Clarke, L., Gelinas, D., van der Kooy, D., Zhen, M., Ciruna, B., and Blencowe, B.J. (2009). Regulation of Vertebrate Nervous System-Specific Alternative Splicing and Development by an SR-Related Protein. Cell, 138: 898-910.


-Recommended by Faculty of 1000.
-Featured in the UofT Faculty of Medicine News.
Raj et al. 2011
Raj, B., O'Hanlon, D., Vessey, J.P., Pan, Q., Ray, D., Buckley, N.J., Miller, F.D., and Blencowe, B.J. (2011) Cross-regulation between an alternative splicing activator and a transcription repressor controls neurogenesis. Mol Cell, 43: 843-850.


Saltzman et al. 2011
Saltzman, A.L., Pan, Q., and Blencowe, B.J. (2011). Regulation of alternative splicing by the core spliceosomal machinery. Genes and Development, 25: 373-384.


Ellis et al. 2012
Ellis, J.D., Barrios-Rodiles, M., Çolak, R., Irimia, M., Kim, T., Calarco, J.A., Wang, X., Pan, Q., O'Hanlon, D., Kim, P.M., Wrana, J.L., and Blencowe, B.J. (2012) Tissue-specific alternative splicing remodels protein-protein interaction networks. Molecular Cell. 46: 884-892.


-Featured on the journal cover.
-Featured in Nature Reviews Genetics Editorial

Regulation of embryonic stem cell-specific alternative splicing reprogramming

Gabut et al. 2011
Gabut, M., Samavarchi-Tehrani, P., Wang, X., Slobodeniuc, V., O'Hanlon, D., Sung, H.K., Alvarez, M., Talukder, S., Pan, Q., Mazzoni, E.O., Nedelec, S., Wichterle, H., Woltjen, K., Hughes, T.R., Zandstra, P.W., Nagy, A., Wrana, J.L., and Blencowe, B.J. (2011) An alternative splicing switch regulates embryonic stem cell pluripotency and reprogramming. Cell, 147: 132-146.


-Featured in Cell Preview Article and in Nature Reviews Genetics Research Highlights.
-Ranked among Top 10 "hottest" research articles in the fields of biochemistry, genetics and molecular biology in 2011
-Recommended by Faculty of 1000.

Han et al 2013
Han, H., Irimia, I., Ross, P.J., Sung, H-K., Alipanahi, B., David, L., Golipour, A., Gabut, M., Michael, I.P., Nachman E.N., Wang, E., Trcka, D., Thompson, T., O'Hanlon, D., Slobodeniuc, V., Barbosa-Morais, N.L., Burge, C.B., Moffat, J., Frey, B.J., Nagy, A., Ellis, J., Wrana, J.L. and Blencowe, B.J. (2013) MBNL proteins repress ES-cell-specific alternative splicing and reprogramming. Nature,


-Highlighted in Nature News and Views article and in Nature Reviews Molecular Cell Biology article.
-Recommended by Faculty of 1000.

Role of epigenetic modifications and the transcriptional machinery and the regulation of alternative splicing

Ip et al. 2011
Ip, J.Y., Schmidt, D., Pan, Q., Ramani, A.K., Fraser, A.G., Odom, D.T., and Blencowe, B.J. (2011). Global impact of RNA polymerase II elongation inhibition on alternative splicing regulation. Genome Research, 21: 390-401.


Luco et al. 2010
Luco, R.F., Pan, Q., Tominaga, K., Blencowe, B.J., Pereira-Smith, O.M. and Misteli, T. (2010) Regulation of alternative splicing by histone modifications. Science, 327:996-1000.


-Recommended by Faculty of 1000.
-Featured in Dev. Cell Editorial and Nature Journal Club

The evolutionary landscape of alternative splicing in vertebrate species

Barbosa-Morais et al. 2012
Barbosa-Morais, N.L., Irimia, M., Pan, Q., Xiong, H.Y., Gueroussov, S., Lee, L.J., Slobodeniuc, V., Kutter, C., Watt, S., Colak, R., Kim, T.H, Misquitta-Ali, C.M., Wilson, M.D., Kim, P.M., Odom, D.T., Frey, B.J. and Blencowe, B.J (2012) The evolutionary landscape of alternative splicing in vertebrate species, Science, 338: 1587-1593.


-Featured in Science perspective article.
-Recommended by Faculty of 1000.
Calarco et al 2007
Calarco, J.A., Xing, Y., Caceres, M., Calarco, J.P., Xiao, X., Pan, Q., Lee, C., Preuss, T.M. and Blencowe, B.J., (2007) Global analysis of alternative splicing differences between human and chimpanzees. Genes and Dev. 21: 2963-2975.


-Featured in CBC news and other media reports.
-Featured in Cell, Leading Edge: Genetics Select

Alternative Splicing and human disease

Misquitta et al. 2011
Misquitta-Ali, C.M., Cheng, E., O’Hanlon, D., Liu, N., McGlade, C.J., Tsao, M.S., and Blencowe, B.J. (2011). Global profiling and molecular characterization of alternative splicing events misregulated in lung cancer. Mol. Cell Biol., 31: 138-150.


Voineagu et al. 2011
Voineagu, I., Wang, X., Johnston, P., Lowe, J., Tian, Y., Horvath, S., Mill, J., Cantor, R., Blencowe, B.J., and Geschwind, D. (2011) Transcriptome Analysis of Autistic Brain Reveals Convergent Molecular Pathology. Nature, 474: 380-400


-Featured in Nature, Nature Review Genetics and Nature Reviews Neuroscience Research highlights
-Recommended by Faculty of 1000.
-Highlighted in BBC, TIME and other International Media reports

Last updated July 4, 2013