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CP - Genome Biology

Brenda Andrews

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Brenda Andrews, Ph.D.

Professor

Address:
University of Toronto
The Donnelly Centre, Rm. 1308
160 College St.
Toronto, ON, M5S 3E1

Phone #: 416-978-8562

Web Site: http://sites.utoronto.ca/andrewslab/homepage.html


Research:

Studying simple yeast cells to understand human cells


Education:

Postdoctoral Fellow: University of California, San Francisco
Ph.D.: University of Toronto
B.Sc.: University of Toronto


Fields of Interest:

  • Genetic Models of Development and Disease

  • Functional Genomics and Proteomics

 

Research Interests:

The Andrews lab uses functional genomics coupled with yeast genetics and cell biology to study cell cycle transcription factor pathways and mechanisms of cell cycle regulation. Current projects include: 1) systematic synthetic dosage lethality (SDL) screens using automated yeast genetics to define targets of protein kinases; 2) a 'phenomics' project that uses high through put fluorescence microscopy to define biological networks and to map cell cycle transcription factor pathways; 3) collaborations with the Boone, Hughes and other labs to map genetic networks controlling cell cycle progression and cell polarity in yeast.

 

Accepting Rotation Students:

Yes

 

 

 

 

Gary Bader

Gary Bader, Ph.D.

Professor

Address:
University of Toronto
The Donnelly Centre, Rm. 602
160 College St.
Toronto, ON, M5S 3E1

Phone #: 416-978-3935

Web Site: http://baderlab.org/


Research:

Organization and evolution of biological systems


Education:

Postdoctoral Fellow:  Memorial Sloan-Kettering Cancer Center
Ph.D.: University of Toronto  
B.Sc.: McGill University


Fields of Interest:

  • Computational and Systems Biology
  • Functional Genomics and Proteomics

 

Research Interests:

We study the organization and evolution of biological systems using computational biology and bioinformatics techniques. This work is supported through the development of open-source biological pathway and network databases and visualization and analysis software.

 

Accepting Rotation Students:

No

 

Benjamin Blencowe

Benjamin Blencowe, Ph.D.

Professor

Address:
University of Toronto
The Donnelly Centre, Rm. 1016
160 College St.
Toronto, ON, M5S 3E1

Phone #: 416-978-3016

Web Site: http://sites.utoronto.ca/intron/


Research:

Regulation of gene expression and alternative splicing


Education:

Postdoctoral Fellow:  Massachusetts Institute of Technology
Ph.D.:  EMBL, Heidelberg, Germany and University of London, UK
B.Sc (Hon):  Imperial College London, UK


Fields of Interest:

  • Cellular and Molecular Structure and Function
  • Functional Genomics and Proteomics

 

Research Interests:

Our research focuses on mechanisms underlying the regulation of gene expression and how these mechanisms go awry in human diseases. Most of our research is directed at understanding how alternative splicing is integrated with other layers of gene regulation to control fundamental biological processes, such as cell fate determination.

 

Accepting Rotation Students:

Yes

 

 

Charles Boone

Charles Boone, Ph.D.

Professor

Address:
University of Toronto
The Donnelly Centre, Room 1312
160 College Street
Toronto, ON M5S 3E1

Phone #: 416-946-7260

Web Site: http://sites.utoronto.ca/boonelab/


Research:

Functional genomics for mapping genetic, chemical-genetic, and protein-protein interactions in yeast


Education:

Postdoctoral Fellow:  University of Oregon
Ph.D.:  McGill University
B.Sc.:  Queen's University


Fields of Interest:

Computational and Systems Biology
Functional Genomics and Proteomics

 

Research Interests:

We are developing and applying functional genomics approaches for mapping genetic, chemical-genetic, and protein-protein interactions on a large-scale using the yeast model system. The ultimate goal is to place all yeast genes and their corresponding products on a functional network.

 

Accepting Rotation Students:

Yes

 

 

 

Alan Davidson

Alan Davidson, Ph.D

Professor

Address:
MaRS Centre, West Tower
661 University Ave., Rm. 1634
Toronto, ON, M5G 1M1

Phone #: 416-978-0332

Web Site: http://individual.utoronto.ca/Davidsonlab/index.html


Research:

Bacteriophages and CRISPR systems


Education:

Postdoctoral Fellow: Massachusetts Institute of Technology
Ph.D.: University of Toronto
B.Sc.: University of Toronto


Fields of Interest:

  • Cellular and Molecular Structure and Function
  • Molecular Microbiology and Infectious Disease

 

Research Interests:

My laboratory focuses on bacteriophages (phages), the viruses that infect bacteria.  We study how phages work, and how we can exploit phage-derived entities for applications in human health.  We also study anti-CRISPRs, which are phage-encoded inhibitors of CRISPR-Cas systems. We discovered these proteins, and are currently endeavouring to understand how they work, and how they can be exploited in genome editing applications.

 

Accepting Rotation Students:

Yes

 

 

Aled Edwards

Aled Edwards, Ph.D.

Professor

Address:
Structural Genome Consortium
MaRS South Tower Rm. 701 
101 College St.
Toronto, ON, M5G 1L5

Phone #:416-946-0237

Web Site: http://www.thesgc.org/about/director


Research:

Developing open access research tools (chemical inhibitors, protein structures and recombinant antibodies)
Additional Affiliations
Structural Genomics Consortium

*currently on leave from Dept. of Molecular Genetics while serving as Director of SGC


Education:

Postdoctoral Fellow: Stanford University
Ph.D.: McGill University
B.Sc.: McGill University


Fields of Interest:

  • Functional Genomics and Proteomics

  • Molecular Medicine and Human Genetics

Research Interests:

Developing open access research tools (chemical inhibitors, protein structures and recombinant antibodies) to increase knowledge of human biology and accelerate drug discovery

 

Lori Frappier

Lori Frappier, Ph.D.

Professor

Address:
MaRS Centre, West Tower
661 University Ave., Rm. 1633
Toronto, ON, M5G 1M1

Phone #: 416-946-3501

Web Site: http://individual.utoronto.ca/frappierlab/index.html


Research:

How herpesvirus promote viral persistence and oncogenesis


Education:

Postdoctoral Fellow: Cornell University Medical College
Ph.D.: McGill University
B.Sc.: Queen's University


Fields of Interest:

  • Cellular and Molecular Structure and Function
  • Molecular Microbiology and Infectious Disease

 

Research Interests:

We study how herpesvirus  proteins (particularly Epstein-Barr virus) manipulate nuclear processes to promote viral persistence and contribute to oncogenesis, often using proteomics methods.  We also study how PML nuclear bodies are regulated and disrupted by viral proteins, and the functions of a novel DNA replication protein that we discovered by proteomics.

 

Accepting Rotation Students:

Yes

 

Jack Greenblatt

Jack Greenblatt, Ph.D.

Professor

Address:
University of Toronto
The Donnelly Centre, Rm. 960
160 College Street
Toronto, ON M5S 3E1

Phone #: 416-978-4141

Web Site: http://sites.utoronto.ca/greenblattlab/


Research:

Protein-protein and protein-RNA interaction networks for chromatin-related proteins and DNA-binding transcription factors


Education:

Postdoctoral Fellow:  Pasteur Institute, Paris
Ph.D.: Harvard University
B.Sc. (Hon): McGill University


Fields of Interest:

  • Cellular and Molecular Structure and Function
  • Computational and Systems Biology

 

Research Interests:

Our current major aims are using affinity purification/mass spectrometry and second-generation sequencing to establish protein-protein and protein-RNA interaction networks for the approximately 900 human chromatin-related proteins and  >1000 human DNA-binding transcription factors, as well as to identify some of their important functions in transcription and their relationships to human diseases.

 

Accepting Rotation Students:

Yes

 

Timothy Hughes

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Timothy Hughes, Ph.D.


Professor

Address:
University of Toronto
The Donnelly Centre, Rm. 1302
160 College St.
Toronto, ON, M5S 3E1

Phone #: 416-946-8260

Web Site: http://hugheslab.med.utoronto.ca/


Research:

How eukarotic cells recognize and interpret the information in the genome, by studying protein-DNA and protein-RNA sequence specificity


Education:

Postdoctoral Fellow:  Rosetta Inpharmatics (now Merck)
Ph.D.:  Baylor College of Medicine
B.Sc., B. Music:  University of Iowa


Fields of Interest:

  • Computational and Systems Biology
  • Functional Genomics and Proteomics

 

Research Interests:

The genome sequence has been described as a blueprint, but it is one that we are largely unable to read.  Our goal is to understand how eukaryotic cells recognize and interpret the information in the genome, by collecting large-scale data on protein-DNA and protein-RNA sequence specificity.

 

Accepting Rotation Students:

Yes

 

Philip Kim

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Philip Kim, Ph.D.

Associate Professor

Address:
University of Toronto
The Donnelly Centre Rm. 606
160 College St.
Toronto, ON, M5S 3E1

Phone #: 416-946-3419

Web Site: http://www.kimlab.org/


Research:

Computational methods to study protein interactions and signaling networks in the context of cancer and other diseases


Education:

Postdoctoral Fellow: Yale University
Ph.D.:  Massachusetts Institute of Technology
Vordiplom/B.S.:  University of Tuebingen


Fields of Interest:

  • Computational and Systems Biology
  • Functional Genomics and Proteomics

 

Research Interests:

The Kim lab uses and develops computational methods to study protein interactions and signaling networks in the context of cancer and other diseases. We use an integrative approach that encompass structural biophysics, systems biology and comparative genomics. Ultimately, we aim to help develop novel therapies.

 

Accepting Rotation Students:

Yes

 

Michael Moran

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Michael Moran, Ph.D.

Professor

Address:
Hospital for Sick Children
Peter Gilgan Centre for Research & Learning, Rm. 17-9705
686 Bay St.
Toronto, ON M5G 0A4

Phone #: 647-235-6435

Admin: katie.jackson@sickkids.ca

Web Site: http://www.sickkids.ca/.../Moran%20.html


Research:

Proteomics and functional genomics to define and stratify cancers focused on signal transduction and metabolic networks


Education:

Postdoctoral Fellow:  Mt. Sinai Hospital, Toronto
Ph.D.:  University of Western Ontario
B.Sc.:  University of Western Ontario


Fields of Interest:

  • Cellular and Molecular Structure and Function

  • Functional Genomics and Proteomics

 

Research Interests:

Proteomics and functional genomics datasets are integrated in order to define and stratify cancers according to their distinctive molecular signatures. Underlying signal transduction and metabolic networks, and their regulation by post-translational modifications, are then molecularly characterized for their contributions to cancer phenotypes.

 

Accepting Rotation Students:

Yes

 

Frederick Roth

Frederick Roth, Ph.D.

Professor

Address:
University of Toronto
The Donnelly Centre, Rm. 912
160 College St. Toronto, ON
M5S 3E1

Phone #: 416-946-5130

Website: http://llama.mshri.on.ca/


Research:

Developing experimental and computational technology to more relate genes and proteins to the functioning of living systems and human disease


Education:

Ph.D.:  Harvard University
B.A.:  University of California, Berkeley


Fields of Interest:

  • Computational and Systems Biology

  • Molecular Medicine and Human Genetics


Research Interests:

Roth's group is focused on developing experimental and computational technology to more efficiently relate genes and proteins to each other and to the functioning of living systems and human disease.

 

Accepting Rotation Students:

Yes

 

Stephen Scherer

Stephen Scherer, Ph.D.

 

Professor

Address:
Hospital for Sick Children,
Peter Gilgan Centre for
Research & Learning,
Rm. 13-9705,
686 Bay St.,
Toronto, ON M5G 0A4

Phone #: 416-813-7613

Admin:  elainec.chang@sickkids.ca

Web Sitehttp://www.tcag.ca/scherer/


Research:

Human genome structure and function, genomic of neurodevelopmental disorders
 

Education:

M.Sc., Ph.D.:  University of Toronto
B.Sc. (Hon):  University of Waterloo
 

Fields of Interest:

  • Computational and Systems Biology

  • Molecular Medicine and Human Genetics

Research Interests:

Human genome structure and function, genomics of autism and other neurodevelopmental disorders

 

Accepting Rotation Students:

No

 

Lincoln Stein

Lincoln Stein, M,D., Ph.D.

Professor

Address:
OICR, MaRS West Tower,
Suite 510
661 University Ave.,
Toronto, ON, M5G 0A3

Phone #: 416-673-8514


Research:

Network and pathway-based analysis to identify common mechanisms in multiple cancer types and to devise prognostic and predictive signatures
 

Education:

Postdoctoral Fellow:  Massachusetts Institute of Technology
Ph.D.:  Harvard University
M.D.:  Harvard Medical School
B.A.:  Johns Hopkins University
 

Fields of Interest:

  • Computational and Systems Biology
  • Functional Genomics and Proteomics


Research Interests:

Stein's research focuses on using network and pathway-based analysis to identify common mechanisms in multiple cancer types and to devise prognostic and predictive signatures to aid in patient management. In addition, his group works on problems relating to the genome structure and function of the nematode Caenorhabditis elegans.

 

Accepting Rotation Students:

Yes

 

Jeff Wrana

Jeff Wrana, Ph.D.

Professor

Address:
Mount Sinai Hospital,
LTRI Rm.1070
600 University Ave.,
Toronto, ON, M5G 1X5

Phone #: 416-586-4800

Web Sitehttp://sites.utoronto.ca/attisano


Research:

Signalling pathways integration into higher order networks that control development cancer initiation and progression

Education:

Postdoctoral Fellow: Memorial Sloan Kettering Cancer Center, NY
Ph.D.:  University of Toronto
B.Sc.:  University of Toronto
 

Fields of Interest:

  • Cellular and Molecular Structure and Function
  • Functional Genomics and Proteomics
     

Research Interests:

We seek to understand how signalling pathways are integrated into higher order networks that control morphogenesis in development and which are aberrantly organized during cancer initiation and progression.

 

Accepting Rotation Students:

Yes

 

Zhaolei Zhang

Zhaolei Zhang, Ph.D.

Professor

Address:
University of Toronto,
The Donnelly Centre, Rm. 608
160 College St.,
Toronto, ON
M5S 3E1

Phone #: 416-946-0924

Websitehttp://sites.utoronto.ca/zhanglab/


Research:

Comparative genomics, genome evolution, microRNAs, genetic variations
 

Education:

Postdoctoral Fellow:  Yale University
Ph.D.:  University of California,Berkeley
B.Sc.:  NanKai University, China
 

Fields of Interest:

  • Computational and Systems Biology
  • Functional Genomics and Proteomics
     

Research Interests:

Comparative genomics, genome evolution, gene duplication, pseudogenes, microRNAs, genetic variations