Viewing entries in
Comp & Sys Biology

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

 

 

 

James Dennis

James Dennis, Ph.D.

Professor

Address:
Mount Sinai Hospital
LTRI Rm. 988
600 University Ave.
Toronto, ON, M5G 1X5

Phone #: 416-586-8233

Web Site: http://dennislab.lunenfeld.ca/


Research:

Cell surface receptors and signaling


Education:

Postdoctoral Fellow:  University of Toronto
M.Sc., Ph.D.:  Queens University
B.Sc.:  Concordia University


Fields of Interest:

  • Computational and Systems Biology
  • Genetic Models of Development and Disease

Research Interests:

We study the regulation of cell surface receptors and signaling. Cell surface expression of receptors is dependent on N-glycosylation in the ER and modifications in the Golgi, which is in turn, sensitive to basic metabolism. Models include cell culture, mice and C. elegans, and phenotypes include cancer, immunity and stem cell maintenance.

 

Anne-Claude Gingras

Anne-Claude Gingras, Ph.D.

Professor

Address:
Mount Sinai Hospital
LTRI, Rm. 992
600 University Ave.
Toronto, ON, M5G 1X5

Phone #: 416-586-5027

Web Site: http://gingraslab.lunenfeld.ca/


Research:

Proteomics, biochemistry cell biology phosphoregulation


Education:

Postdoctoral Fellow:  Institute for Systems Biology, Seattle
Ph.D.:  McGill University
B.Sc.:  Université Laval, Ste-Foy


Fields of Interest:

  • Computational and Systems Biology
  • Functional Genomics and Proteomics

 

Research Interests:

Reversible protein phosphorylation is mediated by a network of protein kinases and phosphatases whose misregulation may result in numerous diseases, including cancer, diabetes and vascular diseases. We are applying quantitative proteomics approaches, as well as an array of biochemical and cell biology techniques, to uncover the basis of phosphoregulation.

 

Accepting Rotation Students:

No

 

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

Hughes.jpg

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

 

Ran Kafri

Kafri.jpg

Ran Kafri, Ph.D.

Assistant Professor

Address:
Hospital for Sick Children
Peter Gilgan Centre for Reserach & Learning, Room 18-9708
686 Bay St.
Toronto, ON M5G 0A4

Phone #: 416-813-7654 x309092

Admin: sandy.hume@sickkids.ca

Web Site: http://www.kafrilab.com/


Research:

Quantitative aspects of cellular identity


Education:

Postdoctoral Fellow: Harvard University
Ph.D.: Weizman Institute of Science
B.Sc.: Ben Gurion University


Fields of Interest:

  • Cellular and Molecular Structure and Function

  • Computational and Systems Biology

 

Research Interests:

The Kafri lab is interested in how quantitative aspects of cellular identity are specified and regulated. For example, in animals, different types are different in size. How is a cell’s particular size specified?

 

Accepting Rotation Students:

No

 

Philip Kim

Kim.jpg

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

 

Quaid Morris

Morris.jpg

Quaid Morris, Ph.D.

Professor

Address:
University of Toronto
The Donnelly Centre, Rm. 616
160 College St.
Toronto, Ontario, M5S 3E1

Phone #: 416-978-8568

Web Site: http://www.morrislab.ca/


Research:

Computational biology, machine learning, gene function prediction, post-transcriptional regulation


Education:

Postdoctoral Fellow:  University of Toronto
Postdoctoral Fellow:  OCI, University Health Network
Ph.D.:  Massachusetts Institute of Technology
B.Sc. (Hon): University of Toronto


Fields of Interest:

  • Computational and Systems Biology
  • 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

 

John Parkinson

John Parkinson, Ph.D.

Professor

Address:
Hospital for Sick Children, Peter Gilgan Centre for Research & Learning, Rm. 21.9709
686 Bay St.
Toronto, ON M5G 0A4

Phone #: 416-813-5746

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


Research:

Evolution and operation of biological systems that pertain to human disease


Education:

Postdoctoral Fellow:   University of Manitoba
Postdoctoral Fellow:   University of Edinburgh, U.K.
Ph.D.:  University of Manchester, U.K.
B.Sc. (Hon): University of Bath, U.K.


Fields of Interest:

  • Computational and Systems Biology
  • Molecular Microbiology and Infectious Disease

 

Research Interests:

Our labs interests are focused on the evolution and operation of biological systems, particularly those that pertain to human disease. Specific systems of interests include those that allow bacterial pathogens and parasites to survive and persist within their human hosts. In collaboration with the NIH, we are actively developing and applying novel integrative strategies that combine mathematical models with functional genomics to target parasite metabolism.

 

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

 

Frank Sicheri

Frank Sicheri, Ph.D.

Professor

Address:
Mount Sinai Hospital,
LTRI Room 1090A,
600 University Ave,
Toronto, ON, M5G 1X5

Phone #: 416-586-8471

Web Sitehttp://research.lunenfeld.ca/sicheri/


Research:

Mechanisms of action of signaling molecules studied with X-ray crystallography and biochemical techniques
 

Education:

Postdoctoral Fellow:  Rockefeller University
Ph.D.:  McMaster University
B.Sc. (Hon):  McMaster University


Fields of Interest:

  • Cellular and Molecular Structure and Function

  • Computational and Systems Biology

Research Interests:

Research in the Sicheri lab is focused on elucidating the mechanism of action of signalling molecules through the use of x-ray crystallography and biochemical techniques.

 

Accepting Rotation Students:

Yes

 

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

 

Boris Steipe

Boris Steipe, M.D., Ph.D.

Associate Professor

Address:
University of Toronto,
Medical Sciences Building, Rm. 5271
1 King's College Circle,
Toronto, ON M5S 1A8

Phone #: 416-946-7741

Web Sitehttp://biochemistry.utoronto.ca/steipe/


Research:

Patterns in molecular structure: computational methods of pattern discovery
 

Education:

Postdoctoral Fellow: Max-Planck-Institute for Biochemistry, Germany
Ph.D., M.D.:  University of Munich, Germany
 

Fields of Interest:

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

Research Interests:

I am interested in recurring patterns in molecular structure: the computational methods of pattern discovery, their characterization regarding features, context and distribution,  their association with function in proteins, and their utility for protein engineering and design.

 

Accepting Rotation Students:

No

 

Derek van der Kooy

Derek van der Kooy, Ph.D.

Professor

Address:
University of Toronto, The Donnelly Centre, Rm. 1102
160 College St., Toronto, ON M5S 3E1

Phone #: 416-978-1960

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

 


Research:

Stem cell and developmental biology

Education:

Postdoctoral Fellow:  Cambridge University, U.K.
Postdoctoral Fellow:  Salk Institute
Ph.D.:  University of Toronto
M.A.:  University of British Columbia
 

Fields of Interest

  • Cellular and Molecular Structure and Function
  • Genetic Models of Development and Disease
     

Research Interests

The van der Kooy lab works on various stem cell biology and developmental biology research projects; specifically, stem cells in organisms from Drosophila to humans. We produced the first report of stem cells in the adult mammalian eye, published in 2000 in Science. We have also isolated a rare stem cell from the adult mouse and human pancreas that can show extensive proliferation under defined conditions in vitro. Of interest to the lab is the lineage of neural stem cells from pluripotent embryonic stem cells, with relevance to the origin of the earliest neural stem cell in the developing embryo.

 

Accepting Rotation Students:

Yes

 

Michael Wilson

Michael Wilson, Ph.D.

Associate Professor

Address:
Hospital for Sick Children,
Peter Gilgan Centre for Research & Learning,
Rm. 14-9713,
686 Bay St., Toronto,
ON M5G 0A4

Phone #: (416) 813-7654 ext. 328699

Admin: catherine.tan@sickkids.ca

Web Site: http://www.wilsonlab.org/


Research:

Comparative genome biology, epigenetics and evolution of regulatory networks

Education:

Postdoctoral Fellow:  University of Cambridge, U.K.
Postoctoral Fellow: University of Victoria, B.C.
Ph.D.:  University of Victoria
B.Sc.:  University of Victoria
 

Fields of Interest

  • Computational and Systems Biology
  • Functional Genomics and Proteomics
     

Research Interests:

  • Comparative genome biology, Functional genomics,  Bioinformatics,  Developmental biology    
  • Characterizing the role that regulatory DNA sequence plays in childhood diseases using comparative genomics, bioinformatics and developmental biology.
  • Epigenetics and evolution of regulatory networks in postnatal germ cells.
  • Modeling of human genome innovations.

 

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