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Philip Awadalla

Philip Awadalla, Ph.D.

Professor

Address:
Ontario Institute for Cancer Research
MaRS Centre, Suite 6-42
661 University Ave.
Toronto, ON, M5G 0A3

Phone #: 647-260-7990

Web Site: http://pawadallalab.org

 


Research:

Organization and evolution of biological systems


Education:

Postdoctoral Fellow:  University of British Columbia and University of California, Davis
Ph.D.: University of Edinburgh
M.Sc.: University of Toronto


Fields of Interest:

  • Molecular Medicine and Human Genetics
  • Computational and Systems Biology

 

Research Interests:

Working with empirical genomic data and modern computational models, the laboratory addresses questions relevant to how genetics and the environment influences the frequency and severity of diseases in human populations. Our work focuses on next generation genomic tools to capture genetic determinants of phenotypes, specifically associated with aging, cancer and infectious diseases, from large population cohorts as well as family based studies.

 

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

 

 

 

Amy Caudy

Amy Caudy, Ph.D.

Associate Professor

Address:
University of Toronto
The Donnelly Centre, Rm. 308
160 College St.
Toronto, ON, M5S 3E1

Phone #: 416-978-4074

Web Site: http://tdccbr.med.utoronto.ca/...caudy.html


Research:

Metabolomics, cell growth and metabolism


Education:

Lewis-Sigler Fellow:  Princeton University
Postdoctoral Fellow:  Washington University
Ph.D.:  Watson School of Biological Sciences, Cold Spring Harbor Laboratory
B.A.:  Washington University


Fields of Interest:

  • Cellular and Molecular Structure and Function

  • Functional Genomics and Proteomics

 

Research Interests:

Discovery of novel enzymatic pathways using full scan LC-MS metabolomics, and characterization of the regulatory connections between cell growth and metabolism.

 

Accepting Rotation Students:

No

 

Hue Sun Chan

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Hue Sun Chan, Ph.D.

Professor

Address:
University of Toronto
Medical Sciences Building, Rm. 5363
1 King's College Circle
Toronto, ON, M5S 1A8

Phone #: 416-978-2697

Web Site: http://biochemistry.utoronto.ca/person/hue-sun-chan/

 


Research:

Theoretical and Computational Investigations of Protein Folding, Interactions, and Evolution


Education:

Postdoctoral Fellow:  University of California at San Francisco
Ph.D., University of California at Berkeley


Fields of Interest:

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

Research Interests

Protein folding and interactions are physico-chemical processes.  Our group's overall research goal is to elucidate their underlying energetics. To this end, a main emphasis of our effort is to develop proteinlike heteropolymer models with coarse-grained interactions and simplified representations of chain geometries. The rationale of these approaches is to capture the essential physics and at the same time allow for a broad coverage of the protein conformational space - and also a broad coverage of the sequence space for evolutionary studies - that is not readily achievable currently in higher-resolution models.

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

 

Hannes Rӧst

Hannes Rost.png

Hannes Rӧst, Ph.D.

Assistant Professor

Address:
University of Toronto
Donnelly Centre for Cellular & Biomolecular Research
Room 604, 160 College St.
Toronto, ON, M5S 3E1

Phone #: 416-978-7224

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

Education:

Postdoctoral Fellow: Stanford University
Ph.D.: ETH Zurich
M.Sc./B.Sc: ETH Zurich

Fields of Interest:

  • Computational and Systems Biology
  • Functional Genomics and Proteomics

 

Research Interests:

We study systems-level molecular changes in health and disease using bioinformatic methods. In our research, we develop open-source algorithms to analyze mass spectrometric data and integrate it with other omics data using network analysis, machine learning and signal processing.

 

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

Contact:  Stephen.Scherer@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