Current Members

Bader Lab

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Gary Bader

Associate Professor

Apr.2006

Post docs

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Jüri Reimand

Jan.2011

Cancer genomics

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Scott Zuyderduyn

Aug.2011

Cancer genomics

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Florence Cavalli

with Michael Taylor

Dec.2011

Cancer genomics

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Andrea Uetrecht

with Jason Moffat

Feb.2012

Protein interactions

Ron

Ron Ammar

Aug. 2013

MedSavant and The Sick Kids Genome Clinic

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Mohamed Helmy

Cancer genomics, Cancer mutations analysis

Sep. 2013

Graduate Students

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Shobhit Jain

Computer Science

Sep.2008

Domain interaction prediction

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Brian Law

Computer Science

Sept.2010

Network alignment

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David Shih

Laboratory Medicine and Pathobiology (co-supervised with Michael D. Taylor)

Jan.2011

Cancer genomics of medulloblastoma

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Marina Olhovsky

Part-time M. Sc. student (co-supervised with Ron Pearlman); software engineer at Tony Pawson's lab

Jan. 2012

Computational predictions of protein-protein interactions

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Pegah Khosravi

Bioinformatics

Oct.2012

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Asha Rostamianfar

Computer Science

Sept.2013

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Patryk Skowron

Laboratory Medicine and Pathobiology (co-supervised with Michael D. Taylor)

Sept.2013

Cancer genomics of medulloblastoma

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Lucas Hu

Molecular Genetics (co-supervised with Andrew Emili)

Sept.2013

WormMap

Undergraduate Students

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Arkady Arkhangorodsky

University of Toronto

July-Aug 2013, June 2014 - present

High dimensional data visualization, EnrichmentMap annotation

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Tristan Frappier-Brinton

Queen's University

July - August 2014

Pubmed Publication trends

Soumil Narayan

McMaster University

May 2013-Aug 2014

Cancer genomics analysis

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Alvin Leung

Mcgill University

May 2013-Aug 2014

Cytoscape

Research Staff

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Veronique Voisin

Research Associate

Jan.2011

Pathway Analysis of Cancer Stem Cells

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Ruth Isserlin

Nov.2007

Active cell map
(Co-supervised with Andrew Emili)

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Shirley Hui

Research Associate

May.2014

Medical Decision Making

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Changjiang Xu

Research Associate

June 2014

Statistical data analysis

Software Developers

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Khalid Zhuberi

Jun.2008

GeneMANIA

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Christian Lopes

Sep.2008

GeneMANIA Cytoscape

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Jason Montojo

Sep.2008

GeneMANIA Cytoscape

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Max Franz

May 2010 (formerly U of Waterloo co-op student Jan-May 2009 and Sept-Dec 2009)

GeneMANIA

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Igor Rodchenkov

Nov.2008

Pathway Commons
BioPAX Cytoscape

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Harold Rodriguez

Feb.2009

Systems Administrator
Build Process
GeneMANIA

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Mike Kucera

Sept.2014

Cytoscape

More Photos

Past Members

Post Docs

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Deena Gendoo

with Annie Huang

Sep. 2012 - Oct. 2013

Cancer genomics on Pediatric Brain Tumours

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Iain Wallace

Co-supervised with Guri Giaever and Corey Nislow

Oct.2007-Mar.2012

Chemical genomics in yeast

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Xiaofeng Xin

Jul.2010-Nov.2011

Protein-protein interactions in C. elegans

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Magali Michaut

Jan.2009-Nov.2011

Multiple perturbations in yeast

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Daniele Merico

Co-supervised with Andrew Emili

Jan.2009-Apr.2011 (formerly visiting student since Nov.2007)

Active cell map

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Oliver Stueker

Dec.2008-Apr.2010

Cancer Stem Cells / Active cell map

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David Gfeller

Feb.2008-Feb.2010

Specificity and robustness in protein interaction networks

Graduate Students

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Omar Wagih

Computer Science

Sept.2012 - Dec.2013

Cancer genomics

Ron

Ron Ammar

Molecular Genetics (co-supervised with Corey Nislow and Guri Giaever)

Sep. 2008 - July 2013

Genomics technology in yeast, chemical screening

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Shirley Hui

Molecular Genetics

May.2007 - April 2013

Domain specificity

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Anastasija Baryshnikova

Molecular Genetics (co-supervised with Charlie Boone)

May.2006-Oct.2012

Genetic interactions in yeast

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Mohammed Alshalalfa

Visiting student from University of Calgary

May.2011-Dec 2011

Master regulators identification using network biology

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Laure Sambourg

Laboratoire TIMC-IMAG, France, Visiting student

June.2011-Dec.2011

Cancer interactome and alternative splicing

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Chris Tan

Molecular Genetics (co-supervised with Tony Pawson)

Jan.2007-Aug.2011

Network evolution

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Xiaojian Shao

China Agricultural University, China, Visiting student

Sept.2008-Sept.2010

Quantitative interaction prediction

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Vuk Pavlovic

Molecular Genetics

May.2007-2011

Protein complex detection from networks

Software Engineers

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Ovi Comes

May.2008-Jun.2010

GeneMANIA

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Rashad Badrawi

Aug.2008-Apr.2010

GeneMANIA/Pathway Commons

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Laetitia Morrison

Sep.2007-Dec.2009

Integrative Biology of Yeast

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Moyez Dharsee

Jan.2007-Oct.2008

Protein interaction prediction

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Michael Matan

Jan-Aug.2007

Integrative Biology of Yeast

Project Manager

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Sylva Donaldson

Project Manager, Coordinator of Training and Outreach

Jun.2008-Jun.2010

GeneMANIA

Quality Assurance

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Farzana Kazi

QA Analyst

Jan.2009-Jun.2010

GeneMANIA/Cytoscape/Pathway Commons

Lab Technicians

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Jun Gu

Technician (co-supervised with Dev Sidhu)

Dec.2010

Protein interaction screening

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Lianet Lopez

Technician (co-supervised with Charlie Boone)

Oct.2007-Jun.2008

Protein interaction screening

Undergraduate Students

Ruth Grace Wong
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University of Western Ontario, Computational Biochemistry

May-Aug 2014

MedSavant Pathway View Extension (Google Summer of code 2014)

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Victor Kofia

University of Toronto

May-Aug 2013, Sep 2013- present

Co-Authorship Cytoscape App, Enrichment Map App

Diana Nicholls

University of Toronto

June-Aug 2013

Pathguide.org

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Yue Dong

University of Toronto

Dec.2011 - Sep.2013

Cytoscape

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Hussam Kaka

University of Toronto

Sep. 2012 - Aug.2013

GeneMANIA

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Luke Chang

Summer Researcher

June-Aug 2013

GeneMANIA

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Xiang Xing

University of Toronto

May 2010-Aug 2012

WW domain prediction, PDZ domain prediction

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Adrian Zhu

Jan. 2011

GeneMANIA

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Ameen Modhafar

University of Waterloo Systems Design Engineering co-op student

Jan to Apr.2010

Yeast systems analysis

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Anson Maitland

University of Waterloo Mathematics co-op student

May to Aug.2009

GeneMANIA

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Quentin Shao

McMaster University Applied Mathematics co-op student

May to Aug.2009

GeneMANIA

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Michael Tsui

University of Toronto Bioinformatics

May to Aug.2009

GeneMANIA

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George Wright

McMaster University Biology and Pharmacology co-op student

May to Aug.2009

GeneMANIA

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Pauline Chao

University of Waterloo

Jan-May.2009

GeneMANIA

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Benjamin Elliott

University of Toronto Electrical Engineering

May-August.2008

Yeast systems analysis

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Ioana Ivan

University of Toronto Computational Biology 299Y student (co-supervised with Reinhart Reithmeier)

Sep.2006-Aug.2007

Membrane interactions with PDZ domains

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Kevin Ha

University of Waterloo Co-op Bioinformatics (co-supervised with Steve Gallinger)

Sep-Dec.2006,
Apr-Aug.2007

Colorectal Cancer biomarkers

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Stacy Hung

Bioinformatics, UWaterloo

Apr-Aug.2007

Protein interaction prediction

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Natalie Yeung

University of Toronto Immunology, 4th year

Jan-July.2007

Cytoscape usability

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Aseel Al Dallal

University of Waterloo Co-op Bioinformatics (co-supervised with Steve Gallinger)

Jan-Apr.2007

Colorectal Cancer biomarkers

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Faisal Naqib

University of Waterloo Faculty of Math(co-supervised with Steve Gallinger)

May-Aug.2006

Colorectal Cancer biomarkers

Project Students

Yue Dong

University of Toronto

May-Aug 2012

App Manager for Cytoscape, Cytoscape Web 2 renderers (Google Summer of Code 2012)

Bimal Ramdoyal

University of Toronto

May-Aug 2011

Proteomics analysis (4th year project course)

Marek Zaluski

Concordia University, Montreal

May-Aug 2011

HTML5 prototype for Cytoscape Web (Google Summer of Code 2011)

Yue Dong

University of Toronto

May-Aug 2011

3D Renderer for Cytoscape (Google Summer of Code 2011)

Layla Oesper

University of Wisconsin, Madison, WI

May-Aug 2010

WordCloud Plugin for Cytoscape (Google Summer of Code 2010)

Monica Raj

University of British Columbia

July.2007-April.2008

Predicting in vivo PDZ domain protein interactions (4th year research project)

Maital Ashkenazi

Hebrew University, Jerusalem

May-Aug 2007

Enhanced search feature for Cytoscape (Google Summer of Code with David States and Allan Kuchinsky)

Anna Rukosuyeva

University of Toronto, Computer Science

Sep.2007-Dec.2008

Viewing compound nodes in Cytoscape (4th year project course)

Victoria Mui

University of Toronto, Computer Science

May-Aug 2008

Label layout algorithm for Cytoscape (Google Summer of Code with Greg Wilson)

Visiting Scientists

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Carolyn Cummins

Visiting Scientist (Assistant Professor of Pharmacy)

Nov 2013

Pathway and RNA-seq analysis

Graduate Rotation Students

Alyssa Molinaro

Molecular Genetics

Sept.2014

Pathway analysis

Rong Huang

Molecular Genetics

Oct.2013

Pathway analysis

Shixuan Liu

Molecular Genetics

Sep.2013

Pathway analysis

Huy Nguyen

Molecular Genetics

Nov.2012

Enrichment maps

Huayun Hou

Molecular Genetics

Oct.2012

Pathway analysis

Jochen Weile

Molecular Genetics

Sep.2011

Pathway analysis

Akiko Sekikawa

Molecular Genetics

Sep.2010

Protein interaction network evolution

Carl Song

Molecular Genetics

Dec.2009

Pathway analysis

Gavin Wilson

Molecular Genetics

Sep.2009

Protein interaction network evolution

Brad Arshinoff

Molecular Genetics

Jan.2009

Analyzing yeast high content screening data

Devon Radford

Molecular Genetics

Nov.2008

Predicting genetic interactions in yeast from mutations in cell structure

Ron Ammar

Molecular Genetics

Oct.2008

Predicting active biomolecules in yeast

Adrian Verster

Molecular Genetics

Sept.2008

Predicting trigenic synthetic lethalic in yeast

Harshika Seepany

Medical Genetics

Oct.2007

PDZ protein interaction specificity analysis

Shirley Hui

Medical Genetics

Mar.2007

Gene expression correlation analysis

Vuk Pavlovic

Medical Genetics

Feb.2007

Protein complex detection

Trevis Alleyne

Medical Genetics

Nov.2006

Protein interactions involving SH3 domains - specificity prediction

Graham Cromar

Medical Genetics

Oct.2006

Protein interactions involving SH3 domains - interaction prediction

Chris Tan

Medical Genetics

Sep.2006

Protein interactions involving SH3 domains - specificity analysis

Members (last edited 2014-10-31 18:44:25 by GaryBader)

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