Current Members

Bader Lab

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Gary Bader

Professor

Apr.2006

Post docs

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Shamini Ayyadhury

Co-supervised with Dr. Trevor Pugh

Sept.2020

Cancer Drug Targets

Graduate Students

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Stuart Matan-Lithwick

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

May.2015

Metastasis in cancer

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Brendan Innes

Molecular Genetics

Jan.2016

Intercellular Signalling

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Hamed Heydari

Molecular Genetics

Jan.2016

Genetic interaction network analysis

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Duncan Forster

Molecular Genetics (co-supervised with Charlie Boone)

Feb.2017

Building a Unified Model of Cellular Function

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Gurnit Atwal

Molecular Genetics (co-supervised with Quaid Morris)

Jan.2017

The Genomic Evolution of Pancreatic Ductal Adenocarcinoma

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John Giorgi

Computer Science

Sept.2017

Information extraction in the biomedical domain using deep learning

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Owen Whitley

Molecular Genetics

Jan.2018

The Analysis and Integration of various types of '-omics' data to characterize cancer stem cells

[ATTACH]

Zoe Clarke

Molecular Genetics

Jan.2020

Cellular ecosystems, liver cancer evolution

[ATTACH]

Aiden Sababi

Molecular Genetics

Jan.2020

Cellular ecosystems and Single Cell Mutational analyses

[ATTACH]

Ronald Xie

Molecular Genetics

Jan.2020

Deep learning applications in electron microscopy, Single cell omics

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Daniel Stueckmann

Molecular Genetics

Jan.2020

Kidney cancer single cell genomics

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Delaram Pouyabahar

Molecular Genetics

Jan.2020

Single cell data integration, liver disease

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Qi Wu

Molecular Genetics

Jan.2021

Building a unified model of cellular function

Visiting Graduate Students

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Mehrshad Sadria

Co-supervised with Dr. Sid Goyal)

Feb 2021

Single Cell Analysis of Regeneration

Research Staff

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Ruth Isserlin

Research Staff

Nov.2007

Active cell map
(Co-supervised with Andrew Emili)

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Veronique Voisin

Research Associate

Jan.2011

Pathway Analysis of Cancer Stem Cells

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Scott Zuyderduyn

Research Associate

Aug.2011

Cancer genomics

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Changjiang Xu

Research Associate

June.2014

Statistical data analysis

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Jeff Liu

Research Associate

November.2015

Pathway Analysis of Cancer Stem Cells

Jeffrey Wong

Jeffrey Wong

Research Associate

Jan.2016

Computational Biology

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Maria Abou Chakra

Research Associate

July.2016

Modeling Organoid Development

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Tallulah Andrews

University Health Network (co-supervised with Sonya MacParland)

Jan 2020

Single Cell Genomics

Software Developers

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Christian Lopes

Sep.2008

GeneMANIA Cytoscape

Max Franz

Max Franz

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

GeneMANIA Pathway Commons Cytoscape

Mike Kucera

Mike Kucera

Sept.2014

Cytoscape

Masoud Sarabadani

Masoud Sarabadani

May 2020

Genetic interaction network analysis

Financial Staff

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Anna Corpuz

Apr.2019

Financial and Research Assistant

Undergraduate Students

Anweshi Anavadya

University of Waterloo Computer Engineering co-op student

Jan-Apr.2021

Biofactoid

More Photos

Past Members

Post Docs

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Shraddha Pai

Jan.2015-Jan 2021

Predicting disease risk/prognosis in mental illness

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Florian Goebels

Jan.2015-Sep.2017

Protein Protein interactions

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Mohamed Helmy

Sep. 2013-Aug.2017

Cancer genomics, Cancer mutations analysis

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Jüri Reimand

Jan.2011-July.2015

Cancer genomics

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Florence Cavalli

with Michael Taylor

Dec.2011 - June.2015

Cancer genomics

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Andrea Uetrecht

with Jason Moffat

Feb.2012-Aug.2015

Protein interactions

Ron

Ron Ammar

Aug. 2013-Feb.2015

MedSavant and The Sick Kids Genome Clinic

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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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Patryk Skowron

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

Sept.2013-Jan.2020

Cancer genomics of medulloblastoma

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Lucas Hu

Molecular Genetics (co-supervised with Andrew Emili)

Sept.2013-Sept.2019

WormMap

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Brian Law

Computer Science

Sept.2010-Aug.2019

Network alignment

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Thinh Tran

Molecular Genetics

Feb.2018-Jul.2019

Single cell RNAseq analysis of heart development lineages

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Catherine Ross

Molecular Genetics (co-supervised with Boone/Andrews lab)

Dec.2015-Apr.2018

Computational pipeline to determine signs of natural positive selection for certain biological pathways among different human ethnic populations.

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Shobhit Jain

Computer Science

Graduated 2018

Domain interaction prediction

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Timothy Lau

Computer Science

Sept.2015-Aug.2017

Domain-peptide interaction

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David Shih

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

Jan.2011-Aug.2015

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-Aug.2015

Computational predictions of protein-protein interactions

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Asha Rostamianfar

Computer Science

Sept.2013-May.2015

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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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Chris Tan

Molecular Genetics (co-supervised with Tony Pawson)

Jan.2007-Aug.2011

Network evolution

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Vuk Pavlovic

Molecular Genetics

May.2007-2011

Protein complex detection from networks

Visiting Graduate Students

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Anne Nohr

Visiting student from Copenhagen

Jul. 2019-Aug. 2019

Precision Medicine for Mental Health

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Laura Fedrizzi

Visiting student from Italy

Apr. 2019-May 2019

Single Cell Network Analysis

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Philipp Weber

Department of Mathematics and Computer Science, University of Southern Denmark

Sept.2018-Feb.2019

Development of new methods for the processing and analysis of breath and biogas data with the help of machine learning and deep neural network architectures. Analysis of biological networks and detection and treatment of cancer in a personalized setting.

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Valentina Corso

Visiting Student From Italy

Aug.2017-Feb.2018

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Luca Giudice

Visiting Student From Italy

Aug.2017-Feb.2018

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Rosario Distefano

Visiting student from University of Verona, Italy

Jan-Jul 2016

Biological pathway simulation

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Pegah Khosravi

Bioinformatics

Oct.2012 - Sep.2014

Gene expression regulation

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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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Xiaojian Shao

China Agricultural University, China, Visiting student

Sept.2008-Sept.2010

Quantitative interaction prediction

Research Associates

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Shirley Hui

Research Associate

May.2014-Nov.2018

Medical Decision Making

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Ahmad Shah

Research Staff

Sept.2014-Aug.2018

Precision medicine

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Shaheena Bashir

Research Associate

March 2013 - March 2014

Biostatistics

Software Developers

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Dylan Fong

Nov.2016-Dec.2018

Pathway Commons

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Igor Rodchenkov, PhD

Senior Research Associate

Nov.2008-Jan.2019

Pathway Commons
BioPAX Cytoscape

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Harold Rodriguez

Feb.2009-Jun.2018

Systems Administrator
Build Process
GeneMANIA

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Patrick Magee

Oct.2014-Aug.2015

Pharmacogenetics app, MedSavant

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Khalid Zhuberi

Jun.2008-Jan.2015

GeneMANIA

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Jason Montojo

Sep.2008-Aug.2014

GeneMANIA Cytoscape

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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

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James Wu

Thesis Project Student

Sept.2018

Text mining biomedical literature

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Dina Issakova

Undergraduate Project Student

May.2018

Evolutionary biology, computer vision/image processing, genomics data mining

Michael Wrana

University of Toronto Summer Student

May.2018

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Caitlin Christina O'Callaghan

University of Waterloo Co-Op Student

May.2018

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Rex Wen

University of Waterloo Co-Op Student

May.2018

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Logan Mosier

University of Waterloo Co-Op Student

Jan.2018-Apr.2018

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Wanxin Li

University of Waterloo Co-Op Student

Jan.2018-Apr.2018

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Jonah Dlin

University of Waterloo Co-Op Student

Sept - Dec 2017

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Harsh Mistry

University of Waterloo Co-Op Student

Sept - Dec 2017

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Geoffry Elder

University of Waterloo Co-Op Student

Sept - Dec 2017

Farzan Taj

Farzan Taj

University of Toronto

May- August 2017

Pathway Commons

Alexander Li

Alexander Li

University of Toronto

May- August 2017

Pathway Commons

Manfred

Manfred Cheung

University of Waterloo

Jan - April 2017

Pathway Commons

Peter Smith

Peter Smith

University of Waterloo

Jan - April 2017

Pathway Commons

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Victor Kofia

University of Toronto

Apr.2013 - Sept.2013, Sep 2014 - Aug.2015

Co-Authorship Cytoscape App, Enrichment Map App, 3D molecule visualization for Google Cardboard

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Arkady Arkhangorodsky

University of Toronto

July-Aug 2013, June-Sep 2014

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 2015 (3 summers)

Cancer genomics analysis

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Alvin Leung

Mcgill University

May 2013-Aug 2014

Cytoscape

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Ruth Grace Wong

University of Western Ontario, Computational Biochemistry

May-Aug 2014

MedSavant Pathway View Extension (Google Summer of code 2014)

Nickolas Goncharenko

McMaster University

May-Aug.2016

Biological pathway simulation

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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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Susan Thomas

Scientist, Biomedical Informatics Center, Mumbai, India

Sept.2018-Jan.2019

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Carolyn Cummins

Visiting Scientist (Assistant Professor of Pharmacy)

Nov 2013

Pathway and RNA-seq analysis

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Alberto Ocana

Visiting Scientist (Hospital Clínico San Carlos. Madrid)

Summer 2013

Pathway and RNA-seq analysis

Financial Staff

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Patrick Scopa

Aug.2017-Oct.2018

Financial and Research Assistant

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Shan Gao

May.2017 - Aug.2018
Jun.2016 - May.2017

Financial Administrator

Financial and Research Assistant

Graduate Rotation Students

Michael Geuenich

Molecular Genetics

Sept.2020

Qi Wu

Molecular Genetics

Sept.2020

Delaram Pouyabahar

Molecular Genetics

Nov.2019

Aiden Sababi

Molecular Genetics

Nov.2019

Sara Gordillo Sampedro

Molecular Genetics

Nov.2019

Daniel Stueckmann

Molecular Genetics

Sep.2019

Zoe Clarke

Molecular Genetics

Sep.2019

Matthaeus Ware

Molecular Genetics

Sep.2018

Jessie Medeiros

Molecular Genetics

Feb.2018

Thinh Tran

Molecular Genetics

Jan.2018

Kevin Wang

Molecular Genetics

Jan.2018

Charlotte Michelle Nguyen

Molecular Genetics

Nov.2017

Shubham Gupta

Molecular Genetics

Nov.2017

Owen Whitley

Molecular Genetics

Nov.2017

Zain Patel

Molecular Genetics

Nov.2017

James St. Pierre

Molecular Genetics

Oct.2017

Yu-Xi Xiao

Molecular Genetics

Sept.2017

Dustin Sokolowski

Molecular Genetics

Sept.2017

Alexandra Rasnitsyn

Molecular Genetics

Jul.2017-Aug.2017

Ibrahim El-Hamamy

Molecular Genetics

Mar.2017

Network/pathway analysis

Katelyn Kozma

Molecular Genetics

Feb.2017

Network/pathway analysis

Ahmad Malik

Molecular Genetics

Jan.2017

Network/pathway analysis

Duncan Forster

Molecular Genetics

Nov.2016

Network/pathway analysis

Gurnit Atwal

Molecular Genetics

Nov.2016

Network/pathway analysis

Hamed Heydari

Molecular Genetics

Nov.2015

Network/pathway analysis

Heather Gibling

Molecular Genetics

Sep.2015

Network/pathway analysis

Jeff Luong

Molecular Genetics

Sep.2015

Network/pathway analysis

Patrick Magee

Molecular Genetics

Oct.2014

Network/pathway analysis

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 2021-02-05 05:43:15 by GaryBader)

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