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| ||<style="text-align:center;"> {{attachment:Andrea.jpg}} ||Andrea Uetrecht ||with Jason Moffat ||Feb.2012 ||Protein interactions || ||<style="text-align:center;"> {{attachment:RonAmmar/ron_profile.jpg|Ron|width="250"}} ||[[RonAmmar|Ron Ammar]] || ||Aug. 2013 ||MedSavant and The Sick Kids Genome Clinic || |
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| ||<style="text-align:center;"> {{attachment:asha.JPG}} ||[[AshaRostamianfar|Asha Rostamianfar]] ||Computer Science ||Sept.2013 ||- || | |
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| ||<style="text-align:center;"> ||[[StuartMatanLithwick|Stuart Matan-Lithwick]] ||Laboratory Medicine & Pathobiology ||May 2015 ||- || | ||<style="text-align:center;"> {{attachment:StuartPhoto.JPG}} ||[[StuartMatanLithwick|Stuart Matan-Lithwick]] ||Laboratory Medicine & Pathobiology (co-supervised with [[http://www.sickkids.ca/AboutSickKids/Directory/People/T/Michael-D-Taylor.html|Michael D. Taylor]]) ||May 2015 ||- || ||<style="text-align:center;"> ||[[TimothyLau|Timothy Lau]] || Computer Science || Sept 2015 || Domain-peptide interaction || |
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| ||<style="text-align:center;"> {{attachment:Khalid.jpg}} ||[[KhalidZhumber|Khalid Zhuberi]] ||Jun.2008 ||||<style="text-align:center;">[[http://www.genemania.org/|GeneMANIA]] || | |
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| ||<style="text-align:center;"> {{attachment:Andrea.jpg}} ||Andrea Uetrecht ||with Jason Moffat ||Feb.2012-Aug.2015 ||Protein interactions || ||<style="text-align:center;"> {{attachment:RonAmmar/ron_profile.jpg|Ron|width="250"}} ||[[RonAmmar|Ron Ammar]] || ||Aug. 2013-Feb.2015 ||MedSavant and The Sick Kids Genome Clinic || |
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| ||<style="text-align:center;"> {{attachment:Pegah.png||height="200px",width="239px"}} ||[[PegahKhosravi|Pegah Khosravi]] ||Bioinformatics ||Oct.2012 - Sep.2014 ||Gene expression regulation || | ||<style="text-align:center;"> {{attachment:asha.JPG}} ||[[AshaRostamianfar|Asha Rostamianfar]] ||Computer Science ||Sept.2013 ||- || ||<style="text-align:center;"> {{attachment:Pegah.png||height="100px",width="120px"}} ||[[PegahKhosravi|Pegah Khosravi]] ||Bioinformatics ||Oct.2012 - Sep.2014 ||Gene expression regulation || |
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| ||<style="text-align:center;"> {{attachment:Jason.jpg}} ||[[JasonMontojo|Jason Montojo]] ||Sep.2008 ||||<style="text-align:center;">[[http://www.genemania.org/|GeneMANIA]] [[http://www.cytoscape.org|Cytoscape]] || | ||<style="text-align:center;"> {{attachment:patrick.jpg||height="116",width="116"}} ||Patrick Magee || ||Oct.2014-Aug.2015 ||||<style="text-align:center;">Pharmacogenetics app, MedSavant || ||<style="text-align:center;"> {{attachment:Khalid.jpg}} ||[[KhalidZhumber|Khalid Zhuberi]] ||Jun.2008-Jan.2015 ||||<style="text-align:center;">[[http://www.genemania.org/|GeneMANIA]] || ||<style="text-align:center;"> {{attachment:Jason.jpg}} ||[[JasonMontojo|Jason Montojo]] || ||Sep.2008-Aug.2014 ||||<style="text-align:center;">[[http://www.genemania.org/|GeneMANIA]] [[http://www.cytoscape.org|Cytoscape]] || |
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| ||<style="text-align:center;"> ||<style="text-align:center;">Soumil Narayan ||McMaster University ||May 2013-Aug 2014 ||Cancer genomics analysis || | ||<style="text-align:center;"> ||<style="text-align:center;">Soumil Narayan ||McMaster University ||May 2013-Aug 2015 (3 summers) ||Cancer genomics analysis || |
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| ||||<style="text-align:center;">Ruth Grace Wong <<BR>> {{attachment:RuthGraceWong.jpg}} ||University of Western Ontario, Computational Biochemistry ||May-Aug 2014 ||MedSavant Pathway View Extension (Google Summer of code 2014) || | ||<style="text-align:center;">{{attachment:RuthGraceWong.jpg}} || Ruth Grace Wong ||University of Western Ontario, Computational Biochemistry ||May-Aug 2014 ||MedSavant Pathway View Extension (Google Summer of code 2014) || |
Current Members
Bader Lab |
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Associate Professor |
Apr.2006 |
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Post docs |
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Jan.2011 |
Cancer genomics |
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Aug.2011 |
Cancer genomics |
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Florence Cavalli |
with Michael Taylor |
Dec.2011 |
Cancer genomics |
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Sep. 2013 |
Cancer genomics, Cancer mutations analysis |
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Jan. 2015 |
Protein Protein interactions |
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Jan. 2015 |
Predicting disease risk/prognosis in mental illness |
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Graduate Students |
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Computer Science |
Sep.2008 |
Domain interaction prediction |
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Computer Science |
Sept.2010 |
Network alignment |
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Laboratory Medicine and Pathobiology (co-supervised with Michael D. Taylor) |
Jan.2011 |
Cancer genomics of medulloblastoma |
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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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Laboratory Medicine and Pathobiology (co-supervised with Michael D. Taylor) |
Sept.2013 |
Cancer genomics of medulloblastoma |
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Molecular Genetics (co-supervised with Andrew Emili) |
Sept.2013 |
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Computer Science |
Sept.2014 |
- |
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Laboratory Medicine & Pathobiology (co-supervised with Michael D. Taylor) |
May 2015 |
- |
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Computer Science |
Sept 2015 |
Domain-peptide interaction |
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Undergraduate Students |
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University of Toronto |
May-Aug 2013, Sep 2013- Apr 2013, Sep 2014 - present |
Co-Authorship Cytoscape App, Enrichment Map App, 3D molecule visualization for Google Cardboard |
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Research Staff |
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Research Associate |
Jan.2011 |
Pathway Analysis of Cancer Stem Cells |
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Nov.2007 |
Active cell map |
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Research Associate |
May.2014 |
Medical Decision Making |
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Research Associate |
June 2014 |
Statistical data analysis |
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Software Developers |
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Sep.2008 |
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May 2010 (formerly U of Waterloo co-op student Jan-May 2009 and Sept-Dec 2009) |
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Nov.2008 |
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Feb.2009 |
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Sept.2014 |
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Past Members
Post Docs |
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Andrea Uetrecht |
with Jason Moffat |
Feb.2012-Aug.2015 |
Protein interactions |
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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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Co-supervised with Guri Giaever and Corey Nislow |
Oct.2007-Mar.2012 |
Chemical genomics in yeast |
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Xiaofeng Xin |
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Jul.2010-Nov.2011 |
Protein-protein interactions in C. elegans |
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Jan.2009-Nov.2011 |
Multiple perturbations in yeast |
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Co-supervised with Andrew Emili |
Jan.2009-Apr.2011 (formerly visiting student since Nov.2007) |
Active cell map |
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Dec.2008-Apr.2010 |
Cancer Stem Cells / Active cell map |
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Feb.2008-Feb.2010 |
Specificity and robustness in protein interaction networks |
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Graduate Students |
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Computer Science |
Sept.2013 |
- |
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Bioinformatics |
Oct.2012 - Sep.2014 |
Gene expression regulation |
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Computer Science |
Sept.2012 - Dec.2013 |
Cancer genomics |
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Molecular Genetics (co-supervised with Corey Nislow and Guri Giaever) |
Sep. 2008 - July 2013 |
Genomics technology in yeast, chemical screening |
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Molecular Genetics |
May.2007 - April 2013 |
Domain specificity |
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Molecular Genetics (co-supervised with Charlie Boone) |
May.2006-Oct.2012 |
Genetic interactions in yeast |
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Visiting student from University of Calgary |
May.2011-Dec 2011 |
Master regulators identification using network biology |
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Laboratoire TIMC-IMAG, France, Visiting student |
June.2011-Dec.2011 |
Cancer interactome and alternative splicing |
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Molecular Genetics (co-supervised with Tony Pawson) |
Jan.2007-Aug.2011 |
Network evolution |
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China Agricultural University, China, Visiting student |
Sept.2008-Sept.2010 |
Quantitative interaction prediction |
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Molecular Genetics |
May.2007-2011 |
Protein complex detection from networks |
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Software Engineers |
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Patrick Magee |
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Oct.2014-Aug.2015 |
Pharmacogenetics app, MedSavant |
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Jun.2008-Jan.2015 |
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Sep.2008-Aug.2014 |
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May.2008-Jun.2010 |
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Aug.2008-Apr.2010 |
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Sep.2007-Dec.2009 |
Integrative Biology of Yeast |
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Jan.2007-Oct.2008 |
Protein interaction prediction |
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Michael Matan |
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Jan-Aug.2007 |
Integrative Biology of Yeast |
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Project Manager |
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Project Manager, Coordinator of Training and Outreach |
Jun.2008-Jun.2010 |
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Quality Assurance |
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QA Analyst |
Jan.2009-Jun.2010 |
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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 |
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Undergraduate Students |
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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 |
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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) |
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University of Toronto |
May-Aug 2013, Sep 2013- present |
Co-Authorship Cytoscape App, Enrichment Map App |
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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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University of Toronto |
May 2010-Aug 2012 |
WW domain prediction, PDZ domain prediction |
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Adrian Zhu |
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Jan. 2011 |
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University of Waterloo Systems Design Engineering co-op student |
Jan to Apr.2010 |
Yeast systems analysis |
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University of Waterloo Mathematics co-op student |
May to Aug.2009 |
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McMaster University Applied Mathematics co-op student |
May to Aug.2009 |
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University of Toronto Bioinformatics |
May to Aug.2009 |
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McMaster University Biology and Pharmacology co-op student |
May to Aug.2009 |
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University of Waterloo |
Jan-May.2009 |
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University of Toronto Electrical Engineering |
May-August.2008 |
Yeast systems analysis |
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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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University of Waterloo Co-op Bioinformatics (co-supervised with Steve Gallinger) |
Sep-Dec.2006, |
Colorectal Cancer biomarkers |
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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 |
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Project Students |
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Yue Dong |
University of Toronto |
May-Aug 2012 |
App Manager for Cytoscape, Cytoscape Web 2 renderers (Google Summer of Code 2012) |
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Bimal Ramdoyal |
University of Toronto |
May-Aug 2011 |
Proteomics analysis (4th year project course) |
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Marek Zaluski |
Concordia University, Montreal |
May-Aug 2011 |
HTML5 prototype for Cytoscape Web (Google Summer of Code 2011) |
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Yue Dong |
University of Toronto |
May-Aug 2011 |
3D Renderer for Cytoscape (Google Summer of Code 2011) |
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Layla Oesper |
University of Wisconsin, Madison, WI |
May-Aug 2010 |
WordCloud Plugin for Cytoscape (Google Summer of Code 2010) |
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Monica Raj |
University of British Columbia |
July.2007-April.2008 |
Predicting in vivo PDZ domain protein interactions (4th year research project) |
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Maital Ashkenazi |
Hebrew University, Jerusalem |
May-Aug 2007 |
Enhanced search feature for Cytoscape (Google Summer of Code with David States and Allan Kuchinsky) |
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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 |
|
||||
|
Carolyn Cummins |
Visiting Scientist (Assistant Professor of Pharmacy) |
Nov 2013 |
Pathway and RNA-seq analysis |
|
Graduate Rotation Students |
|
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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 |
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 |