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| ||<style="text-align:center;"> {{attachment:Peter.jpg|Peter Smith|width=150 height=150}}} ||[[PeterSmith|Peter Smith]] ||Jan. 2017 ||||<style="text-align:center;">[[http://www.cytoscape.org|Cytoscape]] || ||<style="text-align:center;"> {{attachment:Manfred.jpg|Manfred Cheung}}||[[Manfred Cheung]]||Jan. 2017||||<style="text-align:left;">Manfred Cheung is a web developer and student currently studying Systems Design Engineering at the University of Waterloo. He does front end development for a web based application built to facilitate access to the Pathway Commons REST interface, as well as contributes to the development of the CytoscapeJS library. Manfred brings experience doing development work for a wide variety of organizations, from small startups to national corporations. || |
||<class="table-header">Undergraduate Students ||||||||<class="table-header" style="text-align:center;"> || ||<style="text-align:center;"> {{attachment:Peter.jpg|Peter Smith|width=150 height=150}} ||[[PeterSmith|Peter Smith]] ||University of Waterloo||||Jan.-April 2017 ||||<style="text-align:center;">[[http://www.cytoscape.org|Cytoscape]] || ||<style="text-align:center;"> {{attachment:Manfred.jpg|Manfred Cheung}}||[[Manfred Cheung]]||University of Waterloo||||Jan.-April 2017||||<style="text-align:center;">[[http://www.pathwaycommons.org|Pathway Commons]]<<BR>>[[http://www.cytoscape.org|Cytoscape]] || |
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| ||<class="table-header">Staff ||||||||<class="table-header" style="text-align:center;"> || ||<style="text-align:center;"> {{attachment:Shan.jpg}} ||[[ShanGao|Shan Gao]] ||Jun.2016 ||||<style="text-align:center;">Financial and Research Assistant || |
||<class="table-header">Financial Staff ||||||||<class="table-header" style="text-align:center;"> || ||<style="text-align:center;"> {{attachment:Shan.jpg||width="200"}} ||[[ShanGao|Shan Gao]] ||Jun.2016 ||||<style="text-align:center;">Financial and Research Assistant || |
Current Members
Bader Lab |
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Professor |
Apr.2006 |
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Post docs |
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Aug.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) |
Sept.2013 |
Cancer genomics of medulloblastoma |
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Molecular Genetics (co-supervised with Andrew Emili) |
Sept.2013 |
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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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Molecular Genetics |
Jan 2016 |
Intercellular Signalling |
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Research Staff |
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Research Associate |
Jan.2011 |
Pathway Analysis of Cancer Stem Cells |
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Research Staff |
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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Research Staff |
Sept.2014 |
- |
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Research Associate |
November 2015 |
Pathway Analysis of Cancer Stem Cells |
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Research Associate |
July 2016 |
Modeling Organoid Development |
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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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Undergraduate Students |
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University of Waterloo |
Jan.-April 2017 |
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University of Waterloo |
Jan.-April 2017 |
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Financial Staff |
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Jun.2016 |
Financial and Research Assistant |
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Past Members
Post Docs |
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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 |
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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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Laboratory Medicine and Pathobiology (co-supervised with Michael D. Taylor) |
Jan.2011-Aug.2015 |
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-Aug.2015 |
Computational predictions of protein-protein interactions |
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Computer Science |
Sept.2013-May.2015 |
- |
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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 |
May-Aug 2013, Sep 2013- Apr 2013, Sep 2014 - Aug.2015 |
Co-Authorship Cytoscape App, Enrichment Map App, 3D molecule visualization for Google Cardboard |
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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 |
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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- Aug.2015 |
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) |
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Victoria Mui |
University of Toronto, Computer Science |
May-Aug 2008 |
Label layout algorithm for Cytoscape (Google Summer of Code with Greg Wilson) |
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Visiting Scientists |
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Carolyn Cummins |
Visiting Scientist (Assistant Professor of Pharmacy) |
Nov 2013 |
Pathway and RNA-seq analysis |
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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 |
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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 |