|
Size: 22331
Comment:
|
Size: 23558
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 7: | Line 7: |
| ||<style="text-align:center;"> {{attachment:Florence.jpg}} ||Florence Cavalli ||with Michael Taylor ||Dec.2011 ||Cancer genomics || | |
| Line 11: | Line 10: |
| Line 16: | Line 13: |
| ||<style="text-align:center;"> {{attachment:Catherine.jpeg|width:"100"}} ||[[Catherine Ross|Catherine Ross]] ||Second year Master's student in the Boone/Andrews lab (co-supervised by Gary Bader)|| ||Computational pipeline to determine signs of natural positive selection for certain biological pathways among different human ethnic populations.|| | |
| Line 18: | Line 16: |
| ||<style="text-align:center;"> {{attachment:AhmadShah.JPG}} ||[[AhmadShah|Ahmad Shah]] ||Computer Science ||Sept.2014 ||- || | |
| Line 24: | Line 21: |
| ||<style="text-align:center;"> {{attachment:ruth.png}} ||[[RuthIsserlin|Ruth Isserlin]] ||Nov.2007 ||||<style="text-align:center;">Active cell map <<BR>>(Co-supervised with Andrew Emili) || | ||<style="text-align:center;"> {{attachment:ruth.png}} ||[[RuthIsserlin|Ruth Isserlin]] ||Research Staff ||Nov.2007 || Active cell map <<BR>>(Co-supervised with Andrew Emili) || |
| Line 27: | Line 24: |
| ||<style="text-align:center;"> {{attachment:AhmadShah.JPG}} ||[[AhmadShah|Ahmad Shah]] ||Research Staff ||Sept.2014 ||- || | |
| Line 35: | Line 33: |
| ||<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]] || |
|
| Line 36: | Line 37: |
| ||<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 || |
|
| Line 43: | Line 46: |
| ||<style="text-align:center;"> {{attachment:Florence.jpg}} ||Florence Cavalli ||with Michael Taylor ||Dec.2011 - June.2015 ||Cancer genomics || |
Current Members
Bader Lab |
|
|||||
|
Professor |
Apr.2006 |
|
|||
Post docs |
|
|||||
|
|
Aug.2011 |
Cancer genomics |
|||
|
|
Sep. 2013 |
Cancer genomics, Cancer mutations analysis |
|||
|
|
Jan. 2015 |
Protein Protein interactions |
|||
|
|
Jan. 2015 |
Predicting disease risk/prognosis in mental illness |
|||
Graduate Students |
|
|||||
|
Computer Science |
Sep.2008 |
Domain interaction prediction |
|||
|
Computer Science |
Sept.2010 |
Network alignment |
|||
|
Second year Master's student in the Boone/Andrews lab (co-supervised by Gary Bader) |
|
Computational pipeline to determine signs of natural positive selection for certain biological pathways among different human ethnic populations. |
|||
|
Laboratory Medicine and Pathobiology (co-supervised with Michael D. Taylor) |
Sept.2013 |
Cancer genomics of medulloblastoma |
|||
|
Molecular Genetics (co-supervised with Andrew Emili) |
Sept.2013 |
||||
|
Laboratory Medicine & Pathobiology (co-supervised with Michael D. Taylor) |
May 2015 |
- |
|||
|
Computer Science |
Sept 2015 |
Domain-peptide interaction |
|||
|
Molecular Genetics |
Jan 2016 |
Intercellular Signalling |
|||
Research Staff |
|
|||||
|
Research Associate |
Jan.2011 |
Pathway Analysis of Cancer Stem Cells |
|||
|
Research Staff |
Nov.2007 |
Active cell map |
|||
|
Research Associate |
May.2014 |
Medical Decision Making |
|||
|
Research Associate |
June 2014 |
Statistical data analysis |
|||
|
Research Staff |
Sept.2014 |
- |
|||
|
Research Associate |
November 2015 |
Pathway Analysis of Cancer Stem Cells |
|||
|
Research Associate |
July 2016 |
Modeling Organoid Development |
|||
Software Developers |
|
|||||
|
Sep.2008 |
|||||
|
May 2010 (formerly U of Waterloo co-op student Jan-May 2009 and Sept-Dec 2009) |
|||||
|
Nov.2008 |
|||||
|
Feb.2009 |
|||||
|
Sept.2014 |
|||||
Undergraduate Students |
|
|||||
|
University of Waterloo |
Jan.-April 2017 |
||||
|
University of Waterloo |
Jan.-April 2017 |
||||
Financial Staff |
|
|||
|
Jun.2016 |
Financial and Research Assistant |
||
Past Members
Post Docs |
|
||||
|
|
Jan.2011-July.2015 |
Cancer genomics |
||
|
Florence Cavalli |
with Michael Taylor |
Dec.2011 - June.2015 |
Cancer genomics |
|
|
Andrea Uetrecht |
with Jason Moffat |
Feb.2012-Aug.2015 |
Protein interactions |
|
|
|
Aug. 2013-Feb.2015 |
MedSavant and The Sick Kids Genome Clinic |
||
|
Deena Gendoo |
with Annie Huang |
Sep. 2012 - Oct. 2013 |
Cancer genomics on Pediatric Brain Tumours |
|
|
Co-supervised with Guri Giaever and Corey Nislow |
Oct.2007-Mar.2012 |
Chemical genomics in yeast |
||
|
Xiaofeng Xin |
|
Jul.2010-Nov.2011 |
Protein-protein interactions in C. elegans |
|
|
|
Jan.2009-Nov.2011 |
Multiple perturbations in yeast |
||
|
Co-supervised with Andrew Emili |
Jan.2009-Apr.2011 (formerly visiting student since Nov.2007) |
Active cell map |
||
|
|
Dec.2008-Apr.2010 |
Cancer Stem Cells / Active cell map |
||
|
|
Feb.2008-Feb.2010 |
Specificity and robustness in protein interaction networks |
||
Graduate Students |
|
||||
|
Laboratory Medicine and Pathobiology (co-supervised with Michael D. Taylor) |
Jan.2011-Aug.2015 |
Cancer genomics of medulloblastoma |
||
|
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 |
||
|
Computer Science |
Sept.2013-May.2015 |
- |
||
|
Bioinformatics |
Oct.2012 - Sep.2014 |
Gene expression regulation |
||
|
Computer Science |
Sept.2012 - Dec.2013 |
Cancer genomics |
||
|
Molecular Genetics (co-supervised with Corey Nislow and Guri Giaever) |
Sep. 2008 - July 2013 |
Genomics technology in yeast, chemical screening |
||
|
Molecular Genetics |
May.2007 - April 2013 |
Domain specificity |
||
|
Molecular Genetics (co-supervised with Charlie Boone) |
May.2006-Oct.2012 |
Genetic interactions in yeast |
||
|
Visiting student from University of Calgary |
May.2011-Dec 2011 |
Master regulators identification using network biology |
||
|
Laboratoire TIMC-IMAG, France, Visiting student |
June.2011-Dec.2011 |
Cancer interactome and alternative splicing |
||
|
Molecular Genetics (co-supervised with Tony Pawson) |
Jan.2007-Aug.2011 |
Network evolution |
||
|
China Agricultural University, China, Visiting student |
Sept.2008-Sept.2010 |
Quantitative interaction prediction |
||
|
Molecular Genetics |
May.2007-2011 |
Protein complex detection from networks |
||
Software Engineers |
|
||||
|
Patrick Magee |
|
Oct.2014-Aug.2015 |
Pharmacogenetics app, MedSavant |
|
|
Jun.2008-Jan.2015 |
||||
|
|
Sep.2008-Aug.2014 |
|||
|
|
May.2008-Jun.2010 |
|||
|
|
Aug.2008-Apr.2010 |
|||
|
|
Sep.2007-Dec.2009 |
Integrative Biology of Yeast |
||
|
|
Jan.2007-Oct.2008 |
Protein interaction prediction |
||
|
Michael Matan |
|
Jan-Aug.2007 |
Integrative Biology of Yeast |
|
Project Manager |
|
||||
|
Project Manager, Coordinator of Training and Outreach |
Jun.2008-Jun.2010 |
|||
Quality Assurance |
|
||||
|
QA Analyst |
Jan.2009-Jun.2010 |
|||
Lab Technicians |
|
||||
|
Jun Gu |
Technician (co-supervised with Dev Sidhu) |
Dec.2010 |
Protein interaction screening |
|
|
Lianet Lopez |
Technician (co-supervised with Charlie Boone) |
Oct.2007-Jun.2008 |
Protein interaction screening |
|
Undergraduate Students |
|
||||
|
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 |
||
|
University of Toronto |
July-Aug 2013, June-Sep 2014 |
High dimensional data visualization, EnrichmentMap annotation |
||
|
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 |
|
|
Alvin Leung |
Mcgill University |
May 2013-Aug 2014 |
Cytoscape |
|
|
Ruth Grace Wong |
University of Western Ontario, Computational Biochemistry |
May-Aug 2014 |
MedSavant Pathway View Extension (Google Summer of code 2014) |
|
|
University of Toronto |
May-Aug 2013, Sep 2013- Aug.2015 |
Co-Authorship Cytoscape App, Enrichment Map App |
||
|
Diana Nicholls |
University of Toronto |
June-Aug 2013 |
Pathguide.org |
|
|
Yue Dong |
University of Toronto |
Dec.2011 - Sep.2013 |
Cytoscape |
|
|
Hussam Kaka |
University of Toronto |
Sep. 2012 - Aug.2013 |
GeneMANIA |
|
|
Luke Chang |
Summer Researcher |
June-Aug 2013 |
GeneMANIA |
|
|
University of Toronto |
May 2010-Aug 2012 |
WW domain prediction, PDZ domain prediction |
||
|
Adrian Zhu |
|
Jan. 2011 |
||
|
University of Waterloo Systems Design Engineering co-op student |
Jan to Apr.2010 |
Yeast systems analysis |
||
|
University of Waterloo Mathematics co-op student |
May to Aug.2009 |
|||
|
McMaster University Applied Mathematics co-op student |
May to Aug.2009 |
|||
|
University of Toronto Bioinformatics |
May to Aug.2009 |
|||
|
McMaster University Biology and Pharmacology co-op student |
May to Aug.2009 |
|||
|
University of Waterloo |
Jan-May.2009 |
|||
|
University of Toronto Electrical Engineering |
May-August.2008 |
Yeast systems analysis |
||
|
University of Toronto Computational Biology 299Y student (co-supervised with Reinhart Reithmeier) |
Sep.2006-Aug.2007 |
Membrane interactions with PDZ domains |
||
|
University of Waterloo Co-op Bioinformatics (co-supervised with Steve Gallinger) |
Sep-Dec.2006, |
Colorectal Cancer biomarkers |
||
|
Bioinformatics, UWaterloo |
Apr-Aug.2007 |
Protein interaction prediction |
||
|
Natalie Yeung |
University of Toronto Immunology, 4th year |
Jan-July.2007 |
Cytoscape usability |
|
|
Aseel Al Dallal |
University of Waterloo Co-op Bioinformatics (co-supervised with Steve Gallinger) |
Jan-Apr.2007 |
Colorectal Cancer biomarkers |
|
|
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 |
|
||||
|
Carolyn Cummins |
Visiting Scientist (Assistant Professor of Pharmacy) |
Nov 2013 |
Pathway and RNA-seq analysis |
|
Graduate Rotation Students |
|
||
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 |