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| Deletions are marked like this. | Additions are marked like this. |
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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 || ||<style="text-align:center;"> {{attachment:mhelmy3.png}} ||[[MohamedHelmy|Mohamed Helmy]] ||Cancer genomics, Cancer mutations analysis||Sep. 2013 || || ||<style="text-align:center;"> {{attachment:Florian.png}} ||[[FlorianGoebels|Florian Goebels]] || ||Jan. 2014 || Protein Protein interactions || ||<style="text-align:center;"> {{attachment:Shraddha.png}} ||[[ShraddhaPai|Shraddha Pai]] || ||Jan. 2014 || Predicting disease risk/prognosis in psychiatry || |
||<style="text-align:center;"> {{attachment:mhelmy3.png}} ||[[MohamedHelmy|Mohamed Helmy]] || ||Sep. 2013 ||Cancer genomics, Cancer mutations analysis || ||<style="text-align:center;"> {{attachment:Florian.png}} ||[[FlorianGoebels|Florian Goebels]] || ||Jan. 2015 ||Protein Protein interactions || ||<style="text-align:center;"> {{attachment:Shraddha.jpg}} ||[[ShraddhaPai|Shraddha Pai]] || ||Jan. 2015 ||Predicting disease risk/prognosis in mental illness || |
| Line 20: | Line 19: |
| ||<style="text-align:center;"> {{attachment:Pegah.png||height="200px",width="239px"}} ||[[PegahKhosravi|Pegah Khosravi]] ||Bioinformatics ||Oct.2012 ||- || ||<style="text-align:center;"> {{attachment:asha.JPG}} ||[[AshaRostamianfar|Asha Rostamianfar]] ||Computer Science ||Sept.2013 ||- || ||<style="text-align:center;"> {{attachment:Patryk.jpg}} ||[[Patryk Skowron|Patryk Skowron]] ||Laboratory Medicine and Pathobiology (co-supervised with [[http://www.sickkids.ca/AboutSickKids/Directory/People/T/Michael-D-Taylor.html|Michael D. Taylor]]) ||Sept.2013 ||Cancer genomics of medulloblastoma || |
||<style="text-align:center;"> {{attachment:Patryk.jpg}} ||[[Patryk Skowron]] ||Laboratory Medicine and Pathobiology (co-supervised with [[http://www.sickkids.ca/AboutSickKids/Directory/People/T/Michael-D-Taylor.html|Michael D. Taylor]]) ||Sept.2013 ||Cancer genomics of medulloblastoma || |
| Line 24: | Line 21: |
| ||<style="text-align:center;"> {{attachment:AhmadShah.JPG}} ||[[AhmadShah|Ahmad Shah]] ||Computer Science ||Sept.2014 ||- || ||<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;"> {{attachment:Tim.jpg}} ||[[TimothyLau|Timothy Lau]] || Computer Science || Sept 2015 || Domain-peptide interaction || |
|
| Line 25: | Line 25: |
| ||<style="text-align:center;"> {{attachment:arkady.jpg}} ||<style="text-align:center;"> [[ArkadyArk|Arkady Arkhangorodsky]] || University of Toronto || July-Aug 2013, June 2014 - present ||High dimensional data visualization, EnrichmentMap annotation|| ||<style="text-align:center;"> {{attachment:tristan.jpg}} ||<style="text-align:center;"> Tristan Frappier-Brinton || Queen's University || July - August 2014 ||Pubmed Publication trends|| ||<style="text-align:center;"> ||<style="text-align:center;">Soumil Narayan ||McMaster University ||May 2013-Aug 2014 ||Cancer genomics analysis || ||<style="text-align:center;"> {{attachment:Alvin.png|xx.jpg|height="116",width="116"}} ||<style="text-align:center;">Alvin Leung ||Mcgill University ||May 2013-Aug 2014 ||Cytoscape || |
||<style="text-align:center;"> {{attachment:victor.jpg}} ||<style="text-align:center;">[[kofiav|Victor Kofia]] ||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 || |
| Line 32: | Line 29: |
| ||<style="text-align:center;"> {{attachment:Shirley.jpg}} ||[[ShirleyHui|Shirley Hui]] ||Research Associate ||May.2014||Medical Decision Making || ||<style="text-align:center;"> {{attachment:Changjiang.jpg}} ||[[ChangjiangXu|Changjiang Xu]] ||Research Associate ||June 2014||Statistical data analysis || |
||<style="text-align:center;"> {{attachment:Shirley.jpg}} ||[[ShirleyHui|Shirley Hui]] ||Research Associate ||May.2014 ||Medical Decision Making || ||<style="text-align:center;"> {{attachment:Changjiang.jpg}} ||[[ChangjiangXu|Changjiang Xu]] ||Research Associate ||June 2014 ||Statistical data analysis || |
| Line 35: | Line 32: |
| ||<style="text-align:center;"> {{attachment:Khalid.jpg}} ||[[KhalidZhumber|Khalid Zhuberi]] ||Jun.2008 ||||<style="text-align:center;">[[http://www.genemania.org/|GeneMANIA]] || | |
| Line 37: | Line 33: |
| ||<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:qrcode.png}} ||[[MaxFranz|Max Franz]] ||May 2010 (formerly U of Waterloo co-op student Jan-May 2009 and Sept-Dec 2009) ||||<style="text-align:center;">[[http://www.genemania.org/|GeneMANIA]] || |
||<style="text-align:center;"> {{attachment:qrcode.png|Max Franz|height=120 width=120}} ||[[MaxFranz|Max Franz]] ||May 2010 (formerly U of Waterloo co-op student Jan-May 2009 and Sept-Dec 2009) ||||<style="text-align:center;">[[http://www.genemania.org/|GeneMANIA]] || |
| Line 41: | Line 36: |
| ||<style="text-align:center;"> {{attachment:mike-pic.jpg}} ||[[MikeKucera|Mike Kucera]] ||Sept.2014 ||||<style="text-align:center;">[[http://www.cytoscape.org|Cytoscape]] || | ||<style="text-align:center;"> {{attachment:mike-pic.jpg|Mike Kucera|width=150 height=150}} ||[[MikeKucera|Mike Kucera]] ||Sept.2014 ||||<style="text-align:center;">[[http://www.cytoscape.org|Cytoscape]] || |
| Line 48: | Line 44: |
| ||<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 || |
|
| Line 56: | Line 54: |
| ||<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 || |
|
| Line 57: | Line 57: |
| ||<style="text-align:center;"> {{attachment:RonAmmar/ron_profile.jpg|Ron|width="250"}} ||[[RonAmmar|Ron Ammar]] || Molecular Genetics (co-supervised with Corey Nislow and Guri Giaever)||Sep. 2008 - July 2013 ||Genomics technology in yeast, chemical screening || | ||<style="text-align:center;"> {{attachment:RonAmmar/ron_profile.jpg|Ron|width="250"}} ||[[RonAmmar|Ron Ammar]] ||Molecular Genetics (co-supervised with Corey Nislow and Guri Giaever) ||Sep. 2008 - July 2013 ||Genomics technology in yeast, chemical screening || |
| Line 66: | Line 66: |
| ||<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]] || |
|
| Line 79: | Line 82: |
| ||||<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:arkady.jpg}} ||<style="text-align:center;">[[ArkadyArk|Arkady Arkhangorodsky]] ||University of Toronto ||July-Aug 2013, June 2014 - present ||High dimensional data visualization, EnrichmentMap annotation || ||<style="text-align:center;"> {{attachment:tristan.jpg}} ||<style="text-align:center;">Tristan Frappier-Brinton ||Queen's University ||July - August 2014 ||Pubmed Publication trends || ||<style="text-align:center;"> ||<style="text-align:center;">Soumil Narayan ||McMaster University ||May 2013-Aug 2015 (3 summers) ||Cancer genomics analysis || ||<style="text-align:center;"> {{attachment:Alvin.png|xx.jpg|height="116",width="116"}} ||<style="text-align:center;">Alvin Leung ||Mcgill University ||May 2013-Aug 2014 ||Cytoscape || ||<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) || |
| Line 115: | Line 122: |
| ||Patrick Magee ||Molecular Genetics ||Oct.2014 ||Network/pathway analysis || | |
| Line 116: | Line 124: |
| ||Rong Huang||Molecular Genetics ||Oct.2013 ||Pathway analysis || ||Shixuan Liu||Molecular Genetics ||Sep.2013 ||Pathway analysis || |
||Rong Huang ||Molecular Genetics ||Oct.2013 ||Pathway analysis || ||Shixuan Liu ||Molecular Genetics ||Sep.2013 ||Pathway analysis || |
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 |
|
|
Florence Cavalli |
with Michael Taylor |
Dec.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 |
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|||
|
Computer Science |
Sep.2008 |
Domain interaction prediction |
|
|
Computer Science |
Sept.2010 |
Network alignment |
|
|
Laboratory Medicine and Pathobiology (co-supervised with Michael D. Taylor) |
Jan.2011 |
Cancer genomics of medulloblastoma |
|
|
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 |
|
|
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 |
||
|
Computer Science |
Sept.2014 |
- |
|
|
Laboratory Medicine & Pathobiology (co-supervised with Michael D. Taylor) |
May 2015 |
- |
|
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Computer Science |
Sept 2015 |
Domain-peptide interaction |
|
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 |
|
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 |
|
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 |
|||
|
Sept.2014 |
|||
![[ATTACH]](/Members?action=AttachFile&do=upload_form&ticket=006724334d.1c198dcc68d64bf2aee7948cde002d934d2923c4&target=Tim.jpg "[ATTACH]"){kind=small}
Past Members
Post Docs |
|
||||
|
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 |
|
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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 |
|
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 |
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||||
|
Computer Science |
Sept.2013 |
- |
||
|
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 |
July-Aug 2013, June 2014 - present |
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- present |
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 |