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| ||<style="text-align:center;"> {{attachment:duncan.jpg}} ||[[Duncan Forster|Duncan Forster]] || Molecular Genetics (co-supervised with Charlie Boone) ||Feb.2017 || The unknownome || ||<style="text-align:center;"> {{attachment:gurnit.jpg}} ||[[Gurnit Atwal |Gurnit Atwal ]] || Molecular Genetics (co-supervised with Quaid Morris) || Jan.2017 || Tumour evolution || ||<style="text-align:center;"> {{attachment:johngiorgi.jpg|}}||[[John Giorgi]]||Computer Science||Sept.2017||||<style="text-align:center;">[[http://www.pathwaycommons.org|Pathway Commons]]|| ||<style="text-align:center;"> {{attachment:owenwhitney.jpg||width=120}}||[[Owen Whitley]]||Molecular Genetics||Sept.2017||||<style="text-align:center;">The Analysis and Integration of various types of '-omics' data to characterize cancer stem cells|| |
||<style="text-align:center;"> {{attachment:duncan.jpg}} ||[[Duncan Forster|Duncan Forster]] || Molecular Genetics (co-supervised with Charlie Boone) ||Feb.2017 || Building a Unified Model of Cellular Function || ||<style="text-align:center;"> {{attachment:gurnit.jpg}} ||[[Gurnit Atwal |Gurnit Atwal ]] || Molecular Genetics (co-supervised with Quaid Morris) || Jan.2017 || The Genomic Evolution of Pancreatic Ductal Adenocarcinoma || ||<style="text-align:center;"> {{attachment:johngiorgi.jpg|}}||[[John Giorgi]]||Computer Science||Sept.2017||||<style="text-align:center;">Information extraction in the biomedical domain using deep learning|| ||<style="text-align:center;"> {{attachment:owenwhitney.jpg||width=120}}||[[Owen Whitley]]||Molecular Genetics||Jan.2018||||<style="text-align:center;">The Analysis and Integration of various types of '-omics' data to characterize cancer stem cells|| |
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| ||<style="text-align:center;"> {{attachment:anon.png||width=200}}||[[Philipp Weber]]||Department of Mathematics and Computer Science, University of Southern Denmark||Sept.2018|||| | ||<style="text-align:center;"> {{attachment:pweb.png||width=200}}||[[Philipp Weber]]||Department of Mathematics and Computer Science, University of Southern Denmark||Sept.2018||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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| ||<style="text-align:center;"> {{attachment:anon.png}} ||[[Susan Thomas]] ||Scientist, Biomedical Informatics Center, Mumbai, India||Sept.2018|||| | |
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| ||<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]] || ||<style="text-align:center;"> {{attachment:IgorRodchenkov.jpg}} ||[[IgorRodchenkov|Igor Rodchenkov]] ||Nov.2008 ||||<style="text-align:center;">[[http://www.pathwaycommons.org|Pathway Commons]]<<BR>>[[http://www.biopax.org|BioPAX]] [[http://www.cytoscape.org|Cytoscape]] || |
||<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]] [[http://www.pathwaycommons.org|Pathway Commons]] [[http://www.cytoscape.org|Cytoscape]] || |
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| ||<style="text-align:center;"> {{attachment:anon.png||width="100"}} ||Dina Issakova ||University of Toronto Summer Student||May.2018 |||| |
||<style="text-align:center;"> {{attachment:dina.png||width="200"}} ||Dina Issakova ||Undergraduate Project Student||May.2018 ||Evolutionary biology, computer vision/image processing, genomics data mining|| ||<style="text-align:center;"> {{attachment:jameswu.jpg||width="200"}} ||James Wu ||Thesis Project Student||Sept.2018 ||Text mining biomedical literature|| ||<class="table-header">Visiting Scientists ||||||||<class="table-header" style="text-align:center;"> || ||<style="text-align:center;"> {{attachment:anon.png}} ||[[Susan Thomas]] ||Scientist, Biomedical Informatics Center, Mumbai, India||Sept.2018|||| |
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| ||<style="text-align:center;"> {{attachment:IgorRodchenkov.jpg}} ||[[IgorRodchenkov|Igor Rodchenkov, PhD]] ||Senior Research Associate ||Nov.2008-Jan.2019 ||||<style="text-align:center;">[[http://www.pathwaycommons.org|Pathway Commons]]<<BR>>[[http://www.biopax.org|BioPAX]] [[http://www.cytoscape.org|Cytoscape]] || | |
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| ||||Michael Wrana ||University of Toronto Summer Student||May.2018 |||| | ||<style="text-align:center;">||<style="text-align:center;">Michael Wrana||University of Toronto Summer Student ||May.2018 |||| |
Current Members
Bader Lab |
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Professor |
Apr.2006 |
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Post docs |
|
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|
|
Jan.2015 |
Predicting disease risk/prognosis in mental illness |
||
Graduate Students |
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||||
|
Computer Science |
Sept.2010 |
Network alignment |
||
|
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 |
Metastasis in cancer |
||
|
Molecular Genetics (co-supervised with Boone/Andrews lab) |
Dec.2015 |
Computational pipeline to determine signs of natural positive selection for certain biological pathways among different human ethnic populations. |
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|
Molecular Genetics |
Jan.2016 |
Intercellular Signalling |
||
|
Molecular Genetics |
Jan.2016 |
Genetic interaction network analysis |
||
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Molecular Genetics (co-supervised with Charlie Boone) |
Feb.2017 |
Building a Unified Model of Cellular Function |
||
|
Molecular Genetics (co-supervised with Quaid Morris) |
Jan.2017 |
The Genomic Evolution of Pancreatic Ductal Adenocarcinoma |
||
|
Computer Science |
Sept.2017 |
Information extraction in the biomedical domain using deep learning |
||
|
Molecular Genetics |
Jan.2018 |
The Analysis and Integration of various types of '-omics' data to characterize cancer stem cells |
||
|
Molecular Genetics |
Feb. 2018 |
Single cell RNAseq analysis of heart development lineages |
||
|
Department of Mathematics and Computer Science, University of Southern Denmark |
Sept.2018 |
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. |
||
Research Staff |
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||||
|
Research Staff |
Nov.2007 |
Active cell map |
||
|
Research Associate |
Jan.2011 |
Pathway Analysis of Cancer Stem Cells |
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Research Associate |
Aug.2011 |
Cancer genomics |
||
|
Research Associate |
May.2014 |
Medical Decision Making |
||
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Research Associate |
June.2014 |
Statistical data analysis |
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Research Associate |
November.2015 |
Pathway Analysis of Cancer Stem Cells |
||
|
Research Associate |
Jan.2016 |
Computational Biology |
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Research Associate |
July.2016 |
Modeling Organoid Development |
||
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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Sept.2014 |
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Nov.2016 |
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Financial Staff |
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Aug.2017 |
Financial and Research Assistant |
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Undergraduate Students |
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Dina Issakova |
Undergraduate Project Student |
May.2018 |
Evolutionary biology, computer vision/image processing, genomics data mining |
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James Wu |
Thesis Project Student |
Sept.2018 |
Text mining biomedical literature |
|
Visiting Scientists |
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Scientist, Biomedical Informatics Center, Mumbai, India |
Sept.2018 |
|||
Past Members
Post Docs |
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|
|
Jan.2015-Sep.2017 |
Protein Protein interactions |
|||
|
|
Sep. 2013-Aug.2017 |
Cancer genomics, Cancer mutations analysis |
|||
|
|
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 |
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|
|
Dec.2008-Apr.2010 |
Cancer Stem Cells / Active cell map |
|||
|
|
Feb.2008-Feb.2010 |
Specificity and robustness in protein interaction networks |
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Graduate Students |
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|||||
|
Computer Science |
Graduated 2018 |
Domain interaction prediction |
|||
|
Summer student, Molecular Genetics |
Jul.2017-Aug.2017 |
Precision medicine |
|||
|
Computer Science |
Sept.2015-Aug.2017 |
Domain-peptide interaction |
|||
|
Visiting student from University of Verona, Italy |
Jan-Jul 2016 |
Biological pathway simulation |
|||
|
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 |
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|
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 |
|||
Research Associates |
|
|||||
|
Research Staff |
Sept.2014-Aug.2018 |
Precision medicine |
|||
Software Developers |
|
|||||
|
Senior Research Associate |
Nov.2008-Jan.2019 |
||||
|
Feb.2009-Jun.2018 |
|||||
|
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 |
|
|||||
Michael Wrana |
University of Toronto Summer Student |
May.2018 |
||||
|
Caitlin Christina O'Callaghan |
University of Waterloo Co-Op Student |
May.2018 |
|||
|
Rex Wen |
University of Waterloo Co-Op Student |
May.2018 |
|||
|
Logan Mosier |
University of Waterloo Co-Op Student |
Jan.2018-Apr.2018 |
|||
|
Wanxin Li |
University of Waterloo Co-Op Student |
Jan.2018-Apr.2018 |
|||
|
Visiting Student From Italy |
Aug. 2017 - Feb. 2018 |
||||
|
Visiting Student From Italy |
Aug. 2017 - Feb. 2018 |
||||
|
Jonah Dlin |
University of Waterloo Co-Op Student |
Sept - Dec 2017 |
|||
|
Harsh Mistry |
University of Waterloo Co-Op Student |
Sept - Dec 2017 |
|||
|
Geoffry Elder |
University of Waterloo Co-Op Student |
Sept - Dec 2017 |
|||
|
University of Toronto |
May- August 2017 |
||||
|
University of Toronto |
May- August 2017 |
||||
|
University of Waterloo |
Jan - April 2017 |
||||
|
University of Waterloo |
Jan - April 2017 |
||||
|
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) |
||
|
McMaster University |
May-Aug.2016 |
Biological pathway simulation |
|||
|
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 |
||
Financial Staff |
|
|||||
|
May.2017 - Aug.2018 |
Financial Administrator |
||||
Graduate Rotation Students |
|
||
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 |
|
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 |
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 |