Diff for "Members" - Bader Lab @ The University of Toronto

Differences between revisions 187 and 246 (spanning 59 versions)

Current Members

Bader Lab
	Gary Bader	Associate Professor	Apr.2006
Post docs
	Jüri Reimand		Jan.2011	Cancer genomics
	Scott Zuyderduyn		Aug.2011	Cancer genomics
	Florence Cavalli	with Michael Taylor	Dec.2011	Cancer genomics
	Mohamed Helmy		Sep. 2013	Cancer genomics, Cancer mutations analysis
	Florian Goebels		Jan. 2015	Protein Protein interactions
	Shraddha Pai		Jan. 2015	Predicting disease risk/prognosis in mental illness

Graduate Students
	Shobhit Jain	Computer Science	Sep.2008	Domain interaction prediction
	Brian Law	Computer Science	Sept.2010	Network alignment
	David Shih	Laboratory Medicine and Pathobiology (co-supervised with Michael D. Taylor)	Jan.2011	Cancer genomics of medulloblastoma
	Marina Olhovsky	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
	Patryk Skowron	Laboratory Medicine and Pathobiology (co-supervised with Michael D. Taylor)	Sept.2013	Cancer genomics of medulloblastoma
	Lucas Hu	Molecular Genetics (co-supervised with Andrew Emili)	Sept.2013	WormMap
	Ahmad Shah	Computer Science	Sept.2014	-
	Stuart Matan-Lithwick	Laboratory Medicine & Pathobiology (co-supervised with Michael D. Taylor)	May 2015	-
	Timothy Lau	Computer Science	Sept 2015	Domain-peptide interaction
Undergraduate Students
	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
Research Staff
	Veronique Voisin	Research Associate	Jan.2011	Pathway Analysis of Cancer Stem Cells
	Ruth Isserlin	Nov.2007	Active cell map (Co-supervised with Andrew Emili)
	Shirley Hui	Research Associate	May.2014	Medical Decision Making
	Changjiang Xu	Research Associate	June 2014	Statistical data analysis
Software Developers
	Christian Lopes	Sep.2008	GeneMANIA Cytoscape
	Max Franz	May 2010 (formerly U of Waterloo co-op student Jan-May 2009 and Sept-Dec 2009)	GeneMANIA
	Igor Rodchenkov	Nov.2008	Pathway Commons BioPAX Cytoscape
	Harold Rodriguez	Feb.2009	Systems Administrator Build Process GeneMANIA
	Mike Kucera	Sept.2014	Cytoscape

More Photos

Past Members

Post Docs
	Andrea Uetrecht	with Jason Moffat	Feb.2012-Aug.2015	Protein interactions
	Ron Ammar		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
	Iain Wallace	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
	Magali Michaut		Jan.2009-Nov.2011	Multiple perturbations in yeast
	Daniele Merico	Co-supervised with Andrew Emili	Jan.2009-Apr.2011 (formerly visiting student since Nov.2007)	Active cell map
	Oliver Stueker		Dec.2008-Apr.2010	Cancer Stem Cells / Active cell map
	David Gfeller		Feb.2008-Feb.2010	Specificity and robustness in protein interaction networks
Graduate Students
	Asha Rostamianfar	Computer Science	Sept.2013	-
	Pegah Khosravi	Bioinformatics	Oct.2012 - Sep.2014	Gene expression regulation
	Omar Wagih	Computer Science	Sept.2012 - Dec.2013	Cancer genomics
	Ron Ammar	Molecular Genetics (co-supervised with Corey Nislow and Guri Giaever)	Sep. 2008 - July 2013	Genomics technology in yeast, chemical screening
	Shirley Hui	Molecular Genetics	May.2007 - April 2013	Domain specificity
	Anastasija Baryshnikova	Molecular Genetics (co-supervised with Charlie Boone)	May.2006-Oct.2012	Genetic interactions in yeast
	Mohammed Alshalalfa	Visiting student from University of Calgary	May.2011-Dec 2011	Master regulators identification using network biology
	Laure Sambourg	Laboratoire TIMC-IMAG, France, Visiting student	June.2011-Dec.2011	Cancer interactome and alternative splicing
	Chris Tan	Molecular Genetics (co-supervised with Tony Pawson)	Jan.2007-Aug.2011	Network evolution
	Xiaojian Shao	China Agricultural University, China, Visiting student	Sept.2008-Sept.2010	Quantitative interaction prediction
	Vuk Pavlovic	Molecular Genetics	May.2007-2011	Protein complex detection from networks
Software Engineers
	Patrick Magee		Oct.2014-Aug.2015	Pharmacogenetics app, MedSavant
	Khalid Zhuberi	Jun.2008-Jan.2015	GeneMANIA
	Jason Montojo		Sep.2008-Aug.2014	GeneMANIA Cytoscape
	Ovi Comes		May.2008-Jun.2010	GeneMANIA
	Rashad Badrawi		Aug.2008-Apr.2010	GeneMANIA/Pathway Commons
	Laetitia Morrison		Sep.2007-Dec.2009	Integrative Biology of Yeast
	Moyez Dharsee		Jan.2007-Oct.2008	Protein interaction prediction
	Michael Matan		Jan-Aug.2007	Integrative Biology of Yeast
Project Manager
	Sylva Donaldson	Project Manager, Coordinator of Training and Outreach	Jun.2008-Jun.2010	GeneMANIA
Quality Assurance
	Farzana Kazi	QA Analyst	Jan.2009-Jun.2010	GeneMANIA/Cytoscape/Pathway Commons
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
	Arkady Arkhangorodsky	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)
	Victor Kofia	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
	Xiang Xing	University of Toronto	May 2010-Aug 2012	WW domain prediction, PDZ domain prediction
	Adrian Zhu		Jan. 2011	GeneMANIA
	Ameen Modhafar	University of Waterloo Systems Design Engineering co-op student	Jan to Apr.2010	Yeast systems analysis
	Anson Maitland	University of Waterloo Mathematics co-op student	May to Aug.2009	GeneMANIA
	Quentin Shao	McMaster University Applied Mathematics co-op student	May to Aug.2009	GeneMANIA
	Michael Tsui	University of Toronto Bioinformatics	May to Aug.2009	GeneMANIA
	George Wright	McMaster University Biology and Pharmacology co-op student	May to Aug.2009	GeneMANIA
	Pauline Chao	University of Waterloo	Jan-May.2009	GeneMANIA
	Benjamin Elliott	University of Toronto Electrical Engineering	May-August.2008	Yeast systems analysis
	Ioana Ivan	University of Toronto Computational Biology 299Y student (co-supervised with Reinhart Reithmeier)	Sep.2006-Aug.2007	Membrane interactions with PDZ domains
	Kevin Ha	University of Waterloo Co-op Bioinformatics (co-supervised with Steve Gallinger)	Sep-Dec.2006, Apr-Aug.2007	Colorectal Cancer biomarkers
	Stacy Hung	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
Huy Nguyen	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

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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:Deena.jpg|alt text|width="150"}} ||Deena Gendoo ||with Annie Huang ||Sept. 2012 ||Cancer genomics on Pediatric Brain Tumours ||
||<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]] || ||Sep. 2013 || ||
+||<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 ||
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-||<style="text-align:center;"> {{attachment:omarwagih.jpg}} ||[[OmarWagih|Omar Wagih]] ||Computer Science ||Sept.2012 ||Cancer genomics ||
||<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]] ||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:Lucas.jpg}} ||[[LucasHu|Lucas Hu]] ||Molecular Genetics (co-supervised with [[http://www.utoronto.ca/emililab/|Andrew Emili]]) ||Sept.2013 ||WormMap ||
||<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 ||
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-||<style="text-align:center;"> {{attachment:victor.jpg}} ||<style="text-align:center;">[[kofiav|Victor Kofia]] ||University of Toronto ||May-Aug 2013, Sep 2013- present ||Co-Authorship Cytoscape App, Enrichment Map App ||
+||<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 ||
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+||<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 ||
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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: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]] ||
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-||<class="table-header">Visiting Scientists ||||||||<class="table-header" style="text-align:center;"> ||
||<style="text-align:center;"> {{attachment:Carolyn.jpg|alt text|width="150"}} ||Carolyn Cummins ||Visiting Scientist (Assistant Professor of Pharmacy) ||Nov 2013 ||Pathway and RNA-seq analysis ||
+||<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]] ||
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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 ||
||<style="text-align:center;"> {{attachment:Deena.jpg|alt text|width="150"}} ||Deena Gendoo ||with Annie Huang ||Sep. 2012 - Oct. 2013 ||Cancer genomics on Pediatric Brain Tumours ||
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-||<style="text-align:center;"> {{attachment:Shirley.jpg}} ||[[ShirleyHui|Shirley Hui]] ||Molecular Genetics ||May.2007 ||Domain specificity ||
+||<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 ||
||<style="text-align:center;"> {{attachment:omarwagih.jpg}} ||[[OmarWagih|Omar Wagih]] ||Computer Science ||Sept.2012 - Dec.2013 ||Cancer genomics ||
||<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:Shirley.jpg}} ||[[ShirleyHui|Shirley Hui]] ||Molecular Genetics ||May.2007 - April 2013 ||Domain specificity ||
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+||<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;"> {{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) ||
||<style="text-align:center;"> {{attachment:victor.jpg}} ||<style="text-align:center;">[[kofiav|Victor Kofia]] ||University of Toronto ||May-Aug 2013, Sep 2013- present ||Co-Authorship Cytoscape App, Enrichment Map App ||
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-||<style="text-align:center;"> ||<style="text-align:center;">Soumil Narayan ||McMaster University ||May-Aug 2013 ||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-Sep 2013 ||Cytoscape ||
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-||||<style="text-align:center;">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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-||<class="table-header">High School Students ||||||||<class="table-header" style="text-align:center;"> ||
||<style="text-align:center;"> {{attachment:arkady.jpg}} ||<style="text-align:center;">Arkady Arkhangorodsky ||Summer Researcher ||July-Aug 2013 ||High dimensional data visualization ||
+||<class="table-header">Visiting Scientists ||||||||<class="table-header" style="text-align:center;"> ||
||<style="text-align:center;"> {{attachment:Carolyn.jpg|alt text|width="150"}} ||Carolyn Cummins ||Visiting Scientist (Assistant Professor of Pharmacy) ||Nov 2013 ||Pathway and RNA-seq analysis ||
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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 ||