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| *[:GaryBader:Gary Bader] - Assistant Professor | #acl All:read == Current Members == ||<class=""table-header"">Bader Lab ||||||||<class=""table-header"" style=""text-align:center; ""> || ||<style=""text-align:center; ""> {{attachment:gary.png}} ||[[GaryBader|Gary Bader]] ||Professor ||Apr.2006 || || ||<class=""table-header"">Post docs ||||||||<class=""table-header"" style=""text-align:center; "">|| ||<style=""text-align:center; ""> {{attachment:S.Ayyadhury.JPG}} ||[[ShaminiAyyadhury|Shamini Ayyadhury]] ||Co-supervised with [[https://medbio.utoronto.ca/faculty/pugh|Dr. Trevor Pugh]] ||Sept.2020 ||Cancer Drug Targets || ||<class=""table-header"">Graduate Students ||||||||<class=""table-header"" style=""text-align:center; ""> || ||<style=""text-align:center; ""> {{attachment:binnes.jpg}} ||[[BrendanInnes|Brendan Innes]] ||Molecular Genetics ||Jan.2016 ||Intercellular Signalling || ||<style=""text-align:center; ""> {{attachment:hamed.jpg}} ||[[Hamed Heydari]] ||Molecular Genetics ||Jan.2016 ||Genetic interaction network analysis || ||<style=""text-align:center; ""> {{attachment:duncan.jpg}} ||[[Duncan Forster]] ||Molecular Genetics (co-supervised with Charlie Boone) ||Feb.2017 ||Building a Unified Model of Cellular Function || ||<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="150"}} ||[[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 || ||<style=""text-align:center; ""> {{attachment:Z.Clarke.jpg||width="150"}} ||[[Zoe Clarke]] ||Molecular Genetics ||Jan.2020 ||||<style=""text-align:center; "">Cellular ecosystems, liver cancer evolution || ||<style=""text-align:center; ""> {{attachment:A.Sabibi.JPG||width="150"}} ||[[Aiden Sababi]] ||Molecular Genetics ||Jan.2020 ||||<style=""text-align:center; "">Cellular ecosystems and Single Cell Mutational analyses || ||<style=""text-align:center; ""> {{attachment:R.Xie.JPG||width="150"}} ||[[Ronald Xie]] ||Molecular Genetics ||Jan.2020 ||||<style=""text-align:center; "">Deep learning applications in electron microscopy, Single cell omics || ||<style=""text-align:center; ""> {{attachment:D.Stuekmann.JPG||width="150"}} ||[[Daniel Stueckmann]] ||Molecular Genetics ||Jan.2020 ||||<style=""text-align:center; "">Kidney cancer single cell genomics || ||<style=""text-align:center; ""> {{attachment:D.Pouyabahar.jpg||width="150"}} ||[[Delaram Pouyabahar]] ||Molecular Genetics ||Jan.2020 ||||<style=""text-align:center; "">Single cell data integration, liver disease || ||<style=""text-align:center; ""> {{attachment:Q.Wu.jpg||width="150"}} ||[[Qi Wu]] ||Molecular Genetics ||Jan.2021 ||||<style=""text-align:center; "">Building a unified model of cellular function || ||<class=""table-header"">Visiting Graduate Students ||||||||<class=""table-header"" style=""text-align:center; ""> || ||<style=""text-align:center; ""> {{attachment:M.Sadria.jpg||width="150"}} ||[[MehrshadSadria|Mehrshad Sadria]] ||Co-supervised with [[https://goyallab.wordpress.com/|Dr. Sid Goyal]]) ||Feb 2021 ||Single Cell Analysis of Regeneration || ||<class=""table-header"">Research Staff ||||||||<class=""table-header"" style=""text-align:center; ""> || ||<style=""text-align:center; ""> {{attachment:ruth.png}} ||[[RuthIsserlin|Ruth Isserlin]] ||Research Staff ||Nov.2007 ||Pathway and Network Analysis || ||<style=""text-align:center; ""> {{attachment:Veronique.png}} ||[[VeroniqueVoisin|Veronique Voisin]] ||Research Associate ||Jan.2011 ||Pathway Analysis of Cancer Stem Cells || ||<style=""text-align:center; ""> {{attachment:scott.jpg}} ||[[ScottZuyderduyn|Scott Zuyderduyn]] ||Research Associate ||Aug.2011 ||Cancer genomics || ||<style=""text-align:center; ""> {{attachment:Changjiang.jpg}} ||[[ChangjiangXu|Changjiang Xu]] ||Research Associate ||June.2014 ||Statistical data analysis || ||<style=""text-align:center; ""> {{attachment:Jeff.jpg}} ||[[JeffLiu|Jeff Liu]] ||Research Associate ||November.2015 ||Pathway Analysis of Cancer Stem Cells || ||<style=""text-align:center; ""> {{attachment:jeffwong.jpg|Jeffrey Wong|height="120 width=120"}} ||[[JeffreyWong|Jeffrey Wong]] ||Research Associate ||Jan.2016 ||Computational Biology || ||<style=""text-align:center; ""> {{attachment:MAC_UTO.jpg}} ||[[MariaAbouChakra|Maria Abou Chakra]] ||Research Associate ||July.2016 || Organoid Development || ||<style=""text-align:center; ""> {{attachment:T.Andrews.JPG|alt text|width="150"}} ||Tallulah Andrews ||University Health Network (co-supervised with [[https://www.uhnresearch.ca/researcher/sonya-macparland/|Sonya MacParland)]] ||Jan 2020 ||Single Cell Genomics || ||<style=""text-align:center; ""> {{attachment:anon.png}} ||[[Kevin Nixon]] ||Research Associate ||May 2020 || Princess Margaret multi-omics data interpretation team || ||<style=""text-align:center; ""> {{attachment:anon.png}} ||[[Arvind Singh Mer]] ||Research Associate ||April 2021 || Princess Margaret multi-omics data interpretation team || ||<style=""text-align:center; ""> {{attachment:anon.png}} ||[[Wail Ba-alawi]] ||Research Associate ||May 2021 || Princess Margaret multi-omics data interpretation team || ||<class=""table-header"">Software Developers ||||||||<class=""table-header"" style=""text-align:center; ""> || ||<style=""text-align:center; ""> {{attachment:Christian.jpg}} ||[[ChristianLopes|Christian Lopes]] ||Sep.2008 ||||<style=""text-align:center; "">[[http://www.genemania.org/|GeneMANIA]] [[http://www.cytoscape.org|Cytoscape]] || ||<style=""text-align:center; "">{{attachment:Max.jpeg|Max Franz|width="150 height=150"}} ||[[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]] || ||<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]] [[https://apps.cytoscape.org/apps/enrichmentmap|EnrichmentMap]]|| ||<style=""text-align:center; ""> {{attachment:M.Sarabadani.jpg|Masoud Sarabadani|width="150 height=150"}} ||[[MasoudSarabadani|Masoud Sarabadani]] ||May 2020 ||||<style=""text-align:center; "">[[Genetic interaction network analysis]] || ||<class=""table-header"">Financial Staff ||||||||<class=""table-header"" style=""text-align:center; ""> || ||<style=""text-align:center; ""> {{attachment:Anna.jpg||width="130"}} ||[[AnnaCorpuz|Anna Corpuz]] ||Apr.2019 ||||<style=""text-align:center; "">Financial and Research Assistant || ||<class=""table-header"">Undergraduate Students ||||||||<class=""table-header"" style=""text-align:center; ""> || ||<style=""text-align:center; ""> ||Anweshi Anavadya ||University of Waterloo Computer Engineering co-op student ||Jan-Apr.2021 ||[[https://biofactoid.org/|Biofactoid]] || ||<class=""table-header"">[[Members/Photos|More Photos]] || == Past Members == ||<class=""table-header"">Post Docs ||||||||<class=""table-header"" style=""text-align:center; ""> || ||<style=""text-align:center; ""> {{attachment:Shraddha.jpg}} ||[[ShraddhaPai|Shraddha Pai]] || ||Jan.2015-Jan 2021||Predicting disease risk/prognosis in mental illness || ||<style=""text-align:center; ""> {{attachment:Florian.png}} ||[[FlorianGoebels|Florian Goebels]] || ||Jan.2015-Sep.2017 ||Protein Protein interactions || ||<style=""text-align:center; ""> {{attachment:mhelmy3.png}} ||[[MohamedHelmy|Mohamed Helmy]] || ||Sep. 2013-Aug.2017 ||Cancer genomics, Cancer mutations analysis || ||<style=""text-align:center; ""> {{attachment:Juri_Reimand_th.jpg}} ||[[JuriReimand|Jüri Reimand]] || ||Jan.2011-July.2015 ||Cancer genomics || ||<style=""text-align:center; ""> {{attachment:Florence.jpg}} ||Florence Cavalli ||with Michael Taylor ||Dec.2011 - June.2015 ||Cancer genomics || ||<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 || ||<style=""text-align:center; ""> {{attachment:iain.png}} ||[[IainWallace|Iain Wallace]] ||Co-supervised with [[http://chemogenomics.med.utoronto.ca/|Guri Giaever and Corey Nislow]] ||Oct.2007-Mar.2012 ||Chemical genomics in yeast || ||<style=""text-align:center; ""> {{attachment:xiaofeng.jpeg}} ||Xiaofeng Xin || ||Jul.2010-Nov.2011 ||Protein-protein interactions in C. elegans || ||<style=""text-align:center; ""> {{attachment:magali.png}} ||[[MagaliMichaut|Magali Michaut]] || ||Jan.2009-Nov.2011 ||Multiple perturbations in yeast || ||<style=""text-align:center; ""> {{attachment:DanieleM.jpg}} ||[[DanieleMerico|Daniele Merico]] ||Co-supervised with [[http://www.emililab.org/home/|Andrew Emili]] ||Jan.2009-Apr.2011 (formerly visiting student since Nov.2007) ||Active cell map || ||<style=""text-align:center; ""> {{attachment:oliver.jpg}} ||[[OliverStueker|Oliver Stueker]] || ||Dec.2008-Apr.2010 ||Cancer Stem Cells / Active cell map || ||<style=""text-align:center; ""> {{attachment:david.jpg}} ||[[DavidGfeller|David Gfeller]] || ||Feb.2008-Feb.2010 ||Specificity and robustness in protein interaction networks || ||<class=""table-header"">Graduate Students ||||||||<class=""table-header"" style=""text-align:center; ""> || ||<style=""text-align:center; ""> {{attachment:gurnit.jpg}} ||[[Gurnit Atwal]] ||Molecular Genetics (co-supervised with Quaid Morris) ||Jan.2017-Mar.2021 ||The Genomic Evolution of Pancreatic Ductal Adenocarcinoma || ||<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-Feb.2021 ||Metastasis in cancer || ||<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-Jan.2020 ||Cancer genomics of medulloblastoma || ||<style=""text-align:center; ""> {{attachment:Lucas.jpg}} ||[[LucasHu|Lucas Hu]] ||Molecular Genetics (co-supervised with [[https://www.emililab.org/home/|Andrew Emili]]) ||Sept.2013-Sept.2019 ||WormMap || ||<style=""text-align:center; ""> {{attachment:Brian.jpg}} ||[[BrianLaw|Brian Law]] ||Computer Science ||Sept.2010-Aug.2019 ||Network alignment || ||<style=""text-align:center; ""> {{attachment:thinh2.png||width="200"}} ||[[Thinh Tran]] ||Molecular Genetics ||Feb.2018-Jul.2019 ||Single cell RNAseq analysis of heart development lineages || ||<style=""text-align:center; ""> {{attachment:Catherine.jpeg|width:"100"}} ||[[Catherine Ross]] ||Molecular Genetics (co-supervised with Boone/Andrews lab) ||Dec.2015-Apr.2018 ||Computational pipeline to determine signs of natural positive selection for certain biological pathways among different human ethnic populations. || ||<style=""text-align:center; ""> {{attachment:shobhit.png}} ||[[ShobhitJain|Shobhit Jain]] ||Computer Science ||Graduated 2018 ||Domain interaction prediction || ||<style=""text-align:center; ""> {{attachment:tim.jpg}} ||[[TimothyLau|Timothy Lau]] ||Computer Science ||Sept.2015-Aug.2017 ||Domain-peptide interaction || ||<style=""text-align:center; ""> {{attachment:davids_tn.jpg}} ||[[DavidShih|David Shih]] ||Laboratory Medicine and Pathobiology (co-supervised with [[http://www.sickkids.ca/AboutSickKids/Directory/People/T/Michael-D-Taylor.html|Michael D. Taylor]]) ||Jan.2011-Aug.2015 ||Cancer genomics of medulloblastoma || ||<style=""text-align:center; ""> {{attachment:olhovsky.jpg}} ||[[http://baderlab.org/MarinaOlhovsky|Marina Olhovsky]] ||Part-time M. Sc. student (co-supervised with [[http://www.yorku.ca/ronp/|Ron Pearlman]]); software engineer at [[http://pawsonlab.mshri.on.ca|Tony Pawson]]'s lab ||Jan. 2012-Aug.2015 ||Computational predictions of protein-protein interactions || ||<style=""text-align:center; ""> {{attachment:asha.JPG}} ||[[AshaRostamianfar|Asha Rostamianfar]] ||Computer Science ||Sept.2013-May.2015 ||- || ||<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 || ||<style=""text-align:center; ""> {{attachment:anastasija.jpg}} ||[[AnastasijaBaryshnikova|Anastasija Baryshnikova]] ||Molecular Genetics (co-supervised with [[http://sites.utoronto.ca/boonelab/|Charlie Boone]]) ||May.2006-Oct.2012 ||Genetic interactions in yeast || ||<style=""text-align:center; ""> {{attachment:Chris.jpg}} ||[[ChrisTan|Chris Tan]] ||Molecular Genetics (co-supervised with [[http://pawsonlab.mshri.on.ca/|Tony Pawson]]) ||Jan.2007-Aug.2011 ||Network evolution || ||<style=""text-align:center; ""> {{attachment:vuk.png}} ||[[VukPavlovic|Vuk Pavlovic]] ||Molecular Genetics ||May.2007-2011 ||Protein complex detection from networks || ||<class=""table-header"">Visiting Graduate Students ||||||||<class=""table-header"" style=""text-align:center; ""> || ||<style=""text-align:center; ""> {{attachment:AnneNohr.JPG||width="200"}} ||[[AnneNohr|Anne Nohr]] ||Visiting student from Copenhagen ||Jul. 2019-Aug. 2019 ||Precision Medicine for Mental Health || ||<style=""text-align:center; ""> {{attachment:anon.png}} ||[[LauraFedrizzi|Laura Fedrizzi]] ||Visiting student from Italy ||Apr. 2019-May 2019 ||Single Cell Network Analysis || ||<style=""text-align:center; ""> {{attachment:pweb.png||width="200"}} ||[[Philipp Weber]] ||Department of Mathematics and Computer Science, University of Southern Denmark ||Sept.2018-Feb.2019 ||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. || ||<style=""text-align:center; ""> {{attachment:valentina.jpg||width="150"}} ||[[Valentina Corso]] ||Visiting Student From Italy ||Aug.2017-Feb.2018 ||||<style=""text-align:center; ""> || ||<style=""text-align:center; ""> {{attachment:luca.jpg||width="200"}} ||[[Luca Giudice]] ||Visiting Student From Italy ||Aug.2017-Feb.2018 ||||<style=""text-align:center; ""> || ||<style=""text-align:center; ""> {{attachment:Rosario.png}} ||[[Rosario Distefano]] ||Visiting student from University of Verona, Italy ||Jan-Jul 2016 ||Biological pathway simulation || ||<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:MohammedAlshalalfa.jpg|width="250}} ||[[Mohammed Alshalalfa]] ||Visiting student from University of Calgary ||May.2011-Dec 2011 ||Master regulators identification using network biology || ||<style=""text-align:center; ""> {{attachment:sambourg.png}} ||[[LaureSambourg|Laure Sambourg]] ||[[http://www-timc.imag.fr/?lang=en|Laboratoire TIMC-IMAG]], France, Visiting student ||June.2011-Dec.2011 ||Cancer interactome and alternative splicing || ||<style=""text-align:center; ""> {{attachment:xiaojian.png}} ||[[XiaojianShao|Xiaojian Shao]] ||[[http://www.cau.edu.cn/|China Agricultural University]], China, Visiting student ||Sept.2008-Sept.2010 ||Quantitative interaction prediction || ||<class=""table-header"">Research Associates ||||||||<class=""table-header"" style=""text-align:center; ""> || ||<style=""text-align:center; ""> {{attachment:Shirley.jpg}} ||[[ShirleyHui|Shirley Hui]] ||Research Associate ||May.2014-Nov.2018 ||Medical Decision Making || ||<style=""text-align:center; ""> {{attachment:AhmadShah.JPG}} ||[[AhmadShah|Ahmad Shah]] ||Research Staff ||Sept.2014-Aug.2018 ||Precision medicine || ||<style=""text-align:center; ""> {{attachment:shaheena.jpg}} ||Shaheena Bashir ||Research Associate ||March 2013 - March 2014 ||Biostatistics || ||<class=""table-header"">Software Developers ||||||||<class=""table-header"" style=""text-align:center; ""> || ||<style=""text-align:center; ""> {{attachment:dylan.jpg||width="150"}} ||[[Dylan Fong]] ||Nov.2016-Dec.2018 ||||<style=""text-align:center; "">[[http://www.pathwaycommons.org|Pathway Commons]] || ||<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]] || ||<style=""text-align:center; ""> {{attachment:Harold.jpg}} ||[[HaroldRodriguez|Harold Rodriguez]] ||Feb.2009-Jun.2018 ||||<style=""text-align:center; "">[[http://baderlab.org/Intranet/SysAdmin|Systems Administrator]]<<BR>> [[http://baderlab.org/Genemania/BuildProcess|Build Process]] <<BR>> [[http://www.genemania.org/|GeneMANIA]] || ||<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]] || ||<style=""text-align:center; ""> {{attachment:Ovi.jpg}} ||[[OviComes|Ovi Comes]] || ||May.2008-Jun.2010 ||<style=""text-align:center; "">[[http://www.genemania.org/|GeneMANIA]] || ||<style=""text-align:center; ""> {{attachment:Rashad.jpg}} ||[[RashadBadrawi|Rashad Badrawi]] || ||Aug.2008-Apr.2010 ||<style=""text-align:center; "">[[http://www.genemania.org/|GeneMANIA]]/[[http://www.pathwaycommons.org/pc/|Pathway Commons]] || ||<style=""text-align:center; ""> {{attachment:Laetitia.jpg}} ||[[LaetitiaMorrison|Laetitia Morrison]] || ||Sep.2007-Dec.2009 ||<style=""text-align:center; "">Integrative Biology of Yeast || ||<style=""text-align:center; ""> {{attachment:moyez.png}} ||[[MoyezDharsee|Moyez Dharsee]] || ||Jan.2007-Oct.2008 ||<style=""text-align:center; "">Protein interaction prediction || ||<style=""text-align:center; ""> {{attachment:matan.png}} ||Michael Matan || ||Jan-Aug.2007 ||<style=""text-align:center; "">Integrative Biology of Yeast || ||<class=""table-header"">Project Manager ||||||||<class=""table-header"" style=""text-align:center; ""> || ||<style=""text-align:center; ""> {{attachment:Sylva.jpg}} ||[[SylvaDonaldson|Sylva Donaldson]] ||Project Manager, Coordinator of Training and Outreach ||Jun.2008-Jun.2010 ||[[http://www.genemania.org|GeneMANIA]] || ||<class=""table-header"">Quality Assurance ||||||||<class=""table-header"" style=""text-align:center; ""> || ||<style=""text-align:center; ""> {{attachment:Farzana.jpg}} ||[[FarzanaKazi|Farzana Kazi]] ||QA Analyst ||Jan.2009-Jun.2010 ||[[http://www.genemania.org|GeneMANIA]]/[[http://www.cytoscape.org|Cytoscape]]/[[http://www.pathwaycommons.org/pc/|Pathway Commons]] || ||<class=""table-header"">Lab Technicians ||||||||<class=""table-header"" style=""text-align:center; ""> || ||<style=""text-align:center; ""> {{attachment:Jun.jpg}} ||Jun Gu ||Technician (co-supervised with [[http://sites.utoronto.ca/sidhulab/|Dev Sidhu]]) ||Dec.2010 ||Protein interaction screening || ||<style=""text-align:center; ""> {{attachment:lianet.jpg}} ||Lianet Lopez ||Technician (co-supervised with [[http://sites.utoronto.ca/boonelab/|Charlie Boone]]) ||Oct.2007-Jun.2008 ||Protein interaction screening || ||<class=""table-header"">Undergraduate Students ||||||||<class=""table-header"" style=""text-align:center; ""> || ||<style=""text-align:center; ""> {{attachment:jameswu.jpg||width="200"}} ||James Wu ||Thesis Project Student ||Sept.2018 ||Text mining biomedical literature || ||<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; ""> ||<style=""text-align:center; "">Michael Wrana ||University of Toronto Summer Student ||May.2018 || || ||<style=""text-align:center; ""> {{attachment:caitlin.png||width="200"}} ||Caitlin Christina O'Callaghan ||University of Waterloo Co-Op Student ||May.2018 || || ||<style=""text-align:center; ""> {{attachment:anon.png||width="100"}} ||Rex Wen ||University of Waterloo Co-Op Student ||May.2018 || || ||<style=""text-align:center; ""> {{attachment:anon.png||width="100"}} ||Logan Mosier ||University of Waterloo Co-Op Student ||Jan.2018-Apr.2018 || || ||<style=""text-align:center; ""> {{attachment:anon.png||width="100"}} ||Wanxin Li ||University of Waterloo Co-Op Student ||Jan.2018-Apr.2018 || || ||<style=""text-align:center; ""> {{attachment:anon.png}} ||Jonah Dlin ||University of Waterloo Co-Op Student ||Sept - Dec 2017 || || ||<style=""text-align:center; ""> {{attachment:harsh.jpg||width="200"}} ||Harsh Mistry ||University of Waterloo Co-Op Student ||Sept - Dec 2017 || || ||<style=""text-align:center; ""> {{attachment:anon.png}} ||Geoffry Elder ||University of Waterloo Co-Op Student ||Sept - Dec 2017 || || ||<style=""text-align:center; ""> {{attachment:Farzan.jpg|Farzan Taj|width="150 height=150"}} ||[[Farzan Taj]] ||University of Toronto ||May- August 2017 ||||<style=""text-align:center; "">[[http://www.pathwaycommons.org|Pathway Commons]] || ||<style=""text-align:center; ""> {{attachment:Alex li.jpg|Alexander Li|width="150 height=150"}} ||[[AlexanderLi|Alexander Li]] ||University of Toronto ||May- August 2017 ||||<style=""text-align:center; "">[[http://www.pathwaycommons.org|Pathway Commons]] || || ||<style=""text-align:center; ""> {{attachment:Manfred.jpg|Manfred|width="150 height=150"}} ||[[ManfredCheung|Manfred Cheung]] ||University of Waterloo ||Jan - April 2017 ||||<style=""text-align:center; "">[[http://www.pathwaycommons.org|Pathway Commons]] || || ||<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.pathwaycommons.org|Pathway Commons]] || || ||<style=""text-align:center; ""> {{attachment:victor.jpg}} ||<style=""text-align:center; "">[[kofiav|Victor Kofia]] ||University of Toronto ||Apr.2013 - Sept.2013, Sep 2014 - Aug.2015 ||Co-Authorship Cytoscape App, Enrichment Map App, 3D molecule visualization for Google Cardboard || ||<style=""text-align:center; ""> {{attachment:arkady.jpg}} ||<style=""text-align:center; "">[[ArkadyArk|Arkady Arkhangorodsky]] ||University of Toronto ||July-Aug 2013, June-Sep 2014 ||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; ""> ||<style=""text-align:center; "">[[Nickolas Goncharenko]] ||McMaster University ||May-Aug.2016 ||Biological pathway simulation || ||<style=""text-align:center; ""> {{attachment:anon.png}} ||<style=""text-align:center; "">Diana Nicholls ||University of Toronto ||June-Aug 2013 ||Pathguide.org || ||<style=""text-align:center; ""> {{attachment:yue.jpg}} ||<style=""text-align:center; "">Yue Dong ||University of Toronto ||Dec.2011 - Sep.2013 ||Cytoscape || ||<style=""text-align:center; ""> {{attachment:hussam.jpg|xx.jpg|height="116",width="116"}} ||<style=""text-align:center; "">Hussam Kaka ||University of Toronto ||Sep. 2012 - Aug.2013 ||GeneMANIA || ||<style=""text-align:center; ""> {{attachment:luke.jpg}} ||<style=""text-align:center; "">Luke Chang ||Summer Researcher ||June-Aug 2013 ||GeneMANIA || ||<style=""text-align:center; ""> {{attachment:xx.jpg}} ||[[XiangXing|Xiang Xing]] ||University of Toronto ||May 2010-Aug 2012 ||WW domain prediction, PDZ domain prediction || ||<style=""text-align:center; ""> {{attachment:adrian.jpg}} ||Adrian Zhu || ||Jan. 2011 ||||<style=""text-align:center; "">[[http://www.genemania.org/|GeneMANIA]] || ||<style=""text-align:center; ""> {{attachment:Ameen.png}} ||[[AmeenModhafar|Ameen Modhafar]] ||University of Waterloo Systems Design Engineering co-op student ||Jan to Apr.2010 ||Yeast systems analysis || ||<style=""text-align:center; ""> {{attachment:Anson.jpg}} ||[[AnsonMaitland|Anson Maitland]] ||University of Waterloo Mathematics co-op student ||May to Aug.2009 ||[[http://beta.genemania.org/|GeneMANIA]] || ||<style=""text-align:center; ""> {{attachment:Quentin.jpg}} ||[[QuentinShao|Quentin Shao]] ||McMaster University Applied Mathematics co-op student ||May to Aug.2009 ||[[http://beta.genemania.org/|GeneMANIA]] || ||<style=""text-align:center; ""> {{attachment:Michael.jpg}} ||[[MichaelTsui|Michael Tsui]] ||University of Toronto Bioinformatics ||May to Aug.2009 ||[[http://beta.genemania.org/|GeneMANIA]] || ||<style=""text-align:center; ""> {{attachment:George.jpg}} ||[[GeorgeWright|George Wright]] ||McMaster University Biology and Pharmacology co-op student ||May to Aug.2009 ||[[http://beta.genemania.org/|GeneMANIA]] || ||<style=""text-align:center; ""> {{attachment:Pauline.jpg}} ||[[PaulineChao|Pauline Chao]] ||University of Waterloo ||Jan-May.2009 ||[[http://beta.genemania.org/|GeneMANIA]] || ||<style=""text-align:center; ""> {{attachment:ben.jpg}} ||[[BenElliott|Benjamin Elliott]] ||University of Toronto Electrical Engineering ||May-August.2008 ||Yeast systems analysis || ||<style=""text-align:center; ""> {{attachment:ioana.jpg}} ||[[IoanaIvan|Ioana Ivan]] ||University of Toronto Computational Biology 299Y student (co-supervised with [[http://biochemistry.utoronto.ca/reithmeier/bch.html|Reinhart Reithmeier]]) ||Sep.2006-Aug.2007 ||Membrane interactions with PDZ domains || ||<style=""text-align:center; ""> {{attachment:kevin.jpg}} ||[[KevinHa|Kevin Ha]] ||University of Waterloo Co-op Bioinformatics (co-supervised with [[http://www.lunenfeld.ca/researchers/gallinger/|Steve Gallinger]]) ||Sep-Dec.2006,<<BR>>Apr-Aug.2007 ||Colorectal Cancer biomarkers || ||<style=""text-align:center; ""> {{attachment:stacy.png}} ||[[StacyHung|Stacy Hung]] ||Bioinformatics, UWaterloo ||Apr-Aug.2007 ||Protein interaction prediction || ||<style=""text-align:center; ""> {{attachment:natalie.png}} ||Natalie Yeung ||University of Toronto Immunology, 4th year ||Jan-July.2007 ||Cytoscape usability || ||<style=""text-align:center; ""> {{attachment:aseel2.png}} ||Aseel Al Dallal ||University of Waterloo Co-op Bioinformatics (co-supervised with [[http://www.lunenfeld.ca/researchers/gallinger/|Steve Gallinger]]) ||Jan-Apr.2007 ||Colorectal Cancer biomarkers || ||<style=""text-align:center; ""> {{attachment:faisal.gif}} ||Faisal Naqib ||University of Waterloo Faculty of Math(co-supervised with [[http://www.lunenfeld.ca/researchers/gallinger/|Steve Gallinger]]) ||May-Aug.2006 ||Colorectal Cancer biomarkers || ||<class=""table-header"">Project Students ||||||||<class=""table-header"" style=""text-align:center; ""> || ||||<style=""text-align:center; "">Yue Dong ||University of Toronto ||May-Aug 2012 ||App Manager for Cytoscape, Cytoscape Web 2 renderers (Google Summer of Code 2012) || ||||<style=""text-align:center; "">Bimal Ramdoyal ||University of Toronto ||May-Aug 2011 ||Proteomics analysis (4th year project course) || ||||<style=""text-align:center; "">Marek Zaluski ||Concordia University, Montreal ||May-Aug 2011 ||HTML5 prototype for Cytoscape Web (Google Summer of Code 2011) || ||||<style=""text-align:center; "">Yue Dong ||University of Toronto ||May-Aug 2011 ||3D Renderer for Cytoscape (Google Summer of Code 2011) || ||||<style=""text-align:center; "">Layla Oesper ||University of Wisconsin, Madison, WI ||May-Aug 2010 ||WordCloud Plugin for Cytoscape (Google Summer of Code 2010) || ||||<style=""text-align:center; "">Monica Raj ||University of British Columbia ||July.2007-April.2008 ||Predicting in vivo PDZ domain protein interactions (4th year research project) || ||||<style=""text-align:center; "">Maital Ashkenazi ||Hebrew University, Jerusalem ||May-Aug 2007 ||Enhanced search feature for Cytoscape (Google Summer of Code with David States and Allan Kuchinsky) || ||||<style=""text-align:center; "">Anna Rukosuyeva ||University of Toronto, Computer Science ||Sep.2007-Dec.2008 ||Viewing compound nodes in Cytoscape (4th year project course) || ||||<style=""text-align:center; "">Victoria Mui ||University of Toronto, Computer Science ||May-Aug 2008 ||Label layout algorithm for Cytoscape (Google Summer of Code with Greg Wilson) || ||<class=""table-header"">Visiting Scientists ||||||||<class=""table-header"" style=""text-align:center; ""> || ||<style=""text-align:center; ""> {{attachment:susan-ICMR.jpg||width="200"}} ||[[Susan Thomas]] ||Scientist, Biomedical Informatics Center, Mumbai, India ||Sept.2018-Jan.2019 || || ||<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:Alberto.jpg|alt text|width="150"}} ||Alberto Ocana ||Visiting Scientist (Hospital Clínico San Carlos. Madrid) ||Summer 2013 ||Pathway and RNA-seq analysis || ||<class=""table-header"">Financial Staff ||||||||<class=""table-header"" style=""text-align:center; ""> || ||<style=""text-align:center; ""> {{attachment:patty.jpg||width="200"}} ||[[PatrickScopa|Patrick Scopa]] ||Aug.2017-Oct.2018 ||||<style=""text-align:center; "">Financial and Research Assistant || ||<style=""text-align:center; ""> {{attachment:Shan.jpg||width="200"}} ||[[ShanGao|Shan Gao]] ||May.2017 - Aug.2018 <<BR>> Jun.2016 - May.2017 ||||<style=""text-align:center; "">Financial Administrator <<BR>> <<BR>> Financial and Research Assistant || ||<class=""table-header"">Graduate Rotation Students ||||||<class=""table-header"" style=""text-align:center; ""> || ||Michael Geuenich ||Molecular Genetics ||Sept.2020 || || ||Qi Wu ||Molecular Genetics ||Sept.2020 || || ||Delaram Pouyabahar ||Molecular Genetics ||Nov.2019 || || ||Aiden Sababi ||Molecular Genetics ||Nov.2019 || || ||Sara Gordillo Sampedro ||Molecular Genetics ||Nov.2019 || || ||Daniel Stueckmann ||Molecular Genetics ||Sep.2019 || || ||Zoe Clarke ||Molecular Genetics ||Sep.2019 || || ||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 || || ||Alexandra Rasnitsyn ||Molecular Genetics ||Jul.2017-Aug.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 || ||[[HuyNguyen|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 || |
Current Members
Bader Lab |
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Professor |
Apr.2006 |
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Post docs |
|||||
|
Co-supervised with Dr. Trevor Pugh |
Sept.2020 |
Cancer Drug Targets |
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Graduate Students |
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Molecular Genetics |
Jan.2016 |
Intercellular Signalling |
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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 |
||
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Computer Science |
Sept.2017 |
Information extraction in the biomedical domain using deep learning |
||
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Molecular Genetics |
Jan.2018 |
The Analysis and Integration of various types of '-omics' data to characterize cancer stem cells |
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Molecular Genetics |
Jan.2020 |
Cellular ecosystems, liver cancer evolution |
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Molecular Genetics |
Jan.2020 |
Cellular ecosystems and Single Cell Mutational analyses |
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Molecular Genetics |
Jan.2020 |
Deep learning applications in electron microscopy, Single cell omics |
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Molecular Genetics |
Jan.2020 |
Kidney cancer single cell genomics |
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Molecular Genetics |
Jan.2020 |
Single cell data integration, liver disease |
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Molecular Genetics |
Jan.2021 |
Building a unified model of cellular function |
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Visiting Graduate Students |
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Co-supervised with Dr. Sid Goyal) |
Feb 2021 |
Single Cell Analysis of Regeneration |
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Research Staff |
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Research Staff |
Nov.2007 |
Pathway and Network Analysis |
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Research Associate |
Jan.2011 |
Pathway Analysis of Cancer Stem Cells |
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Research Associate |
Aug.2011 |
Cancer genomics |
||
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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 |
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Research Associate |
Jan.2016 |
Computational Biology |
||
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Research Associate |
July.2016 |
Organoid Development |
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Tallulah Andrews |
University Health Network (co-supervised with Sonya MacParland) |
Jan 2020 |
Single Cell Genomics |
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Research Associate |
May 2020 |
Princess Margaret multi-omics data interpretation team |
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Research Associate |
April 2021 |
Princess Margaret multi-omics data interpretation team |
||
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Research Associate |
May 2021 |
Princess Margaret multi-omics data interpretation team |
||
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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May 2020 |
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Financial Staff |
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Apr.2019 |
Financial and Research Assistant |
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Undergraduate Students |
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Anweshi Anavadya |
University of Waterloo Computer Engineering co-op student |
Jan-Apr.2021 |
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![[ATTACH]](/Members?action=AttachFile&do=upload_form&ticket=00676e94d8.3c330d52c709709dab9d67fa33479bb069a7fbda&target=Z.Clarke.jpg "[ATTACH]"){kind=small}
![[ATTACH]](/Members?action=AttachFile&do=upload_form&ticket=00676e94d8.3c330d52c709709dab9d67fa33479bb069a7fbda&target=A.Sabibi.JPG "[ATTACH]"){kind=small}
![[ATTACH]](/Members?action=AttachFile&do=upload_form&ticket=00676e94d8.3c330d52c709709dab9d67fa33479bb069a7fbda&target=R.Xie.JPG "[ATTACH]"){kind=small}
![[ATTACH]](/Members?action=AttachFile&do=upload_form&ticket=00676e94d8.3c330d52c709709dab9d67fa33479bb069a7fbda&target=Max.jpeg "[ATTACH]"){kind=small}
Past Members
Post Docs |
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Jan.2015-Jan 2021 |
Predicting disease risk/prognosis in mental illness |
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Jan.2015-Sep.2017 |
Protein Protein interactions |
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Sep. 2013-Aug.2017 |
Cancer genomics, Cancer mutations analysis |
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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 |
|
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 |
||
Graduate Students |
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||||
|
Molecular Genetics (co-supervised with Quaid Morris) |
Jan.2017-Mar.2021 |
The Genomic Evolution of Pancreatic Ductal Adenocarcinoma |
||
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Laboratory Medicine & Pathobiology (co-supervised with Michael D. Taylor) |
May.2015-Feb.2021 |
Metastasis in cancer |
||
|
Laboratory Medicine and Pathobiology (co-supervised with Michael D. Taylor) |
Sept.2013-Jan.2020 |
Cancer genomics of medulloblastoma |
||
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Molecular Genetics (co-supervised with Andrew Emili) |
Sept.2013-Sept.2019 |
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|
Computer Science |
Sept.2010-Aug.2019 |
Network alignment |
||
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Molecular Genetics |
Feb.2018-Jul.2019 |
Single cell RNAseq analysis of heart development lineages |
||
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Molecular Genetics (co-supervised with Boone/Andrews lab) |
Dec.2015-Apr.2018 |
Computational pipeline to determine signs of natural positive selection for certain biological pathways among different human ethnic populations. |
||
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Computer Science |
Graduated 2018 |
Domain interaction prediction |
||
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Computer Science |
Sept.2015-Aug.2017 |
Domain-peptide interaction |
||
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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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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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Molecular Genetics (co-supervised with Tony Pawson) |
Jan.2007-Aug.2011 |
Network evolution |
||
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Molecular Genetics |
May.2007-2011 |
Protein complex detection from networks |
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Visiting Graduate Students |
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Visiting student from Copenhagen |
Jul. 2019-Aug. 2019 |
Precision Medicine for Mental Health |
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Visiting student from Italy |
Apr. 2019-May 2019 |
Single Cell Network Analysis |
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Department of Mathematics and Computer Science, University of Southern Denmark |
Sept.2018-Feb.2019 |
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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Visiting Student From Italy |
Aug.2017-Feb.2018 |
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Visiting Student From Italy |
Aug.2017-Feb.2018 |
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Visiting student from University of Verona, Italy |
Jan-Jul 2016 |
Biological pathway simulation |
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Bioinformatics |
Oct.2012 - Sep.2014 |
Gene expression regulation |
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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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China Agricultural University, China, Visiting student |
Sept.2008-Sept.2010 |
Quantitative interaction prediction |
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Research Associates |
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Research Associate |
May.2014-Nov.2018 |
Medical Decision Making |
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Research Staff |
Sept.2014-Aug.2018 |
Precision medicine |
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|
Shaheena Bashir |
Research Associate |
March 2013 - March 2014 |
Biostatistics |
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Software Developers |
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|
Nov.2016-Dec.2018 |
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Senior Research Associate |
Nov.2008-Jan.2019 |
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Feb.2009-Jun.2018 |
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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 |
|
Jan-Aug.2007 |
Integrative Biology of Yeast |
||
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 |
||||
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 |
|
|||||
|
James Wu |
Thesis Project Student |
Sept.2018 |
Text mining biomedical literature |
||
|
Dina Issakova |
Undergraduate Project Student |
May.2018 |
Evolutionary biology, computer vision/image processing, genomics data mining |
||
|
Michael Wrana |
University of Toronto Summer Student |
May.2018 |
|
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|
Caitlin Christina O'Callaghan |
University of Waterloo Co-Op Student |
May.2018 |
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|
Rex Wen |
University of Waterloo Co-Op Student |
May.2018 |
|
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|
Logan Mosier |
University of Waterloo Co-Op Student |
Jan.2018-Apr.2018 |
|
||
|
Wanxin Li |
University of Waterloo Co-Op Student |
Jan.2018-Apr.2018 |
|
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|
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 |
Apr.2013 - Sept.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 |
|||
|
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) |
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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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Scientist, Biomedical Informatics Center, Mumbai, India |
Sept.2018-Jan.2019 |
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Carolyn Cummins |
Visiting Scientist (Assistant Professor of Pharmacy) |
Nov 2013 |
Pathway and RNA-seq analysis |
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Alberto Ocana |
Visiting Scientist (Hospital Clínico San Carlos. Madrid) |
Summer 2013 |
Pathway and RNA-seq analysis |
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Financial Staff |
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Aug.2017-Oct.2018 |
Financial and Research Assistant |
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May.2017 - Aug.2018 |
Financial Administrator |
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Graduate Rotation Students |
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Michael Geuenich |
Molecular Genetics |
Sept.2020 |
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Qi Wu |
Molecular Genetics |
Sept.2020 |
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Delaram Pouyabahar |
Molecular Genetics |
Nov.2019 |
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Aiden Sababi |
Molecular Genetics |
Nov.2019 |
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Sara Gordillo Sampedro |
Molecular Genetics |
Nov.2019 |
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Daniel Stueckmann |
Molecular Genetics |
Sep.2019 |
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Zoe Clarke |
Molecular Genetics |
Sep.2019 |
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Matthaeus Ware |
Molecular Genetics |
Sep.2018 |
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Jessie Medeiros |
Molecular Genetics |
Feb.2018 |
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Thinh Tran |
Molecular Genetics |
Jan.2018 |
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Kevin Wang |
Molecular Genetics |
Jan.2018 |
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Charlotte Michelle Nguyen |
Molecular Genetics |
Nov.2017 |
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Shubham Gupta |
Molecular Genetics |
Nov.2017 |
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Owen Whitley |
Molecular Genetics |
Nov.2017 |
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Zain Patel |
Molecular Genetics |
Nov.2017 |
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James St. Pierre |
Molecular Genetics |
Oct.2017 |
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Yu-Xi Xiao |
Molecular Genetics |
Sept.2017 |
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Dustin Sokolowski |
Molecular Genetics |
Sept.2017 |
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Alexandra Rasnitsyn |
Molecular Genetics |
Jul.2017-Aug.2017 |
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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 |