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Principal Investigator | Graduate Students | Research Associates - | Post-doctoral Fellows | Programmers | Technicians | Visiting Scientists | Past Members

Lab picture at IBM Toronto Lab, December 2005.

Principal Investigator


Igor Jurisica, PhD.
Senior Scientist, Krembil Research Institute, Data Science Discovery Centre for Chronic Disease
Tier I Canada Research Chair in Integrative Cancer Informatics

Physical Science Lead, Informatics and Communications Technology, TECHNA Institute for the Advancement of Technology for Health

Principal Investigator

Professor, Departments of Computer Science and Medical Biophysics, University of Toronto.
Adjunct Professor, School of Computing & Dept. Pathology and Molecular Medicine, Queen's University, Kingston, ON.
Adjunct Professor, Graduate Program in Computer Science, York University, Toronto, ON.
Affiliated member, Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia

Honorary Professor, Shanghai Jiao Tong University, College of Stomatology

Visiting Scientist, IBM Centre for Advance Studies.

F1000Prime Member; F1000 Advisory Board Member

Associate Editor, BMC Bioinformatics.

Associate Editor, Proteomes.
Associate Editor, Cancer informatics.
Associate Editor, International Journal of Knowledge Discovery in Bioinformatics.
Associate Editor, Interdisciplinary Sciences: Computational Life Sciences.

Founding Associate Editor: J Big Data& Information Analytics
Editorial Board: Biology Direct



Administrative Assistant


Soleil Miron

Soleil Miron

Soleil Miron is an assistant to Dr. Igor Jurisica. She overlooks all the administrative operations of the lab.

 





Graduate Students

 

 Sara Rahmati
  PhD. candidate, University of Toronto, Department of Medical Biophysics

Sara is interested in linking protein-protein interactions, protein disorder and structure to determine tissue and condition specific interaction dynamics

 Rosanne McQuaid
  PhD candidate, University of Toronto, Department of Physiology
  Co-supervised with Dr. A. Jurisicova

Rosanne works on novel approaches to ovarian cancer treatment

 Mamatha Bhat, MD, MSc

 

 CIHR Fellow

 

Mamatha joined the lab in September 2015 and works on network analysis approach to determine gene signatures in HCC

 

 

 


Undergraduate Students



 

Research Associates

 

 Christian Anders Cumbaa

Christian has been with the lab since August 2001. His research area is machine learning and image analysis in high-throughput protein crystallography

 Chiara Pastrello, PhD

Chiara joined the lab in May 2010. Her research focusses on integrative cancer biology.

 Max Kotlyar, PhD

Max finished his PhD research on predicting protein-protein interactions and esential genes by data mining, and continues to work on integrative cancer informatics.

 

 

Post-doctoral Fellows

 Serene Wong, PhD

Serene joined the lab in May 2014 and works on graph theory approach to characterize the relationship between disease and structure of protein-protein interaction networks.

 Tomas Tokar, PhD

 

Tomas joined the lab in October 2013 and works on network modeling

 Anne-Christin Hauschild, PhD

 

Anne-Christine joined the lab in July 2016, working on integrative analytics in arthritis and cancer biomarker pattern family detection.

 

 

Research Programmers

 

 Richard Lu

Richard is our System Administrator. He joined the lab in May 2003.

 Mark Abovsky

Mark joined the lab in October 2013 to work on CDIP, ADIP and other lab portals.

 Dylan Bethune-Waddell


Dylan joined the lab in September 2013 to work on protein interaction prediction

 

Technicians

 Han Li

Han joined the lab in August 2006 as a research technician, working on ovarian cancer.

 

 

 

 

 

Visiting Scientists

Eric K Morgen, MD MPH
[Co-supervisor] with Dr. G. Liu






Visiting Students


 

Past members




Students Deg, Year, Dept. Title
Simon Larsen Visiting student 2015  
Maisa Pinheiro Visiting student 2015  
Bruno Fantinatti Visiting student 2014  
Nathan Braniff MSc, 2015,

Queen's U

School of Computing

Novel algorithms for prognostic signature discovery. Co-supervised with Dr. P. Mousavi

Joshua Armenia Visiting student 2013  
Fabio Marchi Visiting student 2012  
Naiara da Costa Cinegaglia MSc 2015 UNESP  
Lili Wang

PhD 2015, Queen's U

School of Computing

 
Brendan Innes 2015  
Serene Wong PhD 2014, York U, Computer Science Exploiting structure information for network dissimilarity characterization. Application to disease network analysis and treatment prediction
Abraham Heifets PhD 2013, DCS Automated synthetic feasibility assessment: A data-driven derivation of computational tools for medicinal chemistry
Giuseppe Agapito PhD 2013 Integration, analysis and efficient visualization of biological data
Alison Pon MSc 2013, DCS Selection of gene signatures for brain metastasis in non-small cell lung cancer from neural development genes
Daniela Rosu PhD 2013, DCS Practical Ontologies: Requirements, Design and Applications to Semantic Integration and Knowledge
Discovery
Kristen Fortney PhD 2012, MBP Bioinformatics approaches to biomarker and drug discovery in aging and disease
Elize Shirdel PhD 2012, MBP Navigating the micronome A systematic study of both the external effects of microRNAs on gene repression networks, and the contribution of microRNA terminal loops to microRNA function
Rui Yan PhD 2012, DCS Pattern discovery in DNA sequences
Max Kotlyar PhD 2011, MBP Prediction of protein-protein interactions and essential genes through data integration
Jifang Jiang MSc 2009, DCS Investigation of the Correlation Between CNPs in the Human Cancer Genome and Protein-Protein Interactions Using Oligonucleotide SNP Arrays
Paul Boutros PhD 2008, MBP Integrated molecular prediction of patient prognosis
Kevin Brown PhD 2007, MBP Interpreting gene expression in human cancer through integration with model organism protein-protein interaction data.
Edward Xia PhD 2007, DCS Optimal grid scheduling by dynamic selection of scheduling heuristics
Niloofar Arshadi PhD 2007, DCS Case-based reasoning system maintenance
Julia Chae MSc 2005, DCS Integration of clustering and statistical analysis of microarray data
Linghai Zhang MSc 2005, DCS Effective and efficient high-dimensional data clustering using self-organizing maps
Natasha Przulj  PhD 2005, DCS Analyzing large networks: Protein interactions example
Marlena Marziarz MSc 2003, DCS A computational analysis tool for clinical correlation of microarray data.
Kartik Desai MEng 2002, ME Effective and efficient data management in life sciences
Ian van Toch MBP Modeling of protein-protein interaction networks
Amr Abu-Zeid MBP  
     
Programmers/Technicians    
David Otasek 2005 to 01-2015 NAViGaTOR developer
Arpad Szabo 01-2014 to 02-2015 Database administrator
Nazgol Shahbandi 01-2013 to 07-2014 Drug repositioning
Renatas Minkstinas 05-2012 to 02-2015 Research programmer
Marc Angeli 01-2012 to 02-2015 Research technician
Adrian M. Teisanu 04-2010 to 04-2014 Database administrator
Shima Khoshraftar 11-2012 to 11-2013 I2D extensions
Wing Xie 09-2008 to 01-2014 mirDIP and CDIP development
Fabio Accorsi 11-2012 to 08-2013 Validation studies
Varune Rohan Ramnarine 01-2009 to 10-2011 Analyzing and integrating CGH and microRNA data
Muhammad Ali 06-2007 to 07-2011 NAViGaTOR: Protein-protein interaction network visualization and analysis
Uzma Khan 07-2009 to 12-2010 Design and development of web-based bioinformatics resources for the lab, including high-throughput data analysis
Tejaswini Ganapathi 02-2010 to 08-2010 Automated cell dynamics analysis
Attila Barta 01-2010 to 04-2010 IBM DB2 Database Administrator
Stephen Grant 03-2006 to 2009 Complex data sonification
Frederic Breard 04-2006 to 07-2008 IBM DB2 database design and administration
Mahima Agochiya 04-2005 to 08-2008 Integrated computational biology approach to biomarker identification in ovarian cancer
Mikhail Soloviev 06-2006 to 05-2008 Protein-protein interaction network analysis and modeling
Wing Xie 05-2007 to 02-2008 Protein-protein interaction network analysis
Andrew Morrison 06-2007 to 11-2007 Machine learning and visualization techniques for high dimensional datasets
Vyacheslav Morozov 03-2006 to 03-2007 Protein data analysis
Baiju Devani 08-2004 to 01-2007 NAViGaTOR: Protein-protein interaction network visualization
Salimah Shariff 04-2006 to 08-2006 Protein data analysis
Cosmin Truta 10-2005 to 07-2006 Image analysis and compression in high-throughput protein crystallography
Cheryl Chan 10-2005 to 04-2006 Integrated ovarian cancer analysis
Gareth Morrison 12-2004 to 07-2005 Androgen and estrogen metabolic network modeling
Xin Zhang 08-2002 to 06-2005 Clustering and visualization of high-throughput data in ovarian cancer
Akhil Patel 07-2003 to 09-2004 Time series data analysis and visualization
Mujahid Sultan 05-2001 to 05-2003 Machine learning and visualization techniques for high dimensional datasets
Patrick Rogers 03-1998 to 12-2003 TA3: Interactive case-based reasoning system
     
Scientific Associates    
     
Mike Tsay 2013 to 12 2016 Modeling of signaling cascades
Dr. Waheed Sangrar 09 2013 to 03 2015 Modeling of signaling cascades
     
Dr. Elize Shirdel 2012 to 09 2013 microRNA structure and function
Liz Sauter 2012 to 07 2013 Project manager on ORF Gl2
Dr. Dan Strumpf 11 2005 to 05 2013 Integrative data mining and modeling in non-small cell lung cancer
Dr. Fiona Broackes-Carter 06 2010 to 01 2013 Protein-protein interaction curation
Dr. Amira Djebbari 07 2010 to 10 2011 Network modeling and characterization of cancer
Dr. Periklis Andritos 08 2010 to 08 2011 Text mining
Dr. Kevin Brown 01 2007 to 01 2010 Integrative computational biology
     
PDFs    
Dr. Ramanuja Simha 10 2016 to 05 2017
Dr. Lisa Yan 01 2014 to 02 2015 High-throughput protein crystallography
Dr. Kalpana Venkat 05 2011 to 10 2013 Non-small cell lung cancer.
Dr. Fatemeh Vafaee 09 2011 to 09 2012 Gene association prediction.
Dr. Levi Waldron 10 2008 to 05 2010 Dynamics of interactions in head and neck cancer.
Dr. Joseph Geraci 09 2008 to 12 2009 Mathematical modeling of cancer. Jointly supervised with Dr. Geoffrei Liu.
Dr. Yun Niu 01 2007 to 08 2009 Computational linguistic approach to automated protein interaction extraction from PubMed.
Dr. Ata Ghavidel 06 2007 to 05 2009 Dynamics of complex formation in DNA damage repair and relation to cancer. Co-supervised with Dr. T. Kislinger.
Dr. Michael McGuffin 09 2006 to 08 2007 Advanced graphical user interfaces for biological data visualization.
Dr. Natasha Przulj 03 2005 to 06 2005 Protein-protein interaction network structure-function relationship.Co-supervised by J. Wrana, SLRI.
     
Technicians    
Christine Frantz 2008 - 03 2010 Prognostic and predictive biomarker validation in lung cancer
Lina Qi 04 2010 - 01 2012 Lab technician
     
Undergraduate and high school trainees    
Edward Feng 2013 Novel approaches to cancer treatment
Carrie Wei 2013 Novel approaches to cancer treatment
Andrea Vargas 2011 Automated cell dynamics analysis from images
Alex Yue 2011 Roche-Tecan integration and automation
Adilya Rafikova 2011 Lung cancer data portal
Mukul Raina 2011 Protein-protein interaction prediction
Rajesh Nair 2010 Protein-protein interaction characterization and curation
Curtis Foong 2010-2011 Network-based prognostic signature optimization
Polina Binder 2010-2011 GPU-optimized layout algorithms for NAViGaTOR
Raymond Chu 2010 Topology-directed layout algorithms for NAViGaTOR.
Adrien J.Guillon 2008 Scalable graph theory algorithms on the linux cluster for protein interaction network analysis
Mark Aldham 2008 Experiment automation on Tecan robot
Christian Popovici 2008 High-throughput protein crystallography image analysis
Dene Ringuette 2005-2008 Protein binding signature discovery using protein-protein interaction profile similarity
Joni Iljazi 2008 Modeling of cancer signaling
Joanna Yeung 2007 Prostate cancer data integration and analysis portal
Rick Valenzano 2006, 2007 Scalable layout algorithms for protein-protein interaction network visualization
Ian van Toch 2006, 2007 Modeling of protein-protein interaction networks
Ruchi Prasad 2006 Structural aspects of protein-protein interaction networks
Topaz Chiu 2006 Predicting dynamic protein interaction network from differential gene expression data
Marc Tyndel 2005  
Chi Hay Tong 2005  
Alice Ho 2004  
Conor McKinley 2004  
Matthew Lam 2004   
Kate Harris 2004  
Nasimeh Asharian 2004  
Wing Xie 2003  
Minzhi Lu 2003  
Brian Hacko 2002  
Colin Kong 2002  
Alan Grosskurth 2002  
Akhil Patel 2002, 2003  
James Bergstra 2002  
Bilal Ahmed 2002, 2003  
Satish Mathew 2002  
Alex Andreoopoulos 2002   
Stefan Pintilie 2002   
Roman Podolny 2002   
Xing Zhang 2002   
Gerard Quon 2001   
Aaron Rehaag 2001   
Jakob Mouka 2000  
Jing Duan 1999, 2000  
Jinhe chen 1998, 1999  
Tungyat Wong 1998, 1999