Lab picture at IBM Toronto Lab, December 2005.
Physical Science Lead, Informatics and Communications Technology, TECHNA Institute for the Advancement of Technology for Health
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
Mamatha Bhat, MD, MSc
Mamatha joined the lab in September 2015 and works on network analysis approach to determine gene signatures in HCC
Christian has been with the lab since August 2001. His research area is machine learning and image analysis in high-throughput protein crystallography
Chiara joined the lab in May 2010. Her research focusses on integrative cancer biology.
Max finished his PhD research on predicting protein-protein interactions and esential genes by data mining, and continues to work on integrative cancer informatics.
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-Christine joined the lab in July 2016, working on integrative analytics in arthritis and cancer biomarker pattern family detection.
Richard is our System Administrator. He joined the lab in May 2003.
Mark joined the lab in October 2013 to work on CDIP, ADIP and other lab portals.
Han joined the lab in August 2006 as a research technician, working on ovarian cancer.
|Students||Deg, Year, Dept.||Title|
|Simon Larsen||Visiting student 2015|
|Maisa Pinheiro||Visiting student 2015|
|Bruno Fantinatti||Visiting student 2014|
|Nathan Braniff||MSc, 2015,
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|
PhD 2015, Queen's U
School of Computing
|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
|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|
|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|
|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|
|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.|
|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|
|Chi Hay Tong||2005|
|Akhil Patel||2002, 2003|
|Bilal Ahmed||2002, 2003|
|Jing Duan||1999, 2000|
|Jinhe chen||1998, 1999|
|Tungyat Wong||1998, 1999|