People - Wodak Lab

Shoshana Wodak

Dr. Shoshana J. Wodak obtained her PhD degree from Columbia University, New York, USA. She was Professor and Director of the Centre for Structural Biology and Bioinformatics, at the Free University of Brussels, Belgium, and a Group Leader at the European Bioinformatics Institute, Cambridge UK, before joining the Hospital for Sick Children in Toronto, in 2004. She currently occupies there the post of Scientific Director of the Center for Computational Biology and Senior Scientist in the Structural Biology Program. She also is a Tier I Canada Research Chair in Computational Biology and Bioinformatics and Professor at the Departments of Biochemistry and of Molecular Genetics at the University of Toronto. Dr. Wodak gained recognition for her pioneering work on many computational methods for the analysis, prediction and simulations of protein structures and protein interactions. More recently she has been developing advanced database tools for the representation and analysis of protein-protein interaction networks and biochemical pathways, as well as computational methods for protein design and the analysis of protein-protein and protein-DNA interactions.

Andrei Turinsky

I joined the Wodak lab in December 2007. I am currently a technical co-ordinator of the large-scale CIHR Team project Model Organism Interactomes and Human Diseases [link to CIHR project site] and perform other R&D duties. My research interests include machine-learning applications in bioinformatics, spatio-temporal data mining, and biomedical image analysis. I hold a PhD in Mathematical Computer Science (2002) and M.Sc. degrees in Mathematical Computer Science (1997) and Applied Mathematics (1995).

Prior to joining the Wodak lab, I worked at the Sun Center of Excellence for Visual Genomics (COE), University of Calgary, where I led the development of the 4D Bioinformatics research initiative and the CAVEman project. My earlier work at the COE (2002-2005) was within the scope of the Bioinformatics Platform, a project funded by the Genome Canada to create a unified national infrastructure for research in bioinformatics. Between 1998 and 2002, I worked at the National Center for Data Mining in Chicago, USA, where I was involved in the Project DataSpace, an infrastructure for exploring, analyzing, and mining remote and distributed data. I have developed numerous software projects since 1992, and managed several large-scale software initiatives (combined value over $7M) since 2004. I am also certified in teaching, and have taught extensively in both academia (13 semesters) and in industry (7 years).

Brian Turner

If asked where I would be twenty years after high school, I would have said I'd never be working in anything like computers or biology, never mind computational biology. At that point in time, I wanted to be an architect, and was enrolled in the School of Architecture at the University of Waterloo. However that did not prove to my liking and so I left thinking maybe I'd rather be a director. That led me to producing and production-managing TV commercials for a decade all over North America, including Toronto, Los Angeles, Miami, Seattle, Calgary, and Halifax for agencies and clients including Leo Burnett (Paris, Chicago, Toronto), JWT (New York, Toronto), TBWA Chiat Day (Toronto), BBDO (Detroit), General Motors, Molsons, Coca-Cola, Kodak, UPS, to name a few.

As PCs infiltrated the workplace, including studios and production offices, I became interested in programming and decided to get a degree in computer science, which I did at the University of Toronto. From there I held a variety of positions, including consulting with clients such as Rogers Media (Toronto), Lehman Brothers (New York), Baby Center (San Francisco), and Swiss Re (Toronto).

With a desire to work in more challenging domain and no small amount of serendipity I joined the Wodak lab. The focus of my work here is to bring software engineering best practices to projects at the lab as well as to explore and expand the possibilities of network visualization, data representation and storage.

James Vlasblom

I am an PhD student in the department of biochemistry at the University of Toronto. After graduating with a BASc in computer engineering from the University of Toronto, I worked for two years as a software developer before returning to school. My research interests are in the areas of systems biology, machine learning, and the many types of interaction networks found within the cell.

Miguel A. Santos

I graduated in Theoretical Physics by the Universitat of Barcelona and got my Ph.D in the same university on the front dynamics of phase transitions in the presence of external noise, having as advisor Prof. J.M. Sancho. After that, I joined the Molecular Modeling Group lead by Prof. Lourdes F. Vega at the time when she moved from the Universitat Rovira i Virgili to the Institut de Ciècia de Materials de Barcelona ICMAB-CSIC (spanish national council for scientific research). There I worked on the characterization of nano-porous materials.

From 1993 to 2003 I've been adjunct professor at the Engineering School of the Universitat Rovira i Virgili, where I taught and managed the freshman physics laboratories for Chemical, Electrical and Electronic Engineering, and at the same time, lecturer at the UNED (Spanish National at Distance University, aka, spanish Open University), teaching Physics and Mathematical Logic for Computer Science.

I joined the group of Prof. Wodak at the Université Libre de Bruxelles in september 2003, before moving to the Hospital for Sick Children in January 2005. I have been working on problems on protein design (implementing the use of NOE restraints and backbone flexibility in DESIGNER), homology modeling and Protein-DNA interaction (analyzing the factors that determine the affinity and specificity of these interactions).

As manager of our group's cluster, I also have some fun in dismantling the hardware and changing some burned out pieces.

Shuye Pu

I joined Dr. Shoshana Wodak's lab in 2004. My current position is research project manager and I oversee several research projects. I graduated from Lanzhou medical college in China in 1988. Since then, I have spent most of my time as a biomedical researcher in the United States and Canada. My earlier work was mostly in the field of neuroscience, particularly, neuroendocrine regulation of reproductive functions and feeding behaviors. Later on, I have re-focused my research activities on computational biology and bioinformatics.

My current research interests include the following:

• Biological network analysis:
  • identification of multi-protein complexes from physical protein-protein interaction networks using graph clustering algorithms
  • prediction of protein-protein interactions by data integration
  • identification of multi-functional proteins from genetic interaction networks
  • investigation of metabolic enzyme evolution by metabolic network analysis.
• Algorithm design: development of efficient biclustering algorithms for high-throughput data analysis.
• Chromatin modification and human diseases: identification of human disease related genes that are involved in chromatin remodeling and histone modification.

Recent publications:

• Pu S, Vlasblom J, Emili A, Greenblatt J, Wodak SJ. Identifying functional modules in the physical interactome of Saccharomyces cerevisiae. Proteomics. 2007 Mar;7(6):944-60.
• Vlasblom J, Wu S, Pu S, Superina M, Liu G, Orsi C, Wodak SJ. GenePro: a Cytoscape plug-in for advanced visualization and analysis of interaction networks. Bioinformatics. 2006 Sep 1;22(17):2178-9.
• Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, Ignatchenko A, Li J, Pu S, et al. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature. 2006 Mar 30;440(7084):637-43. Epub 2006 Mar 22.