Brief Biography

Dr. Shoshana Wodak obtained her PhD from Columbia University, New York. She was a professor at the Free University of Brussels for over 20 years, where she founded and co-directed the Centre of Structural Biology and Bioinformatics and started a Master’s program in Bioinformatics with colleagues in 2001. She also occupied the position of Group Leader at the European Bioinformatics Institute (EBI) between 1996 and 2001, and has been a member of the European Molecular Biology Organization (EMBO) since 1992.

Since joining SickKids in the spring of 2004, Dr. Wodak has served as the Scientific Director of the Centre for Computational Biology. She also holds a Tier 1 Canada Research Chair in Computational Biology and Bioinformatics.

Dr. Wodak developed the first Docking algorithm for the prediction of protein-protein interactions from the structure of the independent components. She also developed one of the first procedures for defining structural domains from the atomic coordinates of proteins, and wrote a number of key papers on the role of local interactions (those between residues close-by along the chain) in stabilizing the native state, in protein structure prediction, protein folding and in fold recognition. She has also contributed to the problem of assessing the quality of protein X-ray structures, and to the analysis of dynamic and thermodynamic properties of proteins, and protein-solvent interactions. More recently, Dr. Wodak and her team have developed efficient procedures for automatic protein design, for simulating protein interactions and conformational changes, and for analyzing protein interactions networks and cellular pathways.

Dr. Wodak serves on the management committee of the CAPRI (Critical Assessment of Predicted Interactions) experiment, which is similar in spirit to CASP but focuses on protein-protein docking methods. She heads the team responsible for assessing the quality of the docking predictions submitted by groups across the world.

Dr. Wodak is a member of the Editorial Boards of:

• Protein, Structure Function and Bioinformatics
• Plos Bioinformatics
• BMC Bioinformatics
• Database

Research Interests

Our research spans the fields of computational structural biology and bioinformatics.

We use molecular simulation and modeling techniques to study protein-protein, protein-DNA and protein-small molecular interactions at the atomic scale. We furthermore analyze the properties of known protein structures and sequences in order to gain insight into how evolution has shaped their functional specificity.

On-going projects in this area include:

• Deciphering the recognition code of DNA binding regulatory proteins
• Unraveling the mechanism of oligomer formation of the prion protein
• Prediction of ligand binding sites from protein sequence and 3D structure
• Mapping the molecular functions of proteins involved in chromatin modifications

In parallel to these molecular level investigations we are also actively engaged in developing quantitative and integrative computational approaches at the cellular level.

On-going projects in this area include:

• Development of software tools for the visualization and analysis of metabolic and signaling pathways
• Increasing the coverage and reliability of protein interaction networks through the integration of multiple sources of data
• Identifying functional modules from protein and genetic interaction data

All of our research activities closely combine the development of methods and software tools with their application to important biological problems with relevance to human health. Many of these applications are carried out in collaboration with the staff of the Centre for Computational Biology and SickKids PIs.

External Funding

• Canadian Institutes of Health Research (CIHR)
• PrioNet Canada
• Canada Foundation for Innovation (CFI)

Publications

Wodak SJ, Pu S, Vlasblom J, Séraphin B. (2008), Challenges and rewards of interaction proteomics, Mol Cell Proteomics. Sep 17;1535-9484.

Malevanets A, Sirota FL, Wodak SJ. (2008), Mechanism and energy landscape of domain swapping in the B1 domain of protein G., J Mol Biol. Sep 26;382(1):223-35.

Pu S, Ronen K, Vlasblom J, Greenblatt J, Wodak SJ. (2008), Local coherence in genetic interaction patterns reveals prevalent functional versatility, Bioinformatics. Aug 20;1460-2059.

Roca M, De Maria L, Wodak SJ, Moliner V, Tunon I, Giraldo J. (2008), Coupling of the guanoisne glycosidic bond confirmation and the ribonucleotidecleavage reaction: implications for barnase catalysis, Proteins. Feb 1;1097-0134

Sirota FL, Héry-Huynh S, Maurer-Stroh S, Wodak SJ.(2008), Role of the amino acid sequence in domain swapping of the B1 domain of protein G. Proteins, Jan 10;1097-0134.

Dessailly BH, Lensink MF, Orengo CA, Wodak SJ. (2008), LigASite--a database of biologically relevant binding sites in proteins with known apo-structures, Nucleic Acids Res. Jan 36; Database issue:D667-73

Pu S, Vlasblom J, Emili A, Greenblatt J, Wodak SJ. (2007), Identifying functional modules in the physical interactome of Saccharomyces cerevisiae. Proteomics, 7, 944-60.

Lensink MF, Mendez R, Wodak SJ. (2007), Docking and scoring protein complexes: CAPRI 3rd Edition Proteins 69, 704-18.

Croes D, Couche F, Wodak SJ, van Helden J. (2006) Inferring meaningful pathways in weighted metabolic networks, J Mol Biol. Feb 10;356(1):222-36.

Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, Ignatchenko A, Li J, Pu S, Datta N, Tikuisis AP, Punna T, Peregrin-Alvarez JM, Shales M, Zhang X, Davey M, Robinson MD, Paccanaro A, Bray JE, Sheung A, Beattie B, Richards DP, Canadien V, Lalev A, Mena F, Wong P, Starostine A, Canete MM, Vlasblom J, Wu S, Orsi C, Collins SR, Chandran S, Haw R, Rilstone JJ, Gandi K, Thompson NJ, Musso G, St Onge P, Ghanny S, Lam MH, Butland G, Altaf-Ul AM, Kanaya S, Shilatifard A, O'Shea E, Weissman JS, Ingles CJ, Hughes TR, Parkinson J, Gerstein M, Wodak SJ, Emili A, Greenblatt JF. (2006), Global landscape of protein complexes in the yeast Saccharomyces cerevisiae, Nature. Mar 30;440(7084):637-43. Epub Mar 22.

Billingsley G, Santhiya ST, Paterson AD, Ogata K, Wodak S, Hosseini SM, Manisastry SM, Vijayalakshmi P, Gopinath PM, Graw J, Heon E. (2006), CRYBA4, a novel human cataract gene, is also involved in microphthalmia. Am J Hum Genet. Oct;79(4):702-9.

Vlasblom J, Wu S, Pu S, Superina M, Liu G, Orsi C, Wodak SJ. (2006), GenePro: a cytoscape plug-in for advanced visualization and analysis of interaction networks (2006), Bioinformatics. Sep 1;22(17):2178-9.

Simonis N, Gonze D, Orsi C, van Helden J, Wodak SJ. (2006), Modularity of the transcriptional response of protein complexes in yeast, J Mol Biol. Oct 20;363(2):589-610.

Croes D, Couche F, Wodak SJ, van Helden J. (2005), Metabolic PathFinding: inferring relevant pathways in biochemical networks, Nucleic Acids Res. Jul 1;33(Web Server issue):W326-30.

Jaramillo A, Wodak SJ. (2005), Protein design is a challenge for implicit solvation models, Biophysical J. Jan ;88(1) :156-71.

A complete list of publications can be found pm the Wodak Lab website.