Molecular Systematics in Three Dimensions. - Shoshana J. Wodak (German Conference on Bioinformatics, 1997)

Logical Tools for Quering and Assisting Annotation of a Biochemical Pathway Database. - Jacques van Helden; David R. Gilbert; Lorenz Wernisch; Renato Mancuso 002; Matthew D. Eldridge; Kirill Degtyarenko; Shoshana J. Wodak (German Conference on Bioinformatics, 1999)

Application of Regulatory Sequence Analysis and Metabolic Network Analysis to the Interpretation of Gene Expression Data. - Jacques van Helden; David R. Gilbert; Lorenz Wernisch; Michael Schroeder 001; Shoshana J. Wodak (JOBIM, 2000)

From Molecular Activities and Processes to Biological Function. - Jacques van Helden; Avi Naim; Christian Lemer; Renato Mancuso 002; Matthew D. Eldridge; Shoshana J. Wodak (Briefings Bioinform., 2001)

Advanced pairwise structure alignments of proteins and analysis of conformational changes. - Maria Elena Ochagavía; Jean Richelle; Shoshana J. Wodak (Bioinform., 2002)

An overview of data models for the analysis of biochemical pathways. - Yves Deville; David R. Gilbert; Jacques van Helden; Shoshana J. Wodak (Briefings Bioinform., 2003)

Combining pattern discovery and discriminant analysis to predict gene co-regulation. - Nicolas Simonis; Shoshana J. Wodak; G. N. Cohen; Jacques van Helden (Bioinform., 2004)

The aMAZE LightBench: a web interface to a relational database of cellular processes. - Christian Lemer; Erick Antezana; Fabian Couche; Frédéric Fays; Xavier Santolaria; Rekin's Janky; Yves Deville; Jean Richelle; Shoshana J. Wodak (Nucleic Acids Res., 2004)

ACLAME: A CLAssification of Mobile genetic Elements. - Raphaël Leplae; Aline Hebrant; Shoshana J. Wodak; Ariane Toussaint (Nucleic Acids Res., 2004)

Metabolic PathFinding: inferring relevant pathways in biochemical networks. - Didier Croes; Fabian Couche; Shoshana J. Wodak; Jacques van Helden (Nucleic Acids Res., 2005)

CYGD: the Comprehensive Yeast Genome Database. - Ulrich Güldener; Martin Münsterkötter; Gabi Kastenmüller; Normann Strack; Jacques van Helden; Christian Lemer; J. Richelles; Shoshana J. Wodak; J. García-Martínez; José E. Pérez-Ortín; Holger Michael; Andreas Kaps; et al. (Nucleic Acids Res., 2005)

GenePro: a cytoscape plug-in for advanced visualization and analysis of interaction networks. - James Vlasblom; Samuel Wu; Shuye Pu; Mark Superina; Gina Liu; Chris Orsi; Shoshana J. Wodak (Bioinform., 2006)

Relating destabilizing regions to known functional sites in proteins. - Benoit H. Dessailly; Marc F. Lensink; Shoshana J. Wodak (BMC Bioinform., 2007)

Recognizing protein-protein interfaces with empirical potentials and reduced amino acid alphabets. - Guillaume Launay; Raul Mendez; Shoshana J. Wodak; Thomas Simonson (BMC Bioinform., 2007)

Local coherence in genetic interaction patterns reveals prevalent functional versatility. - Shuye Pu; Karen Ronen; James Vlasblom; Jack Greenblatt; Shoshana J. Wodak (Bioinform., 2008)

LigASite - a database of biologically relevant binding sites in proteins with known apo-structures. - Benoit H. Dessailly; Marc F. Lensink; Christine A. Orengo; Shoshana J. Wodak (Nucleic Acids Res., 2008)

Markov clustering versus affinity propagation for the partitioning of protein interaction graphs. - James Vlasblom; Shoshana J. Wodak (BMC Bioinform., 2009)

Literature curation of protein interactions: measuring agreement across major public databases. - Andrei L. Turinsky; Sabry Razick; Brian Turner; Ian M. Donaldson; Shoshana J. Wodak (Database J. Biol. Databases Curation, 2010)

iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence. - Brian Turner; Sabry Razick; Andrei L. Turinsky; James Vlasblom; Edgard K. Crowdy; Emerson Cho; Kyle Morrison; Ian M. Donaldson; Shoshana J. Wodak (Database J. Biol. Databases Curation, 2010)

OrthoNets: simultaneous visual analysis of orthologs and their interaction neighborhoods across different organisms. - Yanqi Hao; Anna Merkoulovitch; James Vlasblom; Shuye Pu; Andrei L. Turinsky; Denitza Roudeva; Brian Turner; Jack Greenblatt; Shoshana J. Wodak (Bioinform., 2011)

DAnCER: Disease-Annotated Chromatin Epigenetics Resource. - Andrei L. Turinsky; Brian Turner; Rosanne C. Borja; James A. Gleeson; Michael Heath; Shuye Pu; Thomas Switzer; Dong Dong; Yunchen Gong; Tuan On; Xuejian Xiong; Andrew Emili; et al. (Nucleic Acids Res., 2011)

Savant Genome Browser 2: visualization and analysis for population-scale genomics. - Marc Fiume; Eric J. M. Smith; Andrew Brook; Dario Strbenac; Brian Turner; Aziz M. Mezlini; Mark D. Robinson; Shoshana J. Wodak; Michael Brudno (Nucleic Acids Res., 2012)

Topic Pages: PLoS Computational Biology Meets Wikipedia. - Shoshana J. Wodak; Daniel Mietchen; Andrew M. Collings; Robert B. Russell; Philip E. Bourne (PLoS Comput. Biol., 2012)

Submit a Topic Page to PLOS Computational Biology and Wikipedia. - Daniel Mietchen; Shoshana J. Wodak; Szymon Wasik; Natalia Szostak; Christophe Dessimoz (PLoS Comput. Biol., 2018)

The impact of structural bioinformatics tools and resources on SARS-CoV-2 research and therapeutic strategies. - Vaishali P. Waman; Neeladri Sen; Mihaly Varadi; Antoine Daina; Shoshana J. Wodak; Vincent Zoete; Sameer Velankar; Christine A. Orengo (Briefings Bioinform., 2021)