COMBOSA3D: combining sequence alignments with three-dimensional structures. - P. M. Stothard (Bioinform., 2001)

PlasMapper: a web server for drawing and auto-annotating plasmid maps. - Xiaoli Dong; Paul Stothard; Ian J. Forsythe; David S. Wishart (Nucleic Acids Res., 2004)

The CyberCell Database (CCDB): a comprehensive, self-updating, relational database to coordinate and facilitate in silico modeling of Escherichia coli. - Shan Sundararaj; Anchi Guo; Bahram Habibi-Nazhad; Melania Rouani; Paul Stothard; Michael Ellison; David S. Wishart (Nucleic Acids Res., 2004)

Circular genome visualization and exploration using CGView. - Paul Stothard; David S. Wishart (Bioinform., 2005)

BASys: a web server for automated bacterial genome annotation. - Gary H. Van Domselaar; Paul Stothard; Savita Shrivastava; Joseph A. Cruz; Anchi Guo; Xiaoli Dong; Paul Lu; Duane Szafron; Russell Greiner; David S. Wishart (Nucleic Acids Res., 2005)

BacMap: an interactive picture atlas of annotated bacterial genomes. - Paul Stothard; Gary H. Van Domselaar; Savita Shrivastava; Anchi Guo; Brian O'Neill; Joseph A. Cruz; Michael Ellison; David S. Wishart (Nucleic Acids Res., 2005)

DrugBank: a comprehensive resource for in silico drug discovery and exploration. - David S. Wishart; Craig Knox; Anchi Guo; Savita Shrivastava; Murtaza Hassanali; Paul Stothard; Zhan Chang; Jennifer Woolsey (Nucleic Acids Res., 2006)

Biospider: A Web Server for Automating Metabolome Annotations. - Craig Knox; Savita Shrivastava; Paul Stothard; Roman Eisner; David S. Wishart (Pacific Symposium on Biocomputing, 2007)

HMDB: the Human Metabolome Database. - David S. Wishart; Dan Tzur; Craig Knox; Roman Eisner; Anchi Guo; Nelson Young; Dean Cheng; Kevin Jewell; David Arndt; Summit Sawhney; Chris Fung; Lisa Nikolai; et al. (Nucleic Acids Res., 2007)

PolySearch: a web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites. - Dean Cheng; Craig Knox; Nelson Young; Paul Stothard; Sambasivarao Damaraju; David S. Wishart (Nucleic Acids Res., 2008)

The CGView Server: a comparative genomics tool for circular genomes. - Jason R. Grant; Paul Stothard (Nucleic Acids Res., 2008)

Most parsimonious haplotype allele sharing determination. - Zhipeng Cai 001; Hadi Sabaa; Yining Wang; Randy Goebel; Zhiquan Wang; Jiaofen Xu; Paul Stothard; Guohui Lin (BMC Bioinform., 2009)

Interactive microbial genome visualization with GView. - Aaron J. Petkau; Matthew Stuart-Edwards; Paul Stothard; Gary H. Van Domselaar (Bioinform., 2010)

PROSESS: a protein structure evaluation suite and server. - Mark V. Berjanskii; Yongjie Liang; Jianjun Zhou; Peter Tang; Paul Stothard; You Zhou; Joseph A. Cruz; Cam Macdonell; Guohui Lin; Paul Lu; David S. Wishart (Nucleic Acids Res., 2010)

In-depth annotation of SNPs arising from resequencing projects using NGS-SNP. - Jason R. Grant; Adriano S. Arantes; Xiaoping Liao; Paul Stothard (Bioinform., 2011)

BacMap: an up-to-date electronic atlas of annotated bacterial genomes. - Joseph A. Cruz; Yifeng Liu 001; Yongjie Liang; You Zhou; Michael Wilson 002; Jonathan J. Dennis; Paul Stothard; Gary H. Van Domselaar; David S. Wishart (Nucleic Acids Res., 2012)

Whole genome SNP genotype piecemeal imputation. - Yining Wang; Tim Wylie; Paul Stothard; Guohui Lin (BMC Bioinform., 2015)

Visualizing and comparing circular genomes using the CGView family of tools. - Paul Stothard; Jason R. Grant; Gary H. Van Domselaar (Briefings Bioinform., 2019)

Proksee: in-depth characterization and visualization of bacterial genomes. - Jason R. Grant; Eric Enns; Eric Marinier; Arnab Mandal; Emily K. Herman; Chih-Yu Chen; Morag Graham; Gary H. Van Domselaar; Paul Stothard (Nucleic Acids Res., 2023)

PHASTEST: faster than PHASTER, better than PHAST. - David S. Wishart; Scott Han; Sukanta Saha; Eponine Oler; Harrison Peters; Jason R. Grant; Paul Stothard; Vasuk Gautam (Nucleic Acids Res., 2023)

PlasMapper 3.0 - a web server for generating, editing, annotating and visualizing publication quality plasmid maps. - David S. Wishart; Leah Ren; Jacques Leong-Sit; Sukanta Saha; Jason R. Grant; Paul Stothard; Upasana Singh; Abby Kropielnicki; Eponine Oler; Harrison Peters; Vasuk Gautam (Nucleic Acids Res., 2023)