Constrained multiple sequence alignment using XALIGN. - David S. Wishart; Robert F. Boyko; Brian D. Sykes (Comput. Appl. Biosci., 1994)

SEQSEE: a comprehensive program suite for protein sequence analysis. - David S. Wishart; Robert F. Boyko; Leigh Willard; Frederic M. Richards; Brian D. Sykes (Comput. Appl. Biosci., 1994)

A platform-independent graphical user interface for SEQSEE and XALIGN. - David S. Wishart; Scott Fortin; David R. Woloschuk; Warren Wong; Timothy Rosborough; Gary H. Van Domselaar; Jonathan Schaeffer 001; Duane Szafron (Comput. Appl. Biosci., 1997)

Prediction of genetic structure in eukaryotic DNA using reference point logistic regression and sequence alignment. - Peter M. Hooper; Haiyan Zhang; David S. Wishart (Bioinform., 2000)

Bioinformatics: Tools for Protein Technologies. - David S. Wishart (Essentials of Genomics and Bioinformatics, 2002)

VADAR: a web server for quantitative evaluation of protein structure quality. - Leigh Willard; Anuj Ranjan; Haiyan Zhang; Hassan Monzavi; Robert F. Boyko; Brian D. Sykes; David S. Wishart (Nucleic Acids Res., 2003)

Predicting subcellular localization of proteins using machine-learned classifiers. - Zhiyong Lu; Duane Szafron; Russell Greiner; Paul Lu; David S. Wishart; Brett Poulin; John Anvik; Cam Macdonell; Roman Eisner (Bioinform., 2004)

GelScape: a web-based server for interactively annotating, manipulating, comparing and archiving 1D and 2D gel images. - Nelson Young; Zhan Chang; David S. Wishart (Bioinform., 2004)

Dynamic cellular automata: a simple but powerful approach to cellular simulation. - David S. Wishart; Robert Yang; David Arndt; Peter Tang; Joseph A. Cruz (Silico Biol., 2004)

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)

SuperPose: a simple server for sophisticated structural superposition. - Rajarshi Maiti; Gary H. Van Domselaar; Haiyan Zhang; 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)

Proteome Analyst: custom predictions with explanations in a web-based tool for high-throughput proteome annotations. - Duane Szafron; Paul Lu; Russell Greiner; David S. Wishart; Brett Poulin; Roman Eisner; Zhiyong Lu; John Anvik; Cam Macdonell; Alona Fyshe; David Meeuwis (Nucleic Acids Res., 2004)

The Proteome Analyst Suite of Automated Function Prediction Tools. - Brett Poulin; Duane Szafron; Paul Lu; Russell Greiner; David S. Wishart; Roman Eisner; Alona Fyshe; Brandon Pearcy; Luca Pireddu (AAAI, 2005)

Pathway Analyst–Automated Metabolic Pathway Prediction. - Luca Pireddu; Brett Poulin; Duane Szafron; Paul Lu; David S. Wishart (CIBCB, 2005)

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)

PA-GOSUB: a searchable database of model organism protein sequences with their predicted Gene Ontology molecular function and subcellular localization. - Paul Lu; Duane Szafron; Russell Greiner; David S. Wishart; Alona Fyshe; Brandon Pearcy; Brett Poulin; Roman Eisner; Danny Ngo; Nicholas Lamb (Nucleic Acids Res., 2005)

MovieMaker: a web server for rapid rendering of protein motions and interactions. - Rajarshi Maiti; Gary H. Van Domselaar; 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)

Visual Explanation of Evidence with Additive Classifiers. - Brett Poulin; Roman Eisner; Duane Szafron; Paul Lu; Russell Greiner; David S. Wishart; Alona Fyshe; Brandon Pearcy; Cam Macdonell; John Anvik (AAAI, 2006)

Improving the accuracy of protein secondary structure prediction using structural alignment. - Scott Montgomerie; Shan Sundararaj; Warren J. Gallin; David S. Wishart (BMC Bioinform., 2006)

PREDITOR: a web server for predicting protein torsion angle restraints. - Mark V. Berjanskii; Stephen Neal; David S. Wishart (Nucleic Acids Res., 2006)

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)

Session Introduction. - David S. Wishart; Russell Greiner (Pacific Symposium on Biocomputing, 2007)

Current Progress in computational metabolomics. - David S. Wishart (Briefings Bioinform., 2007)

The RCI server: rapid and accurate calculation of protein flexibility using chemical shifts. - Mark V. Berjanskii; David S. Wishart (Nucleic Acids Res., 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)

Protein contact order prediction from primary sequences. - Yi Shi 005; Jianjun Zhou; David Arndt; David S. Wishart; Guohui Lin (BMC Bioinform., 2008)

MetaboMiner - semi-automated identification of metabolites from 2D NMR spectra of complex biofluids. - Jianguo Xia; Trent C. Bjorndahl; Peter Tang; David S. Wishart (BMC Bioinform., 2008)

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)

PROTEUS2: a web server for comprehensive protein structure prediction and structure-based annotation. - Scott Montgomerie; Joseph A. Cruz; Savita Shrivastava; David Arndt; Mark V. Berjanskii; David S. Wishart (Nucleic Acids Res., 2008)

PPT-DB: the protein property prediction and testing database. - David S. Wishart; David Arndt; Mark V. Berjanskii; Anchi Guo; Yi Shi 005; Savita Shrivastava; Jianjun Zhou; You Zhou; Guohui Lin (Nucleic Acids Res., 2008)

CS23D: a web server for rapid protein structure generation using NMR chemical shifts and sequence data. - David S. Wishart; David Arndt; Mark V. Berjanskii; Peter Tang; Jianjun Zhou; Guohui Lin (Nucleic Acids Res., 2008)

DrugBank: a knowledgebase for drugs, drug actions and drug targets. - David S. Wishart; Craig Knox; Anchi Guo; Dean Cheng; Savita Shrivastava; Dan Tzur; Bijaya Gautam; Murtaza Hassanali (Nucleic Acids Res., 2008)

GeNMR: a web server for rapid NMR-based protein structure determination. - Mark V. Berjanskii; Peter Tang; Jack Liang; Joseph A. Cruz; Jianjun Zhou; You Zhou; Edward Bassett; Cam Macdonell; Paul Lu; Guohui Lin; David S. Wishart (Nucleic Acids Res., 2009)

HMDB: a knowledgebase for the human metabolome. - David S. Wishart; Craig Knox; Anchi Guo; Roman Eisner; Nelson Young; Bijaya Gautam; David D. Hau; Nick Psychogios; Edison Dong; Souhaila Bouatra; Rupasri Mandal; Igor Sinelnikov; et al. (Nucleic Acids Res., 2009)

MetaboAnalyst: a web server for metabolomic data analysis and interpretation. - Jianguo Xia; Nick Psychogios; Nelson Young; David S. Wishart (Nucleic Acids Res., 2009)

Phenol-Explorer: an online comprehensive database on polyphenol contents in foods. - Vanessa Neveu; Jara Perez-Jimenez; Femke Vos; Vanessa Crespy; Lerman du Chaffaut; Louise Mennen; Craig Knox; Roman Eisner; Joseph A. Cruz; David S. Wishart; Augustin Scalbert (Database J. Biol. Databases Curation, 2010)

MetPA: a web-based metabolomics tool for pathway analysis and visualization. - Jianguo Xia; David S. Wishart (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)

SMPDB: The Small Molecule Pathway Database. - Alex Frolkis; Craig Knox; Emilia Lim; Timothy Jewison; Vivian Law; David D. Hau; Philip Liu; Bijaya Gautam; Son Ly; Anchi Guo; Jianguo Xia; Yongjie Liang; et al. (Nucleic Acids Res., 2010)

T3DB: a comprehensively annotated database of common toxins and their targets. - Emilia Lim; Allison Pon; Yannick Djoumbou; Craig Knox; Savita Shrivastava; Anchi Guo; Vanessa Neveu; David S. Wishart (Nucleic Acids Res., 2010)

MSEA: a web-based tool to identify biologically meaningful patterns in quantitative metabolomic data. - Jianguo Xia; David S. Wishart (Nucleic Acids Res., 2010)

MetATT: a web-based metabolomics tool for analyzing time-series and two-factor datasets. - Jianguo Xia; Igor Sinelnikov; David S. Wishart (Bioinform., 2011)

DrugBank 3.0: a comprehensive resource for 'Omics' research on drugs. - Craig Knox; Vivian Law; Timothy Jewison; Philip Liu; Son Ly; Alex Frolkis; Allison Pon; Kelly Banco; Christine Mak; Vanessa Neveu; Yannick Djoumbou; Roman Eisner; et al. (Nucleic Acids Res., 2011)

PHAST: A Fast Phage Search Tool. - You Zhou; Yongjie Liang; Karlene H. Lynch; Jonathan J. Dennis; David S. Wishart (Nucleic Acids Res., 2011)

Phenol-Explorer 2.0: a major update of the Phenol-Explorer database integrating data on polyphenol metabolism and pharmacokinetics in humans and experimental animals. - Joseph A. Rothwell; Mireia Urpi-Sarda; Maria Boto-Ordoñez; Craig Knox; Rafael Llorach; Roman Eisner; Joseph A. Cruz; Vanessa Neveu; David S. Wishart; Claudine Manach; Cristina Andres-Lacueva; Augustin Scalbert (Database J. Biol. Databases Curation, 2012)

Development of Ecom50 and Retention Index Models for Nontargeted Metabolomics: Identification of 1, 3-Dicyclohexylurea in Human Serum by HPLC/Mass Spectrometry. - L. Mark Hall; Lowell H. Hall; Tzipporah M. Kertesz; Dennis W. Hill; Thomas R. Sharp; Edward Z. Oblak; Ying W. Dong; David S. Wishart; Ming-Hui Chen; David F. Grant (J. Chem. Inf. Model., 2012)

METAGENassist: a comprehensive web server for comparative metagenomics. - David Arndt; Jianguo Xia; Yifeng Liu 001; You Zhou; Anchi Guo; Joseph A. Cruz; Igor Sinelnikov; Karen Budwill; Camilla L. Nesbø; David S. Wishart (Nucleic Acids Res., 2012)

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)

YMDB: the Yeast Metabolome Database. - Timothy Jewison; Craig Knox; Vanessa Neveu; Yannick Djoumbou; Anchi Guo; Jacqueline Lee; Philip Liu; Rupasri Mandal; Ram Krishnamurthy 002; Igor Sinelnikov; Michael Wilson 002; David S. Wishart (Nucleic Acids Res., 2012)

MetaboAnalyst 2.0 - a comprehensive server for metabolomic data analysis. - Jianguo Xia; Rupasri Mandal; Igor Sinelnikov; David Broadhurst; David S. Wishart (Nucleic Acids Res., 2012)

Chapter 3: Small Molecules and Disease. - David S. Wishart (PLoS Comput. Biol., 2012)

Phenol-Explorer 3.0: a major update of the Phenol-Explorer database to incorporate data on the effects of food processing on polyphenol content. - Joseph A. Rothwell; Jara Perez-Jimenez; Vanessa Neveu; Alexander Medina-Remón; Nouha M'Hiri; Paula García-Lobato; Claudine Manach; Craig Knox; Roman Eisner; David S. Wishart; Augustin Scalbert (Database J. Biol. Databases Curation, 2013)

An improved method to detect correct protein folds using partial clustering. - Jianjun Zhou; David S. Wishart (BMC Bioinform., 2013)

Competitive Fragmentation Modeling of ESI-MS/MS spectra for metabolite identification. - Felicity Allen; Russell Greiner; David S. Wishart (CoRR, 2013)

ECMDB: The E. coli Metabolome Database. - Anchi Guo; Timothy Jewison; Michael Wilson 002; Yifeng Liu 001; Craig Knox; Yannick Djoumbou; Patrick Lo; Rupasri Mandal; Ram Krishnamurthy 002; David S. Wishart (Nucleic Acids Res., 2013)

HMDB 3.0 - The Human Metabolome Database in 2013. - David S. Wishart; Timothy Jewison; Anchi Guo; Michael Wilson 002; Craig Knox; Yifeng Liu 001; Yannick Djoumbou; Rupasri Mandal; Farid Aziat; Edison Dong; Souhaila Bouatra; Igor Sinelnikov; et al. (Nucleic Acids Res., 2013)

INMEX - a web-based tool for integrative meta-analysis of expression data. - Jianguo Xia; Christopher D. Fjell; Matthew L. Mayer; Olga M. Pena; David S. Wishart; Robert E. W. Hancock (Nucleic Acids Res., 2013)

Accurate, fully-automated NMR spectral profiling for metabolomics. - Siamak Ravanbakhsh; Philip Liu; Trent C. Bjorndahl; Rupasri Mandal; Jason R. Grant; Michael Wilson 002; Roman Eisner; Igor Sinelnikov; Xiaoyu Hu; Claudio Luchinat; Russell Greiner; David S. Wishart (CoRR, 2014)

CFM-ID: a web server for annotation, spectrum prediction and metabolite identification from tandem mass spectra. - Felicity Allen; Allison Pon; Michael Wilson 002; Russell Greiner; David S. Wishart (Nucleic Acids Res., 2014)

SMPDB 2.0: Big Improvements to the Small Molecule Pathway Database. - Timothy Jewison; Yilu Su; Fatemeh Miri Disfany; Yongjie Liang; Craig Knox; Adam Maciejewski; Jenna Poelzer; Jessica Huynh; You Zhou; David Arndt; Yannick Djoumbou; Yifeng Liu 001; et al. (Nucleic Acids Res., 2014)

DrugBank 4.0: shedding new light on drug metabolism. - Vivian Law; Craig Knox; Yannick Djoumbou; Timothy Jewison; Anchi Guo; Yifeng Liu 001; Adam Maciejewski; David Arndt; Michael Wilson 002; Vanessa Neveu; Alexandra Tang; Geraldine Gabriel; et al. (Nucleic Acids Res., 2014)

pE-DB: a database of structural ensembles of intrinsically disordered and of unfolded proteins. - Mihaly Varadi; Simone Kosol; Pierre Lebrun; Erica Valentini; Martin Blackledge; A. Keith Dunker; Isabella C. Felli; Julie D. Forman-Kay; Richard W. Kriwacki; Roberta Pierattelli; Joel L. Sussman; Dmitri I. Svergun; et al. (Nucleic Acids Res., 2014)

Guest Editorial - Special Issue on '-Omics' Based Companion Diagnostics for Personalized Medicine. - Jie Chen 002; Shankar Subramaniam; David S. Wishart; Stephen T. Wong (IEEE Trans. Biomed. Circuits Syst., 2014)

Developing Trends in Aptamer-Based Biosensor Devices and Their Applications. - Scott MacKay; David S. Wishart; James Z. Xing; Jie Chen 002 (IEEE Trans. Biomed. Circuits Syst., 2014)

Simulating electrical properties of interdigitated electrode designs for impedance-based biosensing applications. - Scott MacKay; Peter Hermansen; David S. Wishart; Wayne Hiebert; Jie Chen 002 (CCECE, 2015)

Role of Water in Ligand Binding to Maltose-Binding Protein: Insight from a New Docking Protocol Based on the 3D-RISM-KH Molecular Theory of Solvation. - Wenjuan Huang; Nikolay Blinov; David S. Wishart; Andriy Kovalenko 001 (J. Chem. Inf. Model., 2015)

CSI 3.0: a web server for identifying secondary and super-secondary structure in proteins using NMR chemical shifts. - Noor E. Hafsa; David Arndt; David S. Wishart (Nucleic Acids Res., 2015)

PolySearch2: a significantly improved text-mining system for discovering associations between human diseases, genes, drugs, metabolites, toxins and more. - Yifeng Liu 001; Yongjie Liang; David S. Wishart (Nucleic Acids Res., 2015)

Pathways with PathWhiz. - Allison Pon; Timothy Jewison; Yilu Su; Yongjie Liang; Craig Knox; Adam Maciejewski; Michael Wilson 002; David S. Wishart (Nucleic Acids Res., 2015)

T3DB: the toxic exposome database. - David S. Wishart; David Arndt; Allison Pon; Tanvir Sajed; Anchi Guo; Yannick Djoumbou; Craig Knox; Michael Wilson 002; Yongjie Liang; Jason R. Grant; Yifeng Liu 001; Seyed Ali Goldansaz; et al. (Nucleic Acids Res., 2015)

MetaboAnalyst 3.0 - making metabolomics more meaningful. - Jianguo Xia; Igor Sinelnikov; Beomsoo Han; David S. Wishart (Nucleic Acids Res., 2015)

Simulations of Interdigitated Electrode Interactions with Gold Nanoparticles for Impedance-Based Biosensing Applications. - Scott MacKay; Peter Hermansen; David S. Wishart; Jie Chen 002 (Sensors, 2015)

Live demonstration: Portable impedance-based biosensor system for metabolomic sensing. - Scott MacKay; Ryan Corpuz; Calvin Chong; Jie Chen 002; David S. Wishart (BioCAS, 2016)

Simulations and design of microfabricated interdigitated electrodes for use in a gold nanoparticle enhanced biosensor. - Peter Hermansen; Scott MacKay; David S. Wishart; Jie Chen 002 (EMBC, 2016)

An impedance detection circuit for applications in a portable biosensor system. - Xiaojian Yu; Mihai Esanu; Scott MacKay; Jie Chen 002; Mohamad Sawan; David S. Wishart; Wayne Hiebert (ISCAS, 2016)

ClassyFire: automated chemical classification with a comprehensive, computable taxonomy. - Yannick Djoumbou; Roman Eisner; Craig Knox; Leonid L. Chepelev; Janna Hastings; Gareth I. Owen; Eoin Fahy; Christoph Steinbeck; Shankar Subramanian; Evan Bolton; Russell Greiner; David S. Wishart (J. Cheminformatics, 2016)

PHASTER: a better, faster version of the PHAST phage search tool. - David Arndt; Jason R. Grant; Ana Marcu; Tanvir Sajed; Allison Pon; Yongjie Liang; David S. Wishart (Nucleic Acids Res., 2016)

Heatmapper: web-enabled heat mapping for all. - Sasha Babicki; David Arndt; Ana Marcu; Yongjie Liang; Jason R. Grant; Adam Maciejewski; David S. Wishart (Nucleic Acids Res., 2016)

ECMDB 2.0: A richer resource for understanding the biochemistry of E. coli. - Tanvir Sajed; Ana Marcu; Miguel Ramirez-Gaona; Allison Pon; An Chi Guo; Craig Knox; Michael Wilson 002; Jason R. Grant; Yannick Djoumbou; David S. Wishart (Nucleic Acids Res., 2016)

Exposome-Explorer: a manually-curated database on biomarkers of exposure to dietary and environmental factors. - Vanessa Neveu; Alice Moussy; Héloïse Rouaix; Roland Wedekind; Allison Pon; Craig Knox; David S. Wishart; Augustin Scalbert (Nucleic Acids Res., 2017)

YMDB 2.0: a significantly expanded version of the yeast metabolome database. - Miguel Ramirez-Gaona; Ana Marcu; Allison Pon; An Chi Guo; Tanvir Sajed; Noah A. Wishart; Naama Karu; Yannick Djoumbou Feunang; David Arndt; David S. Wishart (Nucleic Acids Res., 2017)

CypReact: A Software Tool for in Silico Reactant Prediction for Human Cytochrome P450 Enzymes. - Siyang Tian; Yannick Djoumbou Feunang; Russell Greiner; David S. Wishart (J. Chem. Inf. Model., 2018)

MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis. - Jasmine Chong; Othman Soufan; Carin Li; Iurie Caraus; Shuzhao Li; Guillaume Bourque; David S. Wishart; Jianguo Xia (Nucleic Acids Res., 2018)

PAMDB: a comprehensive Pseudomonas aeruginosa metabolome database. - Weiliang Huang; Luke K. Brewer; Jace W. Jones; Angela T. Nguyen; Ana Marcu; David S. Wishart; Amanda G. Oglesby-Sherrouse; Maureen A. Kane; Angela Wilks (Nucleic Acids Res., 2018)

DrugBank 5.0: a major update to the DrugBank database for 2018. - David S. Wishart; Yannick D. Feunang; An Chi Guo; Elvis J. Lo; Ana Marcu; Jason R. Grant; Tanvir Sajed; Daniel Johnson; Carin Li; Zinat Sayeeda; Nazanin Assempour; Ithayavani Iynkkaran; et al. (Nucleic Acids Res., 2018)

HMDB 4.0: the human metabolome database for 2018. - David S. Wishart; Yannick Djoumbou Feunang; Ana Marcu; An Chi Guo; Kevin Y. H. Liang; Rosa Vázquez-Fresno; Tanvir Sajed; Daniel Johnson; Carin Li; Naama Karu; Zinat Sayeeda; Elvis J. Lo; et al. (Nucleic Acids Res., 2018)

PHAST, PHASTER and PHASTEST: Tools for finding prophage in bacterial genomes. - David Arndt; Ana Marcu; Yongjie Liang; David S. Wishart (Briefings Bioinform., 2019)

The role of hydration effects in 5-fluorouridine binding to SOD1: insight from a new 3D-RISM-KH based protocol for including structural water in docking simulations. - Vijaya Kumar Hinge; Nikolay Blinov; Dipankar Roy; David S. Wishart; Andriy Kovalenko 001 (J. Comput. Aided Mol. Des., 2019)

BioTransformer: a comprehensive computational tool for small molecule metabolism prediction and metabolite identification. - Yannick Djoumbou Feunang; Jarlei Fiamoncini; Alberto Gil-de-la-Fuente; Russell Greiner; Claudine Manach; David S. Wishart (J. Cheminformatics, 2019)

FOBI: an ontology to represent food intake data and associate it with metabolomic data. - Pol Castellano-Escuder; Raúl González-Domínguez; David S. Wishart; Cristina Andres-Lacueva; Alex Sánchez-Pla (Database J. Biol. Databases Curation, 2020)

Exposome-Explorer 2.0: an update incorporating candidate dietary biomarkers and dietary associations with cancer risk. - Vanessa Neveu; Geneviève Nicolas; Reza M. Salek; David S. Wishart; Augustin Scalbert (Nucleic Acids Res., 2020)

PathBank: a comprehensive pathway database for model organisms. - David S. Wishart; Carin Li; Ana Marcu; Hasan Badran; Allison Pon; Zachary Budinski; Jonas Patron; Debra Lipton; Xuan Cao; Eponine Oler; Krissa Li; Maïlys Paccoud; et al. (Nucleic Acids Res., 2020)

Predicting PAMPA permeability using the 3D-RISM-KH theory: are we there yet? - Dipankar Roy; Devjyoti Dutta; David S. Wishart; Andriy Kovalenko 001 (J. Comput. Aided Mol. Des., 2021)

CyProduct: A Software Tool for Accurately Predicting the Byproducts of Human Cytochrome P450 Metabolism. - Siyang Tian; Xuan Cao; Russell Greiner; Carin Li; Anchi Guo; David S. Wishart (J. Chem. Inf. Model., 2021)

MarkerDB: an online database of molecular biomarkers. - David S. Wishart; Brendan Bartok; Eponine Oler; Kevin Y. H. Liang; Zachary Budinski; Mark V. Berjanskii; Anchi Guo; Xuan Cao; Michael Wilson 002 (Nucleic Acids Res., 2021)

Chemical language models enable navigation in sparsely populated chemical space. - Michael A. Skinnider; R. Greg Stacey; David S. Wishart; Leonard J. Foster (Nat. Mach. Intell., 2021)

A deep generative model enables automated structure elucidation of novel psychoactive substances. - Michael A. Skinnider; Fei Wang 062; Daniel Pasin; Russell Greiner; Leonard J. Foster; Petur W. Dalsgaard; David S. Wishart (Nat. Mach. Intell., 2021)

CFM-ID 4.0 - a web server for accurate MS-based metabolite identification. - Fei Wang 062; Dana Allen; Siyang Tian; Eponine Oler; Vasuk Gautam; Russell Greiner; Thomas O. Metz; David S. Wishart (Nucleic Acids Res., 2022)

HMDB 5.0: the Human Metabolome Database for 2022. - David S. Wishart; Anchi Guo; Eponine Oler; Fei Wang 062; Afia Anjum; Harrison Peters; Raynard Dizon; Zinat Sayeeda; Siyang Tian; Brian L. Lee; Mark V. Berjanskii; Robert Mah; et al. (Nucleic Acids Res., 2022)

NP-MRD: the Natural Products Magnetic Resonance Database. - David S. Wishart; Zinat Sayeeda; Zachary Budinski; Anchi Guo; Brian L. Lee; Mark V. Berjanskii; Manoj Rout; Harrison Peters; Raynard Dizon; Robert Mah; Claudia Torres-Calzada; Mickel Hiebert-Giesbrecht; et al. (Nucleic Acids Res., 2022)

BioTransformer 3.0 - a web server for accurately predicting metabolic transformation products. - David S. Wishart; Siyang Tian; Dana Allen; Eponine Oler; Harrison Peters; Vicki W. Lui; Vasuk Gautam; Yannick Djoumbou Feunang; Russell Greiner; Thomas O. Metz (Nucleic Acids Res., 2022)

ChemFOnt: the chemical functional ontology resource. - David S. Wishart; Sagan Girod; Harrison Peters; Eponine Oler; Juan Jovel; Zachary Budinski; Ralph Milford; Vicki W. Lui; Zinat Sayeeda; Robert Mah; William Wei; Hasan Badran; et al. (Nucleic Acids Res., 2023)

MiMeDB: the Human Microbial Metabolome Database. - David S. Wishart; Eponine Oler; Harrison Peters; Anchi Guo; Sagan Girod; Scott Han; Sukanta Saha; Vicki W. Lui; Marcia Levatte; Vasuk Gautam; Rima Kaddurah-Daouk; Naama Karu (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)

MassSpecGym: A benchmark for the discovery and identification of molecules. - Roman Bushuiev; Anton Bushuiev; Niek F. de Jonge; Adamo Young; Fleming Kretschmer; Raman Samusevich; Janne Heirman; Fei Wang 062; Luke Zhang; Kai Dührkop; Marcus Ludwig; Nils A. Haupt; et al. (NeurIPS, 2024)

FraGNNet: A Deep Probabilistic Model for Mass Spectrum Prediction. - Adamo Young; Fei Wang 062; David S. Wishart; Bo Wang 044; Hannes L. Röst; Russ Greiner (CoRR, 2024)

FraGNNet: A Deep Probabilistic Model for Tandem Mass Spectrum Prediction. - Adamo Young; Fei Wang 062; David S. Wishart; Bo Wang 044; Russell Greiner; Hannes Rost (Trans. Mach. Learn. Res., 2025)