David S. Wishart

113 papers A* 3C 2Misc 2Journal 102Unranked 3

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	FraGNNet: A Deep Probabilistic Model for Tandem Mass Spectrum Prediction. Trans. Mach. Learn. Res. Adamo Young, Fei Wang, David S. Wishart, Bo Wang, Russell Greiner, Hannes Rost
2024	J	`jnl`	FraGNNet: A Deep Probabilistic Model for Mass Spectrum Prediction. CoRR Adamo Young, Fei Wang, David S. Wishart, Bo Wang, Hannes L. Röst, Russ Greiner
2024	A*	`conf`	MassSpecGym: A benchmark for the discovery and identification of molecules. NeurIPS Roman Bushuiev, Anton Bushuiev, Niek F. de Jonge, Adamo Young, Fleming Kretschmer, Raman Samusevich, Janne Heirman, Fei Wang, Luke Zhang, Kai Dührkop, Marcus Ludwig, Nils A. Haupt, Apurva Kalia, Corinna Brungs, Robin Schmid, Russell Greiner, Bo Wang, David S. Wishart, Liping Liu, Juho Rousu, Wout Bittremieux, Hannes Rost, Tytus D. Mak, Soha Hassoun, Florian Huber, Justin J. J. van der Hooft, Michael A. Stravs, Sebastian Böcker, Josef Sivic, Tomás Pluskal
2024	J	`jnl`	MassSpecGym: A benchmark for the discovery and identification of molecules. CoRR Roman Bushuiev, Anton Bushuiev, Niek F. de Jonge, Adamo Young, Fleming Kretschmer, Raman Samusevich, Janne Heirman, Fei Wang, Luke Zhang, Kai Dührkop, Marcus Ludwig, Nils A. Haupt, Apurva Kalia, Corinna Brungs, Robin Schmid, Russell Greiner, Bo Wang, David S. Wishart, Li-Ping Liu, Juho Rousu, Wout Bittremieux, Hannes Rost, Tytus D. Mak, Soha Hassoun, Florian Huber, Justin J. J. van der Hooft, Michael A. Stravs, Sebastian Böcker, Josef Sivic, Tomás Pluskal
2023	J	`jnl`	ChemFOnt: the chemical functional ontology resource. Nucleic Acids Res. 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, Elvis J. Lo, Mai Yamamoto, Yannick Djoumbou Feunang, Naama Karu, Vasuk Gautam
2023	J	`jnl`	MiMeDB: the Human Microbial Metabolome Database. Nucleic Acids Res. 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
2023	J	`jnl`	PHASTEST: faster than PHASTER, better than PHAST. Nucleic Acids Res. David S. Wishart, Scott Han, Sukanta Saha, Eponine Oler, Harrison Peters, Jason R. Grant, Paul Stothard, Vasuk Gautam
2023	J	`jnl`	PlasMapper 3.0 - a web server for generating, editing, annotating and visualizing publication quality plasmid maps. Nucleic Acids Res. 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
2022	J	`jnl`	BioTransformer 3.0 - a web server for accurately predicting metabolic transformation products. Nucleic Acids Res. David S. Wishart, Siyang Tian, Dana Allen, Eponine Oler, Harrison Peters, Vicki W. Lui, Vasuk Gautam, Yannick Djoumbou Feunang, Russell Greiner, Thomas O. Metz
2022	J	`jnl`	CFM-ID 4.0 - a web server for accurate MS-based metabolite identification. Nucleic Acids Res. Fei Wang, Dana Allen, Siyang Tian, Eponine Oler, Vasuk Gautam, Russell Greiner, Thomas O. Metz, David S. Wishart
2022	J	`jnl`	HMDB 5.0: the Human Metabolome Database for 2022. Nucleic Acids Res. David S. Wishart, Anchi Guo, Eponine Oler, Fei Wang, Afia Anjum, Harrison Peters, Raynard Dizon, Zinat Sayeeda, Siyang Tian, Brian L. Lee, Mark V. Berjanskii, Robert Mah, Mai Yamamoto, Juan Jovel, Claudia Torres-Calzada, Mickel Hiebert-Giesbrecht, Vicki W. Lui, Dorna Varshavi, Dorsa Varshavi, Dana Allen, David Arndt, Nitya Khetarpal, Aadhavya Sivakumaran, Karxena Harford, Selena Sanford, Kristen Yee, Xuan Cao, Zachary Budinski, Jaanus Liigand, Lun Zhang, Jiamin Zheng, Rupasri Mandal, Naama Karu, Maija Dambrova, Helgi B. Schiöth, Russell Greiner, Vasuk Gautam
2022	J	`jnl`	NP-MRD: the Natural Products Magnetic Resonance Database. Nucleic Acids Res. 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, Dorna Varshavi, Dorsa Varshavi, Eponine Oler, Dana Allen, Xuan Cao, Vasuk Gautam, Andrew Maras, Ella F. Poynton, Pegah Tavangar, Vera Yang, Jeffrey A. van Santen, Rajarshi Ghosh, Saurav Sarma, Eleanor Knutson, Victoria Sullivan, Amy M. Jystad, Ryan S. Renslow, Lloyd W. Sumner, Roger G. Linington, John R. Cort
2021	J	`jnl`	A deep generative model enables automated structure elucidation of novel psychoactive substances. Nat. Mach. Intell. Michael A. Skinnider, Fei Wang, Daniel Pasin, Russell Greiner, Leonard J. Foster, Petur W. Dalsgaard, David S. Wishart
2021	J	`jnl`	Chemical language models enable navigation in sparsely populated chemical space. Nat. Mach. Intell. Michael A. Skinnider, R. Greg Stacey, David S. Wishart, Leonard J. Foster
2021	J	`jnl`	CyProduct: A Software Tool for Accurately Predicting the Byproducts of Human Cytochrome P450 Metabolism. J. Chem. Inf. Model. Siyang Tian, Xuan Cao, Russell Greiner, Carin Li, Anchi Guo, David S. Wishart
2021	J	`jnl`	MarkerDB: an online database of molecular biomarkers. Nucleic Acids Res. David S. Wishart, Brendan Bartok, Eponine Oler, Kevin Y. H. Liang, Zachary Budinski, Mark V. Berjanskii, Anchi Guo, Xuan Cao, Michael Wilson
2021	J	`jnl`	Predicting PAMPA permeability using the 3D-RISM-KH theory: are we there yet? J. Comput. Aided Mol. Des. Dipankar Roy, Devjyoti Dutta, David S. Wishart, Andriy Kovalenko
2020	J	`jnl`	Exposome-Explorer 2.0: an update incorporating candidate dietary biomarkers and dietary associations with cancer risk. Nucleic Acids Res. Vanessa Neveu, Geneviève Nicolas, Reza M. Salek, David S. Wishart, Augustin Scalbert
2020	J	`jnl`	FOBI: an ontology to represent food intake data and associate it with metabolomic data. Database J. Biol. Databases Curation Pol Castellano-Escuder, Raúl González-Domínguez, David S. Wishart, Cristina Andres-Lacueva, Alex Sánchez-Pla
2020	J	`jnl`	PathBank: a comprehensive pathway database for model organisms. Nucleic Acids Res. 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, Chelsea Hong, An Chi Guo, Christopher Chan, William Wei, Miguel Ramirez-Gaona
2019	J	`jnl`	BioTransformer: a comprehensive computational tool for small molecule metabolism prediction and metabolite identification. J. Cheminformatics Yannick Djoumbou Feunang, Jarlei Fiamoncini, Alberto Gil-de-la-Fuente, Russell Greiner, Claudine Manach, David S. Wishart
2019	J	`jnl`	PHAST, PHASTER and PHASTEST: Tools for finding prophage in bacterial genomes. Briefings Bioinform. David Arndt, Ana Marcu, Yongjie Liang, David S. Wishart
2019	J	`jnl`	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. J. Comput. Aided Mol. Des. Vijaya Kumar Hinge, Nikolay Blinov, Dipankar Roy, David S. Wishart, Andriy Kovalenko
2018	J	`jnl`	CypReact: A Software Tool for in Silico Reactant Prediction for Human Cytochrome P450 Enzymes. J. Chem. Inf. Model. Siyang Tian, Yannick Djoumbou Feunang, Russell Greiner, David S. Wishart
2018	J	`jnl`	DrugBank 5.0: a major update to the DrugBank database for 2018. Nucleic Acids Res. 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, Yifeng Liu, Adam Maciejewski, Nicola Gale, Alex Wilson, Lucy Chin, Ryan Cummings, Diana Le, Allison Pon, Craig Knox, Michael Wilson
2018	J	`jnl`	HMDB 4.0: the human metabolome database for 2018. Nucleic Acids Res. 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, Nazanin Assempour, Mark V. Berjanskii, Sandeep Singhal, David Arndt, Yongjie Liang, Hasan Badran, Jason R. Grant, Arnau Serra-Cayuela, Yifeng Liu, Rupa Mandal, Vanessa Neveu, Allison Pon, Craig Knox, Michael Wilson, Claudine Manach, Augustin Scalbert
2018	J	`jnl`	MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis. Nucleic Acids Res. Jasmine Chong, Othman Soufan, Carin Li, Iurie Caraus, Shuzhao Li, Guillaume Bourque, David S. Wishart, Jianguo Xia
2018	J	`jnl`	PAMDB: a comprehensive Pseudomonas aeruginosa metabolome database. Nucleic Acids Res. 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
2017	J	`jnl`	Exposome-Explorer: a manually-curated database on biomarkers of exposure to dietary and environmental factors. Nucleic Acids Res. Vanessa Neveu, Alice Moussy, Héloïse Rouaix, Roland Wedekind, Allison Pon, Craig Knox, David S. Wishart, Augustin Scalbert
2017	J	`jnl`	YMDB 2.0: a significantly expanded version of the yeast metabolome database. Nucleic Acids Res. 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
2016	C	`conf`	An impedance detection circuit for applications in a portable biosensor system. ISCAS Xiaojian Yu, Mihai Esanu, Scott MacKay, Jie Chen, Mohamad Sawan, David S. Wishart, Wayne Hiebert
2016	J	`jnl`	ClassyFire: automated chemical classification with a comprehensive, computable taxonomy. J. Cheminformatics 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
2016	J	`jnl`	ECMDB 2.0: A richer resource for understanding the biochemistry of Nucleic Acids Res. Tanvir Sajed, Ana Marcu, Miguel Ramirez-Gaona, Allison Pon, An Chi Guo, Craig Knox, Michael Wilson, Jason R. Grant, Yannick Djoumbou, David S. Wishart
2016	J	`jnl`	Heatmapper: web-enabled heat mapping for all. Nucleic Acids Res. Sasha Babicki, David Arndt, Ana Marcu, Yongjie Liang, Jason R. Grant, Adam Maciejewski, David S. Wishart
2016	—	`conf`	Live demonstration: Portable impedance-based biosensor system for metabolomic sensing. BioCAS Scott MacKay, Ryan Corpuz, Calvin Chong, Jie Chen, David S. Wishart
2016	J	`jnl`	PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res. David Arndt, Jason R. Grant, Ana Marcu, Tanvir Sajed, Allison Pon, Yongjie Liang, David S. Wishart
2016	—	`conf`	Simulations and design of microfabricated interdigitated electrodes for use in a gold nanoparticle enhanced biosensor. EMBC Peter Hermansen, Scott MacKay, David S. Wishart, Jie Chen
2015	J	`jnl`	CSI 3.0: a web server for identifying secondary and super-secondary structure in proteins using NMR chemical shifts. Nucleic Acids Res. Noor E. Hafsa, David Arndt, David S. Wishart
2015	J	`jnl`	MetaboAnalyst 3.0 - making metabolomics more meaningful. Nucleic Acids Res. Jianguo Xia, Igor Sinelnikov, Beomsoo Han, David S. Wishart
2015	J	`jnl`	Pathways with PathWhiz. Nucleic Acids Res. Allison Pon, Timothy Jewison, Yilu Su, Yongjie Liang, Craig Knox, Adam Maciejewski, Michael Wilson, David S. Wishart
2015	J	`jnl`	PolySearch2: a significantly improved text-mining system for discovering associations between human diseases, genes, drugs, metabolites, toxins and more. Nucleic Acids Res. Yifeng Liu, Yongjie Liang, David S. Wishart
2015	J	`jnl`	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. J. Chem. Inf. Model. Wenjuan Huang, Nikolay Blinov, David S. Wishart, Andriy Kovalenko
2015	—	`conf`	Simulating electrical properties of interdigitated electrode designs for impedance-based biosensing applications. CCECE Scott MacKay, Peter Hermansen, David S. Wishart, Wayne Hiebert, Jie Chen
2015	J	`jnl`	Simulations of Interdigitated Electrode Interactions with Gold Nanoparticles for Impedance-Based Biosensing Applications. Sensors Scott MacKay, Peter Hermansen, David S. Wishart, Jie Chen
2015	J	`jnl`	T3DB: the toxic exposome database. Nucleic Acids Res. David S. Wishart, David Arndt, Allison Pon, Tanvir Sajed, Anchi Guo, Yannick Djoumbou, Craig Knox, Michael Wilson, Yongjie Liang, Jason R. Grant, Yifeng Liu, Seyed Ali Goldansaz, Stephen M. Rappaport
2014	J	`jnl`	Accurate, fully-automated NMR spectral profiling for metabolomics. CoRR Siamak Ravanbakhsh, Philip Liu, Trent C. Bjorndahl, Rupasri Mandal, Jason R. Grant, Michael Wilson, Roman Eisner, Igor Sinelnikov, Xiaoyu Hu, Claudio Luchinat, Russell Greiner, David S. Wishart
2014	J	`jnl`	CFM-ID: a web server for annotation, spectrum prediction and metabolite identification from tandem mass spectra. Nucleic Acids Res. Felicity Allen, Allison Pon, Michael Wilson, Russell Greiner, David S. Wishart
2014	J	`jnl`	Developing Trends in Aptamer-Based Biosensor Devices and Their Applications. IEEE Trans. Biomed. Circuits Syst. Scott MacKay, David S. Wishart, James Z. Xing, Jie Chen
2014	J	`jnl`	DrugBank 4.0: shedding new light on drug metabolism. Nucleic Acids Res. Vivian Law, Craig Knox, Yannick Djoumbou, Timothy Jewison, Anchi Guo, Yifeng Liu, Adam Maciejewski, David Arndt, Michael Wilson, Vanessa Neveu, Alexandra Tang, Geraldine Gabriel, Carol Ly, Sakina Adamjee, Zerihun T. Dame, Beomsoo Han, You Zhou, David S. Wishart
2014	J	`jnl`	Guest Editorial - Special Issue on '-Omics' Based Companion Diagnostics for Personalized Medicine. IEEE Trans. Biomed. Circuits Syst. Jie Chen, Shankar Subramaniam, David S. Wishart, Stephen T. Wong
2014	J	`jnl`	SMPDB 2.0: Big Improvements to the Small Molecule Pathway Database. Nucleic Acids Res. 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, Lu Deng, Anchi Guo, Beomsoo Han, Allison Pon, Michael Wilson, Shahrzad Rafatnia, Philip Liu, David S. Wishart
2014	J	`jnl`	pE-DB: a database of structural ensembles of intrinsically disordered and of unfolded proteins. Nucleic Acids Res. 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, Vladimir N. Uversky, Michele Vendruscolo, David S. Wishart, Peter E. Wright, Peter Tompa
2013	J	`jnl`	An improved method to detect correct protein folds using partial clustering. BMC Bioinform. Jianjun Zhou, David S. Wishart
2013	J	`jnl`	Competitive Fragmentation Modeling of ESI-MS/MS spectra for metabolite identification. CoRR Felicity Allen, Russell Greiner, David S. Wishart
2013	J	`jnl`	ECMDB: The Nucleic Acids Res. Anchi Guo, Timothy Jewison, Michael Wilson, Yifeng Liu, Craig Knox, Yannick Djoumbou, Patrick Lo, Rupasri Mandal, Ram Krishnamurthy, David S. Wishart
2013	J	`jnl`	HMDB 3.0 - The Human Metabolome Database in 2013. Nucleic Acids Res. David S. Wishart, Timothy Jewison, Anchi Guo, Michael Wilson, Craig Knox, Yifeng Liu, Yannick Djoumbou, Rupasri Mandal, Farid Aziat, Edison Dong, Souhaila Bouatra, Igor Sinelnikov, David Arndt, Jianguo Xia, Philip Liu, Faizath Yallou, Trent C. Bjorndahl, Rolando Perez-Pineiro, Roman Eisner, Felicity Allen, Vanessa Neveu, Russell Greiner, Augustin Scalbert
2013	J	`jnl`	INMEX - a web-based tool for integrative meta-analysis of expression data. Nucleic Acids Res. Jianguo Xia, Christopher D. Fjell, Matthew L. Mayer, Olga M. Pena, David S. Wishart, Robert E. W. Hancock
2013	J	`jnl`	Phenol-Explorer 3.0: a major update of the Phenol-Explorer database to incorporate data on the effects of food processing on polyphenol content. Database J. Biol. Databases Curation 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
2012	J	`jnl`	BacMap: an up-to-date electronic atlas of annotated bacterial genomes. Nucleic Acids Res. Joseph A. Cruz, Yifeng Liu, Yongjie Liang, You Zhou, Michael Wilson, Jonathan J. Dennis, Paul Stothard, Gary H. Van Domselaar, David S. Wishart
2012	J	`jnl`	Chapter 3: Small Molecules and Disease. PLoS Comput. Biol. David S. Wishart
2012	J	`jnl`	Development of Ecom J. Chem. Inf. Model. 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
2012	J	`jnl`	METAGENassist: a comprehensive web server for comparative metagenomics. Nucleic Acids Res. David Arndt, Jianguo Xia, Yifeng Liu, You Zhou, Anchi Guo, Joseph A. Cruz, Igor Sinelnikov, Karen Budwill, Camilla L. Nesbø, David S. Wishart
2012	J	`jnl`	MetaboAnalyst 2.0 - a comprehensive server for metabolomic data analysis. Nucleic Acids Res. Jianguo Xia, Rupasri Mandal, Igor Sinelnikov, David Broadhurst, David S. Wishart
2012	J	`jnl`	Phenol-Explorer 2.0: a major update of the Phenol-Explorer database integrating data on polyphenol metabolism and pharmacokinetics in humans and experimental animals. Database J. Biol. Databases Curation 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
2012	J	`jnl`	YMDB: the Yeast Metabolome Database. Nucleic Acids Res. Timothy Jewison, Craig Knox, Vanessa Neveu, Yannick Djoumbou, Anchi Guo, Jacqueline Lee, Philip Liu, Rupasri Mandal, Ram Krishnamurthy, Igor Sinelnikov, Michael Wilson, David S. Wishart
2011	J	`jnl`	DrugBank 3.0: a comprehensive resource for 'Omics' research on drugs. Nucleic Acids Res. Craig Knox, Vivian Law, Timothy Jewison, Philip Liu, Son Ly, Alex Frolkis, Allison Pon, Kelly Banco, Christine Mak, Vanessa Neveu, Yannick Djoumbou, Roman Eisner, Anchi Guo, David S. Wishart
2011	J	`jnl`	MetATT: a web-based metabolomics tool for analyzing time-series and two-factor datasets. Bioinform. Jianguo Xia, Igor Sinelnikov, David S. Wishart
2011	J	`jnl`	PHAST: A Fast Phage Search Tool. Nucleic Acids Res. You Zhou, Yongjie Liang, Karlene H. Lynch, Jonathan J. Dennis, David S. Wishart
2010	J	`jnl`	MSEA: a web-based tool to identify biologically meaningful patterns in quantitative metabolomic data. Nucleic Acids Res. Jianguo Xia, David S. Wishart
2010	J	`jnl`	MetPA: a web-based metabolomics tool for pathway analysis and visualization. Bioinform. Jianguo Xia, David S. Wishart
2010	J	`jnl`	PROSESS: a protein structure evaluation suite and server. Nucleic Acids Res. 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
2010	J	`jnl`	Phenol-Explorer: an online comprehensive database on polyphenol contents in foods. Database J. Biol. Databases Curation 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
2010	J	`jnl`	SMPDB: The Small Molecule Pathway Database. Nucleic Acids Res. 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, Savita Shrivastava, David S. Wishart
2010	J	`jnl`	T3DB: a comprehensively annotated database of common toxins and their targets. Nucleic Acids Res. Emilia Lim, Allison Pon, Yannick Djoumbou, Craig Knox, Savita Shrivastava, Anchi Guo, Vanessa Neveu, David S. Wishart
2009	J	`jnl`	GeNMR: a web server for rapid NMR-based protein structure determination. Nucleic Acids Res. 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
2009	J	`jnl`	HMDB: a knowledgebase for the human metabolome. Nucleic Acids Res. 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, Jianguo Xia, Leslie Jia, Joseph A. Cruz, Emilia Lim, Constance A. Sobsey, Savita Shrivastava, Paul Huang, Philip Liu, Lydia Fang, Jun Peng, Ryan Fradette, Dean Cheng, Dan Tzur, Melisa Clements, Avalyn Lewis, Andrea De Souza, Azaret Zuniga, Margot Dawe, Yeping Xiong, Derrick Clive, Russell Greiner, Alsu Nazyrova, Rustem Shaykhutdinov, Liang Li, Hans J. Vogel, Ian J. Forsythe
2009	J	`jnl`	MetaboAnalyst: a web server for metabolomic data analysis and interpretation. Nucleic Acids Res. Jianguo Xia, Nick Psychogios, Nelson Young, David S. Wishart
2008	J	`jnl`	CS23D: a web server for rapid protein structure generation using NMR chemical shifts and sequence data. Nucleic Acids Res. David S. Wishart, David Arndt, Mark V. Berjanskii, Peter Tang, Jianjun Zhou, Guohui Lin
2008	J	`jnl`	DrugBank: a knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Res. David S. Wishart, Craig Knox, Anchi Guo, Dean Cheng, Savita Shrivastava, Dan Tzur, Bijaya Gautam, Murtaza Hassanali
2008	J	`jnl`	MetaboMiner - semi-automated identification of metabolites from 2D NMR spectra of complex biofluids. BMC Bioinform. Jianguo Xia, Trent C. Bjorndahl, Peter Tang, David S. Wishart
2008	J	`jnl`	PPT-DB: the protein property prediction and testing database. Nucleic Acids Res. David S. Wishart, David Arndt, Mark V. Berjanskii, Anchi Guo, Yi Shi, Savita Shrivastava, Jianjun Zhou, You Zhou, Guohui Lin
2008	J	`jnl`	PROTEUS2: a web server for comprehensive protein structure prediction and structure-based annotation. Nucleic Acids Res. Scott Montgomerie, Joseph A. Cruz, Savita Shrivastava, David Arndt, Mark V. Berjanskii, David S. Wishart
2008	J	`jnl`	PolySearch: a web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites. Nucleic Acids Res. Dean Cheng, Craig Knox, Nelson Young, Paul Stothard, Sambasivarao Damaraju, David S. Wishart
2008	J	`jnl`	Protein contact order prediction from primary sequences. BMC Bioinform. Yi Shi, Jianjun Zhou, David Arndt, David S. Wishart, Guohui Lin
2007	Misc	`conf`	Biospider: A Web Server for Automating Metabolome Annotations. Pacific Symposium on Biocomputing Craig Knox, Savita Shrivastava, Paul Stothard, Roman Eisner, David S. Wishart
2007	J	`jnl`	Current Progress in computational metabolomics. Briefings Bioinform. David S. Wishart
2007	J	`jnl`	HMDB: the Human Metabolome Database. Nucleic Acids Res. 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, Mike Lewis, Marie-Aude Coutouly, Ian J. Forsythe, Peter Tang, Savita Shrivastava, Kevin Jeroncic, Paul Stothard, Godwin Amegbey, David Block, David D. Hau, James Wagner, Jessica Miniaci, Melisa Clements, Mulu Gebremedhin, Natalie Guo, Ying Zhang, Gavin E. Duggan, Glen D. MacInnis, Alim M. Weljie, Reza Dowlatabadi, Fiona Bamforth, Derrick Clive, Russell Greiner, Liang Li, Tom Marrie, Brian D. Sykes, Hans J. Vogel, Lori Querengesser
2007	Misc	`conf`	Session Introduction. Pacific Symposium on Biocomputing David S. Wishart, Russell Greiner
2007	J	`jnl`	The RCI server: rapid and accurate calculation of protein flexibility using chemical shifts. Nucleic Acids Res. Mark V. Berjanskii, David S. Wishart
2006	J	`jnl`	DrugBank: a comprehensive resource for Nucleic Acids Res. David S. Wishart, Craig Knox, Anchi Guo, Savita Shrivastava, Murtaza Hassanali, Paul Stothard, Zhan Chang, Jennifer Woolsey
2006	J	`jnl`	Improving the accuracy of protein secondary structure prediction using structural alignment. BMC Bioinform. Scott Montgomerie, Shan Sundararaj, Warren J. Gallin, David S. Wishart
2006	J	`jnl`	PREDITOR: a web server for predicting protein torsion angle restraints. Nucleic Acids Res. Mark V. Berjanskii, Stephen Neal, David S. Wishart
2006	A*	`conf`	Visual Explanation of Evidence with Additive Classifiers. AAAI Brett Poulin, Roman Eisner, Duane Szafron, Paul Lu, Russell Greiner, David S. Wishart, Alona Fyshe, Brandon Pearcy, Cam Macdonell, John Anvik
2005	J	`jnl`	BASys: a web server for automated bacterial genome annotation. Nucleic Acids Res. Gary H. Van Domselaar, Paul Stothard, Savita Shrivastava, Joseph A. Cruz, Anchi Guo, Xiaoli Dong, Paul Lu, Duane Szafron, Russell Greiner, David S. Wishart
2005	J	`jnl`	BacMap: an interactive picture atlas of annotated bacterial genomes. Nucleic Acids Res. Paul Stothard, Gary H. Van Domselaar, Savita Shrivastava, Anchi Guo, Brian O'Neill, Joseph A. Cruz, Michael Ellison, David S. Wishart
2005	J	`jnl`	Circular genome visualization and exploration using CGView. Bioinform. Paul Stothard, David S. Wishart
2005	J	`jnl`	MovieMaker: a web server for rapid rendering of protein motions and interactions. Nucleic Acids Res. Rajarshi Maiti, Gary H. Van Domselaar, David S. Wishart
2005	J	`jnl`	PA-GOSUB: a searchable database of model organism protein sequences with their predicted Gene Ontology molecular function and subcellular localization. Nucleic Acids Res. Paul Lu, Duane Szafron, Russell Greiner, David S. Wishart, Alona Fyshe, Brandon Pearcy, Brett Poulin, Roman Eisner, Danny Ngo, Nicholas Lamb
2005	C	`conf`	Pathway Analyst--Automated Metabolic Pathway Prediction. CIBCB Luca Pireddu, Brett Poulin, Duane Szafron, Paul Lu, David S. Wishart
2005	A*	`conf`	The Proteome Analyst Suite of Automated Function Prediction Tools. AAAI Brett Poulin, Duane Szafron, Paul Lu, Russell Greiner, David S. Wishart, Roman Eisner, Alona Fyshe, Brandon Pearcy, Luca Pireddu
2004	J	`jnl`	Dynamic cellular automata: a simple but powerful approach to cellular simulation. Silico Biol. David S. Wishart, Robert Yang, David Arndt, Peter Tang, Joseph A. Cruz
2004	J	`jnl`	GelScape: a web-based server for interactively annotating, manipulating, comparing and archiving 1D and 2D gel images. Bioinform. Nelson Young, Zhan Chang, David S. Wishart
2004	J	`jnl`	PlasMapper: a web server for drawing and auto-annotating plasmid maps. Nucleic Acids Res. Xiaoli Dong, Paul Stothard, Ian J. Forsythe, David S. Wishart
2004	J	`jnl`	Predicting subcellular localization of proteins using machine-learned classifiers. Bioinform. Zhiyong Lu, Duane Szafron, Russell Greiner, Paul Lu, David S. Wishart, Brett Poulin, John Anvik, Cam Macdonell, Roman Eisner
2004	J	`jnl`	Proteome Analyst: custom predictions with explanations in a web-based tool for high-throughput proteome annotations. Nucleic Acids Res. Duane Szafron, Paul Lu, Russell Greiner, David S. Wishart, Brett Poulin, Roman Eisner, Zhiyong Lu, John Anvik, Cam Macdonell, Alona Fyshe, David Meeuwis
2004	J	`jnl`	SuperPose: a simple server for sophisticated structural superposition. Nucleic Acids Res. Rajarshi Maiti, Gary H. Van Domselaar, Haiyan Zhang, David S. Wishart
2004	J	`jnl`	The CyberCell Database (CCDB): a comprehensive, self-updating, relational database to coordinate and facilitate in silico modeling of Escherichia coli. Nucleic Acids Res. Shan Sundararaj, Anchi Guo, Bahram Habibi-Nazhad, Melania Rouani, Paul Stothard, Michael Ellison, David S. Wishart
2003	J	`jnl`	VADAR: a web server for quantitative evaluation of protein structure quality. Nucleic Acids Res. Leigh Willard, Anuj Ranjan, Haiyan Zhang, Hassan Monzavi, Robert F. Boyko, Brian D. Sykes, David S. Wishart
2002	—	`ch.`	Bioinformatics: Tools for Protein Technologies. Essentials of Genomics and Bioinformatics David S. Wishart
2000	J	`jnl`	Prediction of genetic structure in eukaryotic DNA using reference point logistic regression and sequence alignment. Bioinform. Peter M. Hooper, Haiyan Zhang, David S. Wishart
1997	J	`jnl`	A platform-independent graphical user interface for SEQSEE and XALIGN. Comput. Appl. Biosci. David S. Wishart, Scott Fortin, David R. Woloschuk, Warren Wong, Timothy Rosborough, Gary H. Van Domselaar, Jonathan Schaeffer, Duane Szafron
1994	J	`jnl`	Constrained multiple sequence alignment using XALIGN. Comput. Appl. Biosci. David S. Wishart, Robert F. Boyko, Brian D. Sykes
1994	J	`jnl`	SEQSEE: a comprehensive program suite for protein sequence analysis. Comput. Appl. Biosci. David S. Wishart, Robert F. Boyko, Leigh Willard, Frederic M. Richards, Brian D. Sykes