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ORCIDDavid S. Wishart
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- affiliation: University of Alberta, Edmonton, Canada
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2020 – today
- 2024
[i3]Adamo Young, Fei Wang, David S. Wishart, Bo Wang, Hannes L. Röst, Russ Greiner:
FraGNNet: A Deep Probabilistic Model for Mass Spectrum Prediction. CoRR abs/2404.02360 (2024)- 2023
- [j97]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:
MiMeDB: the Human Microbial Metabolome Database. Nucleic Acids Res. 51(D1): 611-620 (2023) - [j96]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:
ChemFOnt: the chemical functional ontology resource. Nucleic Acids Res. 51(D1): 1220-1229 (2023) - [j95]David S. Wishart, Scott Han, Sukanta Saha, Eponine Oler, Harrison Peters, Jason R. Grant, Paul Stothard, Vasuk Gautam:
PHASTEST: faster than PHASTER, better than PHAST. Nucleic Acids Res. 51(W1): 443-450 (2023) - [j94]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:
PlasMapper 3.0 - a web server for generating, editing, annotating and visualizing publication quality plasmid maps. Nucleic Acids Res. 51(W1): 459-467 (2023) - 2022
- [j93]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:
HMDB 5.0: the Human Metabolome Database for 2022. Nucleic Acids Res. 50(D1): 622-631 (2022) - [j92]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:
NP-MRD: the Natural Products Magnetic Resonance Database. Nucleic Acids Res. 50(D1): 665-677 (2022) - [j91]David S. Wishart, Siyang Tian, Dana Allen, Eponine Oler, Harrison Peters, Vicki W. Lui, Vasuk Gautam, Yannick Djoumbou Feunang, Russell Greiner, Thomas O. Metz:
BioTransformer 3.0 - a web server for accurately predicting metabolic transformation products. Nucleic Acids Res. 50(W1): 115-123 (2022) - [j90]Fei Wang, Dana Allen, Siyang Tian, Eponine Oler, Vasuk Gautam, Russell Greiner, Thomas O. Metz, David S. Wishart:
CFM-ID 4.0 - a web server for accurate MS-based metabolite identification. Nucleic Acids Res. 50(W1): 165-174 (2022) - 2021
- [j89]Dipankar Roy, Devjyoti Dutta, David S. Wishart, Andriy Kovalenko:
Predicting PAMPA permeability using the 3D-RISM-KH theory: are we there yet? J. Comput. Aided Mol. Des. 35(2): 261-269 (2021) - [j88]Siyang Tian, Xuan Cao, Russell Greiner, Carin Li, Anchi Guo, David S. Wishart:
CyProduct: A Software Tool for Accurately Predicting the Byproducts of Human Cytochrome P450 Metabolism. J. Chem. Inf. Model. 61(6): 3128-3140 (2021) - [j87]David S. Wishart, Brendan Bartok, Eponine Oler, Kevin Y. H. Liang, Zachary Budinski, Mark V. Berjanskii, Anchi Guo, Xuan Cao, Michael Wilson:
MarkerDB: an online database of molecular biomarkers. Nucleic Acids Res. 49(Database-Issue): D1259-D1267 (2021) - [j86]Michael A. Skinnider, R. Greg Stacey, David S. Wishart, Leonard J. Foster:
Chemical language models enable navigation in sparsely populated chemical space. Nat. Mach. Intell. 3(9): 759-770 (2021) - [j85]Michael A. Skinnider, Fei Wang, Daniel Pasin, Russell Greiner, Leonard J. Foster, Petur W. Dalsgaard, David S. Wishart:
A deep generative model enables automated structure elucidation of novel psychoactive substances. Nat. Mach. Intell. 3(11): 973-984 (2021) - 2020
- [j84]Pol Castellano-Escuder, Raúl González-Domínguez, David S. Wishart, Cristina Andres-Lacueva, Alex Sánchez-Pla:
FOBI: an ontology to represent food intake data and associate it with metabolomic data. Database J. Biol. Databases Curation 2020 (2020) - [j83]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:
PathBank: a comprehensive pathway database for model organisms. Nucleic Acids Res. 48(Database-Issue): D470-D478 (2020) - [j82]Vanessa Neveu, Geneviève Nicolas, Reza M. Salek, David S. Wishart, Augustin Scalbert:
Exposome-Explorer 2.0: an update incorporating candidate dietary biomarkers and dietary associations with cancer risk. Nucleic Acids Res. 48(Database-Issue): D908-D912 (2020)
2010 – 2019
- 2019
- [j81]David Arndt, Ana Marcu, Yongjie Liang, David S. Wishart:
PHAST, PHASTER and PHASTEST: Tools for finding prophage in bacterial genomes. Briefings Bioinform. 20(4): 1560-1567 (2019) - [j80]Vijaya Kumar Hinge, Nikolay Blinov, Dipankar Roy, David S. Wishart, Andriy Kovalenko:
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. 33(10): 913-926 (2019) - [j79]Yannick Djoumbou Feunang, Jarlei Fiamoncini, Alberto Gil-de-la-Fuente, Russell Greiner, Claudine Manach, David S. Wishart:
BioTransformer: a comprehensive computational tool for small molecule metabolism prediction and metabolite identification. J. Cheminformatics 11(1): 2:1-2:25 (2019) - 2018
- [j78]Siyang Tian, Yannick Djoumbou Feunang, Russell Greiner, David S. Wishart:
CypReact: A Software Tool for in Silico Reactant Prediction for Human Cytochrome P450 Enzymes. J. Chem. Inf. Model. 58(6): 1282-1291 (2018) - [j77]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:
DrugBank 5.0: a major update to the DrugBank database for 2018. Nucleic Acids Res. 46(Database-Issue): D1074-D1082 (2018) - [j76]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:
PAMDB: a comprehensive Pseudomonas aeruginosa metabolome database. Nucleic Acids Res. 46(Database-Issue): D575-D580 (2018) - [j75]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:
HMDB 4.0: the human metabolome database for 2018. Nucleic Acids Res. 46(Database-Issue): D608-D617 (2018) - [j74]Jasmine Chong, Othman Soufan, Carin Li, Iurie Caraus, Shuzhao Li, Guillaume Bourque, David S. Wishart, Jianguo Xia:
MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis. Nucleic Acids Res. 46(Webserver-Issue): W486-W494 (2018) - 2017
- [j73]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:
YMDB 2.0: a significantly expanded version of the yeast metabolome database. Nucleic Acids Res. 45(Database-Issue): D440-D445 (2017) - [j72]Vanessa Neveu, Alice Moussy, Héloïse Rouaix, Roland Wedekind, Allison Pon, Craig Knox, David S. Wishart, Augustin Scalbert:
Exposome-Explorer: a manually-curated database on biomarkers of exposure to dietary and environmental factors. Nucleic Acids Res. 45(Database-Issue): D979-D984 (2017) - 2016
- [j71]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:
ClassyFire: automated chemical classification with a comprehensive, computable taxonomy. J. Cheminformatics 8(1): 61:1-61:20 (2016) - [j70]Tanvir Sajed, Ana Marcu, Miguel Ramirez-Gaona, Allison Pon, An Chi Guo, Craig Knox, Michael Wilson, Jason R. Grant, Yannick Djoumbou, David S. Wishart:
ECMDB 2.0: A richer resource for understanding the biochemistry of E. coli. Nucleic Acids Res. 44(Database-Issue): 495-501 (2016) - [j69]Sasha Babicki, David Arndt, Ana Marcu, Yongjie Liang, Jason R. Grant, Adam Maciejewski, David S. Wishart:
Heatmapper: web-enabled heat mapping for all. Nucleic Acids Res. 44(Webserver-Issue): W147-W153 (2016) - [j68]David Arndt, Jason R. Grant, Ana Marcu, Tanvir Sajed, Allison Pon, Yongjie Liang, David S. Wishart:
PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res. 44(Webserver-Issue): W16-W21 (2016) - [c9]Scott MacKay, Ryan Corpuz, Calvin Chong, Jie Chen, David S. Wishart:
Live demonstration: Portable impedance-based biosensor system for metabolomic sensing. BioCAS 2016: 129 - [c8]Peter Hermansen, Scott MacKay, David S. Wishart, Jie Chen:
Simulations and design of microfabricated interdigitated electrodes for use in a gold nanoparticle enhanced biosensor. EMBC 2016: 299-302 - [c7]Xiaojian Yu, Mihai Esanu, Scott MacKay, Jie Chen, Mohamad Sawan, David S. Wishart, Wayne Hiebert:
An impedance detection circuit for applications in a portable biosensor system. ISCAS 2016: 1518-1521 - 2015
- [j67]Wenjuan Huang, Nikolay Blinov, David S. Wishart, Andriy Kovalenko:
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. 55(2): 317-328 (2015) - [j66]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:
T3DB: the toxic exposome database. Nucleic Acids Res. 43(Database-Issue): 928-934 (2015) - [j65]Jianguo Xia, Igor Sinelnikov, Beomsoo Han, David S. Wishart:
MetaboAnalyst 3.0 - making metabolomics more meaningful. Nucleic Acids Res. 43(Webserver-Issue): W251-W257 (2015) - [j64]Noor E. Hafsa, David Arndt, David S. Wishart:
CSI 3.0: a web server for identifying secondary and super-secondary structure in proteins using NMR chemical shifts. Nucleic Acids Res. 43(Webserver-Issue): W370-W377 (2015) - [j63]Yifeng Liu, Yongjie Liang, David S. Wishart:
PolySearch2: a significantly improved text-mining system for discovering associations between human diseases, genes, drugs, metabolites, toxins and more. Nucleic Acids Res. 43(Webserver-Issue): W535-W542 (2015) - [j62]Allison Pon, Timothy Jewison, Yilu Su, Yongjie Liang, Craig Knox, Adam Maciejewski, Michael Wilson, David S. Wishart:
Pathways with PathWhiz. Nucleic Acids Res. 43(Webserver-Issue): W552-W559 (2015) - [j61]Scott MacKay, Peter Hermansen, David S. Wishart, Jie Chen:
Simulations of Interdigitated Electrode Interactions with Gold Nanoparticles for Impedance-Based Biosensing Applications. Sensors 15(9): 22192-22208 (2015) - [c6]Scott MacKay, Peter Hermansen, David S. Wishart, Wayne Hiebert, Jie Chen:
Simulating electrical properties of interdigitated electrode designs for impedance-based biosensing applications. CCECE 2015: 370-375 - 2014
- [j60]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:
pE-DB: a database of structural ensembles of intrinsically disordered and of unfolded proteins. Nucleic Acids Res. 42(Database-Issue): 326-335 (2014) - [j59]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:
SMPDB 2.0: Big Improvements to the Small Molecule Pathway Database. Nucleic Acids Res. 42(Database-Issue): 478-484 (2014) - [j58]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:
DrugBank 4.0: shedding new light on drug metabolism. Nucleic Acids Res. 42(Database-Issue): 1091-1097 (2014) - [j57]Felicity Allen, Allison Pon, Michael Wilson, Russell Greiner, David S. Wishart:
CFM-ID: a web server for annotation, spectrum prediction and metabolite identification from tandem mass spectra. Nucleic Acids Res. 42(Webserver-Issue): 94-99 (2014) - [j56]Jie Chen, Shankar Subramaniam, David S. Wishart, Stephen T. Wong:
Guest Editorial - Special Issue on '-Omics' Based Companion Diagnostics for Personalized Medicine. IEEE Trans. Biomed. Circuits Syst. 8(1): 1-3 (2014) - [j55]Scott MacKay, David S. Wishart, James Z. Xing, Jie Chen:
Developing Trends in Aptamer-Based Biosensor Devices and Their Applications. IEEE Trans. Biomed. Circuits Syst. 8(1): 4-14 (2014) - [i2]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:
Accurate, fully-automated NMR spectral profiling for metabolomics. CoRR abs/1409.1456 (2014) - 2013
- [j54]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:
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 2013 (2013) - [j53]Jianjun Zhou, David S. Wishart:
An improved method to detect correct protein folds using partial clustering. BMC Bioinform. 14: 11 (2013) - [j52]Anchi Guo, Timothy Jewison, Michael Wilson, Yifeng Liu, Craig Knox, Yannick Djoumbou, Patrick Lo, Rupasri Mandal, Ram Krishnamurthy, David S. Wishart:
ECMDB: The E. coli Metabolome Database. Nucleic Acids Res. 41(Database-Issue): 625-630 (2013) - [j51]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:
HMDB 3.0 - The Human Metabolome Database in 2013. Nucleic Acids Res. 41(Database-Issue): 801-807 (2013) - [j50]Jianguo Xia, Christopher D. Fjell, Matthew L. Mayer, Olga M. Pena, David S. Wishart, Robert E. W. Hancock:
INMEX - a web-based tool for integrative meta-analysis of expression data. Nucleic Acids Res. 41(Webserver-Issue): 63-70 (2013) - [i1]Felicity Allen, Russell Greiner, David S. Wishart:
Competitive Fragmentation Modeling of ESI-MS/MS spectra for metabolite identification. CoRR abs/1312.0264 (2013) - 2012
- [j49]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:
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 2012 (2012) - [j48]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:
Development of Ecom50 and Retention Index Models for Nontargeted Metabolomics: Identification of 1, 3-Dicyclohexylurea in Human Serum by HPLC/Mass Spectrometry. J. Chem. Inf. Model. 52(5): 1222-1237 (2012) - [j47]Joseph A. Cruz, Yifeng Liu, Yongjie Liang, You Zhou, Michael Wilson, Jonathan J. Dennis, Paul Stothard, Gary H. Van Domselaar, David S. Wishart:
BacMap: an up-to-date electronic atlas of annotated bacterial genomes. Nucleic Acids Res. 40(Database-Issue): 599-604 (2012) - [j46]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:
YMDB: the Yeast Metabolome Database. Nucleic Acids Res. 40(Database-Issue): 815-820 (2012) - [j45]David Arndt, Jianguo Xia, Yifeng Liu, You Zhou, Anchi Guo, Joseph A. Cruz, Igor Sinelnikov, Karen Budwill, Camilla L. Nesbø, David S. Wishart:
METAGENassist: a comprehensive web server for comparative metagenomics. Nucleic Acids Res. 40(Web-Server-Issue): 88-95 (2012) - [j44]Jianguo Xia, Rupasri Mandal, Igor Sinelnikov, David Broadhurst, David S. Wishart:
MetaboAnalyst 2.0 - a comprehensive server for metabolomic data analysis. Nucleic Acids Res. 40(Web-Server-Issue): 127-133 (2012) - [j43]David S. Wishart:
Chapter 3: Small Molecules and Disease. PLoS Comput. Biol. 8(12) (2012) - 2011
- [j42]Jianguo Xia, Igor Sinelnikov, David S. Wishart:
MetATT: a web-based metabolomics tool for analyzing time-series and two-factor datasets. Bioinform. 27(17): 2455-2456 (2011) - [j41]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:
DrugBank 3.0: a comprehensive resource for 'Omics' research on drugs. Nucleic Acids Res. 39(Database-Issue): 1035-1041 (2011) - [j40]You Zhou, Yongjie Liang, Karlene H. Lynch, Jonathan J. Dennis, David S. Wishart:
PHAST: A Fast Phage Search Tool. Nucleic Acids Res. 39(Web-Server-Issue): 347-352 (2011) - 2010
- [j39]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:
Phenol-Explorer: an online comprehensive database on polyphenol contents in foods. Database J. Biol. Databases Curation 2010 (2010) - [j38]Jianguo Xia, David S. Wishart:
MetPA: a web-based metabolomics tool for pathway analysis and visualization. Bioinform. 26(18): 2342-2344 (2010) - [j37]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:
SMPDB: The Small Molecule Pathway Database. Nucleic Acids Res. 38(Database-Issue): 480-487 (2010) - [j36]Emilia Lim, Allison Pon, Yannick Djoumbou, Craig Knox, Savita Shrivastava, Anchi Guo, Vanessa Neveu, David S. Wishart:
T3DB: a comprehensively annotated database of common toxins and their targets. Nucleic Acids Res. 38(Database-Issue): 781-786 (2010) - [j35]Jianguo Xia, David S. Wishart:
MSEA: a web-based tool to identify biologically meaningful patterns in quantitative metabolomic data. Nucleic Acids Res. 38(Web-Server-Issue): 71-77 (2010) - [j34]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:
PROSESS: a protein structure evaluation suite and server. Nucleic Acids Res. 38(Web-Server-Issue): 633-640 (2010)
2000 – 2009
- 2009
- [j33]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:
HMDB: a knowledgebase for the human metabolome. Nucleic Acids Res. 37(Database-Issue): 603-610 (2009) - [j32]Jianguo Xia, Nick Psychogios, Nelson Young, David S. Wishart:
MetaboAnalyst: a web server for metabolomic data analysis and interpretation. Nucleic Acids Res. 37(Web-Server-Issue): 652-660 (2009) - [j31]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:
GeNMR: a web server for rapid NMR-based protein structure determination. Nucleic Acids Res. 37(Web-Server-Issue): 670-677 (2009) - 2008
- [j30]Yi Shi, Jianjun Zhou, David Arndt, David S. Wishart, Guohui Lin:
Protein contact order prediction from primary sequences. BMC Bioinform. 9 (2008) - [j29]Jianguo Xia, Trent C. Bjorndahl, Peter Tang, David S. Wishart:
MetaboMiner - semi-automated identification of metabolites from 2D NMR spectra of complex biofluids. BMC Bioinform. 9 (2008) - [j28]David S. Wishart, David Arndt, Mark V. Berjanskii, Anchi Guo, Yi Shi, Savita Shrivastava, Jianjun Zhou, You Zhou, Guohui Lin:
PPT-DB: the protein property prediction and testing database. Nucleic Acids Res. 36(Database-Issue): 222-229 (2008) - [j27]David S. Wishart, Craig Knox, Anchi Guo, Dean Cheng, Savita Shrivastava, Dan Tzur, Bijaya Gautam, Murtaza Hassanali:
DrugBank: a knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Res. 36(Database-Issue): 901-906 (2008) - [j26]Scott Montgomerie, Joseph A. Cruz, Savita Shrivastava, David Arndt, Mark V. Berjanskii, David S. Wishart:
PROTEUS2: a web server for comprehensive protein structure prediction and structure-based annotation. Nucleic Acids Res. 36(Web-Server-Issue): 202-209 (2008) - [j25]Dean Cheng, Craig Knox, Nelson Young, Paul Stothard, Sambasivarao Damaraju, David S. Wishart:
PolySearch: a web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites. Nucleic Acids Res. 36(Web-Server-Issue): 399-405 (2008) - [j24]David S. Wishart, David Arndt, Mark V. Berjanskii, Peter Tang, Jianjun Zhou, Guohui Lin:
CS23D: a web server for rapid protein structure generation using NMR chemical shifts and sequence data. Nucleic Acids Res. 36(Web-Server-Issue): 496-502 (2008) - 2007
- [j23]David S. Wishart:
Current Progress in computational metabolomics. Briefings Bioinform. 8(5): 279-293 (2007) - [j22]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:
HMDB: the Human Metabolome Database. Nucleic Acids Res. 35(Database-Issue): 521-526 (2007) - [j21]Mark V. Berjanskii, David S. Wishart:
The RCI server: rapid and accurate calculation of protein flexibility using chemical shifts. Nucleic Acids Res. 35(Web-Server-Issue): 531-537 (2007) - [c5]David S. Wishart, Russell Greiner:
Session Introduction. Pacific Symposium on Biocomputing 2007: 112-114 - [c4]Craig Knox, Savita Shrivastava, Paul Stothard, Roman Eisner, David S. Wishart:
Biospider: A Web Server for Automating Metabolome Annotations. Pacific Symposium on Biocomputing 2007: 145-156 - 2006
- [j20]Scott Montgomerie, Shan Sundararaj, Warren J. Gallin, David S. Wishart:
Improving the accuracy of protein secondary structure prediction using structural alignment. BMC Bioinform. 7: 301 (2006) - [j19]David S. Wishart, Craig Knox, Anchi Guo, Savita Shrivastava, Murtaza Hassanali, Paul Stothard, Zhan Chang, Jennifer Woolsey:
DrugBank: a comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Res. 34(Database-Issue): 668-672 (2006) - [j18]Mark V. Berjanskii, Stephen Neal, David S. Wishart:
PREDITOR: a web server for predicting protein torsion angle restraints. Nucleic Acids Res. 34(Web-Server-Issue): 63-69 (2006) - [c3]Brett Poulin, Roman Eisner, Duane Szafron, Paul Lu, Russell Greiner, David S. Wishart, Alona Fyshe, Brandon Pearcy, Cam Macdonell, John Anvik:
Visual Explanation of Evidence with Additive Classifiers. AAAI 2006: 1822-1829 - 2005
- [j17]Paul Stothard, David S. Wishart:
Circular genome visualization and exploration using CGView. Bioinform. 21(4): 537-539 (2005) - [j16]Paul Lu, Duane Szafron, Russell Greiner, David S. Wishart, Alona Fyshe, Brandon Pearcy, Brett Poulin, Roman Eisner, Danny Ngo, Nicholas Lamb:
PA-GOSUB: a searchable database of model organism protein sequences with their predicted Gene Ontology molecular function and subcellular localization. Nucleic Acids Res. 33(Database-Issue): 147-153 (2005) - [j15]Paul Stothard, Gary H. Van Domselaar, Savita Shrivastava, Anchi Guo, Brian O'Neill, Joseph A. Cruz, Michael Ellison, David S. Wishart:
BacMap: an interactive picture atlas of annotated bacterial genomes. Nucleic Acids Res. 33(Database-Issue): 317-320 (2005) - [j14]Rajarshi Maiti, Gary H. Van Domselaar, David S. Wishart:
MovieMaker: a web server for rapid rendering of protein motions and interactions. Nucleic Acids Res. 33(Web-Server-Issue): 358-362 (2005) - [j13]Gary H. Van Domselaar, Paul Stothard, Savita Shrivastava, Joseph A. Cruz, Anchi Guo, Xiaoli Dong, Paul Lu, Duane Szafron, Russell Greiner, David S. Wishart:
BASys: a web server for automated bacterial genome annotation. Nucleic Acids Res. 33(Web-Server-Issue): 455-459 (2005) - [c2]Brett Poulin, Duane Szafron, Paul Lu, Russell Greiner, David S. Wishart, Roman Eisner, Alona Fyshe, Brandon Pearcy, Luca Pireddu:
The Proteome Analyst Suite of Automated Function Prediction Tools. AAAI 2005: 1698-1699 - [c1]Luca Pireddu, Brett Poulin, Duane Szafron, Paul Lu, David S. Wishart:
Pathway Analyst--Automated Metabolic Pathway Prediction. CIBCB 2005: 243-250 - 2004
- [j12]Zhiyong Lu, Duane Szafron, Russell Greiner, Paul Lu, David S. Wishart, Brett Poulin, John Anvik, Cam Macdonell, Roman Eisner:
Predicting subcellular localization of proteins using machine-learned classifiers. Bioinform. 20(4): 547-556 (2004) - [j11]Nelson Young, Zhan Chang, David S. Wishart:
GelScape: a web-based server for interactively annotating, manipulating, comparing and archiving 1D and 2D gel images. Bioinform. 20(6): 976-978 (2004) - [j10]David S. Wishart, Robert Yang, David Arndt, Peter Tang, Joseph A. Cruz:
Dynamic cellular automata: a simple but powerful approach to cellular simulation. Silico Biol. 5(2): 139-161 (2004) - [j9]Shan Sundararaj, Anchi Guo, Bahram Habibi-Nazhad, Melania Rouani, Paul Stothard, Michael Ellison, David S. Wishart:
The CyberCell Database (CCDB): a comprehensive, self-updating, relational database to coordinate and facilitate in silico modeling of Escherichia coli. Nucleic Acids Res. 32(Database-Issue): 293-295 (2004) - [j8]Duane Szafron, Paul Lu, Russell Greiner, David S. Wishart, Brett Poulin, Roman Eisner, Zhiyong Lu, John Anvik, Cam Macdonell, Alona Fyshe, David Meeuwis:
Proteome Analyst: custom predictions with explanations in a web-based tool for high-throughput proteome annotations. Nucleic Acids Res. 32(Web-Server-Issue): 365-371 (2004) - [j7]Rajarshi Maiti, Gary H. Van Domselaar, Haiyan Zhang, David S. Wishart:
SuperPose: a simple server for sophisticated structural superposition. Nucleic Acids Res. 32(Web-Server-Issue): 590-594 (2004) - [j6]Xiaoli Dong, Paul Stothard, Ian J. Forsythe, David S. Wishart:
PlasMapper: a web server for drawing and auto-annotating plasmid maps. Nucleic Acids Res. 32(Web-Server-Issue): 660-664 (2004) - 2003
- [j5]Leigh Willard, Anuj Ranjan, Haiyan Zhang, Hassan Monzavi, Robert F. Boyko, Brian D. Sykes, David S. Wishart:
VADAR: a web server for quantitative evaluation of protein structure quality. Nucleic Acids Res. 31(13): 3316-3319 (2003) - 2002
- [p1]David S. Wishart:
Bioinformatics: Tools for Protein Technologies. Essentials of Genomics and Bioinformatics 2002: 309-328 - 2000
- [j4]Peter M. Hooper, Haiyan Zhang, David S. Wishart:
Prediction of genetic structure in eukaryotic DNA using reference point logistic regression and sequence alignment. Bioinform. 16(5): 425-438 (2000)
1990 – 1999
- 1997
- [j3]David S. Wishart, Scott Fortin, David R. Woloschuk, Warren Wong, Timothy Rosborough, Gary H. Van Domselaar, Jonathan Schaeffer, Duane Szafron:
A platform-independent graphical user interface for SEQSEE and XALIGN. Comput. Appl. Biosci. 13(5): 561-562 (1997) - 1994
- [j2]David S. Wishart, Robert F. Boyko, Leigh Willard, Frederic M. Richards, Brian D. Sykes:
SEQSEE: a comprehensive program suite for protein sequence analysis. Comput. Appl. Biosci. 10(2): 121-132 (1994) - [j1]David S. Wishart, Robert F. Boyko, Brian D. Sykes:
Constrained multiple sequence alignment using XALIGN. Comput. Appl. Biosci. 10(6): 687-688 (1994)
Coauthor Index
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