Dr Joe Wandy

Publications

List by: Type | Date

Jump to: 2023 | 2022 | 2021 | 2019 | 2018 | 2017 | 2016
Number of items: 16.

2023

McBride, Ross, Wandy, Joe ORCID logoORCID: https://orcid.org/0000-0002-3068-4664, Weidt, Stefan, Rogers, Simon ORCID logoORCID: https://orcid.org/0000-0003-3578-4477, Davies, Vinny ORCID logoORCID: https://orcid.org/0000-0003-1896-8936, Daly, Rónán ORCID logoORCID: https://orcid.org/0000-0002-1275-6820 and Bryson, Kevin ORCID logoORCID: https://orcid.org/0000-0002-1163-6368 (2023) TopNEXt: automatic DDA exclusion framework for multi-sample mass spectrometry experiments. Bioinformatics, 39(7), btad406. (doi: 10.1093/bioinformatics/btad406) (PMID:37364005)

Wandy, Joe ORCID logoORCID: https://orcid.org/0000-0002-3068-4664, Mcbride, Ross, Rogers, Simon ORCID logoORCID: https://orcid.org/0000-0003-3578-4477, Terzis, Nikolaos, Weidt, Stefan, van der Hooft, Justin J.J. ORCID logoORCID: https://orcid.org/0000-0002-9340-5511, Bryson, Kevin ORCID logoORCID: https://orcid.org/0000-0002-1163-6368, Daly, Rónán ORCID logoORCID: https://orcid.org/0000-0002-1275-6820 and Davies, Vinny ORCID logoORCID: https://orcid.org/0000-0003-1896-8936 (2023) Simulated-to-real benchmarking of acquisition methods in untargeted metabolomics. Frontiers in Molecular Biosciences, 10, 1130781. (doi: 10.3389/fmolb.2023.1130781) (PMID:36959982) (PMCID:PMC10027714)

2022

Wandy, Joe ORCID logoORCID: https://orcid.org/0000-0002-3068-4664, Davies, Vinny ORCID logoORCID: https://orcid.org/0000-0003-1896-8936, McBride, Ross, Weidt, Stefan, Rogers, Simon ORCID logoORCID: https://orcid.org/0000-0003-3578-4477 and Daly, Ronan ORCID logoORCID: https://orcid.org/0000-0002-1275-6820 (2022) ViMMS 2.0: A framework to develop, test and optimise fragmentation strategies in LC-MS metabolomics. Journal of Open Source Software, 7(71), 3990. (doi: 10.21105/joss.03990)

2021

Wandy, Joe ORCID logoORCID: https://orcid.org/0000-0002-3068-4664 and Daly, Rónán ORCID logoORCID: https://orcid.org/0000-0002-1275-6820 (2021) GraphOmics: an interactive platform to explore and integrate multi-omics data. BMC Bioinformatics, 22, 603. (doi: 10.1186/s12859-021-04500-1) (PMID:34922446) (PMCID:PMC8684259)

Davies, Vinny ORCID logoORCID: https://orcid.org/0000-0003-1896-8936, Wandy, Joe ORCID logoORCID: https://orcid.org/0000-0002-3068-4664, Weidt, Stefan, van der Hooft, Justin J.J. ORCID logoORCID: https://orcid.org/0000-0002-9340-5511, Miller, Alice ORCID logoORCID: https://orcid.org/0000-0002-0941-1717, Daly, Rónán ORCID logoORCID: https://orcid.org/0000-0002-1275-6820 and Rogers, Simon ORCID logoORCID: https://orcid.org/0000-0003-3578-4477 (2021) Rapid development of improved data-dependent acquisition strategies. Analytical Chemistry, 93(14), pp. 5676-5683. (doi: 10.1021/acs.analchem.0c03895) (PMID:33784814) (PMCID:PMC8047769)

Niu, Mu, Wandy, Joe ORCID logoORCID: https://orcid.org/0000-0002-3068-4664, Daly, Rónán ORCID logoORCID: https://orcid.org/0000-0002-1275-6820, Rogers, Simon ORCID logoORCID: https://orcid.org/0000-0003-3578-4477 and Husmeier, Dirk ORCID logoORCID: https://orcid.org/0000-0003-1673-7413 (2021) R package for statistical inference in dynamical systems using kernel based gradient matching: KGode. Computational Statistics, 36(1), pp. 715-747. (doi: 10.1007/s00180-020-01014-x)

McLuskey, Karen, Wandy, Joe ORCID logoORCID: https://orcid.org/0000-0002-3068-4664, Vincent, Isabel ORCID logoORCID: https://orcid.org/0000-0003-2663-4389, Van Der Hooft, Justin J.J. ORCID logoORCID: https://orcid.org/0000-0002-9340-5511, Rogers, Simon ORCID logoORCID: https://orcid.org/0000-0003-3578-4477, Burgess, Karl and Daly, Ronan ORCID logoORCID: https://orcid.org/0000-0002-1275-6820 (2021) Ranking metabolite sets by their activity levels. Metabolites, 11(2), 103. (doi: 10.3390/metabo11020103) (PMID:33670102) (PMCID:PMC7916825)

Hjorleifsson Eldjarn, Grimur, Ramsay, Andrew ORCID logoORCID: https://orcid.org/0000-0002-1451-8973, Van Der Hooft, Justin ORCID logoORCID: https://orcid.org/0000-0002-9340-5511, Duncan, Katherine R., Soldatou, Sylvia, Rousu, Juho, Daly, Ronan ORCID logoORCID: https://orcid.org/0000-0002-1275-6820, Wandy, Joe ORCID logoORCID: https://orcid.org/0000-0002-3068-4664 and Rogers, Simon ORCID logoORCID: https://orcid.org/0000-0003-3578-4477 (2021) Ranking microbial metabolomic and genomic links in the NPLinker framework using complementary scoring functions. PLoS Computational Biology, 17(5), e1008920. (doi: 10.1371/journal.pcbi.1008920) (PMID:33945539) (PMCID:PMC8130963)

2019

Wandy, Joe ORCID logoORCID: https://orcid.org/0000-0002-3068-4664, Davies, Vinny ORCID logoORCID: https://orcid.org/0000-0003-1896-8936, van der Hooft, Justin J.J. ORCID logoORCID: https://orcid.org/0000-0002-9340-5511, Weidt, Stefan, Daly, Ronan ORCID logoORCID: https://orcid.org/0000-0002-1275-6820 and Rogers, Simon ORCID logoORCID: https://orcid.org/0000-0003-3578-4477 (2019) In silico optimization of mass spectrometry fragmentation strategies in metabolomics. Metabolites, 9(10), 219. (doi: 10.3390/metabo9100219) (PMID:31600991)

Rogers, Simon ORCID logoORCID: https://orcid.org/0000-0003-3578-4477, Ong, Cher Wei, Wandy, Joe ORCID logoORCID: https://orcid.org/0000-0002-3068-4664, Ernst, Madeleine, Ridder, Lars and Van Der Hooft, Justin J.J. ORCID logoORCID: https://orcid.org/0000-0002-9340-5511 (2019) Deciphering complex metabolite mixtures by unsupervised and supervised substructure discovery and semi-automated annotation from MS/MS spectra. Faraday Discussions, 218, pp. 284-302. (doi: 10.1039/C8FD00235E) (PMID:31120050)

Ernst, M. et al. (2019) MolNetEnhancer: enhanced molecular networks by integrating metabolome mining and annotation tools. Metabolites, 9(7), 144. (doi: 10.3390/metabo9070144) (PMID:31315242)

2018

Wandy, Joe ORCID logoORCID: https://orcid.org/0000-0002-3068-4664, Niu, Mu, Giurghita, Diana, Daly, Rónán ORCID logoORCID: https://orcid.org/0000-0002-1275-6820, Rogers, Simon ORCID logoORCID: https://orcid.org/0000-0003-3578-4477 and Husmeier, Dirk ORCID logoORCID: https://orcid.org/0000-0003-1673-7413 (2018) ShinyKGode: an interactive application for ODE parameter inference using gradient matching. Bioinformatics, 34(13), pp. 2314-2315. (doi: 10.1093/bioinformatics/bty089) (PMID:29490021) (PMCID:PMC6022662)

Wandy, Joe ORCID logoORCID: https://orcid.org/0000-0002-3068-4664, Zhu, Yunfeng, van der Hooft, Justin J.J. ORCID logoORCID: https://orcid.org/0000-0002-9340-5511, Daly, Rónán ORCID logoORCID: https://orcid.org/0000-0002-1275-6820, Barrett, Michael P. ORCID logoORCID: https://orcid.org/0000-0001-9447-3519 and Rogers, Simon ORCID logoORCID: https://orcid.org/0000-0003-3578-4477 (2018) Ms2lda.org: web-based topic modelling for substructure discovery in mass spectrometry. Bioinformatics, 34(2), pp. 317-318. (doi: 10.1093/bioinformatics/btx582) (PMID:28968802) (PMCID:PMC5860206)

2017

Gloaguen, Yoann ORCID logoORCID: https://orcid.org/0000-0003-0493-8592, Morton, Fraser ORCID logoORCID: https://orcid.org/0000-0001-5328-9467, Daly, Rónán ORCID logoORCID: https://orcid.org/0000-0002-1275-6820, Gurden, Ross, Rogers, Simon ORCID logoORCID: https://orcid.org/0000-0003-3578-4477, Wandy, Joe ORCID logoORCID: https://orcid.org/0000-0002-3068-4664, Wilson, David, Barrett, Michael ORCID logoORCID: https://orcid.org/0000-0001-9447-3519 and Burgess, Karl (2017) PiMP my metabolome: An integrated, web-based tool for LC-MS metabolomics data. Bioinformatics, 33(24), pp. 4007-4009. (doi: 10.1093/bioinformatics/btx499) (PMID:28961954) (PMCID:PMC5860087)

van der Hooft, Justin J.J. ORCID logoORCID: https://orcid.org/0000-0002-9340-5511, Wandy, Joe ORCID logoORCID: https://orcid.org/0000-0002-3068-4664, Young, Francesca, Padmanabhan, Sandosh ORCID logoORCID: https://orcid.org/0000-0003-3869-5808, Gerasimidis, Konstantinos ORCID logoORCID: https://orcid.org/0000-0001-9432-2200, Burgess, Karl E.V., Barrett, Michael P. ORCID logoORCID: https://orcid.org/0000-0001-9447-3519 and Rogers, Simon ORCID logoORCID: https://orcid.org/0000-0003-3578-4477 (2017) Unsupervised discovery and comparison of structural families across multiple samples in untargeted metabolomics. Analytical Chemistry, 89(14), pp. 7569-7577. (doi: 10.1021/acs.analchem.7b01391) (PMID:28621528) (PMCID:PMC5524435)

2016

van Der Hooft, Justin Johan Jozias ORCID logoORCID: https://orcid.org/0000-0002-9340-5511, Wandy, Joe ORCID logoORCID: https://orcid.org/0000-0002-3068-4664, Barrett, Michael P. ORCID logoORCID: https://orcid.org/0000-0001-9447-3519, Burgess, Karl E.V. and Rogers, Simon ORCID logoORCID: https://orcid.org/0000-0003-3578-4477 (2016) Topic modeling for untargeted substructure exploration in metabolomics. Proceedings of the National Academy of Sciences of the United States of America, 113(48), pp. 13738-13743. (doi: 10.1073/pnas.1608041113) (PMID:27856765) (PMCID:PMC5137707)

This list was generated on Mon Jun 16 23:53:19 2025 BST.
Jump to: Articles
Number of items: 16.

Articles

McBride, Ross, Wandy, Joe ORCID logoORCID: https://orcid.org/0000-0002-3068-4664, Weidt, Stefan, Rogers, Simon ORCID logoORCID: https://orcid.org/0000-0003-3578-4477, Davies, Vinny ORCID logoORCID: https://orcid.org/0000-0003-1896-8936, Daly, Rónán ORCID logoORCID: https://orcid.org/0000-0002-1275-6820 and Bryson, Kevin ORCID logoORCID: https://orcid.org/0000-0002-1163-6368 (2023) TopNEXt: automatic DDA exclusion framework for multi-sample mass spectrometry experiments. Bioinformatics, 39(7), btad406. (doi: 10.1093/bioinformatics/btad406) (PMID:37364005)

Wandy, Joe ORCID logoORCID: https://orcid.org/0000-0002-3068-4664, Mcbride, Ross, Rogers, Simon ORCID logoORCID: https://orcid.org/0000-0003-3578-4477, Terzis, Nikolaos, Weidt, Stefan, van der Hooft, Justin J.J. ORCID logoORCID: https://orcid.org/0000-0002-9340-5511, Bryson, Kevin ORCID logoORCID: https://orcid.org/0000-0002-1163-6368, Daly, Rónán ORCID logoORCID: https://orcid.org/0000-0002-1275-6820 and Davies, Vinny ORCID logoORCID: https://orcid.org/0000-0003-1896-8936 (2023) Simulated-to-real benchmarking of acquisition methods in untargeted metabolomics. Frontiers in Molecular Biosciences, 10, 1130781. (doi: 10.3389/fmolb.2023.1130781) (PMID:36959982) (PMCID:PMC10027714)

Wandy, Joe ORCID logoORCID: https://orcid.org/0000-0002-3068-4664, Davies, Vinny ORCID logoORCID: https://orcid.org/0000-0003-1896-8936, McBride, Ross, Weidt, Stefan, Rogers, Simon ORCID logoORCID: https://orcid.org/0000-0003-3578-4477 and Daly, Ronan ORCID logoORCID: https://orcid.org/0000-0002-1275-6820 (2022) ViMMS 2.0: A framework to develop, test and optimise fragmentation strategies in LC-MS metabolomics. Journal of Open Source Software, 7(71), 3990. (doi: 10.21105/joss.03990)

Wandy, Joe ORCID logoORCID: https://orcid.org/0000-0002-3068-4664 and Daly, Rónán ORCID logoORCID: https://orcid.org/0000-0002-1275-6820 (2021) GraphOmics: an interactive platform to explore and integrate multi-omics data. BMC Bioinformatics, 22, 603. (doi: 10.1186/s12859-021-04500-1) (PMID:34922446) (PMCID:PMC8684259)

Davies, Vinny ORCID logoORCID: https://orcid.org/0000-0003-1896-8936, Wandy, Joe ORCID logoORCID: https://orcid.org/0000-0002-3068-4664, Weidt, Stefan, van der Hooft, Justin J.J. ORCID logoORCID: https://orcid.org/0000-0002-9340-5511, Miller, Alice ORCID logoORCID: https://orcid.org/0000-0002-0941-1717, Daly, Rónán ORCID logoORCID: https://orcid.org/0000-0002-1275-6820 and Rogers, Simon ORCID logoORCID: https://orcid.org/0000-0003-3578-4477 (2021) Rapid development of improved data-dependent acquisition strategies. Analytical Chemistry, 93(14), pp. 5676-5683. (doi: 10.1021/acs.analchem.0c03895) (PMID:33784814) (PMCID:PMC8047769)

Niu, Mu, Wandy, Joe ORCID logoORCID: https://orcid.org/0000-0002-3068-4664, Daly, Rónán ORCID logoORCID: https://orcid.org/0000-0002-1275-6820, Rogers, Simon ORCID logoORCID: https://orcid.org/0000-0003-3578-4477 and Husmeier, Dirk ORCID logoORCID: https://orcid.org/0000-0003-1673-7413 (2021) R package for statistical inference in dynamical systems using kernel based gradient matching: KGode. Computational Statistics, 36(1), pp. 715-747. (doi: 10.1007/s00180-020-01014-x)

McLuskey, Karen, Wandy, Joe ORCID logoORCID: https://orcid.org/0000-0002-3068-4664, Vincent, Isabel ORCID logoORCID: https://orcid.org/0000-0003-2663-4389, Van Der Hooft, Justin J.J. ORCID logoORCID: https://orcid.org/0000-0002-9340-5511, Rogers, Simon ORCID logoORCID: https://orcid.org/0000-0003-3578-4477, Burgess, Karl and Daly, Ronan ORCID logoORCID: https://orcid.org/0000-0002-1275-6820 (2021) Ranking metabolite sets by their activity levels. Metabolites, 11(2), 103. (doi: 10.3390/metabo11020103) (PMID:33670102) (PMCID:PMC7916825)

Hjorleifsson Eldjarn, Grimur, Ramsay, Andrew ORCID logoORCID: https://orcid.org/0000-0002-1451-8973, Van Der Hooft, Justin ORCID logoORCID: https://orcid.org/0000-0002-9340-5511, Duncan, Katherine R., Soldatou, Sylvia, Rousu, Juho, Daly, Ronan ORCID logoORCID: https://orcid.org/0000-0002-1275-6820, Wandy, Joe ORCID logoORCID: https://orcid.org/0000-0002-3068-4664 and Rogers, Simon ORCID logoORCID: https://orcid.org/0000-0003-3578-4477 (2021) Ranking microbial metabolomic and genomic links in the NPLinker framework using complementary scoring functions. PLoS Computational Biology, 17(5), e1008920. (doi: 10.1371/journal.pcbi.1008920) (PMID:33945539) (PMCID:PMC8130963)

Wandy, Joe ORCID logoORCID: https://orcid.org/0000-0002-3068-4664, Davies, Vinny ORCID logoORCID: https://orcid.org/0000-0003-1896-8936, van der Hooft, Justin J.J. ORCID logoORCID: https://orcid.org/0000-0002-9340-5511, Weidt, Stefan, Daly, Ronan ORCID logoORCID: https://orcid.org/0000-0002-1275-6820 and Rogers, Simon ORCID logoORCID: https://orcid.org/0000-0003-3578-4477 (2019) In silico optimization of mass spectrometry fragmentation strategies in metabolomics. Metabolites, 9(10), 219. (doi: 10.3390/metabo9100219) (PMID:31600991)

Rogers, Simon ORCID logoORCID: https://orcid.org/0000-0003-3578-4477, Ong, Cher Wei, Wandy, Joe ORCID logoORCID: https://orcid.org/0000-0002-3068-4664, Ernst, Madeleine, Ridder, Lars and Van Der Hooft, Justin J.J. ORCID logoORCID: https://orcid.org/0000-0002-9340-5511 (2019) Deciphering complex metabolite mixtures by unsupervised and supervised substructure discovery and semi-automated annotation from MS/MS spectra. Faraday Discussions, 218, pp. 284-302. (doi: 10.1039/C8FD00235E) (PMID:31120050)

Ernst, M. et al. (2019) MolNetEnhancer: enhanced molecular networks by integrating metabolome mining and annotation tools. Metabolites, 9(7), 144. (doi: 10.3390/metabo9070144) (PMID:31315242)

Wandy, Joe ORCID logoORCID: https://orcid.org/0000-0002-3068-4664, Niu, Mu, Giurghita, Diana, Daly, Rónán ORCID logoORCID: https://orcid.org/0000-0002-1275-6820, Rogers, Simon ORCID logoORCID: https://orcid.org/0000-0003-3578-4477 and Husmeier, Dirk ORCID logoORCID: https://orcid.org/0000-0003-1673-7413 (2018) ShinyKGode: an interactive application for ODE parameter inference using gradient matching. Bioinformatics, 34(13), pp. 2314-2315. (doi: 10.1093/bioinformatics/bty089) (PMID:29490021) (PMCID:PMC6022662)

Wandy, Joe ORCID logoORCID: https://orcid.org/0000-0002-3068-4664, Zhu, Yunfeng, van der Hooft, Justin J.J. ORCID logoORCID: https://orcid.org/0000-0002-9340-5511, Daly, Rónán ORCID logoORCID: https://orcid.org/0000-0002-1275-6820, Barrett, Michael P. ORCID logoORCID: https://orcid.org/0000-0001-9447-3519 and Rogers, Simon ORCID logoORCID: https://orcid.org/0000-0003-3578-4477 (2018) Ms2lda.org: web-based topic modelling for substructure discovery in mass spectrometry. Bioinformatics, 34(2), pp. 317-318. (doi: 10.1093/bioinformatics/btx582) (PMID:28968802) (PMCID:PMC5860206)

Gloaguen, Yoann ORCID logoORCID: https://orcid.org/0000-0003-0493-8592, Morton, Fraser ORCID logoORCID: https://orcid.org/0000-0001-5328-9467, Daly, Rónán ORCID logoORCID: https://orcid.org/0000-0002-1275-6820, Gurden, Ross, Rogers, Simon ORCID logoORCID: https://orcid.org/0000-0003-3578-4477, Wandy, Joe ORCID logoORCID: https://orcid.org/0000-0002-3068-4664, Wilson, David, Barrett, Michael ORCID logoORCID: https://orcid.org/0000-0001-9447-3519 and Burgess, Karl (2017) PiMP my metabolome: An integrated, web-based tool for LC-MS metabolomics data. Bioinformatics, 33(24), pp. 4007-4009. (doi: 10.1093/bioinformatics/btx499) (PMID:28961954) (PMCID:PMC5860087)

van der Hooft, Justin J.J. ORCID logoORCID: https://orcid.org/0000-0002-9340-5511, Wandy, Joe ORCID logoORCID: https://orcid.org/0000-0002-3068-4664, Young, Francesca, Padmanabhan, Sandosh ORCID logoORCID: https://orcid.org/0000-0003-3869-5808, Gerasimidis, Konstantinos ORCID logoORCID: https://orcid.org/0000-0001-9432-2200, Burgess, Karl E.V., Barrett, Michael P. ORCID logoORCID: https://orcid.org/0000-0001-9447-3519 and Rogers, Simon ORCID logoORCID: https://orcid.org/0000-0003-3578-4477 (2017) Unsupervised discovery and comparison of structural families across multiple samples in untargeted metabolomics. Analytical Chemistry, 89(14), pp. 7569-7577. (doi: 10.1021/acs.analchem.7b01391) (PMID:28621528) (PMCID:PMC5524435)

van Der Hooft, Justin Johan Jozias ORCID logoORCID: https://orcid.org/0000-0002-9340-5511, Wandy, Joe ORCID logoORCID: https://orcid.org/0000-0002-3068-4664, Barrett, Michael P. ORCID logoORCID: https://orcid.org/0000-0001-9447-3519, Burgess, Karl E.V. and Rogers, Simon ORCID logoORCID: https://orcid.org/0000-0003-3578-4477 (2016) Topic modeling for untargeted substructure exploration in metabolomics. Proceedings of the National Academy of Sciences of the United States of America, 113(48), pp. 13738-13743. (doi: 10.1073/pnas.1608041113) (PMID:27856765) (PMCID:PMC5137707)

This list was generated on Mon Jun 16 23:53:19 2025 BST.

Research datasets

Jump to: 2025 | 2022 | 2021 | 2019 | 2017 | 2016
Number of items: 7.

2025

McBride, R., Weidt, S., Wandy, J. , Davies, V. , Daly, R. and Bryson, K. (2025) Seed .mzML Data for ViMMS Maximum Matching Experiments. [Data Collection]

2022

Wandy, J. , McBride, R., Weidt, S., Rogers, S. , Terzis, N., van der Hooft, J. J. J., Bryson, K. , Daly, R. and Davies, V. (2022) DDA and DIA data for ViMMS 2.0. [Data Collection]

2021

Davies, V. , Wandy, J., Weidt, S., van der Hooft, J., Miller, A. , Daly, R. and Rogers, S. (2021) Rapid Development of Improved Data-Dependent Acquisition Strategies. [Data Collection]

2019

Wandy, J., Davies, V. , van der Hooft, J., Weidt, S., Daly, R. and Rogers, S. (2019) In-silico Optimisation of Mass Spectrometry Fragmentation Strategies in Metabolomics. [Data Collection]

2017

Van Der Hooft, J. and Wandy, J. (2017) Unsupervised discovery and comparison of structural families across multiple samples in untargeted metabolomics. [Data Collection]

2016

Van Der Hooft, J., Rogers, S. , Wandy, J., Barrett, M. and Burgess, K. (2016) Topic Modeling for Untargeted Substructure Exploration in Metabolomics. [Data Collection]

Wandy, J., van der Hooft, J. and Rogers, S. (2016) Ionisation Product Clustering to Improve Peak Alignment in LC-MS-based Metabolomics. [Data Collection]

This list was generated on Mon Jun 16 10:13:40 2025 BST.