Dr Ronan Daly

telephone: 01413307374
email: Ronan.Daly@glasgow.ac.uk

Shared Research Facilities, Room B.309, Joseph Black Building, Gilmorehill Campus

Import to contacts

ORCID iDhttps://orcid.org/0000-0002-1275-6820

Publications

List by: Type | Date

Jump to: 2025 | 2024 | 2023 | 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2012 | 2011 | 2010 | 2009 | 2007 | 2006 | 2005
Number of items: 37.

2025

Delles, C. et al. (2025) Response of blood pressure to renal denervation is not associated with genetic variants. Hypertension, 82(1), pp. 118-125. (doi: 10.1161/HYPERTENSIONAHA.124.23393) (PMID:39569514) (PMCID:PMC11654447)

2024

Cortada Garcia, Joan, Haggarty, Jennifer ORCID logoORCID: https://orcid.org/0000-0002-5041-8785, Weidt, Stefan, Daly, Rónán ORCID logoORCID: https://orcid.org/0000-0002-1275-6820, Arnold, S. Alison and Burgess, Karl (2024) On‐line targeted metabolomics for real‐time monitoring of relevant compounds in fermentation processes. Biotechnology and Bioengineering, 121(2), pp. 683-695. (doi: 10.1002/bit.28599) (PMID:37990977) (PMCID:PMC10953439)

2023

Cortada-Garcia, Joan, Daly, Rónán ORCID logoORCID: https://orcid.org/0000-0002-1275-6820, Alison Arnold, S. and Burgess, Karl (2023) Streamlined identification of strain engineering targets for bioprocess improvement using metabolic pathway enrichment analysis. Scientific Reports, 13, 12990. (doi: 10.1038/s41598-023-39661-x) (PMID:37563133) (PMCID:PMC10415327)

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

Cortada‐Garcia, Joan, Haggarty, Jennifer ORCID logoORCID: https://orcid.org/0000-0002-5041-8785, Moses, Tessa, Daly, Rónán ORCID logoORCID: https://orcid.org/0000-0002-1275-6820, Arnold, Susan Alison and Burgess, Karl (2022) On‐line untargeted metabolomics monitoring of an Escherichia coli succinate fermentation process. Biotechnology and Bioengineering, 119(10), pp. 2757-2769. (doi: 10.1002/bit.28173) (PMID:35798686) (PMCID:PMC9541951)

Salji, M. J. et al. (2022) Multi-omics and pathway analysis identify potential roles for tumour n-acetyl aspartate accumulation in murine models of castration resistant prostate cancer. iScience, 25(4), 104056. (doi: 10.1016/j.isci.2022.104056) (PMID:35345457) (PMCID:PMC8957019)

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)

Rossitto, G. et al. (2021) High sodium intake, glomerular hyperfiltration and protein catabolism in patients with essential hypertension. Cardiovascular Research, 117(5), pp. 1372-1381. (doi: 10.1093/cvr/cvaa205) (PMID:33053160) (PMCID:PMC8064429)

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)

Annese, V. F. et al. (2021) A monolithic single-chip point-of-care platform for metabolomic prostate cancer detection. Microsystems and Nanoengineering, 7, 21. (doi: 10.1038/s41378-021-00243-4) (PMID:34567735) (PMCID:PMC8433377)

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)

2020

Daly, R. et al. (2020) Changes in plasma itaconate elevation in early rheumatoid arthritis patients elucidates disease activity associated macrophage activation. Metabolites, 10(6), 241. (doi: 10.3390/metabo10060241) (PMID:32531990) (PMCID:PMC7344783)

2019

Buckley, James, Daly, Rónán ORCID logoORCID: https://orcid.org/0000-0002-1275-6820, Cobbold, Christina A. ORCID logoORCID: https://orcid.org/0000-0001-8814-7688, Burgess, Karl and Mable, Barbara K. ORCID logoORCID: https://orcid.org/0000-0001-7118-4116 (2019) Changing environments and genetic variation: natural variation in inbreeding does not compromise short-term physiological responses. Proceedings of the Royal Society of London Series B: Biological Sciences, 286(1915), 20192109. (doi: 10.1098/rspb.2019.2109) (PMID:31744436) (PMCID:PMC6892046)

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)

2018

Megalios, Anargyros, Daly, Rónán ORCID logoORCID: https://orcid.org/0000-0002-1275-6820 and Burgess, Karl (2018) MetaboCraft: building a Minecraft plugin for metabolomics. Bioinformatics, 34(15), pp. 2693-2694. (doi: 10.1093/bioinformatics/bty102) (PMID:29608638) (PMCID:PMC6061834)

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

Burgess, K.E.V., Borutzki, Y., Rankin, N. ORCID logoORCID: https://orcid.org/0000-0002-7566-1407, Daly, R. ORCID logoORCID: https://orcid.org/0000-0002-1275-6820 and Jourdan, S. (2017) MetaNetter 2: a Cytoscape plugin for ab initio network analysis and metabolite feature classification. Journal of Chromatography B, 1071, pp. 68-74. (doi: 10.1016/j.jchromb.2017.08.015) (PMID:29030098) (PMCID:PMC5726607)

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)

2016

Vincent, Isabel M. ORCID logoORCID: https://orcid.org/0000-0003-2663-4389, Daly, Rónán ORCID logoORCID: https://orcid.org/0000-0002-1275-6820, Courtioux, Bertrand, Cattanach, Amy M., Biéler, Sylvain, Ndung’u, Joseph M., Bisser, Sylvie and Barrett, Michael P. ORCID logoORCID: https://orcid.org/0000-0001-9447-3519 (2016) Metabolomics Identifies multiple candidate biomarkers to diagnose and stage human African trypanosomiasis. PLoS Neglected Tropical Diseases, 10(12), e0005140. (doi: 10.1371/journal.pntd.0005140) (PMID:27941966) (PMCID:PMC5152828)

2015

Wandy, Joe, Daly, Ronan ORCID logoORCID: https://orcid.org/0000-0002-1275-6820, Breitling, Rainer ORCID logoORCID: https://orcid.org/0000-0001-7173-0922 and Rogers, Simon ORCID logoORCID: https://orcid.org/0000-0003-3578-4477 (2015) Incorporating peak grouping information for alignment of multiple liquid chromatography-mass spectrometry datasets. Bioinformatics, 31(12), pp. 1999-2006. (doi: 10.1093/bioinformatics/btv072) (PMID:25649621) (PMCID:PMC4760236)

2014

Daly, Rónán ORCID logoORCID: https://orcid.org/0000-0002-1275-6820, Rogers, Simon ORCID logoORCID: https://orcid.org/0000-0003-3578-4477, Wandy, Joe, Jankevics, Andris, Burgess, Karl E.V. and Breitling, Rainer ORCID logoORCID: https://orcid.org/0000-0001-7173-0922 (2014) MetAssign: probabilistic annotation of metabolites from LC–MS data using a Bayesian clustering approach. Bioinformatics, 30(19), pp. 2764-2771. (doi: 10.1093/bioinformatics/btu370) (PMID:24916385) (PMCID:PMC4173012)

Jiwaji, M. et al. (2014) Quantification of functionalised gold nanoparticle-targeted knockdown of gene expression in HeLa cells. PLoS ONE, 9(6), e99458. (doi: 10.1371/journal.pone.0099458) (PMID:24926959) (PMCID:PMC4057226)

2012

Rogers, S. ORCID logoORCID: https://orcid.org/0000-0003-3578-4477, Daly, R. ORCID logoORCID: https://orcid.org/0000-0002-1275-6820 and Breitling, R. ORCID logoORCID: https://orcid.org/0000-0001-7173-0922 (2012) Mixture model clustering for peak filtering in metabolomics. In: WCSB2012 - 9th International Workshop on Computational Systems Biology, Ulm, Germany, 4-6 Jun 2012,

Jiwaji, M. et al. (2012) Unique reporter-based sensor platforms to monitor signalling in cells. PLoS ONE, 7(11), e50521. (doi: 10.1371/journal.pone.0050521) (PMID:23209767) (PMCID:PMC3510088)

2011

Daly, R. ORCID logoORCID: https://orcid.org/0000-0002-1275-6820, Shen, Q. and Aitken, S. (2011) Learning Bayesian networks: approaches and issues. Knowledge Engineering Review, 26(2), pp. 99-157. (doi: 10.1017/S0269888910000251)

2010

Jiwaji, M., Daly, R. ORCID logoORCID: https://orcid.org/0000-0002-1275-6820, Pansare, K., McLean, P., Yang, J., Kolch, W. and Pitt, A.R. (2010) The Renilla luciferase gene as a reference gene for normalization of gene expression in transiently transfected cells. BMC Molecular Biology, 11(1), p. 103. (doi: 10.1186/1471-2199-11-103)

2009

Daly, R. ORCID logoORCID: https://orcid.org/0000-0002-1275-6820, Edwards, K.D., O'Neill, J.S., Aitken, S., Millar, A.J. and Girolami, M. (2009) Using higher-order dynamic bayesian networks to model periodic data from the circadian clock of Arabidopsis Thaliana. In: Kadirkamanathan, V., Sanguinetti, G. and Noirel, J. (eds.) Pattern Recognition in Bioinformatics: 4th IAPR International Conference, PRIB 2009, Sheffield, UK, September 7-9, 2009. Proceedings. Series: Lecture notes in computer science (5780). Springer, pp. 67-78. ISBN 9783642040306 (doi: 10.1007/978-3-642-04031-3_7)

Daly, R. ORCID logoORCID: https://orcid.org/0000-0002-1275-6820 and Shen, Q. (2009) Learning bayesian network equivalence classes with ant colony optimization. Journal of Artificial Intelligence Research, 35, pp. 391-447. (doi: 10.1613/jair.2681)

2007

Daly, Rónán ORCID logoORCID: https://orcid.org/0000-0002-1275-6820 and Shen, Qiang (2007) Methods to Accelerate the Learning of Bayesian Network Structures. UK Workshop on Computational Intelligence, Leicester UK, 2007.

2006

Shen, Qiang, Daly, Ronan ORCID logoORCID: https://orcid.org/0000-0002-1275-6820 and Aitken, Stuart (2006) Using Ant Colony Optimisation in Learning Bayesian Network Equivalence Classes. UK Workshop on Computational Intelligence, Leeds UK, 2006.

2005

Aitken, Stuart, Jirapech-Umpai, Thanyaluk and Daly, Ronan ORCID logoORCID: https://orcid.org/0000-0002-1275-6820 (2005) Inferring gene regulatory networks from classified microarray data: Initial results. BMC Bioinformatics, 6(Suppl), S4. (doi: 10.1186/1471-2105-6-S3-S4)

Daly, Ronan ORCID logoORCID: https://orcid.org/0000-0002-1275-6820 and Shen, Qiang (2005) A Framework for the Scoring of Operators on the Search Space of Equivalence Classes of Bayesian Network Structures. UK Workshop on Computational Intelligence, London UK, 2005.

This list was generated on Sat Jul 5 14:49:02 2025 BST.
Jump to: Articles | Book Sections | Conference or Workshop Item | Conference Proceedings
Number of items: 37.

Articles

Delles, C. et al. (2025) Response of blood pressure to renal denervation is not associated with genetic variants. Hypertension, 82(1), pp. 118-125. (doi: 10.1161/HYPERTENSIONAHA.124.23393) (PMID:39569514) (PMCID:PMC11654447)

Cortada Garcia, Joan, Haggarty, Jennifer ORCID logoORCID: https://orcid.org/0000-0002-5041-8785, Weidt, Stefan, Daly, Rónán ORCID logoORCID: https://orcid.org/0000-0002-1275-6820, Arnold, S. Alison and Burgess, Karl (2024) On‐line targeted metabolomics for real‐time monitoring of relevant compounds in fermentation processes. Biotechnology and Bioengineering, 121(2), pp. 683-695. (doi: 10.1002/bit.28599) (PMID:37990977) (PMCID:PMC10953439)

Cortada-Garcia, Joan, Daly, Rónán ORCID logoORCID: https://orcid.org/0000-0002-1275-6820, Alison Arnold, S. and Burgess, Karl (2023) Streamlined identification of strain engineering targets for bioprocess improvement using metabolic pathway enrichment analysis. Scientific Reports, 13, 12990. (doi: 10.1038/s41598-023-39661-x) (PMID:37563133) (PMCID:PMC10415327)

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)

Cortada‐Garcia, Joan, Haggarty, Jennifer ORCID logoORCID: https://orcid.org/0000-0002-5041-8785, Moses, Tessa, Daly, Rónán ORCID logoORCID: https://orcid.org/0000-0002-1275-6820, Arnold, Susan Alison and Burgess, Karl (2022) On‐line untargeted metabolomics monitoring of an Escherichia coli succinate fermentation process. Biotechnology and Bioengineering, 119(10), pp. 2757-2769. (doi: 10.1002/bit.28173) (PMID:35798686) (PMCID:PMC9541951)

Salji, M. J. et al. (2022) Multi-omics and pathway analysis identify potential roles for tumour n-acetyl aspartate accumulation in murine models of castration resistant prostate cancer. iScience, 25(4), 104056. (doi: 10.1016/j.isci.2022.104056) (PMID:35345457) (PMCID:PMC8957019)

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)

Rossitto, G. et al. (2021) High sodium intake, glomerular hyperfiltration and protein catabolism in patients with essential hypertension. Cardiovascular Research, 117(5), pp. 1372-1381. (doi: 10.1093/cvr/cvaa205) (PMID:33053160) (PMCID:PMC8064429)

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)

Annese, V. F. et al. (2021) A monolithic single-chip point-of-care platform for metabolomic prostate cancer detection. Microsystems and Nanoengineering, 7, 21. (doi: 10.1038/s41378-021-00243-4) (PMID:34567735) (PMCID:PMC8433377)

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)

Daly, R. et al. (2020) Changes in plasma itaconate elevation in early rheumatoid arthritis patients elucidates disease activity associated macrophage activation. Metabolites, 10(6), 241. (doi: 10.3390/metabo10060241) (PMID:32531990) (PMCID:PMC7344783)

Buckley, James, Daly, Rónán ORCID logoORCID: https://orcid.org/0000-0002-1275-6820, Cobbold, Christina A. ORCID logoORCID: https://orcid.org/0000-0001-8814-7688, Burgess, Karl and Mable, Barbara K. ORCID logoORCID: https://orcid.org/0000-0001-7118-4116 (2019) Changing environments and genetic variation: natural variation in inbreeding does not compromise short-term physiological responses. Proceedings of the Royal Society of London Series B: Biological Sciences, 286(1915), 20192109. (doi: 10.1098/rspb.2019.2109) (PMID:31744436) (PMCID:PMC6892046)

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)

Megalios, Anargyros, Daly, Rónán ORCID logoORCID: https://orcid.org/0000-0002-1275-6820 and Burgess, Karl (2018) MetaboCraft: building a Minecraft plugin for metabolomics. Bioinformatics, 34(15), pp. 2693-2694. (doi: 10.1093/bioinformatics/bty102) (PMID:29608638) (PMCID:PMC6061834)

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)

Burgess, K.E.V., Borutzki, Y., Rankin, N. ORCID logoORCID: https://orcid.org/0000-0002-7566-1407, Daly, R. ORCID logoORCID: https://orcid.org/0000-0002-1275-6820 and Jourdan, S. (2017) MetaNetter 2: a Cytoscape plugin for ab initio network analysis and metabolite feature classification. Journal of Chromatography B, 1071, pp. 68-74. (doi: 10.1016/j.jchromb.2017.08.015) (PMID:29030098) (PMCID:PMC5726607)

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)

Vincent, Isabel M. ORCID logoORCID: https://orcid.org/0000-0003-2663-4389, Daly, Rónán ORCID logoORCID: https://orcid.org/0000-0002-1275-6820, Courtioux, Bertrand, Cattanach, Amy M., Biéler, Sylvain, Ndung’u, Joseph M., Bisser, Sylvie and Barrett, Michael P. ORCID logoORCID: https://orcid.org/0000-0001-9447-3519 (2016) Metabolomics Identifies multiple candidate biomarkers to diagnose and stage human African trypanosomiasis. PLoS Neglected Tropical Diseases, 10(12), e0005140. (doi: 10.1371/journal.pntd.0005140) (PMID:27941966) (PMCID:PMC5152828)

Wandy, Joe, Daly, Ronan ORCID logoORCID: https://orcid.org/0000-0002-1275-6820, Breitling, Rainer ORCID logoORCID: https://orcid.org/0000-0001-7173-0922 and Rogers, Simon ORCID logoORCID: https://orcid.org/0000-0003-3578-4477 (2015) Incorporating peak grouping information for alignment of multiple liquid chromatography-mass spectrometry datasets. Bioinformatics, 31(12), pp. 1999-2006. (doi: 10.1093/bioinformatics/btv072) (PMID:25649621) (PMCID:PMC4760236)

Daly, Rónán ORCID logoORCID: https://orcid.org/0000-0002-1275-6820, Rogers, Simon ORCID logoORCID: https://orcid.org/0000-0003-3578-4477, Wandy, Joe, Jankevics, Andris, Burgess, Karl E.V. and Breitling, Rainer ORCID logoORCID: https://orcid.org/0000-0001-7173-0922 (2014) MetAssign: probabilistic annotation of metabolites from LC–MS data using a Bayesian clustering approach. Bioinformatics, 30(19), pp. 2764-2771. (doi: 10.1093/bioinformatics/btu370) (PMID:24916385) (PMCID:PMC4173012)

Jiwaji, M. et al. (2014) Quantification of functionalised gold nanoparticle-targeted knockdown of gene expression in HeLa cells. PLoS ONE, 9(6), e99458. (doi: 10.1371/journal.pone.0099458) (PMID:24926959) (PMCID:PMC4057226)

Jiwaji, M. et al. (2012) Unique reporter-based sensor platforms to monitor signalling in cells. PLoS ONE, 7(11), e50521. (doi: 10.1371/journal.pone.0050521) (PMID:23209767) (PMCID:PMC3510088)

Daly, R. ORCID logoORCID: https://orcid.org/0000-0002-1275-6820, Shen, Q. and Aitken, S. (2011) Learning Bayesian networks: approaches and issues. Knowledge Engineering Review, 26(2), pp. 99-157. (doi: 10.1017/S0269888910000251)

Jiwaji, M., Daly, R. ORCID logoORCID: https://orcid.org/0000-0002-1275-6820, Pansare, K., McLean, P., Yang, J., Kolch, W. and Pitt, A.R. (2010) The Renilla luciferase gene as a reference gene for normalization of gene expression in transiently transfected cells. BMC Molecular Biology, 11(1), p. 103. (doi: 10.1186/1471-2199-11-103)

Daly, R. ORCID logoORCID: https://orcid.org/0000-0002-1275-6820 and Shen, Q. (2009) Learning bayesian network equivalence classes with ant colony optimization. Journal of Artificial Intelligence Research, 35, pp. 391-447. (doi: 10.1613/jair.2681)

Aitken, Stuart, Jirapech-Umpai, Thanyaluk and Daly, Ronan ORCID logoORCID: https://orcid.org/0000-0002-1275-6820 (2005) Inferring gene regulatory networks from classified microarray data: Initial results. BMC Bioinformatics, 6(Suppl), S4. (doi: 10.1186/1471-2105-6-S3-S4)

Book Sections

Daly, R. ORCID logoORCID: https://orcid.org/0000-0002-1275-6820, Edwards, K.D., O'Neill, J.S., Aitken, S., Millar, A.J. and Girolami, M. (2009) Using higher-order dynamic bayesian networks to model periodic data from the circadian clock of Arabidopsis Thaliana. In: Kadirkamanathan, V., Sanguinetti, G. and Noirel, J. (eds.) Pattern Recognition in Bioinformatics: 4th IAPR International Conference, PRIB 2009, Sheffield, UK, September 7-9, 2009. Proceedings. Series: Lecture notes in computer science (5780). Springer, pp. 67-78. ISBN 9783642040306 (doi: 10.1007/978-3-642-04031-3_7)

Conference or Workshop Item

Daly, Rónán ORCID logoORCID: https://orcid.org/0000-0002-1275-6820 and Shen, Qiang (2007) Methods to Accelerate the Learning of Bayesian Network Structures. UK Workshop on Computational Intelligence, Leicester UK, 2007.

Shen, Qiang, Daly, Ronan ORCID logoORCID: https://orcid.org/0000-0002-1275-6820 and Aitken, Stuart (2006) Using Ant Colony Optimisation in Learning Bayesian Network Equivalence Classes. UK Workshop on Computational Intelligence, Leeds UK, 2006.

Daly, Ronan ORCID logoORCID: https://orcid.org/0000-0002-1275-6820 and Shen, Qiang (2005) A Framework for the Scoring of Operators on the Search Space of Equivalence Classes of Bayesian Network Structures. UK Workshop on Computational Intelligence, London UK, 2005.

Conference Proceedings

Rogers, S. ORCID logoORCID: https://orcid.org/0000-0003-3578-4477, Daly, R. ORCID logoORCID: https://orcid.org/0000-0002-1275-6820 and Breitling, R. ORCID logoORCID: https://orcid.org/0000-0001-7173-0922 (2012) Mixture model clustering for peak filtering in metabolomics. In: WCSB2012 - 9th International Workshop on Computational Systems Biology, Ulm, Germany, 4-6 Jun 2012,

This list was generated on Sat Jul 5 14:49:02 2025 BST.

Research datasets

Jump to: 2025 | 2022 | 2021 | 2019
Number of items: 4.

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]

This list was generated on Sat Jul 5 17:38:05 2025 BST.