2024

Cortada Garcia, J., Haggarty, J., Weidt, S., Daly, R. , Arnold, S. A. and Burgess, K. (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, J., Daly, R. , Alison Arnold, S. and Burgess, K. (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, R., Wandy, J. , Weidt, S., Rogers, S. , Davies, V. , Daly, R. and Bryson, K. (2023) TopNEXt: automatic DDA exclusion framework for multi-sample mass spectrometry experiments. Bioinformatics, 39(7), btad406. (doi: 10.1093/bioinformatics/btad406) (PMID:37364005)

Wandy, J. , Mcbride, R., Rogers, S. , Terzis, N., Weidt, S., van der Hooft, J. J.J. , Bryson, K. , Daly, R. and Davies, V. (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, J., Haggarty, J., Moses, T., Daly, R. , Arnold, S. A. and Burgess, K. (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, J. , Davies, V. , McBride, R., Weidt, S., Rogers, S. and Daly, R. (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, J. and Daly, R. (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, V. , Wandy, J. , Weidt, S., van der Hooft, J. J.J. , Miller, A. , Daly, R. and Rogers, S. (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, M., Wandy, J. , Daly, R. , Rogers, S. and Husmeier, D. (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, K., Wandy, J. , Vincent, I. , Van Der Hooft, J. J.J. , Rogers, S. , Burgess, K. and Daly, R. (2021) Ranking metabolite sets by their activity levels. Metabolites, 11(2), 103. (doi: 10.3390/metabo11020103) (PMID:33670102) (PMCID:PMC7916825)

Hjorleifsson Eldjarn, G., Ramsay, A. , Van Der Hooft, J. , Duncan, K. R., Soldatou, S., Rousu, J., Daly, R. , Wandy, J. and Rogers, S. (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, J., Daly, R. , Cobbold, C. A. , Burgess, K. and Mable, B. K. (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, J. , Davies, V. , van der Hooft, J. J.J. , Weidt, S., Daly, R. and Rogers, S. (2019) In silico optimization of mass spectrometry fragmentation strategies in metabolomics. Metabolites, 9(10), 219. (doi: 10.3390/metabo9100219) (PMID:31600991)

2018

Megalios, A., Daly, R. and Burgess, K. (2018) MetaboCraft: building a Minecraft plugin for metabolomics. Bioinformatics, 34(15), pp. 2693-2694. (doi: 10.1093/bioinformatics/bty102) (PMID:29608638) (PMCID:PMC6061834)

Wandy, J. , Niu, M., Giurghita, D., Daly, R. , Rogers, S. and Husmeier, D. (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, J. , Zhu, Y., van der Hooft, J. J.J. , Daly, R. , Barrett, M. P. and Rogers, S. (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. , Daly, R. 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, Y. , Morton, F. , Daly, R. , Gurden, R., Rogers, S. , Wandy, J. , Wilson, D., Barrett, M. and Burgess, K. (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, I. M. , Daly, R. , Courtioux, B., Cattanach, A. M., Biéler, S., Ndung’u, J. M., Bisser, S. and Barrett, M. P. (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, J., Daly, R. , Breitling, R. and Rogers, S. (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, R. , Rogers, S. , Wandy, J., Jankevics, A., Burgess, K. E.V. and Breitling, R. (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. , Daly, R. and Breitling, R. (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. , 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. , 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. , 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. 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, R. and Shen, Q. (2007) Methods to Accelerate the Learning of Bayesian Network Structures. UK Workshop on Computational Intelligence, Leicester UK, 2007.

2006

Shen, Q., Daly, R. and Aitken, S. (2006) Using Ant Colony Optimisation in Learning Bayesian Network Equivalence Classes. UK Workshop on Computational Intelligence, Leeds UK, 2006.

2005

Aitken, S., Jirapech-Umpai, T. and Daly, R. (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, R. and Shen, Q. (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.

Articles

Cortada Garcia, J., Haggarty, J., Weidt, S., Daly, R. , Arnold, S. A. and Burgess, K. (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, J., Daly, R. , Alison Arnold, S. and Burgess, K. (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, R., Wandy, J. , Weidt, S., Rogers, S. , Davies, V. , Daly, R. and Bryson, K. (2023) TopNEXt: automatic DDA exclusion framework for multi-sample mass spectrometry experiments. Bioinformatics, 39(7), btad406. (doi: 10.1093/bioinformatics/btad406) (PMID:37364005)

Wandy, J. , Mcbride, R., Rogers, S. , Terzis, N., Weidt, S., van der Hooft, J. J.J. , Bryson, K. , Daly, R. and Davies, V. (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, J., Haggarty, J., Moses, T., Daly, R. , Arnold, S. A. and Burgess, K. (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, J. , Davies, V. , McBride, R., Weidt, S., Rogers, S. and Daly, R. (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, J. and Daly, R. (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, V. , Wandy, J. , Weidt, S., van der Hooft, J. J.J. , Miller, A. , Daly, R. and Rogers, S. (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, M., Wandy, J. , Daly, R. , Rogers, S. and Husmeier, D. (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, K., Wandy, J. , Vincent, I. , Van Der Hooft, J. J.J. , Rogers, S. , Burgess, K. and Daly, R. (2021) Ranking metabolite sets by their activity levels. Metabolites, 11(2), 103. (doi: 10.3390/metabo11020103) (PMID:33670102) (PMCID:PMC7916825)

Hjorleifsson Eldjarn, G., Ramsay, A. , Van Der Hooft, J. , Duncan, K. R., Soldatou, S., Rousu, J., Daly, R. , Wandy, J. and Rogers, S. (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, J., Daly, R. , Cobbold, C. A. , Burgess, K. and Mable, B. K. (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, J. , Davies, V. , van der Hooft, J. J.J. , Weidt, S., Daly, R. and Rogers, S. (2019) In silico optimization of mass spectrometry fragmentation strategies in metabolomics. Metabolites, 9(10), 219. (doi: 10.3390/metabo9100219) (PMID:31600991)

Megalios, A., Daly, R. and Burgess, K. (2018) MetaboCraft: building a Minecraft plugin for metabolomics. Bioinformatics, 34(15), pp. 2693-2694. (doi: 10.1093/bioinformatics/bty102) (PMID:29608638) (PMCID:PMC6061834)

Wandy, J. , Niu, M., Giurghita, D., Daly, R. , Rogers, S. and Husmeier, D. (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, J. , Zhu, Y., van der Hooft, J. J.J. , Daly, R. , Barrett, M. P. and Rogers, S. (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. , Daly, R. 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, Y. , Morton, F. , Daly, R. , Gurden, R., Rogers, S. , Wandy, J. , Wilson, D., Barrett, M. and Burgess, K. (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, I. M. , Daly, R. , Courtioux, B., Cattanach, A. M., Biéler, S., Ndung’u, J. M., Bisser, S. and Barrett, M. P. (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, J., Daly, R. , Breitling, R. and Rogers, S. (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, R. , Rogers, S. , Wandy, J., Jankevics, A., Burgess, K. E.V. and Breitling, R. (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. , 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. , 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. 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, S., Jirapech-Umpai, T. and Daly, R. (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. , 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, R. and Shen, Q. (2007) Methods to Accelerate the Learning of Bayesian Network Structures. UK Workshop on Computational Intelligence, Leicester UK, 2007.

Shen, Q., Daly, R. and Aitken, S. (2006) Using Ant Colony Optimisation in Learning Bayesian Network Equivalence Classes. UK Workshop on Computational Intelligence, Leeds UK, 2006.

Daly, R. and Shen, Q. (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. , Daly, R. and Breitling, R. (2012) Mixture model clustering for peak filtering in metabolomics. In: WCSB2012 - 9th International Workshop on Computational Systems Biology, Ulm, Germany, 4-6 Jun 2012,