Search Results - "Wandy, Joe"

GraphOmics: an interactive platform to explore and integrate multi-omics data by Wandy, Joe, Daly, Rónán

“…An increasing number of studies now produce multiple omics measurements that require using sophisticated computational methods for analysis. While each omics…”
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Topic modeling for untargeted substructure exploration in metabolomics by van der Hooft, Justin Johan Jozias, Wandy, Joe, Barrett, Michael P., Burgess, Karl E. V., Rogers, Simon

“…The potential of untargeted metabolomics to answer important questions across the life sciences is hindered because of a paucity of computational tools that…”
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MolNetEnhancer: Enhanced Molecular Networks by Integrating Metabolome Mining and Annotation Tools by Ernst, Madeleine, Kang, Kyo Bin, Caraballo-Rodríguez, Andrés Mauricio, Nothias, Louis-Felix, Wandy, Joe, Chen, Christopher, Wang, Mingxun, Rogers, Simon, Medema, Marnix H, Dorrestein, Pieter C, van der Hooft, Justin J J

“…Metabolomics has started to embrace computational approaches for chemical interpretation of large data sets. Yet, metabolite annotation remains a key…”
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Deciphering complex metabolite mixtures by unsupervised and supervised substructure discovery and semi-automated annotation from MS/MS spectra by Rogers, Simon, Ong, Cher Wei, Wandy, Joe, Ernst, Madeleine, Ridder, Lars, van der Hooft, Justin J J

“…Complex metabolite mixtures are challenging to unravel. Mass spectrometry (MS) is a widely used and sensitive technique for obtaining structural information of…”
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Unsupervised Discovery and Comparison of Structural Families Across Multiple Samples in Untargeted Metabolomics by van der Hooft, Justin J. J, Wandy, Joe, Young, Francesca, Padmanabhan, Sandosh, Gerasimidis, Konstantinos, Burgess, Karl E. V, Barrett, Michael P, Rogers, Simon

“…In untargeted metabolomics approaches, the inability to structurally annotate relevant features and map them to biochemical pathways is hampering the full…”
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Ranking microbial metabolomic and genomic links in the NPLinker framework using complementary scoring functions by Hjörleifsson Eldjárn, Grímur, Ramsay, Andrew, van der Hooft, Justin J J, Duncan, Katherine R, Soldatou, Sylvia, Rousu, Juho, Daly, Rónán, Wandy, Joe, Rogers, Simon

“…Specialised metabolites from microbial sources are well-known for their wide range of biomedical applications, particularly as antibiotics. When mining paired…”
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R package for statistical inference in dynamical systems using kernel based gradient matching: KGode by Niu, Mu, Wandy, Joe, Daly, Rónán, Rogers, Simon, Husmeier, Dirk

“…Many processes in science and engineering can be described by dynamical systems based on nonlinear ordinary differential equations (ODEs). Often ODE parameters…”
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Ranking Metabolite Sets by Their Activity Levels by McLuskey, Karen, Wandy, Joe, Vincent, Isabel, van der Hooft, Justin J J, Rogers, Simon, Burgess, Karl, Daly, Rónán

“…Related metabolites can be grouped into sets in many ways, e.g., by their participation in series of chemical reactions (forming metabolic pathways), or based…”
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Simulated-to-real benchmarking of acquisition methods in untargeted metabolomics by Wandy, Joe, McBride, Ross, Rogers, Simon, Terzis, Nikolaos, Weidt, Stefan, van der Hooft, Justin J J, Bryson, Kevin, Daly, Rónán, Davies, Vinny

“…Data-Dependent and Data-Independent Acquisition modes (DDA and DIA, respectively) are both widely used to acquire MS2 spectra in untargeted liquid…”
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In Silico Optimization of Mass Spectrometry Fragmentation Strategies in Metabolomics by Wandy, Joe, Davies, Vinny, J. J. van der Hooft, Justin, Weidt, Stefan, Daly, Rónán, Rogers, Simon

“…Liquid chromatography (LC) coupled to tandem mass spectrometry (MS/MS) is widely used in identifying small molecules in untargeted metabolomics. Various…”
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TopNEXt: automatic DDA exclusion framework for multi-sample mass spectrometry experiments by McBride, Ross, Wandy, Joe, Weidt, Stefan, Rogers, Simon, Davies, Vinny, Daly, Rónán, Bryson, Kevin

“…Abstract Motivation Liquid Chromatography Tandem Mass Spectrometry experiments aim to produce high-quality fragmentation spectra, which can be used to annotate…”
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PiMP my metabolome: an integrated, web-based tool for LC-MS metabolomics data by Gloaguen, Yoann, Morton, Fraser, Daly, Rónán, Gurden, Ross, Rogers, Simon, Wandy, Joe, Wilson, David, Barrett, Michael, Burgess, Karl

“…The Polyomics integrated Metabolomics Pipeline (PiMP) fulfils an unmet need in metabolomics data analysis. PiMP offers automated and user-friendly analysis…”
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Ms2lda.org: web-based topic modelling for substructure discovery in mass spectrometry by Wandy, Joe, Zhu, Yunfeng, van der Hooft, Justin J J, Daly, Rónán, Barrett, Michael P, Rogers, Simon

“…Abstract Motivation We recently published MS2LDA, a method for the decomposition of sets of molecular fragment data derived from large metabolomics…”
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Rapid Development of Improved Data-Dependent Acquisition Strategies by Davies, Vinny, Wandy, Joe, Weidt, Stefan, van der Hooft, Justin J. J, Miller, Alice, Daly, Rónán, Rogers, Simon

“…Tandem mass spectrometry (LC-MS/MS) is widely used to identify unknown ions in untargeted metabolomics. Data-dependent acquisition (DDA) chooses which ions to…”
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MetAssign: probabilistic annotation of metabolites from LC-MS data using a Bayesian clustering approach by Daly, Rónán, Rogers, Simon, Wandy, Joe, Jankevics, Andris, Burgess, Karl E V, Breitling, Rainer

“…The use of liquid chromatography coupled to mass spectrometry has enabled the high-throughput profiling of the metabolite composition of biological samples…”
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ShinyKGode: an interactive application for ODE parameter inference using gradient matching by Wandy, Joe, Niu, Mu, Giurghita, Diana, Daly, Rónán, Rogers, Simon, Husmeier, Dirk

“…Abstract Motivation Mathematical modelling based on ordinary differential equations (ODEs) is widely used to describe the dynamics of biological systems,…”
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Incorporating peak grouping information for alignment of multiple liquid chromatography-mass spectrometry datasets by Wandy, Joe, Daly, Rónán, Breitling, Rainer, Rogers, Simon

“…The combination of liquid chromatography and mass spectrometry (LC/MS) has been widely used for large-scale comparative studies in systems biology, including…”
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ViMMS 2.0: A framework to develop, test and optimise fragmentation strategies in LC-MS metabolomics by Wandy, Joe, Davies, Vinny, McBride, Ross, Weidt, Stefan, Rogers, Simon, Daly, Rónán

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Unsupervised bayesian explorations of mass spectrometry data by Wandy, Joe

“…In recent years, the large-scale, untargeted studies of the compounds that serve as workers in the cell (proteins) and the small molecules involved in…”
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