Search Results - "Smilde, Age K."

Corruption of the Pearson correlation coefficient by measurement error and its estimation, bias, and correction under different error models by Saccenti, Edoardo, Hendriks, Margriet H. W. B., Smilde, Age K.

“…Correlation coefficients are abundantly used in the life sciences. Their use can be limited to simple exploratory analysis or to construct association networks…”
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Metabolic fate of polyphenols in the human superorganism by van Duynhoven, John, Vaughan, Elaine E., Jacobs, Doris M., Kemperman, Robèr A., van Velzen, Ewoud J. J., Gross, Gabriele, Roger, Laure C., Possemiers, Sam, Smilde, Age K., Doré, Joël, Westerhuis, Johan A., Van de Wiele, Tom, Gordon, Jeffrey I.

“…Dietary polyphenols are components of many foods such as tea, fruit and vegetables and are associated with several beneficial health effects although, so far,…”
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Repeated measures ASCA+ for analysis of longitudinal intervention studies with multivariate outcome data by Madssen, Torfinn S, Giskeødegård, Guro F, Smilde, Age K, Westerhuis, Johan A

“…Longitudinal intervention studies with repeated measurements over time are an important type of experimental design in biomedical research. Due to the advent…”
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Effect of strigolactones on recruitment of the rice root-associated microbiome by Kim, Bora, Westerhuis, Johan A, Smilde, Age K, Floková, Kristýna, Suleiman, Afnan K A, Kuramae, Eiko E, Bouwmeester, Harro J, Zancarini, Anouk

“…Abstract Strigolactones are endogenous plant hormones regulating plant development and are exuded into the rhizosphere when plants experience nutrient…”
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Centering, scaling, and transformations: improving the biological information content of metabolomics data by van den Berg, Robert A, Hoefsloot, Huub C J, Westerhuis, Johan A, Smilde, Age K, van der Werf, Mariët J

“…Extracting relevant biological information from large data sets is a major challenge in functional genomics research. Different aspects of the data hamper…”
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Exploring dynamic metabolomics data with multiway data analysis: a simulation study by Li, Lu, Hoefsloot, Huub, de Graaf, Albert A, Acar, Evrim, Smilde, Age K

“…Analysis of dynamic metabolomics data holds the promise to improve our understanding of underlying mechanisms in metabolism. For example, it may detect changes…”
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Author Correction: Corruption of the Pearson correlation coefficient by measurement error and its estimation, bias, and correction under different error models by Saccenti, Edoardo, Hendriks, Margriet H. W. B., Smilde, Age K.

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Analyzing postprandial metabolomics data using multiway models: a simulation study by Li, Lu, Yan, Shi, Bakker, Barbara M, Hoefsloot, Huub, Chawes, Bo, Horner, David, Rasmussen, Morten A, Smilde, Age K, Acar, Evrim

“…Analysis of time-resolved postprandial metabolomics data can improve the understanding of metabolic mechanisms, potentially revealing biomarkers for early…”
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A strategy for differential abundance analysis of sparse microbiome data with group-wise structured zeros by Abegaz, Fentaw, Abedini, Davar, White, Fred, Guerrieri, Alessandra, Zancarini, Anouk, Dong, Lemeng, Westerhuis, Johan A., van Eeuwijk, Fred, Bouwmeester, Harro, Smilde, Age K.

“…Comparing the abundance of microbial communities between different groups or obtained under different experimental conditions using count sequence data is a…”
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Increased comparability between RNA-Seq and microarray data by utilization of gene sets by van der Kloet, Frans M, Buurmans, Jeroen, Jonker, Martijs J, Smilde, Age K, Westerhuis, Johan A

“…The field of transcriptomics uses and measures mRNA as a proxy of gene expression. There are currently two major platforms in use for quantifying mRNA,…”
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Large-Scale Human Metabolomics Studies:  A Strategy for Data (Pre-) Processing and Validation by Bijlsma, Sabina, Bobeldijk, Ivana, Verheij, Elwin R, Ramaker, Raymond, Kochhar, Sunil, Macdonald, Ian A, van Ommen, Ben, Smilde, Age K

“…A large metabolomics study was performed on 600 plasma samples taken at four time points before and after a single intake of a high fat test meal by obese and…”
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Common and distinct variation in data fusion of designed experimental data by Alinaghi, Masoumeh, Bertram, Hanne Christine, Brunse, Anders, Smilde, Age K., Westerhuis, Johan A.

“…Introduction Integrative analysis of multiple data sets can provide complementary information about the studied biological system. However, data fusion of…”
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Analysis of high-dimensional metabolomics data with complex temporal dynamics using RM-ASCA by Erdős, Balázs, Westerhuis, Johan A, Adriaens, Michiel E, O'Donovan, Shauna D, Xie, Ren, Singh-Povel, Cécile M, Smilde, Age K, Arts, Ilja C W

“…The intricate dependency structure of biological "omics" data, particularly those originating from longitudinal intervention studies with frequently sampled…”
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Cellular and molecular synergy in AS01-adjuvanted vaccines results in an early IFNγ response promoting vaccine immunogenicity by Coccia, Margherita, Collignon, Catherine, Hervé, Caroline, Chalon, Aurélie, Welsby, Iain, Detienne, Sophie, van Helden, Mary J., Dutta, Sheetij, Genito, Christopher J., Waters, Norman C., Van Deun, Katrijn, Smilde, Age K., van den Berg, Robert A., Franco, David, Bourguignon, Patricia, Morel, Sandra, Garçon, Nathalie, Lambrecht, Bart N., Goriely, Stanislas, van der Most, Robbert, Didierlaurent, Arnaud M.

“…Combining immunostimulants in adjuvants can improve the quality of the immune response to vaccines. Here, we report a unique mechanism of molecular and…”
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The Muscle Metabolome Differs between Healthy and Frail Older Adults by Fazelzadeh, Parastoo, Hangelbroek, Roland W. J, Tieland, Michael, de Groot, Lisette C. P. G. M, Verdijk, Lex B, van Loon, Luc J. C, Smilde, Age K, Alves, Rodrigo D. A. M, Vervoort, Jacques, Müller, Michael, van Duynhoven, John P. M, Boekschoten, Mark V

“…Populations around the world are aging rapidly. Age-related loss of physiological functions negatively affects quality of life. A major contributor to the…”
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Centering and scaling in component analysis by Bro, Rasmus, Smilde, Age K.

“…In this paper the purpose and use of centering and scaling are discussed in depth. The main focus is on two‐way bilinear data analysis, but the results can…”
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A structured overview of simultaneous component based data integration by Van Deun, Katrijn, Smilde, Age K, van der Werf, Mariët J, Kiers, Henk A L, Van Mechelen, Iven

“…Data integration is currently one of the main challenges in the biomedical sciences. Often different pieces of information are gathered on the same set of…”
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Modeling adaptive response profiles in a vaccine clinical trial by Hasdemir, Dicle, van den Berg, Robert A, van Kampen, Antoine, Smilde, Age K

“…Vaccine clinical studies typically provide time-resolved data on adaptive response read-outs in response to the administration of that particular vaccine to a…”
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Statistical validation of megavariate effects in ASCA by Vis, Daniel J, Westerhuis, Johan A, Smilde, Age K, van der Greef, Jan

“…Innovative extensions of (M) ANOVA gain common ground for the analysis of designed metabolomics experiments. ASCA is such a multivariate analysis method; it…”
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Metabolic profiling of the response to an oral glucose tolerance test detects subtle metabolic changes by Wopereis, Suzan, Rubingh, Carina M, van Erk, Marjan J, Verheij, Elwin R, van Vliet, Trinette, Cnubben, Nicole H P, Smilde, Age K, van der Greef, Jan, van Ommen, Ben, Hendriks, Henk F J

“…The prevalence of overweight is increasing globally and has become a serious health problem. Low-grade chronic inflammation in overweight subjects is thought…”
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