Search Results - "Saccenti, Edoardo"

The Power of Microbiome Studies: Some Considerations on Which Alpha and Beta Metrics to Use and How to Report Results by Kers, Jannigje Gerdien, Saccenti, Edoardo

“…Since sequencing techniques have become less expensive, larger sample sizes are applicable for microbiota studies. The aim of this study is to show how, and to…”
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Editorial: Education in systems biology 2022 by Saccenti, Edoardo

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What can go wrong when observations are not independently and identically distributed: A cautionary note on calculating correlations on combined data sets from different experiments or conditions by Saccenti, Edoardo

“…In the scientific literature data analysis results are often presented when samples from different experiments or different conditions, technical replicates or…”
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Approaches to Sample Size Determination for Multivariate Data: Applications to PCA and PLS-DA of Omics Data by Saccenti, Edoardo, Timmerman, Marieke E

“…Sample size determination is a fundamental step in the design of experiments. Methods for sample size determination are abundant for univariate analysis…”
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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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NMR Spectroscopy for Metabolomics Research by Emwas, Abdul-Hamid, Roy, Raja, McKay, Ryan T, Tenori, Leonardo, Saccenti, Edoardo, Gowda, G A Nagana, Raftery, Daniel, Alahmari, Fatimah, Jaremko, Lukasz, Jaremko, Mariusz, Wishart, David S

“…Over the past two decades, nuclear magnetic resonance (NMR) has emerged as one of the three principal analytical techniques used in metabolomics (the other two…”
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In-Pero: Exploiting Deep Learning Embeddings of Protein Sequences to Predict the Localisation of Peroxisomal Proteins by Anteghini, Marco, Martins Dos Santos, Vitor, Saccenti, Edoardo

“…Peroxisomes are ubiquitous membrane-bound organelles, and aberrant localisation of peroxisomal proteins contributes to the pathogenesis of several disorders…”
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The association between breastmilk oligosaccharides and faecal microbiota in healthy breastfed infants at two, six, and twelve weeks of age by Borewicz, Klaudyna, Gu, Fangjie, Saccenti, Edoardo, Hechler, Christine, Beijers, Roseriet, de Weerth, Carolina, van Leeuwen, Sander S., Schols, Henk A., Smidt, Hauke

“…Several factors affect gut microbiota development in early life, among which breastfeeding plays a key role. We followed 24 mother-infant pairs to investigate…”
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Network analysis of the proteome and peptidome sheds light on human milk as a biological system by Dekker, Pieter M., Boeren, Sjef, Saccenti, Edoardo, Hettinga, Kasper A.

“…Proteins and peptides found in human milk have bioactive potential to benefit the newborn and support healthy development. Research has been carried out on the…”
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On the Use of Correlation and MI as a Measure of Metabolite-Metabolite Association for Network Differential Connectivity Analysis by Jahagirdar, Sanjeevan, Saccenti, Edoardo

“…Metabolite differential connectivity analysis has been successful in investigating potential molecular mechanisms underlying different conditions in biological…”
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Correlating Infant Fecal Microbiota Composition and Human Milk Oligosaccharide Consumption by Microbiota of 1‐Month‐Old Breastfed Infants by Borewicz, Klaudyna, Gu, Fangjie, Saccenti, Edoardo, Arts, Ilja C.W., Penders, John, Thijs, Carel, Leeuwen, Sander S., Lindner, Cordula, Nauta, Arjen, Leusen, Ellen, Schols, Henk A., Smidt, Hauke

“…Scope Understanding the biological functions of human milk oligosaccharides (HMOs) in shaping gastrointestinal (GI) tract microbiota during infancy is of great…”
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Milk Metabolomics Data Reveal the Energy Balance of Individual Dairy Cows in Early Lactation by Xu, Wei, Vervoort, Jacques, Saccenti, Edoardo, van Hoeij, Renny, Kemp, Bas, van Knegsel, Ariette

“…In early lactation, dairy cows typically have a negative energy balance which has been related to metabolic disorders, compromised health and fertility, and…”
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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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Impact of a wastewater treatment plant on microbial community composition and function in a hyporheic zone of a eutrophic river by Atashgahi, Siavash, Aydin, Rozelin, Dimitrov, Mauricio R., Sipkema, Detmer, Hamonts, Kelly, Lahti, Leo, Maphosa, Farai, Kruse, Thomas, Saccenti, Edoardo, Springael, Dirk, Dejonghe, Winnie, Smidt, Hauke

“…The impact of the installation of a technologically advanced wastewater treatment plant (WWTP) on the benthic microbial community of a vinyl chloride (VC)…”
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Intraspecies characterization of bacteria via evolutionary modeling of protein domains by Budimir, Iva, Giampieri, Enrico, Saccenti, Edoardo, Suarez-Diez, Maria, Tarozzi, Martina, Dall’Olio, Daniele, Merlotti, Alessandra, Curti, Nico, Remondini, Daniel, Castellani, Gastone, Sala, Claudia

“…The ability to detect and characterize bacteria within a biological sample is crucial for the monitoring of infections and epidemics, as well as for the study…”
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Phenotype and multi-omics comparison of Staphylococcus and Streptococcus uncovers pathogenic traits and predicts zoonotic potential by Zondervan, Niels A, Martins Dos Santos, Vitor A P, Suarez-Diez, Maria, Saccenti, Edoardo

“…Staphylococcus and Streptococcus species can cause many different diseases, ranging from mild skin infections to life-threatening necrotizing fasciitis. Both…”
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Correction to: Phenotype and multi-omics comparison of Staphylococcus and Streptococcus uncovers pathogenic traits and predicts zoonotic potential by Zondervan, Niels A, Martins dos Santos, Vitor A. P, Suarez-Diez, Maria, Saccenti, Edoardo

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Exploration of Blood Lipoprotein and Lipid Fraction Profiles in Healthy Subjects through Integrated Univariate, Multivariate, and Network Analysis Reveals Association of Lipase Activity and Cholesterol Esterification with Sex and Age by Balder, Yasmijn, Vignoli, Alessia, Tenori, Leonardo, Luchinat, Claudio, Saccenti, Edoardo

“…In this study, we investigated blood lipoprotein and lipid fraction profiles, quantified using nuclear magnetic resonance, in a cohort of 844 healthy blood…”
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The Effect of DNA Extraction Methods on Observed Microbial Communities from Fibrous and Liquid Rumen Fractions of Dairy Cows by Vaidya, Jueeli D, van den Bogert, Bartholomeus, Edwards, Joan E, Boekhorst, Jos, van Gastelen, Sanne, Saccenti, Edoardo, Plugge, Caroline M, Smidt, Hauke

“…DNA based methods have been widely used to study the complexity of the rumen microbiota, and it is well known that the method of DNA extraction is a critical…”
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The human milk proteome and allergy of mother and child: Exploring associations with protein abundances and protein network connectivity by Dekker, Pieter M, Azad, Meghan B, Boeren, Sjef, Mandhane, Piushkumar J, Moraes, Theo J, Simons, Elinor, Subbarao, Padmaja, Turvey, Stuart E, Saccenti, Edoardo, Hettinga, Kasper A

“…The human milk proteome comprises a vast number of proteins with immunomodulatory functions, but it is not clear how this relates to allergy of the mother or…”
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