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Metabolites, Volume 10, Issue 12

December 2020 - 42 articles

Cover Story: Filigree is a Java-based tool that implements our previously published Differential Network Enrichment Analysis (DNEA) algorithm. Filigree can build robust data-driven partial correlation networks from high-dimensional metabolomics and lipidomics data. If the number of metabolites far exceeds the number of samples, Filigree can perform feature aggregation to reduce data dimensionality. Our methodology can also handle imbalanced experimental designs. Filigree provides an alternative to traditional knowledge-based enrichment testing methods. We demonstrate the utility of Filigree by applying it to previously published studies analyzing the metabolome in the context of metabolic disorders. View this paper
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Articles (42)

  • Article
  • Open Access
32 Citations
6,734 Views
20 Pages

Using Community Science to Reveal the Global Chemogeography of River Metabolomes

  • Vanessa A. Garayburu-Caruso,
  • Robert E. Danczak,
  • James C. Stegen,
  • Lupita Renteria,
  • Marcy Mccall,
  • Amy E. Goldman,
  • Rosalie K. Chu,
  • Jason Toyoda,
  • Charles T. Resch and
  • Joshua M. Torgeson
  • + 4 authors

20 December 2020

River corridor metabolomes reflect organic matter (OM) processing that drives aquatic biogeochemical cycles. Recent work highlights the power of ultrahigh-resolution mass spectrometry for understanding metabolome composition and river corridor metabo...

  • Article
  • Open Access
28 Citations
4,826 Views
15 Pages

Evaluation of Saliva Stability for NMR Metabolomics: Collection and Handling Protocols

  • Daniela Duarte,
  • Beatriz Castro,
  • Joana Leonor Pereira,
  • Joana Faria Marques,
  • Ana Luísa Costa and
  • Ana M. Gil

19 December 2020

Maintaining a salivary metabolic profile upon sample collection and preparation is determinant in metabolomics. Nuclear magnetic resonance (NMR) spectroscopy was used to identify metabolite changes during short-term storage, at room temperature (RT)/...

  • Article
  • Open Access
10 Citations
4,299 Views
26 Pages

Exploratory Analysis of Commercial Olive-Based Dietary Supplements Using Untargeted and Targeted Metabolomics

  • Mar Garcia-Aloy,
  • Nelli Groff,
  • Domenico Masuero,
  • Mauro Nisi,
  • Antonio Franco,
  • Furio Battelini,
  • Urska Vrhovsek and
  • Fulvio Mattivi

19 December 2020

The market of olive-based dietary supplements (OBDS) is composed of a broad range of natural extracts claiming different health effects and often sold without a clear statement on their chemical composition. The aim of this survey was to characterize...

  • Technical Note
  • Open Access
26 Citations
3,783 Views
10 Pages

Metabolic Changes in Serum Metabolome of Beagle Dogs Fed Black Ginseng

  • Dahye Yoon,
  • Ye Jin Kim,
  • Wan Kyu Lee,
  • Bo Ram Choi,
  • Seon Min Oh,
  • Young Seob Lee,
  • Jae Kwang Kim and
  • Dae Young Lee

19 December 2020

The effects of black ginseng, which has many kinds of biological activities, on dogs was investigated. Serum samples of beagle dogs, which were fed with black ginseng for 8 weeks, were measured using high-resolution magic angle spinning (HR-MAS) nucl...

  • Article
  • Open Access
16 Citations
5,298 Views
12 Pages

Single-Cell Transcriptional Profiling of Mouse Islets Following Short-Term Obesogenic Dietary Intervention

  • Annie R. Piñeros,
  • Hongyu Gao,
  • Wenting Wu,
  • Yunlong Liu,
  • Sarah A. Tersey and
  • Raghavendra G. Mirmira

18 December 2020

Obesity is closely associated with adipose tissue inflammation and insulin resistance. Dysglycemia and type 2 diabetes results when islet β cells fail to maintain appropriate insulin secretion in the face of insulin resistance. To clarify the ea...

  • Article
  • Open Access
32 Citations
4,556 Views
14 Pages

Data-Independent Acquisition for the Quantification and Identification of Metabolites in Plasma

  • Tom van der Laan,
  • Isabelle Boom,
  • Joshua Maliepaard,
  • Anne-Charlotte Dubbelman,
  • Amy C. Harms and
  • Thomas Hankemeier

18 December 2020

A popular fragmentation technique for non-targeted analysis is called data-independent acquisition (DIA), because it provides fragmentation data for all analytes in a specific mass range. In this work, we demonstrated the strengths and weaknesses of...

  • Review
  • Open Access
38 Citations
6,187 Views
8 Pages

17 December 2020

Fatty Acyl esters of Hydroxy Fatty Acids (FAHFA) encompass three different lipid families which have incorrectly been classified as wax esters. These families include (i) Branched-chain FAHFAs, involved in the regulation of glucose metabolism and inf...

  • Review
  • Open Access
33 Citations
4,994 Views
30 Pages

16 December 2020

Asthma, allergic rhinitis, food allergy, and atopic dermatitis are common childhood diseases with several different underlying mechanisms, i.e., endotypes of disease. Metabolomics has the potential to identify disease endotypes, which could beneficia...

  • Article
  • Open Access
10 Citations
3,263 Views
8 Pages

Possible Influence of Weight Gain and Creatinine Levels in Predicting Response to Nivolumab: A Multicenter Analysis

  • Cornelia Nitipir,
  • Cristina Orlov-Slavu,
  • Lucian Alecu,
  • Iulian Slavu,
  • Anca Pantea-Stoian,
  • Ionela Daniela Celmare,
  • Mihaela Olaru,
  • Valentin Calu,
  • Andra-Iulia Suceveanu and
  • Laura Mazilu
  • + 6 authors

14 December 2020

Literature suggests that high body mass index can be correlated with better response to immune checkpoint inhibitors. On the other hand, sarcopenia seems to be a negative predictive marker. The present analysis is a retrospective, multicenter trial t...

  • Article
  • Open Access
12 Citations
4,206 Views
13 Pages

A New Approach for the Production of Selenium-Enriched and Probiotic Yeast Biomass from Agro-Industrial by-Products in a Stirred-Tank Bioreactor

  • Sabrina Evelin Martiniano,
  • Letícia Alves Fernandes,
  • Edith Mier Alba,
  • Rafael Rodrigues Philippini,
  • Stephanie Caroline Tavares Tabuchi,
  • Marek Kieliszek,
  • Júlio César dos Santos and
  • Silvio Silvério da Silva

13 December 2020

The production of biomolecules using agro-industrial by-products as feedstock is a growing trend worldwide. Selenium (Se) is a trace element essential for health, and the Se-enrichment of yeast biomass can enhance its benefits. This study investigate...

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Metabolites - ISSN 2218-1989