MADMAX - Management and analysis database for multiple ~omics experiments
Ke Lin,Harrie J. Kools,Philip J. de Groot,Anand Gavai,Ram Kumar Basnet,Feng Cheng,Jian Wu,Xiaowu Wang,Arjen Lommen,Guido J. E. J. Hooiveld,Guusje Bonnema,Richard G. F. Visser,Michael Müller,Jack A. M. Leunissen +13 more
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TLDR
MADMAX is designed to provide a solution for storage and analysis of complex ~omics datasets and constitutes an ISA-Tab compliant LIMS part which is independent of different analysis pipelines.Abstract:
The rapid increase of ~omics datasets generated by microarray, mass spectrometry and next generation sequencing technologies requires an integrated platform that can combine results from different ~omics datasets to provide novel insights in the understanding of biological systems. MADMAX is designed to provide a solution for storage and analysis of complex ~omics datasets. In addition, analysis results (such as lists of genes) will be merged to reveal candidate genes supported by all datasets. The system constitutes an ISA-Tab compliant LIMS part which is independent of different analysis pipelines. A pilot study of different type of ~omics data in Brassica rapa demonstrates the possible use of MADMAX. The web-based user interface provides easy access to data and analysis tools on top of the database.read more
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Calorie Restriction-like Effects of 30 Days of Resveratrol Supplementation on Energy Metabolism and Metabolic Profile in Obese Humans
Silvie Timmers,Ellen Konings,L. Bilet,Riekelt H. Houtkooper,Tineke van de Weijer,Gijs H. Goossens,Joris Hoeks,Sophie E. van der Krieken,Dongryeol Ryu,Sander Kersten,Esther Moonen-Kornips,Matthijs K. C. Hesselink,Iris Kunz,Vera B. Schrauwen-Hinderling,Ellen E. Blaak,Johan Auwerx,Patrick Schrauwen +16 more
TL;DR: It is demonstrated that 30 days of resveratrol supplementation induces metabolic changes in obese humans, mimicking the effects of calorie restriction.
Journal ArticleDOI
Gut-derived short-chain fatty acids are vividly assimilated into host carbohydrates and lipids
Gijs den Besten,Katja Lange,Rick Havinga,Theo H. van Dijk,Albert Gerding,Karen van Eunen,Michael Müller,Albert K. Groen,Guido J. E. J. Hooiveld,Barbara M. Bakker,Dirk-Jan Reijngoud +10 more
TL;DR: Gut-derived acetate, propionate, and butyrate play important roles as substrates for glucose, cholesterol, and lipid metabolism and microarray data suggested that SCFAs exert a mild regulatory effect on the expression of genes involved in hepatic metabolic pathways during the 6-h infusion period.
Journal ArticleDOI
Systems Biology and Multi-Omics Integration: Viewpoints from the Metabolomics Research Community.
Farhana R. Pinu,David J. Beale,Paten Am,Konstantinos A. Kouremenos,Sanjay Swarup,Horst Joachim Schirra,David S. Wishart +6 more
TL;DR: This document envisage that this document will serve as a guide to metabolomics researchers and other members of the community wishing to perform multi-omics studies and believe that these ideas may allow the full promise of integratedmulti-omics research and, ultimately, of systems biology to be realized.
Journal ArticleDOI
Integration of growth and patterning during vascular tissue formation in Arabidopsis
Bert De Rybel,Milad Adibi,Milad Adibi,Alice S. Breda,Jos R. Wendrich,Margot E. Smit,Ondřej Novák,Nobutoshi Yamaguchi,Saiko Yoshida,Gert Van Isterdael,Joakim Palovaara,Bart Nijsse,Mark V. Boekschoten,Guido J. E. J. Hooiveld,Tom Beeckman,Doris Wagner,Karin Ljung,Christian Fleck,Dolf Weijers +18 more
TL;DR: Experimental and theoretical evidence shows that these cells act as a tissue organizer by positioning the domain of oriented cell divisions, and it is demonstrated that the auxin-cytokinin interaction acts as a spatial incoherent feed-forward loop, which is essential to generate distinct hormonal response zones, thus establishing a stable pattern within a growing vascular tissue.
Journal ArticleDOI
Effects of Gut Microbiota Manipulation by Antibiotics on Host Metabolism in Obese Humans: A Randomized Double-Blind Placebo-Controlled Trial.
Dorien Reijnders,Gijs H. Goossens,Gerben D. A. Hermes,Evelien P. J. G. Neis,Christina M. van der Beek,Jasper Most,Jens J. Holst,Kaatje Lenaerts,Ruud S. Kootte,Max Nieuwdorp,Albert K. Groen,Steven W.M. Olde Damink,Mark V. Boekschoten,Hauke Smidt,Erwin G. Zoetendal,Cornelis H. C. Dejong,Ellen E. Blaak +16 more
TL;DR: Antibiotics did not affect tissue-specific insulin sensitivity, energy/substrate metabolism, postprandial hormones and metabolites, systemic inflammation, gut permeability, and adipocyte size, indicating that interference with adult microbiota by 7-day antibiotic treatment has no clinically relevant impact on metabolic health in obese humans.
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