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ECMDB 2.0: A richer resource for understanding the biochemistry ofE. coli

Tanvir Sajed, Ana Marcu, Miguel Ramirez, Allison Pon, An Chi Guo, Craig Knox, Michael Wilson, Jason R. Grant, Yannick Djoumbou, David S. Wishart
2015 Nucleic Acids Research  
of compounds with NMR or MS spectra (from 412 to 3261) and a massive increase in the number of external links to other E. coli or chemical resources.  ...  ECMDB or the Escherichia coli Metabolome Database (http://www.ecmdb.ca) is a comprehensive database containing detailed information about the genome and metabolome of E. coli (K-12).  ...  ACKNOWLEDGEMENTS The authors would like to thank Sasha Babicki and Anthony Wu for their contributions and the many users of ECMDB for their valuable feedback and suggestions.  ... 
doi:10.1093/nar/gkv1060 pmid:26481353 pmcid:PMC4702790 fatcat:4tp4re4t5rhzth2gs7n4iqtyga

Screening of candidate substrates and coupling ions of transporters by thermostability shift assays [article]

Homa Majd, Martin King, Shane M Palmer, Anthony Smith, Liam Elbourne, Ian Paulsen, David Sharples, Peter Henderson, Edmund R.S. Kunji
2018 bioRxiv   pre-print
In each case, the substrates were identified correctly from a large set of chemically related compounds, including stereo-isoforms.  ...  Substrates of most transport proteins have not been identified, limiting our understanding of their role in physiology and disease.  ...  ECMDB 2.0: A richer resource for understanding the 547 biochemistry of E. coli.  ... 
doi:10.1101/367805 fatcat:kphdqpeacjhzdmj7vl54u4aesq

CHEMINFORMATICS TOOLS FOR ENABLING METABOLOMICS

YANNICK DJOUMBOU FEUNANG
2017
Together, they build a cheminformatics platform that can enable iv metabolomics, and contribute to the understanding of our environment as well as the advancement of science. v Preface  ...  With the integration of a rule-based fragmentation approach for spectra prediction, the development of new ranking functions, and the expansion of the spectral database, CFM-ID 3.0 showed a significant  ...  DrugBank provides comprehensive data for >8,000 drugs and drug metabolites (99) . The E. coli Metabolome Database (ECMDB) provides data for >3,000 E. coli derived compounds (12) .  ... 
doi:10.7939/r3vd6pj8b fatcat:bzwvwij6djby3jh5rnugdebk3e

Application of Multi-Omics Approaches to Maximize Beef Production

Aidin Foroutan Naddafi
2021
Therefore, we decided to conduct a comprehensive multi-omics study (metabolomics, transcriptomics, epigenomics) to understand the biological mechanisms impacted by prenatal nutrition (normal-diet or Ndiet  ...  Similar pathway analysis for the HRFI and LRFI bulls showed overrepresentation of the number of DMRs in four networks involved in "embryonic development", "DNA replication, DNA repair, and RNA processing  ...  metabolome [18] [19] [20] [21] , the yeast metabolome [22, 23] , and the E. coli metabolome [24, 25] .  ... 
doi:10.7939/r3-dmka-4k42 fatcat:ow6ebyoysbbnplbhc4kzvywvza