Identification of bioactive metabolites using activity metabolomics

MM Rinschen, J Ivanisevic, M Giera… - Nature reviews Molecular …, 2019 - nature.com
The metabolome, the collection of small-molecule chemical entities involved in metabolism,
has traditionally been studied with the aim of identifying biomarkers in the diagnosis and …

Applications of multi‐omics analysis in human diseases

C Chen, J Wang, D Pan, X Wang, Y Xu, J Yan… - MedComm, 2023 - Wiley Online Library
Multi‐omics usually refers to the crossover application of multiple high‐throughput screening
technologies represented by genomics, transcriptomics, single‐cell transcriptomics …

Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine

A Heinken, J Hertel, G Acharya, DA Ravcheev… - Nature …, 2023 - nature.com
The human microbiome influences the efficacy and safety of a wide variety of commonly
prescribed drugs. Designing precision medicine approaches that incorporate microbial …

Comprehensive metabolomics expands precision medicine for triple-negative breast cancer

Y Xiao, D Ma, YS Yang, F Yang, JH Ding, Y Gong… - Cell research, 2022 - nature.com
Metabolic reprogramming is a hallmark of cancer. However, systematic characterizations of
metabolites in triple-negative breast cancer (TNBC) are still lacking. Our study profiled the …

RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy

SK Burley, HM Berman, C Bhikadiya, C Bi… - Nucleic acids …, 2019 - academic.oup.com
Abstract The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB
PDB, rcsb. org), the US data center for the global PDB archive, serves thousands of Data …

Ion mobility collision cross-section atlas for known and unknown metabolite annotation in untargeted metabolomics

Z Zhou, M Luo, X Chen, Y Yin, X Xiong, R Wang… - Nature …, 2020 - nature.com
The metabolome includes not just known but also unknown metabolites; however,
metabolite annotation remains the bottleneck in untargeted metabolomics. Ion mobility …

Systems biology and multi-omics integration: viewpoints from the metabolomics research community

FR Pinu, DJ Beale, AM Paten, K Kouremenos… - Metabolites, 2019 - mdpi.com
The use of multiple omics techniques (ie, genomics, transcriptomics, proteomics, and
metabolomics) is becoming increasingly popular in all facets of life science. Omics …

Reconstructing organisms in silico: genome-scale models and their emerging applications

X Fang, CJ Lloyd, BO Palsson - Nature Reviews Microbiology, 2020 - nature.com
Escherichia coli is considered to be the best-known microorganism given the large number
of published studies detailing its genes, its genome and the biochemical functions of its …

Current status and applications of genome-scale metabolic models

C Gu, GB Kim, WJ Kim, HU Kim, SY Lee - Genome biology, 2019 - Springer
Genome-scale metabolic models (GEMs) computationally describe gene-protein-reaction
associations for entire metabolic genes in an organism, and can be simulated to predict …

SBML Level 3: an extensible format for the exchange and reuse of biological models

SM Keating, D Waltemath, M König, F Zhang… - Molecular systems …, 2020 - embopress.org
Abstract Systems biology has experienced dramatic growth in the number, size, and
complexity of computational models. To reproduce simulation results and reuse models …