Please cite this paper if you use mummichog:
Li et al. (2013) Predicting network activity from high throughput metabolomics. PLoS computational biology 9.7 (2013): e1003123.

Review papers that cover mummichog

Johnson, Caroline H., Julijana Ivanisevic, and Gary Siuzdak. "Metabolomics: beyond biomarkers and towards mechanisms." Nature reviews Molecular cell biology 17.7 (2016): 451-459.

Barnes et la. (2016) Training in metabolomics research. II. Processing and statistical analysis of metabolomics data, metabolite identification, pathway analysis, applications of metabolomics and its future. Journal of Mass Spectrometry, 51(8), pp.535-548

Schrimpe-Rutledge et al. "Untargeted metabolomics strategies—challenges and emerging directions." Journal of The American Society for Mass Spectrometry 27.12 (2016): 1897-1905.

Li, Shuzhao, Andrei Todor, and Ruiyan Luo. "Blood transcriptomics and metabolomics for personalized medicine." Computational and structural biotechnology journal 14 (2016): 1-7.

Cho et al. "After the feature presentation: technologies bridging untargeted metabolomics and biology." Current opinion in biotechnology 28 (2014): 143-148.

Li et al. "Systems biological approaches to measure and understand vaccine immunity in humans." Seminars in immunology. Vol. 25. No. 3. Academic Press, 2013.

Johnson et al. "Bioinformatics: the next frontier of metabolomics." Analytical chemistry 87.1 (2014): 147-156.

Jones, Dean P. "Sequencing the exposome: a call to action." Toxicology reports 3 (2016): 29-45.

Uppal et al. "Computational metabolomics: a framework for the million metabolome." Chemical research in toxicology 29.12 (2016): 1956-1975.

Xia, Jianguo. "Computational Strategies for Biological Interpretation of Metabolomics Data." Metabolomics: From Fundamentals to Clinical Applications. Springer International Publishing, 2017. 191-206.


Research papers that use mummichog

Gardinassi et al. (2018) Integrative metabolomics and transcriptomics signatures of clinical tolerance to Plasmodium vivax reveal activation of innate cell immunity and T cell signaling. Redox Biology. DOI: 10.1016/j.redox.2018.04.011

Sinclair et al. (2017) mTOR regulates metabolic adaptation of APCs in the lung microenvironment and controls the outcome of allergic inflammation. Science. 357(6355):1014-1021. PMID: 28798047

Li et al. (2017) Metabolic Phenotypes of Response to Vaccination in Humans. Cell 169(5): p862-877.

Huan, Tao, et al. "Systems biology guided by XCMS Online metabolomics." Nature methods 14.5 (2017): 461.

Xu et al. "Autophagy is essential for effector CD8+ T cell survival and memory formation." Nature immunology 15.12 (2014): 1152-1161.

Ravindran, Rajesh, et al. "Vaccine activation of the nutrient sensor GCN2 in dendritic cells enhances antigen presentation." Science 343.6168 (2014): 313-317.

Hoffman et al. "Effects of age, sex, and genotype on high‐sensitivity metabolomic profiles in the fruit fly, Drosophila melanogaster." Aging Cell 13.4 (2014): 596-604.

Walker, Douglas I., et al. "High-resolution metabolomics of occupational exposure to trichloroethylene." International journal of epidemiology 45.5 (2016): 1517-1527.

Jin, Ran, et al. "Amino acid metabolism is altered in adolescents with nonalcoholic fatty liver disease—an untargeted, high resolution metabolomics study." The Journal of pediatrics 172 (2016): 14-19.

Chandler, Joshua D., et al. "Metabolic pathways of lung inflammation revealed by high-resolution metabolomics (HRM) of H1N1 influenza virus infection in mice." American Journal of Physiology-Regulatory, Integrative and Comparative Physiology 311.5 (2016): R906-R916.

Cribbs, Sushma K., et al. "Metabolomics of bronchoalveolar lavage differentiate healthy HIV-1-infected subjects from controls." AIDS research and human retroviruses 30.6 (2014): 579-585.


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