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 …

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 …

Influence of the microbiome, diet and genetics on inter-individual variation in the human plasma metabolome

L Chen, DV Zhernakova, A Kurilshikov… - Nature medicine, 2022 - nature.com
The levels of the thousands of metabolites in the human plasma metabolome are strongly
influenced by an individual's genetics and the composition of their diet and gut microbiome …

Cell-free chemoenzymatic starch synthesis from carbon dioxide

T Cai, H Sun, J Qiao, L Zhu, F Zhang, J Zhang, Z Tang… - Science, 2021 - science.org
Starches, a storage form of carbohydrates, are a major source of calories in the human diet
and a primary feedstock for bioindustry. We report a chemical-biochemical hybrid pathway …

PICRUSt2 for prediction of metagenome functions

GM Douglas, VJ Maffei, JR Zaneveld, SN Yurgel… - Nature …, 2020 - nature.com
To the Editor—One limitation of microbial community marker-gene sequencing is that it does
not provide information about the functional composition of sampled communities …

Gut microbiome of multiple sclerosis patients and paired household healthy controls reveal associations with disease risk and course

X Zhou, R Baumann, X Gao, M Mendoza, S Singh… - Cell, 2022 - cell.com
Changes in gut microbiota have been associated with several diseases. Here, the
International Multiple Sclerosis Microbiome Study (iMSMS) studied the gut microbiome of …

The IMG/M data management and analysis system v. 6.0: new tools and advanced capabilities

IMA Chen, K Chu, K Palaniappan, A Ratner… - Nucleic acids …, 2021 - academic.oup.com
Abstract The Integrated Microbial Genomes & Microbiomes system (IMG/M: https://img. jgi.
doe. gov/m/) contains annotated isolate genome and metagenome datasets sequenced at …

The gut microbiome modulates the protective association between a Mediterranean diet and cardiometabolic disease risk

DD Wang, LH Nguyen, Y Li, Y Yan, W Ma, E Rinott… - Nature medicine, 2021 - nature.com
To address how the microbiome might modify the interaction between diet and
cardiometabolic health, we analyzed longitudinal microbiome data from 307 male …

[HTML][HTML] Gut microbiome is associated with the clinical response to anti-PD-1 based immunotherapy in hepatobiliary cancers

J Mao, D Wang, J Long, X Yang, J Lin… - … for Immunotherapy of …, 2021 - ncbi.nlm.nih.gov
Background The gut microbiome is associated with the response to immunotherapy for
different cancers. However, the impact of the gut microbiome on hepatobiliary cancers …

Protocol Update for large-scale genome and gene function analysis with the PANTHER classification system (v. 14.0)

H Mi, A Muruganujan, X Huang, D Ebert, C Mills… - Nature protocols, 2019 - nature.com
The PANTHER classification system (http://www. pantherdb. org) is a comprehensive system
that combines genomes, gene function classifications, pathways and statistical analysis …