Title
Unraveling Dark Information in Microbiome Data Through Individual Specific Network
Author
Haiyang Hou
References
- Chen, H.-H. et al. SWEET: a single-sample network inference method for deciphering individual features in disease. Brief. Bioinform. 24, bbad032 (2023).
- Liu, X., Wang, Y., Ji, H., Aihara, K. & Chen, L. Personalized characterization of diseases using sample-specific networks. Nucleic Acids Res. 44, e164 (2016).
- Huang, Y., Chang, X., Zhang, Y., Chen, L. & Liu, X. Disease characterization using a partial correlation-based sample-specific network. Brief. Bioinform. 22, bbaa062 (2021).
- Kuijjer, M. L., Tung, M. G., Yuan, G., Quackenbush, J. & Glass, K. Estimating Sample-Specific Regulatory Networks. iScience 14, 226–240 (2019).
- Xu, Y., Nash, K., Acharjee, A. & Gkoutos, G. V. CACONET: a novel classification framework for microbial correlation networks. Bioinformatics 38, 1639–1647 (2022).
- Yachida, S. et al. Metagenomic and metabolomic analyses reveal distinct stage-specific phenotypes of the gut microbiota in colorectal cancer. Nat. Med. 25, 968–976 (2019).
- Vujkovic-Cvijin, I. et al. Host variables confound gut microbiota studies of human disease. Nature 587, 448–454 (2020).
- Lin, Y. et al. Altered Mycobiota Signatures and Enriched Pathogenic Aspergillus rambellii Are Associated With Colorectal Cancer Based on Multicohort Fecal Metagenomic Analyses. Gastroenterology 163, 908–921 (2022).
- Xiao, L., Zhang, F. & Zhao, F. Large-scale microbiome data integration enables robust biomarker identification. Nat. Comput. Sci. 2, 307–316 (2022).
- Structure, Function and Diversity of the Healthy Human Microbiome. Nature 486, 207–214 (2012).
- Sinha, R., Abnet, C. C., White, O., Knight, R. & Huttenhower, C. The microbiome quality control project: baseline study design and future directions. Genome Biol. 16, 276 (2015).
- Ling, W. et al. Batch effects removal for microbiome data via conditional quantile regression. Nat. Commun. 13, 5418 (2022).
- McDonald, D. et al. American Gut: an Open Platform for Citizen Science Microbiome Research. mSystems 3, e00031-18 (2018).