References of BGI-College Poster and ICG-19 Poster

Title

Unraveling Dark Information in Microbiome Data Through Individual Specific Network

Author

Haiyang Hou

References
  1. Chen, H.-H. et al. SWEET: a single-sample network inference method for deciphering individual features in disease. Brief. Bioinform. 24, bbad032 (2023).
  2. Liu, X., Wang, Y., Ji, H., Aihara, K. & Chen, L. Personalized characterization of diseases using sample-specific networks. Nucleic Acids Res. 44, e164 (2016).
  3. 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).
  4. Kuijjer, M. L., Tung, M. G., Yuan, G., Quackenbush, J. & Glass, K. Estimating Sample-Specific Regulatory Networks. iScience 14, 226–240 (2019).
  5. Xu, Y., Nash, K., Acharjee, A. & Gkoutos, G. V. CACONET: a novel classification framework for microbial correlation networks. Bioinformatics 38, 1639–1647 (2022).
  6. 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).
  7. Vujkovic-Cvijin, I. et al. Host variables confound gut microbiota studies of human disease. Nature 587, 448–454 (2020).
  8. 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).
  9. Xiao, L., Zhang, F. & Zhao, F. Large-scale microbiome data integration enables robust biomarker identification. Nat. Comput. Sci. 2, 307–316 (2022).
  10. Structure, Function and Diversity of the Healthy Human Microbiome. Nature 486, 207–214 (2012).
  11. 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).
  12. Ling, W. et al. Batch effects removal for microbiome data via conditional quantile regression. Nat. Commun. 13, 5418 (2022).
  13. McDonald, D. et al. American Gut: an Open Platform for Citizen Science Microbiome Research. mSystems 3, e00031-18 (2018).
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