Concepedia

Substrate utilization and cross-feeding synergistically determine microbiome resistance to pathogen invasion

Xinrun Yang, Tianjie Yang, Ziru Zhang, Yaozhong Zhang, Xinlan Mei, Ningqi Wang, Gaofei Jiang, Yangchun Xu, Qirong Shen, Marnix H. Medema,

Nature Ecology & Evolution · 2025 · 11 citations · 36 references

DOIFull text

Open access

Concepts

References

36

Trimmomatic: a flexible trimmer for Illumina sequence data

Anthony Bolger, Marc Lohse, Björn Usadel · Bioinformatics · 2014 · 69.7K citations · Full text

, , +13

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

Donovan H. Parks, Michael Imelfort, Connor T. Skennerton et al. · Genome Research · 2015 · 12.8K citations · Full text

, , +17

Canu: scalable and accurate long-read assembly via adaptive <i>k</i> -mer weighting and repeat separation

Sergey Koren, Brian P. Walenz, Konstantin Berlin et al. · Genome Research · 2017 · 8.2K citations · Full text

, , +16

A protocol for generating a high-quality genome-scale metabolic reconstruction

Ines Thiele, Bernhard Ø. Palsson · Nature Protocols · 2010 · 1.9K citations · Full text

, , +11

COBRApy: COnstraints-Based Reconstruction and Analysis for Python

Ali Ebrahim, Joshua A. Lerman, Bernhard Ø. Palsson et al. · BMC Systems Biology · 2013 · 1.5K citations · Full text

, , +13