International audience; In metagenome analysis, computational methods for assembly, taxonomic profilingand binning are key components facilitating downstream biological datainterpretation. However, a lack of consensus about benchmarking datasets andevaluation metrics co... View more
Turaev, D. & Rattei, T. High definition for systems biology of microbial communities: metagenomics gets genome-centric and strain-resolved. Curr Opin Biotechnol 39, 174-181 (2016).
Marx, V. Microbiology: the road to strain-level identification. Nat Methods 13, 401-404 (2016).
Sangwan, N., Xia, F. & Gilbert, J.A. Recovering complete and draft population genomes from metagenome datasets. Microbiome 4, 8 (2016).
Yassour, M. et al. Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability. Sci Transl Med 8, 343ra381 (2016).
Bendall, M.L. et al. Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations. ISME J 10, 1589-1601 (2016).
Li, S.S. et al. Durable coexistence of donor and recipient strains after fecal microbiota transplantation. Science 352, 586-589 (2016).
Nature 528, 364-369 (2015).
Kashtan, N. et al. Single-cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus. Science 344, 416-420 (2014).
Li, D., Liu, C.M., Luo, R., Sadakane, K. & Lam, T.W. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics 31, 1674-1676 (2015).
Chikhi, R. & Rizk, G. Space-efficient and exact de Bruijn graph representation based on a Bloom filter. Algorithms Mol Biol 8, 22 (2013).