Mallick H, Ma S, Franzosa EA, Vatanen T, Morgan XC, Huttenhower C. Experimental design and quantitative analysis of microbial community multiomics. Genome Biol. 2017;18(1):228. doi:10.1186/s13059-017-1359-z
McIver LJ, Abu-Ali G, Franzosa EA, et al. bioBakery: a meta’omic analysis environment. Bioinformatics. 2018;34(7):1235-1237. doi:10.1093/bioinformatics/btx754
Schirmer M, Franzosa EA, Lloyd-Price J, et al. Dynamics of metatranscription in the inflammatory bowel disease gut microbiome. Nat Microbiol. 2018;3(3):337-346. doi:10.1038/s41564-017-0089-z
Abu-Ali GS, Mehta RS, Lloyd-Price J, et al. Metatranscriptome of human faecal microbial communities in a cohort of adult men. Nat Microbiol. 2018;3(3):356-366. doi:10.1038/s41564-017-0084-4
Mehta RS, Abu-Ali GS, Drew DA, et al. Stability of the human faecal microbiome in a cohort of adult men. Nat Microbiol. 2018;3(3):347-355. doi:10.1038/s41564-017-0096-0
Bakker OB, Aguirre-Gamboa R, Sanna S, et al. Integration of multi-omics data and deep phenotyping enables prediction of cytokine responses. Nat Immunol. 2018;19(7):776-786. doi:10.1038/s41590-018-0121-3
Piantadosi A, Kanjilal S, Ganesh V, et al. Rapid Detection of Powassan Virus in a Patient With Encephalitis by Metagenomic Sequencing. Clin Infect Dis. 2018;66(5):789-792. doi:10.1093/cid/cix792
Hupalo DN, Luo Z, Melnikov A, et al. Population genomics studies identify signatures of global dispersal and drug resistance in Plasmodium vivax. Nat Genet. 2016;48(8):953-8. doi:10.1038/ng.3588
Segata N, Izard J, Waldron L, et al. Metagenomic biomarker discovery and explanation. Genome Biol. 2011;12(6):R60. doi:10.1186/gb-2011-12-6-r60
Neafsey DE, Barker BM, Sharpton TJ, et al. Population genomic sequencing of Coccidioides fungi reveals recent hybridization and transposon control. Genome Res. 2010;20(7):938-46. doi:10.1101/gr.103911.109