Robust Identification of Noncoding RNA from Transcriptomes Requires Phylogenetically-Informed Sampling. - Stinus Lindgreen; Sinan Ugur Umu; Alicia Sook-Wei Lai; Hisham Eldai; Wenting Liu; Stephanie McGimpsey; Nicole E. Wheeler; Patrick J. Biggs; Nick R. Thomson; Lars Barquist; Anthony M. Poole; Paul P. Gardner (PLoS Comput. Biol., 2014)

A profile-based method for identifying functional divergence of orthologous genes in bacterial genomes. - Nicole E. Wheeler; Lars Barquist; Robert A. Kingsley; Paul P. Gardner (Bioinform., 2016)

Evaluation of parameters affecting performance and reliability of machine learning-based antibiotic susceptibility testing from whole genome sequencing data. - Allison L. Hicks; Nicole E. Wheeler; Leonor Sánchez-Busó; Jennifer L. Rakeman; Simon R. Harris; Yonatan H. Grad (PLoS Comput. Biol., 2019)

Applying data technologies to combat AMR: current status, challenges, and opportunities on the way forward. - Leonid Chindelevitch; Elita Jauneikaite; Nicole E. Wheeler; Kasim Allel; Bede Yaw Ansiri-Asafoakaa; Wireko A. Awuah; Denis C. Bauer; Stephan Beisken; Kara Fan; Gary Grant; Michael Graz; Yara Khalaf; et al. (CoRR, 2022)

Ten simple rules for the sharing of bacterial genotype - Phenotype data on antimicrobial resistance. - Leonid Chindelevitch; Maarten van Dongen; Heather Graz; Antonio Pedrotta; Anita Suresh; Swapna Uplekar; Elita Jauneikaite; Nicole E. Wheeler (PLoS Comput. Biol., 2023)