xREI: a phylo-grammar visualization webserver. - Lars Barquist; Ian H. Holmes (Nucleic Acids Res., 2008)

HandAlign: Bayesian multiple sequence alignment, phylogeny and ancestral reconstruction. - Oscar Westesson; Lars Barquist; Ian H. Holmes (Bioinform., 2012)

Rfam 11.0: 10 years of RNA families. - Sarah W. Burge; Jennifer Daub; Ruth Y. Eberhardt; John G. Tate; Lars Barquist; Eric P. Nawrocki; Sean R. Eddy; Paul P. Gardner; Alex Bateman (Nucleic Acids Res., 2013)

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)

The TraDIS toolkit: sequencing and analysis for dense transposon mutant libraries. - Lars Barquist; Matthew Mayho; Carla A. Cummins; Amy K. Cain; Christine J. Boinett; Andrew J. Page; Gemma C. Langridge; Michael A. Quail; Jacqueline A. Keane; Julian Parkhill (Bioinform., 2016)

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)