Detecting SNPs and estimating allele frequencies in clonal bacterial populations by sequencing pooled DNA. - Kathryn E. Holt; Yik Y. Teo; Heng Li 002; Satheesh Nair; Gordon Dougan; John Wain; Julian Parkhill (Bioinform., 2009)

Design of multiple sequence alignment algorithms on parallel, distributed memory supercomputers. - Philip C. Church; Andrzej Goscinski; Kathryn E. Holt; Michael Inouye; Amol Ghoting; Konstantin Makarychev; Matthias Reumann (EMBC, 2011)

Bandage: interactive visualization of de novo genome assemblies. - Ryan R. Wick; Mark B. Schultz; Justin Zobel; Kathryn E. Holt (Bioinform., 2015)

A platform for leveraging next generation sequencing for routine microbiology and public health use. - Laura Irina Rusu; Kelly L. Wyres; Matthias Reumann; Carlos Queiroz; Alexe Bojovschi; Tom Conway; Saurabh Kumar Garg 001; David J. Edwards; Geoff Hogg; Kathryn E. Holt (Health Inf. Sci. Syst., 2015)

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. - Ryan R. Wick; Louise M. Judd; Claire L. Gorrie; Kathryn E. Holt (PLoS Comput. Biol., 2017)

Deepbinner: Demultiplexing barcoded Oxford Nanopore reads with deep convolutional neural networks. - Ryan R. Wick; Louise M. Judd; Kathryn E. Holt (PLoS Comput. Biol., 2018)

FastSpar: rapid and scalable correlation estimation for compositional data. - Stephen C. Watts; Scott C. Ritchie; Michael Inouye; Kathryn E. Holt (Bioinform., 2019)

Polypolish: Short-read polishing of long-read bacterial genome assemblies. - Ryan R. Wick; Kathryn E. Holt (PLoS Comput. Biol., 2022)

Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing. - Ryan R. Wick; Louise M. Judd; Kathryn E. Holt (PLoS Comput. Biol., 2023)