Primer Master: a new program for the design and analysis of PCR primers. - V. Proutski; Edward C. Holmes (Comput. Appl. Biosci., 1996)

SWAN: sliding window analysis of nucleotide sequence variability. - V. Proutski; Edward C. Holmes (Bioinform., 1998)

Discovering the Phylodynamics of RNA Viruses. - Edward C. Holmes; Bryan T. Grenfell (PLoS Comput. Biol., 2009)

Estimating evolutionary rates using time-structured data: a general comparison of phylogenetic methods. - Sebastián Duchêne; Jemma L. Geoghegan; Edward C. Holmes; Simon Y. W. Ho (Bioinform., 2016)

Sorting permutations: Games, genomes, and cycles. - Katharine L. M. Adamyk; Edward C. Holmes; G. R. Mayfield; Dennis J. Moritz; Marion Scheepers; Bridget Eileen Tenner; Helen C. Wauck (Discret. Math. Algorithms Appl., 2017)

Virus genomes reveal factors that spread and sustained the Ebola epidemic. - Gytis Dudas; Luiz Max Carvalho; Trevor Bedford; Andrew J. Tatem; Guy Baele; Nuno R. Faria; Daniel J. Park; Jason T. Ladner; Armando Arias; Danny Asogun; Filip Bielejec; Sarah L. Caddy; et al. (Nat., 2017)

Establishment and cryptic transmission of Zika virus in Brazil and the Americas. - Nuno R. Faria; Joshua Quick; I. M. Claro; Julien Thézé; J. G. de Jesus; Marta Giovanetti; Moritz U. G. Kraemer; S. C. Hill; Allison Black; A. C. Da Costa; L. C. Franco; S. P. Silva; et al. (Nat., 2017)

Entrezpy: a Python library to dynamically interact with the NCBI Entrez databases. - Jan P. Buchmann; Edward C. Holmes (Bioinform., 2019)

Bioinformatics resources for SARS-CoV-2 discovery and surveillance. - Tao Hu; Juan Li; Hong Zhou; Cixiu Li; Edward C. Holmes; Weifeng Shi (Briefings Bioinform., 2021)

Collecting and managing taxonomic data with NCBI-taxonomist. - Jan P. Buchmann; Edward C. Holmes (Bioinform., 2021)

SegFinder: an automated tool for identifying complete RNA virus genome segments through co-occurrence in multiple sequenced samples. - Xue Liu; Jianbin Kong; Yongtao Shan; Ziyue Yang; Jiafan Miao; Yuanfei Pan; Tianyang Luo; Zhiyuan Shi; Yingmei Wang; Qinyu Gou; Chunhui Yang; Hanzong Li; et al. (Briefings Bioinform., 2025)

Artificial intelligence for modelling infectious disease epidemics. - Moritz U. G. Kraemer; Joseph L.-H. Tsui; Serina Chang; Spyros Lytras; Mark P. Khurana; Samantha Vanderslott; Sumali Bajaj; Neil Scheidwasser; Jacob Liam Curran-Sebastian; Elizaveta Semenova; Mengyan Zhang; H. Juliette T. Unwin; et al. (Nat., 2025)