mapDamage: testing for damage patterns in ancient DNA sequences. - Aurelien Ginolhac; Morten Rasmussen; M. Thomas P. Gilbert; Eske Willerslev; Ludovic Orlando (Bioinform., 2011)

Environmental genes and genomes: understanding the differences and challenges in the approaches and software for their analyses. - Marie Lisandra Zepeda Mendoza; Thomas Sicheritz-Pontén; M. Thomas P. Gilbert (Briefings Bioinform., 2015)

Odintifier - A computational method for identifying insertions of organellar origin from modern and ancient high-throughput sequencing data based on haplotype phasing. - Jose Samaniego Castruita; Marie Lisandra Zepeda Mendoza; Ross Barnett; Nathan Wales; Marcus Gilbert (BMC Bioinform., 2015)

Assembly-Free and Alignment-Free Sample Identification Using Genome Skims. - Shahab Sarmashghi; Kristine Bohmann; M. Thomas P. Gilbert; Vineet Bafna; Siavash Mirarab (RECOMB, 2018)

HoloFood Data Portal: holo-omic datasets for analysing host-microbiota interactions in animal production. - Alexander B. Rogers; Varsha Kale; Germana Baldi; Antton Alberdi; M. Thomas P. Gilbert; Dipayan Gupta; Morten Tønsberg Limborg; Sen Li; Thomas Payne; Bent Petersen; Jacob A. Rasmussen; Lorna J. Richardson; et al. (Database J. Biol. Databases Curation, 2025)