Resources

Publications

1. PhageClouds

   Rangel-Pineros G, Millard A, Michniewski S, Scanlan D, Sirén K, Reyes A, Petersen B, Clokie MRJ, Sicheritz-Pontén T. From trees to clouds: PhageClouds for fast comparison of ~640,000 phage genomic sequences and host-centric visualisation using genomic network graphs. PHAGE, 2021.

   doi:10.1089/phage.2021.0008 (opens in a new tab)

2. PhageLeads

   Yukgehnaish K, Rajandas H, Parimannan S, Manickam R, Marimuthu K, Petersen B, Clokie MRJ, Millard A, Sicheritz-Pontén T. PhageLeads: Rapid Assessment of Phage Therapeutic Suitability Using an Ensemble Machine Learning Approach. Viruses, 2022;14(2):342.

   doi:10.3390/v14020342 (opens in a new tab)

3. taxMyPhage

   Millard A, Denise R, Lestido M, Nicholas MT, Webster D, Turner D, Sicheritz-Pontén T. taxMyPhage: Automated Taxonomy of dsDNA Phage Genomes at the Genus and Species Level. PHAGE: Therapy, Applications, and Research, Mar 2025.

   doi:10.1089/phage.2024.0050 (opens in a new tab)

4. BAPS

   Perfilyev A, Gæde A, Hooton S, Zahran SA, Kalatzis PG, Winther-Have CS, Ibarra Chavez R, Wilkinson RC, Thanki AM, Liu Z, Zhang Q, Lv Q, Liu Y, Gigante AM, Atterbury RJ, Petersen B, Millard AD, Clokie MRJ & Sicheritz-Pontén T. Large-scale analysis of bacterial genomes reveals thousands of lytic phages. Nature Microbiology, Jan 2026.

   doi:10.1038/s41564-025-02203-4 (opens in a new tab)

5. PhageBoost

   Sirén K, Millard A, Petersen B, Gilbert MTP, Clokie MRJ, Sicheritz-Pontén T. Rapid discovery of novel prophages using biological feature engineering and machine learning. NAR Genom Bioinform, 2021.

   doi:10.1093/nargab/lqaa109 (opens in a new tab)

6. PhageCSR

   Clokie MRJ, Blasdel B, Sicheritz-Pontén T. Rethinking phage ecology by rooting it within an established plant framework. PHAGE, 2020.

   doi:10.1089/phage.2020.0015 (opens in a new tab)

No publication is listed for: Phager, Klebreach, PhiAlpha.