Phage Discovery

where we develop next-gen discovery tools for phage genomics based on machine learning, life science AI, network graphs and supercomputing. All tools can collectively be accessed at www.phagecompass.dk.

  • PhageBoost: Predicting prophage novel regions using biological feature engineering and machine learning. Access the prediction server at www.phageboost.dk

  • PhageClouds: Fast comparison of ~640,000 phage genomic sequences and host-centric visualisation using genomic network graphs. Access PhageClouds at www.phageclouds.dk

  • PhageCSR: Exploring the placement of Bacteriophages in the CSR triangle. Access it at www.phageCSR.ml (temporarily down)

  • PhageLeads: Predicting therapeutic phage suitability. Access it at www.phageleads.dk

  • PhageFun: Functional annotation of phage genomes in feature space

Recent publications in Phage Therapy and Phage Discovery

PhageLeads: Rapid Assessment of Phage Therapeutic Suitability Using an Ensemble Machine Learning Approach.

Yukgehnaish K, Rajandas H, Parimannan S, Manickam R, Marimuthu K, Petersen B, Clokie MRJ, Millard A, Sicheritz-Pontén T.Viruses. 2022 Feb 8

inPhocus: Current State and Challenges of Phage Research in Singapore

Navin Kumar Verma, Si Jia Tan, John Chen, Hanrong Chen, Muhammad Hafiz Ismail, Scott A. Rice, Pablo Bifani, Sukumar Hariharan, Vivek Daniel Paul, Bharathi Sriram, Linh Chi Dam, Chia Ching Chan, Peiying Ho, Boon Chong Goh, Shimin Jasmine Chung, Kenneth Choon Meng Goh, Shu Hua Thong, Andrea Lay-Hoon Kwa, Adam Ostrowski, Thet Tun Aung, Halimah Razali, Shermaine W.Y. Low, Mani Shankar Bhattacharyya, Hemant K. Gautam, Rajamani Lakshminarayanan, Thomas Sicheritz-Pontén, Martha R.J. Clokie, Wilfried Moreira, and Maurice Adrianus Monique van Steensel

PHAGE Therapy, Applications and Research, Vol 3, No. 1, 2022 Mar 18

Development of a Phage Cocktail to Target Salmonella Strains Associated with Swine.

Thanki AM, Clavijo V, Healy K, Wilkinson RC, Sicheritz-Pontén T, Millard AD, Clokie MRJ.Pharmaceuticals (Basel). 2022 Jan 2

From Trees to Clouds: PhageClouds for Fast Comparison of ∼640,000 Phage Genomic Sequences and Host-Centric Visualization Using Genomic Network Graphs

Guillermo Rangel-Pineros, Andrew Millard, Slawomir Michniewski, David Scanlan, Kimmo Sirén, Alejandro Reyes, Bent Petersen, Martha R.J. Clokie, and Thomas Sicheritz-Pontén

PHAGE Therapy, Applications and Research, Vol 2, No. 4, Dec 2021

Phage Genome Annotation: Where to Begin and End

Anastasiya Shen and Andrew Millard

PHAGE Therapy, Applications and Research, Vol 2, No. 4, Dec 2021

Complete Genome Sequence of Salmonella enterica Bacteriophage PRF-SP1.

Mutusamy P, Jaya Jothi S, Lee SY, Petersen B, Sicheritz-Ponten T, Clokie MRJ, Loke S, Millard A, Parimannan S, Rajandas H.

Microbiol Resour Announc. 2021 Nov 24

inPhocus: The Diverse Landscape of Phage Studies in the Association of Southeast Asian Nations Region

Heera Rajandas, Sivachandran Parimannan, Thomas Sicheritz-Pontén, and Martha R.J. Clokie

PHAGE Therapy, Applications and Research, Vol 2, No. 3, 01 Sep 2021

inPhocus: Perspectives of the Application of Bacteriophages in Poultry and Aquaculture Industries Based on Varms in China

Xiaonan Zhao, Qing Zhang, Thomas Sicheritz-Pontén, Yuqing Liu, and Martha R.J. Clokie

PHAGE Therapy, Applications and Research, Vol 2, No. 2, 01 Jun 2021

Analysis of Selection Methods to Develop Novel Phage Therapy Cocktails Against Antimicrobial Resistant Clinical Isolates of Bacteria

Haines MEK, Hodges FE, Nale JY, Mahony J, van Sinderen D, Kaczorowska J, Alrashid B, Akter M, Brown N, Sauvageau D, Sicheritz-Pontén T, Thanki AM, Millard AD, Galyov EE, Clokie MRJ.

Front Microbiol. 2021 Mar 29

The Effect of Oxygen Availability on Bacteriophage Infection: A Review

Francesca E. Hodges, Thomas  Sicheritz-Pontén and Martha R.J. Clokie

PHAGE Therapy, Applications and Research, Vol 2, No. 1 , 2021 Mar 17

“Virus Amigos?” The Journey of the Development of Phage-Based Biocontrol in the Latin American Poultry and Aquaculture Industries

Guillermo Rangel-Pineros. Thomas  Sicheritz-Pontén and Martha R. J. Clokie

PHAGE Therapy, Applications and Research, Vol 2, No. , 2021 Mar 17

Rapid discovery of novel prophages using biological feature engineering and machine learning.

Sirén K, Millard A, Petersen B, Gilbert MTP, Clokie MRJ, Sicheritz-Pontén T.

NAR Genom Bioinform. 2021 Jan 6

Rethinking Phage Ecology by Rooting it Within an Established Plant Framework

Martha R.J. ClokieBob G. BlasdelBenoit O.L. Demars and Thomas Sicheritz-Pontén

PHAGE Therapy, Applications and Research Vol 1, No.3 2020 Dec 16

A Local Perspective on Phage-Based Biocontrol in Agriculture and Aquaculture in India

Kiran Kondabagil, Thomas  Sicheritz-Pontén and Martha R.J. Clokie

PHAGE Therapy, Applications and Research Vol 1, No.3, 2020 Dec 16