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
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
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
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. Clokie, Bob G. Blasdel, Benoit 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