Local version of the virus identification and analysis web server (tool set)
TrIdent- Transduction Identification: Automatic detection, classification and characterization of active transduction events in microbiomes.
SaPhARI: An Adaptable Bioinformatics Tool for the Discovery of Novel Phage Satellites
LLM-powered classification of phage protein functions to identify strong lytic candidates against Klebsiella, using transfer learning and biological embeddings.
Cocktail is a program for mathematical modelling of bacteriophage (phage) infection kinetics. Cocktail is a Windows 64-bit program and the source code can be developed in the directions that users see fit. This will be updated soon with a link to the scientific publication describing the program.
Detect elevations and gaps in read coverage on metagenome contigs or assembled genomes
Computational analysis of bacteriophage genomes including genome feature extraction, metadata integration, QC filtering, and large-scale statistical analysis.
End-to-end bacteriophage genome characterisation and phage-therapy screening — a one-click macOS app.
Prediction of bacterial host for phage
Creation of a local database for bacteriophages
Reproducible, one-command HMM-based homologue discovery for protein families across phage/viral databases (six-frame search, ORF validation, iterative convergence). macOS/Linux; Windows via WSL2.
Langevin dynamics simulation of bacteriophage-bacteria interaction
A multi-modal 3D voxel tracking, co-registration, and parallel spatial filtering pipeline designed to analyze and validate the biophysical, morphological, and pathognomonic convergence between historical 2D phage virus silhouettes and modern 3D cebidiomorphic Pycnogonida parasitic vectors.
Python code for implementing antiviral mass-balance in pre-harvest herbal plants.
A comprehensive pan-immunophagomic analysis of Pseudomonas aeruginosa, characterizing CRISPR-Cas arrays, prophage integrations, and innate bacterial defense repertoires across diverse clinical isolates.
📑Reports and bioinformatics analyses from internship in Indonesia
A Nextflow pipeline for the detection, quality assessment, annotation, and classification of bacteriophages from metagenomically assembled contigs
Scripts used to prepare the "Self-splicing introns in genes of Bastillevirinae bacteriophages" paper
Predicting bacteria-phage interactions given phage and target bacterias sequenced genomes as well as hostrange interaction information. MSc Thesis @ DTU Healthtech
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