ArticleBMC bioinformatics2015
MANTIS: an R package that simulates multilocus models of pathogen evolution.
Article in BMC bioinformatics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
5 citing papers in PubMed.
- Genomic epidemiological models describe pathogen evolution across fitness valleys.Science advances · 2022Article
- Determinants of high residual post-PCV13 pneumococcal vaccine-type carriage in Blantyre, Malawi: a modelling study.BMC medicine · 2019Article
- Competition for hosts modulates vast antigenic diversity to generate persistent strain structure in Plasmodium falciparum.PLoS biology · 2019Article
- Reverse immunodynamics: a new method for identifying targets of protective immunity.Scientific reports · 2019Article
- Lineage structure of Streptococcus pneumoniae may be driven by immune selection on the groEL heat-shock protein.Scientific reports · 2017Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
backgroundIn host-pathogen systems the development of immunity by the host places pressure on pathogens, by setting up competition between genetic variants due to the establishment of cross-protective responses. These pressures can lead to pathogen-specific, ubiquitous dynamic behaviours. Understanding the evolutionary forces that shape these patterns is one of the key goals of computationally simulated epidemiological models. Despite the contribution of such research methods in recent years to our current understanding of pathogen evolution, the availability of free software tools for the general public remains scarce.
resultsWe developed the Multilocus ANTIgenic Simulator (MANTIS) software package for the R statistical environment. MANTIS can simulate and analyse epidemiological time-series generated under the biological assumptions of the strain theory of host-pathogen systems by Gupta et al.
conclusionsMANTIS wraps a C/C++ ordinary-differential equations system and Runge-Kutta solver into a set of user-friendly R functions. These include routines to numerically simulate the system and others to analyse, visualize and export results. For this, the package offers its own set of time-series plotting and exportation functions. MANTIS's main goal is to serve as a free, ready-to-use academic software tool. Its open source nature further provides an opportunity for users with advanced programming skills to expand its capabilities. Here, we describe the background theory, implementation, basic functionality and usage of this package. MANTIS is freely available from http://www.eeid.ox.ac.uk/mantis under the GPL license.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.