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spads 1.0: a toolbox to perform spatial analyses on DNA sequence data sets
spads 1.0 (for ‘Spatial and Population Analysis of DNA Sequences’) is a population genetic toolbox for characterizing genetic variability within and among populations from DNA sequences. In view of… Expand
Virus genomes reveal factors that spread and sustained the Ebola epidemic
We reconstruct the dispersal, proliferation and decline of Ebola virus throughout the region by analysing 1,610 Ebola virus genomes, which represent over 5% of the known cases. Expand
Genomic and epidemiological monitoring of yellow fever virus transmission potential
Arbovirus risk in Brazil Despite the existence of an effective vaccine for yellow fever, there are still almost 80,000 fatalities from this infection each year. Since 2016, there has been a… Expand
Evolution and epidemic spread of SARS-CoV-2 in Brazil
Brazil currently has one of the fastest growing SARS-CoV-2 epidemics in the world. Due to limited available data, assessments of the impact of non-pharmaceutical interventions (NPIs) on virus… Expand
GCALIGNER 1.0: an alignment program to compute a multiple sample comparison data matrix from large eco-chemical datasets obtained by GC.
We propose GCALIGNER 1.0, a program allowing the alignment of samples analyzed by GC based on retention time (RT) or Kovats retention indices (I) without MS information. Expand
Rapid outbreak sequencing of Ebola virus in Sierra Leone identifies transmission chains linked to sporadic cases
Abstract To end the largest known outbreak of Ebola virus disease (EVD) in West Africa and to prevent new transmissions, rapid epidemiological tracing of cases and contacts was required. The ability… Expand
Delimiting Species-Poor Data Sets using Single Molecular Markers: A Study of Barcode Gaps, Haplowebs and GMYC.
Most single-locus molecular approaches to species delimitation available to date have been designed and tested on data sets comprising at least tens of species, whereas the opposite case… Expand
Explaining the geographic spread of emerging epidemics: a framework for comparing viral phylogenies and environmental landscape data
We present and apply a new statistical framework that combines genomic and geographic data to test the impact of environmental variables on the mode and tempo of pathogen dispersal during emerging epidemics. Expand
HIV Rebound Is Predominantly Fueled by Genetically Identical Viral Expansions from Diverse Reservoirs.
- Marie-Angélique De Scheerder, B. Vrancken, +15 authors L. Vandekerckhove
- Biology, Medicine
- Cell host & microbe
- 11 September 2019
Viral rebound upon stopping combined antiretroviral therapy poses a major barrier toward an HIV cure. Cellular and anatomical sources responsible for reinitiating viral replication remain a subject… Expand
SERAPHIM: studying environmental rasters and phylogenetically informed movements
- S. Dellicour, R. Rose, Nuno R. Faria, P. Lemey, O. Pybus
- Computer Science, Medicine
- 15 October 2016
SERAPHIM ("Studying Environmental Rasters and PHylogenetically Informed Movements") is a suite of computational methods developed to study phylogenetic reconstructions of spatial movement in an environmental context. Expand