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# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "VERSO" in publications use:'
type: software
title: 'VERSO: Viral Evolution ReconStructiOn (VERSO)'
version: 1.15.0
abstract: Mutations that rapidly accumulate in viral genomes during a pandemic can
  be used to track the evolution of the virus and, accordingly, unravel the viral
  infection network. To this extent, sequencing samples of the virus can be employed
  to estimate models from genomic epidemiology and may serve, for instance, to estimate
  the proportion of undetected infected people by uncovering cryptic transmissions,
  as well as to predict likely trends in the number of infected, hospitalized, dead
  and recovered people. VERSO is an algorithmic framework that processes variants
  profiles from viral samples to produce phylogenetic models of viral evolution. The
  approach solves a Boolean Matrix Factorization problem with phylogenetic constraints,
  by maximizing a log-likelihood function. VERSO includes two separate and subsequent
  steps; in this package we provide an R implementation of VERSO STEP 1.
authors:
- family-names: Ramazzotti
  given-names: Daniele
  email: daniele.ramazzotti@unimib.it
  orcid: https://orcid.org/0000-0002-6087-2666
- family-names: Angaroni
  given-names: Fabrizio
  email: fabrizio.angaroni@unimib.it
- family-names: Maspero
  given-names: Davide
  email: d.maspero@campus.unimib.it
- family-names: Graudenzi
  given-names: Alex
  email: alex.graudenzi@unimib.it
- family-names: De Sano
  given-names: Luca
  email: luca.desano@gmail.com
  orcid: https://orcid.org/0000-0002-9618-3774
repository: https://bioc.r-universe.dev
repository-code: https://github.com/BIMIB-DISCo/VERSO
url: https://github.com/BIMIB-DISCo/VERSO
date-released: '2024-03-21'
contact:
- family-names: Maspero
  given-names: Davide
  email: d.maspero@campus.unimib.it