publications

2022

  1. phastSim: Efficient simulation of sequence evolution for pandemic-scale datasets
    Nicola De Maio, William Boulton, Lukas Weilguny, Conor R. Walker, Yatish Turakhia, Russell Corbett-Detig, and Nick Goldman
    PLOS Computational Biology 2022

2021

  1. Mutation Rates and Selection on Synonymous Mutations in SARS-CoV-2
    Nicola De Maio, Conor R. Walker, Yatish Turakhia, Robert Lanfear, Russell Corbett-Detig, and Nick Goldman
    Genome Biology and Evolution 2021
  2. Short-range template switching in great ape genomes explored using pair hidden Markov models
    Conor R. Walker, Aylwyn Scally, Nicola De Maio, and Nick Goldman
    PLOS Genetics 2021

2020

  1. A Phylodynamic Workflow to Rapidly Gain Insights into the Dispersal History and Dynamics of SARS-CoV-2 Lineages
    Simon Dellicour, Keith Durkin, Samuel L Hong, Bert Vanmechelen, Joan Martí-Carreras, Mandev S Gill, Cécile Meex, Sébastien Bontems, Emmanuel André, Marius Gilbert, Conor R. Walker, Nicola De Maio, Nuno R Faria, James Hadfield, Marie-Pierre Hayette, Vincent Bours, Tony Wawina-Bokalanga, Maria Artesi, Guy Baele, and Piet Maes
    Molecular Biology and Evolution 2020
  2. Stability of SARS-CoV-2 phylogenies
    Yatish Turakhia, Nicola De Maio, Bryan Thornlow, Landen Gozashti, Robert Lanfear, Conor R. Walker, Angie S. Hinrichs, Jason D. Fernandes, Rui Borges, Greg Slodkowicz, Lukas Weilguny, David Haussler, Nick Goldman, and Russell Corbett-Detig
    PLOS Genetics 2020
  3. Masking strategies for SARS-CoV-2 alignments
    Nicola De Maio, Conor R. Walker, Rui Borges, Lukas Weilguny, Greg Slodkowicz, and Nick Goldman
    virological.org 2020
  4. Issues with SARS-CoV-2 sequencing data
    Nicola De Maio, Conor R. Walker, Rui Borges, Lukas Weilguny, Greg Slodkowicz, and Nick Goldman
    virological.org 2020