Publications

Drivers of epidemic dynamics in real time from daily digital COVID-19 measurements.

Kendall M. et al, (2024), Science (New York, N.Y.)

Estimating the contribution of setting-specific contacts to SARS-CoV-2 transmission using digital contact tracing data.

Wang Z. et al, (2024), Nature communications, 15

Comparing Phylogeographies to Reveal Incompatible Geographical Histories within Genomes.

Singer B. et al, (2024), Molecular biology and evolution

First Molecular Characterisation of Porcine Parvovirus 7 (PPV7) in Italy.

Dei Giudici S. et al, (2024), Viruses, 16

In vitro phenotypic characterisation of two genotype I African swine fever viruses with genomic deletion isolated from Sardinian wild boars.

Franzoni G. et al, (2024), Veterinary research, 55

Prevalence of persistent SARS-CoV-2 in a large community surveillance study.

Ghafari M. et al, (2024), Nature

Digital measurement of SARS-CoV-2 transmission risk from 7 million contacts

Ferretti L. et al, (2024), Nature, 626, 145 - 150

Biased estimates of phylogenetic branch lengths resulting from the discretised Gamma model of site rate heterogeneity

Ferretti L. et al, (2024)

Parthenogenomics: Insights on mutation rates and nucleotide diversity in parthenogenetic Panagrolaimus nematodes.

Villegas LI. et al, (2024), Ecology and evolution, 14

A novel factor modulating X chromosome dosage compensation in Anopheles.

Krzywinska E. et al, (2023), Current biology : CB, 33, 4697 - 4703.e4

Correction: Viral burden is associated with age, vaccination, and viral variant in a population-representative study of SARS-CoV-2 that accounts for time-since-infection-related sampling bias.

Fryer HR. et al, (2023), PLoS pathogens, 19

Allelic Entropy and Times until Loss or Fixation of Neutral Polymorphisms.

Ferretti L. and Ribeca P., (2023), Genes, 14

A General Framework for Neutrality Tests Based on the Site Frequency Spectrum.

Ramos-Onsins SE. et al, (2023), Genes, 14

Viral burden is associated with age, vaccination, and viral variant in a population-representative study of SARS-CoV-2 that accounts for time-since-infection-related sampling bias.

Fryer HR. et al, (2023), PLoS pathogens, 19

Enhancing global preparedness during an ongoing pandemic from partial and noisy data.

Klamser PP. et al, (2023), PNAS nexus, 2

Interpreting the pervasive observation of U-shaped Site Frequency Spectra.

Freund F. et al, (2023), PLoS genetics, 19

Epidemiological impacts of the NHS COVID-19 app in England and Wales throughout its first year

Kendall M. et al, (2023), Nature Communications, 14

Origin, Genetic Variation and Molecular Epidemiology of SARS-CoV-2 Strains Circulating in Sardinia (Italy) during the First and Second COVID-19 Epidemic Waves.

Rocchigiani AM. et al, (2023), Viruses, 15

The mutational spectrum of SARS-CoV-2 genomic and antigenomic RNA

Zhao L. et al, (2022), Proceedings of the Royal Society B: Biological Sciences, 289

A Naturally Occurring Microhomology-Mediated Deletion of Three Genes in African Swine Fever Virus Isolated from Two Sardinian Wild Boars.

Fiori MS. et al, (2022), Viruses, 14

Estimating SARS-CoV-2 variant fitness and the impact of interventions in England using statistical and geo-spatial agent-based models

Hinch R. et al, (2022), Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 380

Statistical and agent-based modelling of the transmissibility of different SARS-CoV-2 variants in England and impact of different interventions

Panovska-Griffiths J. et al, (2022), Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 380

The bounded coalescent model: Conditioning a genealogy on a minimum root date.

Carson J. et al, (2022), Journal of theoretical biology, 548

A framework for reconstructing SARS-CoV-2 transmission dynamics using excess mortality data.

Ghafari M. et al, (2022), Nature communications, 13

Phylogenetic estimation of the viral fitness landscape of HIV-1 set-point viral load

Zhao L. et al, (2022), Virus Evolution, 8

Establishment and a comparative transcriptomic analysis of a male-specific cell line from the African malaria mosquito Anopheles gambiae.

Krzywinska E. et al, (2022), Scientific reports, 12

A highly virulent variant of HIV-1 circulating in the Netherlands

Wymant C. et al, (2022), Science, 375, 540 - 545

Interpreting the pervasive observation of U-shaped Site Frequency Spectra

Freund F. et al, (2022)

Parthenogenomics: insights on mutation rates and nucleotide diversity in parthenogeneticPanagrolaimusnematodes

Villegas LI. et al, (2022)

A Deeper Insight into Evolutionary Patterns and Phylogenetic History of ASFV Epidemics in Sardinia (Italy) through Extensive Genomic Sequencing.

Fiori MS. et al, (2021), Viruses, 13

First Genomic Evidence of Dual African Swine Fever Virus Infection: Case Report from Recent and Historical Outbreaks in Sardinia.

Fiori MS. et al, (2021), Viruses, 13

Evolutionary and Ecological Drivers Shape the Emergence and Extinction of Foot-and-Mouth Disease Virus Lineages.

Di Nardo A. et al, (2021), Molecular biology and evolution, 38, 4346 - 4361

Lessons for preparedness and reasons for concern from the early COVID-19 epidemic in Iran.

Ghafari M. et al, (2021), Epidemics, 36

OpenABM-Covid19—An agent-based model for non-pharmaceutical interventions against COVID-19 including contact tracing

Hinch R. et al, (2021), PLOS Computational Biology, 17, e1009146 - e1009146

The epidemiological impact of the NHS COVID-19 app

Wymant C. et al, (2021), Nature, 594, 408 - 412

SARS-CoV-2 within-host diversity and transmission

Lythgoe KA. et al, (2021), Science, 372

femaleless Controls Sex Determination and Dosage Compensation Pathways in Females of Anopheles Mosquitoes.

Krzywinska E. et al, (2021), Current biology : CB, 31, 1084 - 1091.e4

Time to evaluate COVID-19 contact-tracing apps

Colizza V. et al, (2021), Nature Medicine, 27, 361 - 362

Epidemiological changes on the Isle of Wight after the launch of the NHS Test and Trace programme: a preliminary analysis

Kendall M. et al, (2020), The Lancet Digital Health, 2, e658 - e666

Genomic Diversity and Evolution of Quasispecies in Newcastle Disease Virus Infections.

Jadhav A. et al, (2020), Viruses, 12

Patterns of RNA Editing in Newcastle Disease Virus Infections.

Jadhav A. et al, (2020), Viruses, 12

Correction: Pervasive within-host recombination and epistasis as major determinants of the molecular evolution of the foot-and-mouth disease virus capsid.

Ferretti L. et al, (2020), PLoS pathogens, 16

The timing of COVID-19 transmission

Ferretti L. et al, (2020)

Conserved Patterns in Developmental Processes and Phases, Rather than Genes, Unite the Highly Divergent Bilateria.

Ferretti L. et al, (2020), Life (Basel, Switzerland), 10

COVID-19 incidence and R decreased on the Isle of Wight after the launch of the Test, Trace, Isolate programme

Kendall M. et al, (2020)

Within-host genomics of SARS-CoV-2

Lythgoe KA. et al, (2020)

Quantifying SARS-CoV-2 transmission suggests epidemic control with digital contact tracing

Ferretti L. et al, (2020), Science, 368

Quantifying SARS-CoV-2 transmission suggests epidemic control with digital contact tracing

Ferretti L. et al, (2020)

Comparing Phylogeographies: Incompatible Geographical Histories in Pathogens’ Genomes

Singer B. et al, (2020)

Pervasive within-host recombination and epistasis as major determinants of the molecular evolution of the foot-and-mouth disease virus capsid.

Ferretti L. et al, (2020), PLoS pathogens, 16

Cookies on this website

Publications