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Publications

Revisiting the origins of the Sobemovirus genus: A case for ancient origins of plant viruses.

Journal article

Ghafari M. et al, (2024), PLoS Pathog, 20

A quantitative evaluation of the impact of vaccine roll-out rate and coverage on reducing deaths: insights from the first 2 years of COVID-19 epidemic in Iran.

Journal article

Ghafari M. et al, (2023), BMC medicine, 21

Insights into SARS-CoV-2 in Angola during the COVID-19 peak: Molecular epidemiology and genome surveillance.

Journal article

Francisco NM. et al, (2023), Influenza and other respiratory viruses, 17

The recency and geographical origins of the bat viruses ancestral to SARS-CoV and SARS-CoV-2

Preprint

Pekar JE. et al, (2023)

The evolutionary history of hepaciviruses.

Journal article

Li YQ. et al, (2023), bioRxiv

Reconstructing the evolutionary history of human, simian, and prosimian immunodeficiency viruses

Preprint

Ghafari M. et al, (2023)

Insights into SARS-CoV-2 in Angola during the COVID-19 Peak: Molecular Epidemiology and Genome Surveillance

Preprint

FRANCISCO NM. et al, (2023)

A quantitative evaluation of the impact of vaccine roll-out rate and coverage on reducing deaths from COVID-19: a counterfactual study on the impact of the delayed vaccination programme in Iran

Preprint

Ghafari M. et al, (2023)

The evolution of SARS-CoV-2.

Journal article

Markov PV. et al, (2023), Nature reviews. Microbiology, 21, 361 - 379

High number of SARS-CoV-2 persistent infections uncovered through genetic analysis of samples from a large community-based surveillance study

Preprint

Ghafari M. et al, (2023)

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

Journal article

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

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

Journal article

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

Purifying Selection Determines the Short-Term Time Dependency of Evolutionary Rates in SARS-CoV-2 and pH1N1 Influenza

Journal article

Ghafari M. et al, (2022), Molecular Biology and Evolution, 39

Investigating the evolutionary origins of the first three SARS-CoV-2 variants of concern

Preprint

Ghafari M. et al, (2022)

Investigating the evolutionary origins of the first three SARS-CoV-2 variants of concern

Journal article

Ghafari M. et al, (2022), FRONTIERS IN VIROLOGY, 2

A mechanistic evolutionary model explains the time-dependent pattern of substitution rates in viruses.

Journal article

Ghafari M. et al, (2021), Current biology : CB, 31, 4689 - 4696.e5

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

Journal article

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

Excess deaths associated with the Iranian COVID-19 epidemic: A province-level analysis.

Journal article

Ghafari M. et al, (2021), International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases, 107, 101 - 115

Estimates of anti-SARS-CoV-2 antibody seroprevalence in Iran.

Journal article

Ghafari M. et al, (2021), The Lancet. Infectious diseases, 21, 602 - 603

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

Preprint

Ghafari M. et al, (2021)

A novel variant of interest of SARS-CoV-2 with multiple spike mutations detected through travel surveillance in Africa

Preprint

de Oliveira T. et al, (2021)

Engaging Religious Institutions and Faith-Based Communities in Public Health Initiatives: A Case Study of the Romanian Orthodox Church During the COVID-19 Pandemic.

Journal article

Dascalu S. et al, (2021), Frontiers in public health, 9

Prisoner of War dynamics explains the time-dependent pattern of substitution rates in viruses

Preprint

Ghafari M. et al, (2021)

Purifying selection determines the short-term time dependency of evolutionary rates in SARS-CoV-2 and pH1N1 influenza

Preprint

Ghafari M. et al, (2021)

Estimating the false-negative test probability of SARS-CoV-2 by RT-PCR

Journal article

Wikramaratna PS. et al, (2020), Eurosurveillance, 25

Inferring Transmission Bottleneck Size from Viral Sequence Data Using a Novel Haplotype Reconstruction Method.

Journal article

Ghafari M. et al, (2020), Journal of virology, 94, e00014 - e00020

Estimating false-negative detection rate of SARS-CoV-2 by RT-PCR

Preprint

Wikramaratna P. et al, (2020)

Excess deaths associated with the Iranian COVID-19 epidemic: a province-level analysis

Preprint

Ghafari M. et al, (2020)

Inferring transmission bottleneck size from viral sequence data using a novel haplotype reconstruction method

Preprint

Ghafari M. et al, (2020)

The expected time to cross extended fitness plateaus.

Conference paper

Ghafari M. and Weissman DB., (2019), Theoretical population biology, 129, 54 - 67

The expected time to cross extended fitness plateaus

Preprint

Ghafari M. and Weissman D., (2018)

Luria–Delbrück, revisited: the classic experiment does not rule out Lamarckian evolution

Journal article

Holmes CM. et al, (2017), Physical Biology, 14, 055004 - 055004

On the role of topology in regulating transcriptional cascades

Journal article

Ghafari M. and Mashaghi A., (2017), Physical Chemistry Chemical Physics, 19, 25168 - 25179

Observation of a crossover in kinetic aggregation of Palladium colloids

Journal article

Ghafari M. et al, (2015), APPLIED SURFACE SCIENCE, 353, 1143 - 1149